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Sample records for planctomycete rhodopirellula baltica

  1. A Unique Pool of Compatible Solutes on Rhodopirellula baltica, Member of the Deep-Branching Phylum Planctomycetes.

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    Ana Filipa d'Avó

    Full Text Available The intracellular accumulation of small organic solutes was described in the marine bacterium Rhodopirellula baltica, which belongs to the globally distributed phylum Planctomycetes whose members exhibit an intriguing lifestyle and cell morphology. Sucrose, α-glutamate, trehalose and mannosylglucosylglycerate (MGG are the main solutes involved in the osmoadaptation of R. baltica. The ratio and total intracellular organic solutes varied significantly in response to an increase in salinity, temperature and nitrogen content. R. baltica displayed an initial response to both osmotic and thermal stresses that includes α-glutamate accumulation. This trend was followed by a rather unique and complex osmoadaptation mechanism characterized by a dual response to sub-optimal and supra-optimal salinities. A reduction in the salinity to sub-optimal conditions led primarily to the accumulation of trehalose. In contrast, R. baltica responded to salt stress mostly by increasing the intracellular levels of sucrose. The switch between the accumulation of trehalose and sucrose was by far the most significant effect caused by increasing the salt levels of the medium. Additionally, MGG accumulation was found to be salt- as well as nitrogen-dependent. MGG accumulation was regulated by nitrogen levels replacing α-glutamate as a K(+ counterion in nitrogen-poor environments. This is the first report of the accumulation of compatible solutes in the phylum Planctomycetes and of the MGG accumulation in a mesophilic organism.

  2. Permanent draft genomes of the three Rhodopirellula baltica strains SH28, SWK14 and WH47.

    Science.gov (United States)

    Richter, Michael; Richter-Heitmann, Tim; Klindworth, Anna; Wegner, Carl-Eric; Frank, Carsten S; Harder, Jens; Glöckner, Frank Oliver

    2014-02-01

    The genomes of three Rhodopirellula baltica strains were sequenced as permanent drafts to complement the full genome sequence of the type strain R. baltica SH1(T). The isolates are part of a larger study to infer the biogeography of Rhodopirellula species in European marine waters, as well as to amend the genus description of R. baltica. This genomics resource article is the first of a series of five publications reporting in total eight new permanent daft genomes of Rhodopirellula species. Copyright © 2013 Elsevier B.V. All rights reserved.

  3. Permanent draft genomes of the Rhodopirellula maiorica strain SM1.

    Science.gov (United States)

    Richter, Michael; Richter-Heitmann, Tim; Klindworth, Anna; Wegner, Carl-Eric; Frank, Carsten S; Harder, Jens; Glöckner, Frank Oliver

    2014-02-01

    The genome of Rhodopirellula maiorica strain SM1 was sequenced as a permanent draft to complement the full genome sequence of the type strain Rhodopirellula baltica SH1(T). This isolate is part of a larger study to infer the biogeography of Rhodopirellula species in European marine waters, as well as to amend the genus description of R. baltica. This genomics resource article is the fifth of a series of five publications reporting in total eight new permanent daft genomes of Rhodopirellula species. Copyright © 2013 Elsevier B.V. All rights reserved.

  4. Permanent draft genome of Rhodopirellula sallentina SM41.

    Science.gov (United States)

    Wegner, Carl-Eric; Richter, Michael; Richter-Heitmann, Tim; Klindworth, Anna; Frank, Carsten S; Glöckner, Frank Oliver; Harder, Jens

    2014-02-01

    The genome of Rhodopirellula sallentina SM41 was sequenced as a permanent draft to supplement the full genome sequence of the type strain Rhodopirellula baltica SH1(T). This isolate is part of a larger study to gain insights into the biogeography of Rhodopirellula species in European marine waters, as well as to amend the genus description of R. baltica. This genomics resource article is the third of a series of five publications reporting in total eight new permanent daft genomes of Rhodopirellula species. Copyright © 2013 Elsevier B.V. All rights reserved.

  5. Determining the bacterial cell biology of Planctomycetes.

    Science.gov (United States)

    Boedeker, Christian; Schüler, Margarete; Reintjes, Greta; Jeske, Olga; van Teeseling, Muriel C F; Jogler, Mareike; Rast, Patrick; Borchert, Daniela; Devos, Damien P; Kucklick, Martin; Schaffer, Miroslava; Kolter, Roberto; van Niftrik, Laura; Engelmann, Susanne; Amann, Rudolf; Rohde, Manfred; Engelhardt, Harald; Jogler, Christian

    2017-04-10

    Bacteria of the phylum Planctomycetes have been previously reported to possess several features that are typical of eukaryotes, such as cytosolic compartmentalization and endocytosis-like macromolecule uptake. However, recent evidence points towards a Gram-negative cell plan for Planctomycetes, although in-depth experimental analysis has been hampered by insufficient genetic tools. Here we develop methods for expression of fluorescent proteins and for gene deletion in a model planctomycete, Planctopirus limnophila, to analyse its cell organization in detail. Super-resolution light microscopy of mutants, cryo-electron tomography, bioinformatic predictions and proteomic analyses support an altered Gram-negative cell plan for Planctomycetes, including a defined outer membrane, a periplasmic space that can be greatly enlarged and convoluted, and an energized cytoplasmic membrane. These conclusions are further supported by experiments performed with two other Planctomycetes, Gemmata obscuriglobus and Rhodopirellula baltica. We also provide experimental evidence that is inconsistent with endocytosis-like macromolecule uptake; instead, extracellular macromolecules can be taken up and accumulate in the periplasmic space through unclear mechanisms.

  6. Planctomycetes dominate biofilms on surfaces of the kelp Laminaria hyperborea

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    Øvreås Lise

    2010-10-01

    Full Text Available Abstract Background Bacteria belonging to Planctomycetes display several unique morphological and genetic features and are found in a wide variety of habitats on earth. Their ecological roles in these habitats are still poorly understood. Planctomycetes have previously been detected throughout the year on surfaces of the kelp Laminaria hyperborea from southwestern Norway. We aimed to make a detailed investigation of the abundance and phylogenetic diversity of planctomycetes inhabiting these kelp surfaces. Results Planctomycetes accounted for 51-53% of the bacterial biofilm cells in July and September and 24% in February according to fluorescence in situ hybridization (FISH results. Several separate planctomycetes lineages within Pirellulae, Planctomyces and OM190 were represented in 16S rRNA gene clone libraries and the most abundant clones belonged to yet uncultured lineages. In contrast to the abundance, the diversity of the planctomycete populations increased from July to February and was probably influenced by the aging of the kelp tissue. One planctomycete strain that was closely related to Rhodopirellula baltica was isolated using selective cultivation techniques. Conclusions Biofilms on surfaces of L. hyperborea display an even higher proportion of planctomycetes compared to other investigated planctomycete-rich habitats such as open water, sandy sediments and peat bogs. The findings agree well with the hypothesis of the role of planctomycetes as degraders of sulfated polymeric carbon in the marine environment as kelps produce such substances. In addition, the abundant planctomycete populations on kelp surfaces and in association with other eukaryotes suggest that coexistence with eukaryotes may be a key feature of many planctomycete lifestyles.

  7. Permanent draft genomes of the two Rhodopirellula europaea strains 6C and SH398.

    Science.gov (United States)

    Richter-Heitmann, Tim; Richter, Michael; Klindworth, Anna; Wegner, Carl-Eric; Frank, Carsten S; Glöckner, Frank Oliver; Harder, Jens

    2014-02-01

    The genomes of two Rhodopirellula europaea strains were sequenced as permanent drafts to study the genomic diversity within this genus, especially in comparison with the closed genome of the type strain Rhodopirellula baltica SH1(T). The isolates are part of a larger study to infer the biogeography of Rhodopirellula species in European marine waters, as well as to amend the genus description of R. baltica. This genomics resource article is the second of a series of five publications describing a total of eight new permanent daft genomes of Rhodopirellula species. Copyright © 2013 Elsevier B.V. All rights reserved.

  8. Bringing Planctomycetes into pure culture

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    Olga Maria Lage

    2012-12-01

    Full Text Available Planctomycetes have been known since the description of Planctomyces bekefii by Gimesi at the beginning of the twentieth century (1924, although the first axenic cultures were only obtained in the 1970s. Since then, eleven genera with fourteen species have been validly named and five candidatus genera belonging to the anaerobic ammonium oxidation, anammox bacteria have also been discovered. However, Planctomycetes diversity is much broader than these numbers indicate, as shown by environmental molecular studies. In recent years the authors have attempted to isolate and cultivate additional strains of Planctomycetes. This paper provides a summary of the isolation work that was carried out to obtain in pure culture Planctomycetes from several environmental sources. The following strains and planctomycetes have been successfully isolated: two freshwater strains from the sediments of an aquarium, which were described as a new genus and species, Aquisphaera giovannonii; several Rhodopirellula strains from the sediments of a water treatment recycling tank of a marine fish farm; and more than 140 planctomycetes from the biofilm community of macroalgae. This collection comprises several novel taxa that are being characterized and described. Improvements in the isolation methodology were made in order to optimize and enlarge the number of Planctomycetes isolated from the macroalgae. The existence of an intimate and an important relationship between planctomycetes and macroalgae reported before by molecular studies is therefore supported by culture dependent methods.

  9. Developing techniques for the utilization of Planctomycetes as producers of bioactive molecules

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    Olga Jeske

    2016-08-01

    Full Text Available Planctomycetes are conspicuous, ubiquitous, environmentally important bacteria. They can attach to various surfaces in aquatic habitats and form biofilms. Their unique FtsZ-independent budding cell division mechanism is associated with slow growth and doubling times from six hours up to one month. Despite this putative disadvantage in the struggle to colonize surfaces, Planctomycetes are frequently associated with aquatic phototrophic organisms such as diatoms, cyanobacteria or kelp, whereby Planctomycetes can account for up to 50 % of the biofilm-forming bacterial population. Consequently, Planctomycetes were postulated to play an important role in carbon utilization, for example as scavengers after phototrophic blooms. However, given their observed slow growth, such findings are surprising since other faster- growing heterotrophs tend to colonize similar ecological niches. Accordingly, Planctomycetes were suspected to produce antibiotics for habitat protection in response to the attachment on phototrophs. Recently, we demonstrated their genomic potential to produce nonribosomal peptides, polyketides, bacteriocins, and terpenoids that might have antibiotic activities. In this study, we describe the development of a pipeline that consists of tools and procedures to cultivate Planctomycetes for the production of antimicrobial compounds in a chemically- defined medium and a procedure to chemically mimic their interaction with bacteria such as for example Cyanobacteria. We evaluated and adjusted screening assays to allow the hunt for planctomycetal antibiotics. As proof of principle, we demonstrate antimicrobial activities of planctomycetal extracts from Planctopirus limnophila DSM 3776, Rhodopirellula baltica DSM 10527, and the recently isolated strain Pan216. By combining UV/Vis and high resolution mass spectrometry data from High-Performance Liquid Chromatography fractionations with growth inhibition of indicator strains, we were able to assign

  10. Planctomycetes and macroalgae, a striking association

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    Olga Maria Lage

    2014-06-01

    Full Text Available Planctomycetes are part of the complex microbial biofilm community of a wide range of macroalgae. Recently, some studies began to unveil the great diversity of Planctomycetes present in this microenvironment and the interactions between the two organisms. Culture dependent and independent methods revealed the existence of a great number of species but, so far, only less than ten species have been isolated. Planctomycetes comprise the genera Rhodopirellula, Blastopirellula and Planctomyces, Phycisphaera and the uncultured class OM190 and some other taxa have only been found in this association.Several factors favour the colonization of macroalgal surfaces by planctomycetes. Many species possess holdfasts for attachment. The macroalgae secrete various sulphated polysaccharides that are the substrate for the abundant sulfatases produced by planctomycetes. Specificity between planctomycetes and macroalgae seem to exist which may be related to the chemical nature of the polysaccharides produced by each macroalga. Furthermore, the peptidoglycan-free cell wall of planctomycetes allows them to resist the action of several antimicrobial compounds produced by the macroalgae or other bacteria in the biofilm community that are effective against biofouling by other microorganisms.Despite the increase in our knowledge on the successful planctomycetes-macroalgae association, a great effort to fully understand this interaction is needed.

  11. Different Planctomycetes diversity patterns in latitudinal surface seawater of the open sea and in sediment.

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    Shu, Qinglong; Jiao, Nianzhi

    2008-04-01

    The 16S rRNA gene approach was applied to investigate the diversity of Planctomycetes in latitudinal surface seawater of the Western Pacific Ocean. The results revealed that the Pirellula-Rhodopirellula-Blastopirellula clade dominated the Planctomycetes community at all surface seawater sites while the minority genera Gemmata and Planctomyces were only found at sites H5 and H2 respectively. Although the clone frequency of the PRB clade seemed stable (between 83.3% and 94.1%) for all surface seawater sites, the retrieved Pirellula-Rhodopirellula-Blastopirellula clade presented unexpected diversity. Interestingly, low latitude seawater appeared to have higher diversity than mid-latitudes. integral-LIBSHUFF software analysis revealed significantly different diversity patterns between in latitudinal surface seawater and in the sediment of South China Sea station M2896. Our data suggested that different hydrological and geographic features contributed to the shift of Planctomycetes diversity in marine environments. This is, to our knowledge, the first systematic assessment of Planctomycetes in latitudinal surface seawater of the open sea and the first comparison of diversity pattern between surface seawater and sediments and has broadened our understanding of Planctomycetes diversity in marine environments.

  12. Gidon Kremer ja Kremerata Baltica

    Index Scriptorium Estoniae

    2001-01-01

    G. Kremer ja Kremerata Baltica esitamas Tshaikovski, shostakovitshi ja Desjatnikovi loomingut pühapäeval, 16. detsembril kl.19 Vanemuise Kontserdimajas ja esmaspäeval, 17. detsembril kl.19 Estonia kontserdisaalis

  13. Bringing Planctomycetes into pure culture

    OpenAIRE

    Lage, Olga M.; Bondoso, Joana

    2012-01-01

    Planctomycetes have been known since the description of Planctomyces bekefii by Gimesi at the beginning of the twentieth century (1924), although the first axenic cultures were only obtained in the 1970s. Since then, 11 genera with 14 species have been validly named and five candidatus genera belonging to the anaerobic ammonium oxidation, anammox bacteria have also been discovered. However, Planctomycetes diversity is much broader than these numbers indicate, as shown by environmental molecul...

  14. Bringing Planctomycetes into pure culture

    OpenAIRE

    Olga Maria Lage; Olga Maria Lage; Joana eBondoso; Joana eBondoso

    2012-01-01

    Planctomycetes have been known since the description of Planctomyces bekefii by Gimesi at the beginning of the twentieth century (1924), although the first axenic cultures were only obtained in the 1970s. Since then, eleven genera with fourteen species have been validly named and five candidatus genera belonging to the anaerobic ammonium oxidation, anammox bacteria have also been discovered. However, Planctomycetes diversity is much broader than these numbers indicate, as shown by environment...

  15. Genome Analysis of Planctomycetes Inhabiting Blades of the Red Alga Porphyra umbilicalis.

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    Jay W Kim

    Full Text Available Porphyra is a macrophytic red alga of the Bangiales that is important ecologically and economically. We describe the genomes of three bacteria in the phylum Planctomycetes (designated P1, P2 and P3 that were isolated from blades of Porphyra umbilicalis (P.um.1. These three Operational Taxonomic Units (OTUs belong to distinct genera; P2 belongs to the genus Rhodopirellula, while P1 and P3 represent undescribed genera within the Planctomycetes. Comparative analyses of the P1, P2 and P3 genomes show large expansions of distinct gene families, which can be widespread throughout the Planctomycetes (e.g., protein kinases, sensors/response regulators and may relate to specific habitat (e.g., sulfatase gene expansions in marine Planctomycetes or phylogenetic position. Notably, there are major differences among the Planctomycetes in the numbers and sub-functional diversity of enzymes (e.g., sulfatases, glycoside hydrolases, polysaccharide lyases that allow these bacteria to access a range of sulfated polysaccharides in macroalgal cell walls. These differences suggest that the microbes have varied capacities for feeding on fixed carbon in the cell walls of P.um.1 and other macrophytic algae, although the activities among the various bacteria might be functionally complementary in situ. Additionally, phylogenetic analyses indicate augmentation of gene functions through expansions arising from gene duplications and horizontal gene transfers; examples include genes involved in cell wall degradation (e.g., κ-carrageenase, alginate lyase, fucosidase and stress responses (e.g., efflux pump, amino acid transporter. Finally P1 and P2 contain various genes encoding selenoproteins, many of which are enzymes that ameliorate the impact of environmental stresses that occur in the intertidal habitat.

  16. Personal interests hinder Rail Baltica

    Index Scriptorium Estoniae

    2011-01-01

    Läti seimi liige Janis Reirs leiab, et Rail Baltica ehitus on Moskva ja Riia vahelise raudtee ehitusest prioriteetsem, kuna esimest võib potentsiaalselt finantseerida Euroopa Liit. Transpordiminister Uldis Augulis kohtub oma Venemaa kolleegi Igor Levitiniga 7. aprillil. Peaminister Valdis Dombrovskise sõnul vajavad mõlemad projektid majandusanalüüsi

  17. Ars Baltica-verkoston puheenjohtajuus Suomeen Risto Ruohoselle

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    1999-01-01

    1990. a. loodud võrgustiku Ars Baltica sekretariaat (Ars Baltica Contact Point & Communication Center) tuleb Kielist Tallinnasse Eesti kultuuriministeeriumi kuni aastani 2002 (Suur-Karja 23). Ars Baltica (ühendus)

  18. Rail Baltica waiting at the station

    Index Scriptorium Estoniae

    2010-01-01

    Majandus- ja kommunikatsiooniministeeriumi transpordi asekantsleri Eero Pärgmäe sõnul on Eesti 2012. aastal valmis Tallinn-Riia rongiliini avamiseks. Tallinn-Berliini rongiliinist. Siim Kallas lubas aidata edendada Rail Baltica projekti

  19. BALTICA III. Plant condition and life management

    International Nuclear Information System (INIS)

    Hietanen, S.; Auerkari, P.

    1995-01-01

    The BALTICA III, International Conference on Plant Condition and Life Management was held on June 6 - 8, 1995 on board Silja Serenade on its cruise between Helsinki - Stockholm and at the Forest Lake Hotel Korpilampi in Espoo. BALTICA III provides forum for the transfer of technology from applied research to practise. This is the second volume of the publications, which contain the presentations given at the BALTICA III, Plant Condition and Life Management. A total of 45 articles report recent experience in plant condition and life management. The conference focuses on recent applications that have been demonstrated for the benefit of safe and economical operation of power plants. Practical approach is emphasised, including the presentations that aim to provide insight into new techniques, improvements in assessment methodologies as well as maintenance strategies. Compared to earlier occasions in the BALTICA series, a new aspect is in the applications of knowledge-based systems in the service of power plant life management. (orig.)

  20. Diversity patterns and isolation of Planctomycetes associated with metalliferous deposits from hydrothermal vent fields along the Valu Fa Ridge (SW Pacific).

    Science.gov (United States)

    Storesund, Julia Endresen; Lanzèn, Anders; García-Moyano, Antonio; Reysenbach, Anna-Louise; Øvreås, Lise

    2018-02-08

    The microbial diversity associated with diffuse venting deep-sea hydrothermal deposits is tightly coupled to the geochemistry of the hydrothermal fluids. Previous 16S rRNA gene amplicon sequencing (metabarcoding) of marine iron-hydroxide deposits along the Arctic Mid Ocean Ridge, revealed the presence of diverse bacterial communities associated with these deposits (Storesund and Øvreås in Antonie van Leeuwenhoek 104:569-584, 2013). One of the most abundant and diverse phyla detected was the enigmatic Planctomycetes. Here we report on the comparative analyses of the diversity and distribution patterns of Planctomycetes associated with metalliferous deposits from two diffuse-flow hydrothermal vent fields (Mariner and Vai Lili) from the Valu Fa Ridge in the Southwestern Pacific. Metabarcoding of 16S rRNA genes showed that the major prokaryotic phyla were Proteobacteria (51-73% of all 16S rRNA gene reads), Epsilonbacteraeota (0.5-19%), Bacteriodetes (5-17%), Planctomycetes (0.4-11%), Candidatus Latescibacteria (0-5%) and Marine Benthic Group E (Hydrothermarchaeota) (0-5%). The two different sampling sites differed considerably in overall community composition. The abundance of Planctomycetes also varied substantially between the samples and the sites, with the majority of the sequences affiliated with uncultivated members of the classes Planctomycetacia and Phycisphaerae, and other deep branching lineages. Seven different strains affiliated with the order Planctomycetales were isolated, mostly from the Vai Lili samples, where also the highest Planctomycetales diversity was seen. Most of the isolates were affiliated with the genera Gimesia, Rhodopirellula and Blastopirellula. One isolate was only distantly related to known cultured, but uncharacterized species within the Pir4 group. This study shows that the deep-sea Planctomycetes represent a very heterogeneous group with a high phylogenetic diversity and a substantial potential for novel organism discovery in these

  1. BALTICA IV. Plant maintenance for managing life and performance

    Energy Technology Data Exchange (ETDEWEB)

    Hietanen, S.; Auerkari, P. [eds.] [VTT Manufacturing Technology, Espoo (Finland). Operational Reliability

    1998-12-31

    BALTICA IV International Conference on Plant Maintenance Managing Life and performance held on September 7-9, 1998 on board M/S Silja Symphony on its cruise between Helsinki-Stockholm and at Aavaranta in Kirkkonummi. The BALTICA IV conference provides a forum for the transfer of technology from applied research to practice. This is one of the two volumes of the proceedings of the BALTICA IV International Conference on Plant Maintenance Managing Life and Performance. The BALTICA IV conference focuses on new technology, recent experience and applications of condition and life management, and on improvements in maintenance strategies for safe and economical operation of power plants. (orig.)

  2. BALTICA IV. Plant maintenance for managing life and performance

    Energy Technology Data Exchange (ETDEWEB)

    Hietanen, S; Auerkari, P [eds.; VTT Manufacturing Technology, Espoo (Finland). Operational Reliability

    1999-12-31

    BALTICA IV International Conference on Plant Maintenance Managing Life and performance held on September 7-9, 1998 on board M/S Silja Symphony on its cruise between Helsinki-Stockholm and at Aavaranta in Kirkkonummi. The BALTICA IV conference provides a forum for the transfer of technology from applied research to practice. This is one of the two volumes of the proceedings of the BALTICA IV International Conference on Plant Maintenance Managing Life and Performance. The BALTICA IV conference focuses on new technology, recent experience and applications of condition and life management, and on improvements in maintenance strategies for safe and economical operation of power plants. (orig.)

  3. Tartu ihkab Rail Baltica kiirraudteed endale / Madis Aesma

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    Aesma, Madis

    2005-01-01

    2005. aasta sügisel alustatakse uuringuid, et välja selgitada, millisest Eesti linnast - Tartust, Pärnust või Viljandist - peaks tulevikus läbi minema kiirraudtee Rail Baltica, mis viib kuue tunniga Tallinnast Varssavisse. Kaart: Kiirraudtee Rail Baltica kolm võimalikku suunda. Kommenteerib Andrus Ansip

  4. Rail Baltica keerab Raplale selja? / Toivo Räägel

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    Räägel, Toivo, 1956-

    2007-01-01

    Rapla juhte üllatas kiirraudtee Rail Baltica suunamine Rapla ja Pärnu suunalt Valga peale, majandus- ja kommunikatsiooniministeerium toob valiku põhjenduseks sealse parema infrastruktuuri, kuid kinnitab samas, et 10 aasta pärast peaks ka Pärnu suunal valmima kiirraudtee

  5. Via Baltica : Eesti tee Hansaliidust Euroopa Liitu? = Via Baltica : Viron tie Hansaliitosta Euroopan Unioniin? / Hannu Eerikäinen

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    Eerikäinen, Hannu

    2004-01-01

    Via Baltica moodustab Läänemere regioonis tähtsaima arengutelje, mis avab Põhja-Euroopale tee EL-ist väljaspool olevatesse riikidesse. Tallinnast saab taas tähtis vahendaja Põhja- ja Kesk-Euroopa vahel

  6. [Isolation and characterization of Thermopirellula anaerolimosa gen. nov., sp. nov., an obligate anaerobic hydrogen-producing bacterium of the phylum Planctomycetes].

    Science.gov (United States)

    Liu, Dongying; Liu, Yi; Men, Xuehui; Guo, Qunqun; Guo, Rongbo; Qiu, Yanling

    2012-08-04

    To cultivate various yet-to-be cultured heterotrophs from anaerobic granule sludge, we used a selective culture medium with low concentrations of substrates supplemented a variety of antibiotics. An obligate anaerobic, thermophilic, hydrogen-producing bacterium, strain VM20-7(T), was isolated from an upflow anaerobic sludge blanket (UASB) reactor treating high-strength organic wastewater from isomerized sugar production processes. Cells of strain VM20-7(T) are non-motile, spherical, pear or teardrop shaped, occurring singly(o)r as aggregates (0.7 - 2.0 microm x 0.7 - 2.0 microm). Spore formation was not observed. Growth temperature ranges from 35 - 50 degrees C (optimum 45 degrees C), pH ranges from 6.0 - 8.3 (optimum 7.0 - 7.5) , NaCl tolerant concentration ranges from 0% - 0.5% (w/v, optimum 0% ). Nitrate, sulfate, thiosulfate, sulfite, elemental sulfur and Fe (III)-NTA were not used as terminal electron acceptors. Strain VM20-7(T) utilizes a wide range of carbohydrates, including glucose, maltose, ribose, xylose, sucrose, galactose, mannose, raffinose, pectin, yeast extract and xylan. Acetate and H2 are the main end products of glucose fermentation. The G + C content of the genomic DNA was 60.9 mol%. 16S rRNA gene sequence analysis revealed that it is related to the Pirellula-Rhodopirellula-Blastopirellula (PRB) clade within the order Planctomycetales (82.7 - 84.3% similarity with 16S rRNA genes of other known related species). The first obligate anaerobic bacterium within the phylum Planctomycetes was isolated with low concentration of carbohydrates and antibiotics. On the basis of the physiological and phylogenetic data, the name Thermopirellula anaerolimosa gen. nov. , sp. nov. is proposed for strain VM20-7(T) (= CGMCC 1.5169(T) = JCM 17478(T) = DSM 24165(T)).

  7. Via Baltica ei hakka läbi Harku metsa jooksma / Urmas Seaver

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    Seaver, Urmas, 1973-

    2005-01-01

    Tallinna linnavalitsus loobus plaanist ehitada magistraaltee Via Baltica läbi Harku metsa, kuna selle vastu on keskkonnaministeerium, kogutud on ka 1650 protestiallkirja. Kaart: Magistraaltee läbi rabametsa

  8. Isolation and molecular identification of planctomycete bacteria from postlarvae of the giant tiger prawn, Penaeus monodon.

    Science.gov (United States)

    Fuerst, J A; Gwilliam, H G; Lindsay, M; Lichanska, A; Belcher, C; Vickers, J E; Hugenholtz, P

    1997-01-01

    Bacteria phenotypically resembling members of the phylogenetically distinct planctomycete group of the domain Bacteria were isolated from postlarvae of the giant tiger prawn, Penaeus monodon. A selective medium designed in the light of planctomycete antibiotic resistance characteristics was used for this isolation. Planctomycetes were isolated from both healthy and monodon baculovirus-infected prawn postlarvae. The predominant colony type recovered from postlarvae regardless of viral infection status was nonpigmented. Other, less commonly observed types were pink or orange pigmented. A planctomycete-specific 16S rRNA-directed probe was designed and used to screen the isolates for their identity as planctomycetes prior to molecular phylogenetic characterization. 16S rRNA genes from nine prawn isolates together with two planctomycete reference strains (Planctomyces brasiliensis and Gemmata obscuriglobus) were sequenced and compared with reference sequences from the planctomycetes and other members of the domain Bacteria. Phylogenetic analyses and sequence signatures of the 16S rRNA genes demonstrated that the prawn isolates were members of the planctomycete group. Five representatives of the predominant nonpigmented colony type were members of the Pirellula group within the planctomycetes, as were three pink-pigmented colony type representatives. Homology values and tree topology indicated that representatives of the nonpigmented and pink-pigmented colony types formed two discrete clusters within the Pirellula group, not identical to any known Pirellula species. A sole representative of the orange colony type was a member of the Planctomyces group, virtually identical in 16S rDNA sequence to P. brasiliensis, and exhibited distinctive morphology. PMID:8979353

  9. Isolation and Purification of Planctomycetes associated with Harbor and Lagoon Seagrasses of the Red Sea

    KAUST Repository

    Bream, Holly

    2012-07-01

    Planctomycetes are members of a unique superphylum along with Verrucomicrobia and Chlamydia, situated in the domain Bacteria. They have distinct structural and morphological features, and discoveries made through phylogenetic analysis indicate their important role in nutrient cycling. Their known relationships with marine photosynthetic organisms led to the formation of this study\\'s hypothesis, namely, that Planctomycetes can be isolated from the biofilm of seagrass species of the Red Sea using cultivation techniques adapted for these organisms. Preparation of solid and liquid media using M13 with both agar and gellan, and 2216 Difco Marine Broth full-­ strength, 1/10-­strength, and with antibiotics, resulted in the successful isolation of Planctomycetes as confirmed by morphological examination and transmission electron microscopy. The work performed in this study provides a solid foundation for further studies to elucidate the metabolic pathways and ecological significance of Planctomycetes.

  10. Late Ediacaran magnetostratigraphy of Baltica: Evidence for Magnetic Field Hyperactivity?

    Science.gov (United States)

    Bazhenov, Mikhail L.; Levashova, Natalia M.; Meert, Joseph G.; Golovanova, Inessa V.; Danukalov, Konstantin N.; Fedorova, Natalia M.

    2016-02-01

    Long-term changes in characteristics of the geomagnetic field may signal evolutionary changes within the Earth's interior. Among these long-term variations, the magnetic field reversal rate is probably the best known and most frequently used parameter to evaluate concomitant changes in the Earth's core. Although the reversal rate is well known for the last 150 Ma and reasonably constrained back to 300 Ma, knowledge of the early Paleozoic and earlier times is limited. Hence, the haunting question is whether the reversal pattern for the last 300 Myr is a good representation of the field behavior over a much longer interval. A paleomagnetic study of Upper Ediacaran sediments from the Zigan Fm. (Baltica in the western South Urals) revealed a high-temperature, dual-polarity component that is of primary origin (Levashova et al., 2013). In this paper, we present the results of a magnetostratigraphic study from the same sections that can be summed up as follows: 1) >30 magnetozones are found in the ca. 110 meters thick composite section of the Zigan Fm.; 2) A similar reversal pattern was reported from Upper Ediacaran sediments from the White Sea coast (North Russia) and SW Siberia but has never been found in clastic rocks of any other age; 3) The reversal pattern in three remote Ediacaran sections could not result from remagnetization or extremely slow sedimentation; 4) The reversal rate in the Late Ediacaran exceeded 20 reversals per million years; 5) The field appears to behave in a bipolar fashion during the period of hyperactivity.

  11. Phylum Verrucomicrobia representatives share a compartmentalized cell plan with members of bacterial phylum Planctomycetes

    Directory of Open Access Journals (Sweden)

    Romeo Tony

    2009-01-01

    Full Text Available Abstract Background The phylum Verrucomicrobia is a divergent phylum within domain Bacteria including members of the microbial communities of soil and fresh and marine waters; recently extremely acidophilic members from hot springs have been found to oxidize methane. At least one genus, Prosthecobacter, includes species with genes homologous to those encoding eukaryotic tubulins. A significant superphylum relationship of Verrucomicrobia with members of phylum Planctomycetes possessing a unique compartmentalized cell plan, and members of the phylum Chlamydiae including human pathogens with a complex intracellular life cycle, has been proposed. Based on the postulated superphylum relationship, we hypothesized that members of the two separate phyla Planctomycetes and Verrucomicrobia might share a similar ultrastructure plan differing from classical prokaryote organization. Results The ultrastructure of cells of four members of phylum Verrucomicrobia – Verrucomicrobium spinosum, Prosthecobacter dejongeii, Chthoniobacter flavus, and strain Ellin514 – was examined using electron microscopy incorporating high-pressure freezing and cryosubstitution. These four members of phylum Verrucomicrobia, representing 3 class-level subdivisions within the phylum, were found to possess a compartmentalized cell plan analogous to that found in phylum Planctomycetes. Like all planctomycetes investigated, they possess a major pirellulosome compartment containing a condensed nucleoid and ribosomes surrounded by an intracytoplasmic membrane (ICM, as well as a ribosome-free paryphoplasm compartment between the ICM and cytoplasmic membrane. Conclusion A unique compartmentalized cell plan so far found among Domain Bacteria only within phylum Planctomycetes, and challenging our concept of prokaryote cell plans, has now been found in a second phylum of the Domain Bacteria, in members of phylum Verrucomicrobia. The planctomycete cell plan thus occurs in at least two

  12. Genomic analysis indicates the presence of an asymmetric bilayer outer membrane in Planctomycetes and Verrucomicrobia

    Directory of Open Access Journals (Sweden)

    Daan R Speth

    2012-08-01

    Full Text Available Bacteria of the phylum Planctomycetes are of special interest for the study of compartmental cellular organization. Members of this phylum share a very unusual prokaryotic cell plan, featuring several membrane-bound compartments. Recently, it was shown that this cellular organization might extend to certain members of the phylum Verrucomicrobia. The Planctomycete cell plan has been defined as featuring a proteinaceous cell wall, a cytoplasmic membrane surrounding the paryphoplasm and an intracytoplasmic membrane defining the riboplasm. So far it was presumed that Planctomycetes did not have an asymmetric bilayer outer membrane as observed in Gram-negative bacteria. However, recent work on outer membrane biogenesis has provided several marker genes in the outer membrane protein (OMP assembly and the lipopolysaccharide (LPS insertion complexes. Additionally, advances in computational prediction of OMPs provided new tools to perform more accurate genomic screening for such proteins.Here we searched all 22 Planctomycetes and Verrucomicrobia genomes available in Genbank, plus the recently published genome of ‘Candidatus Scalindua profunda’, for markers of outer membrane biogenesis and OMPs. We were able to identify the key components of LPS insertion, OMP assembly and at least eight OMPs in all genomes tested. Additionally, we have analyzed the transcriptome and proteome data of the Planctomycetes ‘Candidatus Kuenenia stuttgartiensis’ and ‘Ca. S. profunda’ and could confirm high expression of several predicted OMPs, including the biomarkers of outer membrane biogenesis.

  13. Structural studies of planctomycete Gemmata obscuriglobus support cell compartmentalisation in a bacterium.

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    Evgeny Sagulenko

    Full Text Available Members of phylum Planctomycetes have been proposed to possess atypical cell organisation for the Bacteria, having a structure of sectioned cells consistent with internal compartments surrounded by membranes. Here via electron tomography we confirm the presence of compartments in the planctomycete Gemmata obscuriglobus cells. Resulting 3-D models for the most prominent structures, nuclear body and riboplasm, demonstrate their entirely membrane - enclosed nature. Immunogold localization of the FtsK protein also supports the internal organisation of G.obscuriglobus cells and their unique mechanism of cell division. We discuss how these new data expand our knowledge on bacterial cell biology and suggest evolutionary consequences of the findings.

  14. Aeg on otsustada : Rail Baltica : rahvusvaheline raudtee toob Eestile kasu / Vilja Savisaar-Toomast

    Index Scriptorium Estoniae

    Savisaar-Toomast, Vilja, 1962-

    2011-01-01

    Vilja Savisaar-Toomast on kindel, et Rail Baltica projekt tuleb esitada Euroopa Liidu finantsperioodiks 2014-2020 ning eelistab marsruuti Tallinn-Pärnu-Riia-Kaunas. Tõenäoliselt on võimalik saada projektile Euroopa Liidult ka maksimumtoetus ehk määraga 60-70%

  15. Riik hakkab Via Baltica maanteed neljarealiseks joonistama / Eno-Gerrit Link

    Index Scriptorium Estoniae

    Link, Eno-Gerrit

    2008-01-01

    Ilmunud ka: Postimees : na russkom jazõke 25. sept. lk. 2. Pärnu maavalitsuse ja maanteeameti eestvedamisel alustatakse Tallinnast Iklani kulgeva Via Baltica liiklussoone teemaplaneeringut, mille järgi tuleb Pärnumaal leida lahendused Are ja Pärnu ümbersõidule ning Nurme õgvendusele. Arvamust avaldab Are vallavanem Jaanus Männik

  16. Via Baltica Pärnu ümbersõidu trassivalik kulges vaevaliselt / Ester Vilgats

    Index Scriptorium Estoniae

    Vilgats, Ester

    2008-01-01

    Via Baltica Pärnu ümbersõidu trassivaliku probleeme käsitlevast kohtumisest võtsid osa majandusministeeriumi transpordi asekantsler Eero Pärgmäe, rahandusministri nõunik Riho Sõrmus ja sama ameti europrogrammide osakonna juhataja Urmas Konsap

  17. Siim Kallas: Rail Baltica edeneb, aga veel pole mõtet kiirrongi oodata / Urmas Jaagant

    Index Scriptorium Estoniae

    Jaagant, Urmas

    2010-01-01

    Euroopa Komisjoni voliniku Siim Kallase sõnul pole mingit põhjust, miks Eestis ei võiks sõita 200 km/h liikuvad kiirrongid, vajaliku raudtee ehitamine võib olla isegi odavam kui uus maantee. Kuid oluline on küsimus, kuidas tekitada erasektoris piisavalt suur kindlustunne, et Rail Baltica projekt ära tasub

  18. Rail Baltica uus tee viiks rongid nelja tunniga Varssavisse / Tiina Rekand

    Index Scriptorium Estoniae

    Rekand, Tiina, 1985-

    2011-01-01

    Rail Baltica tasuvusuuringus on välja töötatud neli optimaalsemat marsruuti. Aecom Ltd Balti regiooni direktor Arnis Kakulis peab parimaks kiireimat ja lühimat teed, mis kulgeks Tallinnast Varssavisse Pärnu, Riia ja Kaunase kaudu

  19. Uudised : Linnamuusikud Euroraadios. Sumera ja Kremerata Baltica. Vox Clamantis kontserdireisil. Bachi konkurss Saksamaal / Priit Kuusk

    Index Scriptorium Estoniae

    Kuusk, Priit, 1938-

    2001-01-01

    Ans. Linnamuusikud esindab Eestit 29. apr. Euroraadios Põhja- ja Baltimaade muusika õhtul. Kremerata Baltica esines Itaalias ja Saksamaal Sumera teosega "Symphone". 22. apr.-1. maini teeb ans. Vox Clamantis kontsertreisi Prantsusmaale ja Portugali. 11.-21. apr. Saarbrückenis toimunud IV rahvusvahelisest J.S.Bachi klaverikonkursist, kus osales ka kaks eesti pianisti

  20. Sugar Metabolism of the First Thermophilic Planctomycete Thermogutta terrifontis: Comparative Genomic and Transcriptomic Approaches

    Science.gov (United States)

    Elcheninov, Alexander G.; Menzel, Peter; Gudbergsdottir, Soley R.; Slesarev, Alexei I.; Kadnikov, Vitaly V.; Krogh, Anders; Bonch-Osmolovskaya, Elizaveta A.; Peng, Xu; Kublanov, Ilya V.

    2017-01-01

    Xanthan gum, a complex polysaccharide comprising glucose, mannose and glucuronic acid residues, is involved in numerous biotechnological applications in cosmetics, agriculture, pharmaceuticals, food and petroleum industries. Additionally, its oligosaccharides were shown to possess antimicrobial, antioxidant, and few other properties. Yet, despite its extensive usage, little is known about xanthan gum degradation pathways and mechanisms. Thermogutta terrifontis, isolated from a sample of microbial mat developed in a terrestrial hot spring of Kunashir island (Far-East of Russia), was described as the first thermophilic representative of the Planctomycetes phylum. It grows well on xanthan gum either at aerobic or anaerobic conditions. Genomic analysis unraveled the pathways of oligo- and polysaccharides utilization, as well as the mechanisms of aerobic and anaerobic respiration. The combination of genomic and transcriptomic approaches suggested a novel xanthan gum degradation pathway which involves novel glycosidase(s) of DUF1080 family, hydrolyzing xanthan gum backbone beta-glucosidic linkages and beta-mannosidases instead of xanthan lyases, catalyzing cleavage of terminal beta-mannosidic linkages. Surprisingly, the genes coding DUF1080 proteins were abundant in T. terrifontis and in many other Planctomycetes genomes, which, together with our observation that xanthan gum being a selective substrate for many planctomycetes, suggest crucial role of DUF1080 in xanthan gum degradation. Our findings shed light on the metabolism of the first thermophilic planctomycete, capable to degrade a number of polysaccharides, either aerobically or anaerobically, including the biotechnologically important bacterial polysaccharide xanthan gum. PMID:29163426

  1. Novel Mono-, Di-, and Trimethylornithine Membrane Lipids in Northern Wetland Planctomycetes

    NARCIS (Netherlands)

    Moore, E.K.; Hopmans, E.C.; Rijpstra, W.I.C.; Villanueva, L.; Dedysh, S.N.; Kulichevskaya, I.S.; Wienk, H.L.J.; Schoutsen, F.; Sinninghe Damsté, J.S.

    2013-01-01

    Northern peatlands represent a significant global carbon store and commonly originate from Sphagnum moss-dominated wetlands. These ombrotrophic ecosystems are rain fed, resulting in nutrient-poor, acidic conditions. Members of the bacterial phylum Planctomycetes are highly abundant and appear to

  2. Sugar Metabolism of the First Thermophilic Planctomycete Thermogutta terrifontis: Comparative Genomic and Transcriptomic Approaches

    Directory of Open Access Journals (Sweden)

    Alexander G. Elcheninov

    2017-11-01

    Full Text Available Xanthan gum, a complex polysaccharide comprising glucose, mannose and glucuronic acid residues, is involved in numerous biotechnological applications in cosmetics, agriculture, pharmaceuticals, food and petroleum industries. Additionally, its oligosaccharides were shown to possess antimicrobial, antioxidant, and few other properties. Yet, despite its extensive usage, little is known about xanthan gum degradation pathways and mechanisms. Thermogutta terrifontis, isolated from a sample of microbial mat developed in a terrestrial hot spring of Kunashir island (Far-East of Russia, was described as the first thermophilic representative of the Planctomycetes phylum. It grows well on xanthan gum either at aerobic or anaerobic conditions. Genomic analysis unraveled the pathways of oligo- and polysaccharides utilization, as well as the mechanisms of aerobic and anaerobic respiration. The combination of genomic and transcriptomic approaches suggested a novel xanthan gum degradation pathway which involves novel glycosidase(s of DUF1080 family, hydrolyzing xanthan gum backbone beta-glucosidic linkages and beta-mannosidases instead of xanthan lyases, catalyzing cleavage of terminal beta-mannosidic linkages. Surprisingly, the genes coding DUF1080 proteins were abundant in T. terrifontis and in many other Planctomycetes genomes, which, together with our observation that xanthan gum being a selective substrate for many planctomycetes, suggest crucial role of DUF1080 in xanthan gum degradation. Our findings shed light on the metabolism of the first thermophilic planctomycete, capable to degrade a number of polysaccharides, either aerobically or anaerobically, including the biotechnologically important bacterial polysaccharide xanthan gum.

  3. Abundance, diversity and depth distribution of Planctomycetes in northern Sphagnum-dominated wetlands

    Directory of Open Access Journals (Sweden)

    Svetlana N. Dedysh

    2012-01-01

    Full Text Available Members of the bacterial phylum Planctomycetes inhabit various aquatic and terrestrial environments. In this study, fluorescence in situ hybridization (FISH was applied to assess the abundance and depth distribution of these bacteria in nine different Sphagnum-dominated wetlands of Northern Russia. Planctomycetes were most abundant in the oxic part of peat bog profiles. The respective cell numbers were in the range 1.1-6.7×107 cells per gram of wet peat, comprising 2 to 14% of total bacterial cells and displaying linear correlation to the peat water pH. Most peatland sites showed a sharp decline of planctomycete abundance with depth, while in two particular sites this decline was followed by a second population maximum in an anoxic part of the bog profile. Oxic peat layers were dominated by representatives of the Isosphaera-Singulisphaera group, while anoxic part of the bog profile was inhabited mostly by Zavarzinella- and Pirellula-like planctomycetes. Phylogenetically related bacteria of the candidate division OP3 were detected in both oxic and anoxic peat with cell densities of 0.6-4.6×106 cells per gram of wet peat.

  4. Telmatocola sphagniphila gen. nov., sp. nov., a Novel Dendriform Planctomycete from Northern Wetlands

    Science.gov (United States)

    Kulichevskaya, Irina S.; Serkebaeva, Yulia M.; Kim, Yongkyu; Rijpstra, W. Irene C.; Damsté, Jaap S. Sinninghe; Liesack, Werner; Dedysh, Svetlana N.

    2012-01-01

    Members of the phylum Planctomycetes are common inhabitants of northern wetlands. We used barcoded pyrosequencing to survey bacterial diversity in an acidic (pH 4.0) Sphagnum peat sampled from the peat bog Obukhovskoye, European North Russia. A total of 21189 bacterial 16S rRNA gene sequences were obtained, of which 1081 reads (5.1%) belonged to the Planctomycetes. Two-thirds of these sequences affiliated with planctomycete groups for which characterized representatives have not yet been available. Here, we describe two organisms from one of these previously uncultivated planctomycete groups. One isolate, strain OB3, was obtained from the peat sample used in our molecular study, while another strain, SP2T (=DSM 23888T = VKM B-2710T), was isolated from the peat bog Staroselsky moss. Both isolates are represented by aerobic, budding, pink-pigmented, non-motile, spherical cells that are arranged in unusual, dendriform-like structures during growth on solid media. These bacteria are moderately acidophilic and mesophilic, capable of growth at pH 4.0–7.0 (optimum pH 5.0–5.5) and at 6–30°C (optimum 20–26°C). The preferred growth substrates are various heteropolysaccharides and sugars, the latter being utilized only if provided in low concentrations (≤0.025%). In contrast to other described planctomycetes, strains SP2T and OB3 possess weak cellulolytic potential. The major fatty acids are C16:1ω5c, C18:1ω5c, C16:0, and C18:0. Characteristic lipids are the n-C31 polyunsaturated alkene (9–10 double bonds) and C30:1/C32:1 (ω-1) hydroxy fatty acids. The G + C content of the DNA is 58.5–59.0 mol%. Strains SP2T and OB3 share identical 16S rRNA gene sequences, which exhibit only 86 and 87% similarity to those of Gemmata obscuriglobus and Zavarzinella formosa. Based on the characteristics reported here, we propose to classify these novel planctomycetes as representatives of a novel genus and species, Telmatocola sphagniphila gen. nov., sp. nov. PMID

  5. Telmatocola sphagniphila gen. nov., sp. nov., a novel dendriform planctomycete from northern wetlands

    Directory of Open Access Journals (Sweden)

    Irina S. Kulichevskaya

    2012-04-01

    Full Text Available Members of the phylum Planctomycetes are common inhabitants of northern wetlands. We used barcoded pyrosequencing to survey bacterial diversity in an acidic (pH 4.0 Sphagnum peat sampled from the peat bog Obukhovskoye, European North Russia. A total of 21189 bacterial 16S rRNA gene sequences were obtained, of which 1081 reads (5.1% belonged to the Planctomycetes. Two-thirds of these sequences affiliated with planctomycete groups for which characterized representatives have not yet been available. Here, we describe two organisms from one of these previously uncultivated planctomycete groups. One isolate, strain OB3, was obtained from the peat sample used in our molecular study, while another strain, SP2T (=DSM 23888T = VKM B-2710T, was isolated from the peat bog Staroselskiy moss. Both isolates are represented by aerobic, budding, pink-pigmented, non-motile, spherical cells that are arranged in unusual, dendriform-like structures during growth on solid media. These bacteria are moderately acidophilic and mesophilic, capable of growth at pH 4.0-7.0 (optimum pH 5.0-5.5 and at 6-30ºC (optimum 20-26ºC. The preferred growth substrates are various heteropolysaccharides and sugars, the latter being utilized only if provided in low concentrations (≤ 0.025%. In contrast to other described planctomycetes, strains SP2T and OB3 possess weak cellulolytic potential. The major fatty acids are C16:1ω5c, C18:1ω5c, C16:0 and C18:0. Characteristic lipids are the n-C31 polyunsaturated alkene (9-10 double bonds and C30:1/C32:1 (ω-1 hydroxy fatty acids. The G+C content of the DNA is 58.5-59.0 mol%. Strains SP2T and OB3 share identical 16S rRNA gene sequences, which exhibit only 86 and 87% similarity to those of Gemmata obscuriglobus and Zavarzinella formosa. Based on the characteristics reported here, we propose to classify these novel planctomycetes as representatives of a novel genus and species, Telmatocola sphagniphila gen. nov., sp. nov.

  6. Genome Analysis of Fimbriiglobus ruber SP5T, a Planctomycete with Confirmed Chitinolytic Capability.

    Science.gov (United States)

    Ravin, Nikolai V; Rakitin, Andrey L; Ivanova, Anastasia A; Beletsky, Alexey V; Kulichevskaya, Irina S; Mardanov, Andrey V; Dedysh, Svetlana N

    2018-04-01

    Members of the bacterial order Planctomycetales have often been observed in associations with Crustacea. The ability to degrade chitin, however, has never been reported for any of the cultured planctomycetes although utilization of N -acetylglucosamine (GlcNAc) as a sole carbon and nitrogen source is well recognized for these bacteria. Here, we demonstrate the chitinolytic capability of a member of the family Gemmataceae , Fimbriiglobus ruber SP5 T , which was isolated from a peat bog. As revealed by metatranscriptomic analysis of chitin-amended peat, the pool of 16S rRNA reads from F. ruber increased in response to chitin availability. Strain SP5 T displayed only weak growth on amorphous chitin as a sole source of carbon but grew well with chitin as a source of nitrogen. The genome of F. ruber SP5 T is 12.364 Mb in size and is the largest among all currently determined planctomycete genomes. It encodes several enzymes putatively involved in chitin degradation, including two chitinases affiliated with the glycoside hydrolase (GH) family GH18, GH20 family β- N -acetylglucosaminidase, and the complete set of enzymes required for utilization of GlcNAc. The gene encoding one of the predicted chitinases was expressed in Escherichia coli , and the endochitinase activity of the recombinant enzyme was confirmed. The genome also contains genes required for the assembly of type IV pili, which may be used to adhere to chitin and possibly other biopolymers. The ability to use chitin as a source of nitrogen is of special importance for planctomycetes that inhabit N-depleted ombrotrophic wetlands. IMPORTANCE Planctomycetes represent an important part of the microbial community in Sphagnum -dominated peatlands, but their potential functions in these ecosystems remain poorly understood. This study reports the presence of chitinolytic potential in one of the recently described peat-inhabiting members of the family Gemmataceae , Fimbriiglobus ruber SP5 T This planctomycete uses

  7. The cell cycle of the planctomycete Gemmata obscuriglobus with respect to cell compartmentalization

    Directory of Open Access Journals (Sweden)

    Fuerst John A

    2009-01-01

    Full Text Available Abstract Background Gemmata obscuriglobus is a distinctive member of the divergent phylum Planctomycetes, all known members of which are peptidoglycan-less bacteria with a shared compartmentalized cell structure and divide by a budding process. G. obscuriglobus in addition shares the unique feature that its nucleoid DNA is surrounded by an envelope consisting of two membranes forming an analogous structure to the membrane-bounded nucleoid of eukaryotes and therefore G. obscuriglobus forms a special model for cell biology. Draft genome data for G. obscuriglobus as well as complete genome sequences available so far for other planctomycetes indicate that the key bacterial cell division protein FtsZ is not present in these planctomycetes, so the cell division process in planctomycetes is of special comparative interest. The membrane-bounded nature of the nucleoid in G. obscuriglobus also suggests that special mechanisms for the distribution of this nuclear body to the bud and for distribution of chromosomal DNA might exist during division. It was therefore of interest to examine the cell division cycle in G. obscuriglobus and the process of nucleoid distribution and nuclear body formation during division in this planctomycete bacterium via light and electron microscopy. Results Using phase contrast and fluorescence light microscopy, and transmission electron microscopy, the cell division cycle of G. obscuriglobus was determined. During the budding process, the bud was formed and developed in size from one point of the mother cell perimeter until separation. The matured daughter cell acted as a new mother cell and started its own budding cycle while the mother cell can itself initiate budding repeatedly. Fluorescence microscopy of DAPI-stained cells of G. obscuriglobus suggested that translocation of the nucleoid and formation of the bud did not occur at the same time. Confocal laser scanning light microscopy applied to cells stained for membranes as

  8. The complete plastid genomes of the two 'dinotoms' Durinskia baltica and Kryptoperidinium foliaceum.

    Directory of Open Access Journals (Sweden)

    Behzad Imanian

    2010-05-01

    Full Text Available In one small group of dinoflagellates, photosynthesis is carried out by a tertiary endosymbiont derived from a diatom, giving rise to a complex cell that we collectively refer to as a 'dinotom'. The endosymbiont is separated from its host by a single membrane and retains plastids, mitochondria, a large nucleus, and many other eukaryotic organelles and structures, a level of complexity suggesting an early stage of integration. Although the evolution of these endosymbionts has attracted considerable interest, the plastid genome has not been examined in detail, and indeed no tertiary plastid genome has yet been sequenced.Here we describe the complete plastid genomes of two closely related dinotoms, Durinskia baltica and Kryptoperidinium foliaceum. The D. baltica (116470 bp and K. foliaceum (140426 bp plastid genomes map as circular molecules featuring two large inverted repeats that separate distinct single copy regions. The organization and gene content of the D. baltica plastid closely resemble those of the pennate diatom Phaeodactylum tricornutum. The K. foliaceum plastid genome is much larger, has undergone more reorganization, and encodes a putative tyrosine recombinase (tyrC also found in the plastid genome of the heterokont Heterosigma akashiwo, and two putative serine recombinases (serC1 and serC2 homologous to recombinases encoded by plasmids pCf1 and pCf2 in another pennate diatom, Cylindrotheca fusiformis. The K. foliaceum plastid genome also contains an additional copy of serC1, two degenerate copies of another plasmid-encoded ORF, and two non-coding regions whose sequences closely resemble portions of the pCf1 and pCf2 plasmids.These results suggest that while the plastid genomes of two dinotoms share very similar gene content and genome organization with that of the free-living pennate diatom P. tricornutum, the K. folicaeum plastid genome has absorbed two exogenous plasmids. Whether this took place before or after the tertiary

  9. Identification of proteins likely to be involved in morphogenesis, cell division, and signal transduction in Planctomycetes by comparative genomics.

    Science.gov (United States)

    Jogler, Christian; Waldmann, Jost; Huang, Xiaoluo; Jogler, Mareike; Glöckner, Frank Oliver; Mascher, Thorsten; Kolter, Roberto

    2012-12-01

    Members of the Planctomycetes clade share many unusual features for bacteria. Their cytoplasm contains membrane-bound compartments, they lack peptidoglycan and FtsZ, they divide by polar budding, and they are capable of endocytosis. Planctomycete genomes have remained enigmatic, generally being quite large (up to 9 Mb), and on average, 55% of their predicted proteins are of unknown function. Importantly, proteins related to the unusual traits of Planctomycetes remain largely unknown. Thus, we embarked on bioinformatic analyses of these genomes in an effort to predict proteins that are likely to be involved in compartmentalization, cell division, and signal transduction. We used three complementary strategies. First, we defined the Planctomycetes core genome and subtracted genes of well-studied model organisms. Second, we analyzed the gene content and synteny of morphogenesis and cell division genes and combined both methods using a "guilt-by-association" approach. Third, we identified signal transduction systems as well as sigma factors. These analyses provide a manageable list of candidate genes for future genetic studies and provide evidence for complex signaling in the Planctomycetes akin to that observed for bacteria with complex life-styles, such as Myxococcus xanthus.

  10. Uudised : Kremerata Baltica solistid Tallinnas. Jaani Kiriku Oreli Fondis. Edison Classical Music Award 2000 / Heili Vaus-Tamm

    Index Scriptorium Estoniae

    Vaus-Tamm, Heili, 1961-

    2000-01-01

    8. apr. esinevad Kremerata Baltica kuus liiget kavaga "Gulliver Madriidis". Kontserdikava tutvustus. 13. apr. tuleb kokku Tallinna Jaani Kiriku Oreli Fondi nõukogu, et otsustada, millise firmaga sõlmitakse leping oreli taastamiseks. 4. apr. anti Amsterdamis kätte tänavused Edisoni klassikalise muusika auhinnad parimate plaadistuste eest, s.h. T. Kaljustele

  11. Genome Sequences of Shewanella baltica and Shewanella morhuae Strains Isolated from the Gastrointestinal Tract of Freshwater Fish.

    Science.gov (United States)

    Castillo, Daniel; Gram, Lone; Dailey, Frank E

    2018-06-21

    We present here the genome sequences of Shewanella baltica strain CW2 and Shewanella morhuae strain CW7, isolated from the gastrointestinal tract of Salvelinus namaycush (lean lake trout) and Coregonus clupeaformis (whitefish), respectively. These genome sequences provide insights into the niche adaptation of these specific species in freshwater systems. Copyright © 2018 Castillo et al.

  12. Characterization of Planctomyces limnophilus and development of genetic tools for its manipulation establish it as a model species for the phylum Planctomycetes.

    Science.gov (United States)

    Jogler, Christian; Glöckner, Frank Oliver; Kolter, Roberto

    2011-08-15

    Planctomycetes represent a remarkable clade in the domain Bacteria because they play crucial roles in global carbon and nitrogen cycles and display cellular structures that closely parallel those of eukaryotic cells. Studies on Planctomycetes have been hampered by the lack of genetic tools, which we developed for Planctomyces limnophilus.

  13. Abundant Trimethylornithine Lipids and Specific Gene Sequences Are Indicative of Planctomycete Importance at the Oxic/Anoxic Interface in Sphagnum-Dominated Northern Wetlands.

    Science.gov (United States)

    Moore, Eli K; Villanueva, Laura; Hopmans, Ellen C; Rijpstra, W Irene C; Mets, Anchelique; Dedysh, Svetlana N; Sinninghe Damsté, Jaap S

    2015-09-01

    Northern wetlands make up a substantial terrestrial carbon sink and are often dominated by decay-resistant Sphagnum mosses. Recent studies have shown that planctomycetes appear to be involved in degradation of Sphagnum-derived debris. Novel trimethylornithine (TMO) lipids have recently been characterized as abundant lipids in various Sphagnum wetland planctomycete isolates, but their occurrence in the environment has not yet been confirmed. We applied a combined intact polar lipid (IPL) and molecular analysis of peat cores collected from two northern wetlands (Saxnäs Mosse [Sweden] and Obukhovskoye [Russia]) in order to investigate the preferred niche and abundance of TMO-producing planctomycetes. TMOs were present throughout the profiles of Sphagnum bogs, but their concentration peaked at the oxic/anoxic interface, which coincided with a maximum abundance of planctomycete-specific 16S rRNA gene sequences. The sequences detected at the oxic/anoxic interface were affiliated with the Isosphaera group, while sequences present in the anoxic peat layers were related to an uncultured planctomycete group. Pyrosequencing-based analysis identified Planctomycetes as the major bacterial group at the oxic/anoxic interface at the Obukhovskoye peat (54% of total 16S rRNA gene sequence reads), followed by Acidobacteria (19% reads), while in the Saxnäs Mosse peat, Acidobacteria were dominant (46%), and Planctomycetes contributed to 6% of the total reads. The detection of abundant TMO lipids in planctomycetes isolated from peat bogs and the lack of TMO production by cultures of acidobacteria suggest that planctomycetes are the producers of TMOs in peat bogs. The higher accumulation of TMOs at the oxic/anoxic interface and the change in the planctomycete community with depth suggest that these IPLs could be synthesized as a response to changing redox conditions at the oxic/anoxic interface. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  14. The dinoflagellates Durinskia baltica and Kryptoperidinium foliaceum retain functionally overlapping mitochondria from two evolutionarily distinct lineages

    Directory of Open Access Journals (Sweden)

    Keeling Patrick J

    2007-09-01

    Full Text Available Abtract Background The dinoflagellates Durinskia baltica and Kryptoperidinium foliaceum are distinguished by the presence of a tertiary plastid derived from a diatom endosymbiont. The diatom is fully integrated with the host cell cycle and is so altered in structure as to be difficult to recognize it as a diatom, and yet it retains a number of features normally lost in tertiary and secondary endosymbionts, most notably mitochondria. The dinoflagellate host is also reported to retain mitochondrion-like structures, making these cells unique in retaining two evolutionarily distinct mitochondria. This redundancy raises the question of whether the organelles share any functions in common or have distributed functions between them. Results We show that both host and endosymbiont mitochondrial genomes encode genes for electron transport proteins. We have characterized cytochrome c oxidase 1 (cox1, cytochrome oxidase 2 (cox2, cytochrome oxidase 3 (cox3, cytochrome b (cob, and large subunit of ribosomal RNA (LSUrRNA of endosymbiont mitochondrial ancestry, and cox1 and cob of host mitochondrial ancestry. We show that all genes are transcribed and that those ascribed to the host mitochondrial genome are extensively edited at the RNA level, as expected for a dinoflagellate mitochondrion-encoded gene. We also found evidence for extensive recombination in the host mitochondrial genes and that recombination products are also transcribed, as expected for a dinoflagellate. Conclusion Durinskia baltica and K. foliaceum retain two mitochondria from evolutionarily distinct lineages, and the functions of these organelles are at least partially overlapping, since both express genes for proteins in electron transport.

  15. Feeding adult of Artemia salina (Crustacea-Branchiopoda on the dinoflagellate Gyrodinium corsicum (Gymnodiniales and the Chryptophyta Rhodomonas baltica

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    Rauquírio André Albuquerque Marinho da Costa

    2005-07-01

    Full Text Available Experiments were carried out on feeding performance and survival rates of adult Artemia salina exposed to no axenic strains of the dinoflagellate Gyrodinium corsicum and of the Chryptophyta Rhodomonas baltica. Filtration rates on R. baltica and G. corsicum varied from 3.35 to 7.14 ml.artemia-1.h-1 and from 2.97 to 15.86 ml.artemia-1.h-1, respectively. The ingestion rates observed for A. salina did not indicate any digestive dysfunction or physiological impairment for organisms fed on G. corsicum and their functional response were similar to those observed for other organisms like copepod fed on different food concentrations. Mortality rates oscillated from 2.5% to 100% when A. salina was fed on R. baltica or G. corsicum, respectively. Highest mortality rates observed for organisms fed on G. corsicum indicated that this dinoflagellate presented a hazard effect on A. salina that was not possible to confirm if it was related to toxin production or to nutritive inadequacy of this dinoflagellate as food for organisms of this species.Experimentos foram desenvolvidos para estudar as taxas de alimentação e de sobrevivência de Artemia salina alimentada com cepas não tóxicas do dinoflagelado Gyrodinium corsicum e da Chryptophyta Rhodomonas baltica. As taxas de filtração sobre R. baltica e G. corsicum variaram entre 3,35 e 7,14 ml.artemia-1.h-1 e 2,97 e 15,86 ml.artemia-1.h-, respectivamente. As taxas de ingestão observadas para A. salina não indicaram disfunção digestiva ou prejuízo fisiológico nos organismos alimentados com G. corsicum, sendo a resposta funcional destes organismos similar a observada em copépodos alimentados com diferentes concentrações de alimento. As taxas de mortalidade de A. salina oscilaram entre 2,5 e 100% quando alimentada com R. baltica e G. corsicum, respectivamente. As maiores taxas de mortalidade observadas para os organismos alimentados com G. corsicum indicam que este dinoflagelado apresenta algum efeito

  16. Molecular Signatures for the PVC Clade (Planctomycetes, Verrucomicrobia, Chlamydiae and Lentisphaerae of Bacteria Provide Insights into their Evolutionary Relationships

    Directory of Open Access Journals (Sweden)

    Radhey S. Gupta

    2012-09-01

    Full Text Available The PVC superphylum is an amalgamation of species from the phyla Planctomycetes, Verrucomicrobia and Chlamydiae, along with the Lentisphaerae, Poribacteria and two other candidate divisions. The diverse species of this superphylum lack any significant marker that differentiates them from other bacteria. Recently, genome sequences for 37 species covering all of the main PVC groups of bacteria have become available. We have used these sequences to construct a phylogenetic tree based upon concatenated sequences for 16 proteins and identify molecular signatures in protein sequences that are specific for the species from these phyla or those providing molecular links among them. Of the useful molecular markers identified in the present work, 6 conserved signature indels (CSIs in the proteins Cyt c oxidase, UvrD helicase, urease and a helicase-domain containing protein are specific for the species from the Verrucomicrobia phylum; three other CSIs in an ABC transporter protein, cobyrinic acid ac-diamide synthase and SpoVG protein are specific for the Planctomycetes species. Additionally, a 3 aa insert in the RpoB protein is uniquely present in all sequenced Chlamydiae, Verrucomicrobia and Lentisphaerae species, providing evidence for the shared ancestry of the species from these three phyla. Lastly, we have also identified a conserved protein of unknown function that is exclusively found in all sequenced species from the phyla Chlamydiae, Verrucomicrobia, Lentisphaerae and Planctomycetes suggesting a specific linkage among them. The absence of this protein in Poribacteria, which branches separately from other members of the PVC clade, indicates that it is not specifically related to the PVC clade of bacteria. The molecular markers described here in addition to clarifying the evolutionary relationships among the PVC clade of bacteria also provide novel tools for their identification and for genetic and biochemical studies on these organisms.

  17. Trilobites and biofacies in the Early–Middle Ordovician of Baltica and a brief comparison with the Yangtze Plate

    Directory of Open Access Journals (Sweden)

    Jan Bergström †

    2013-11-01

    Full Text Available Baltica except for Baltoscandia was subject to an early Tremadocian immigration of trilobites similar to that on other plates. In Baltoscandia the Olenid biofacies lingered on until it was replaced by the late Tremadocian Ceratopyge biofacies. For the rest of the time (Floian to mid-Darriwilian, Baltoscandia had fairly monotonous lithologies and faunas, constituting a single Asaphid biofacies with lateral variations expressed as differences largely in the relative abundance of species. In the South Urals immigration started in the earliest Tremadocian with fairly rich deep-water faunas. A poorer fauna is known from the Polar Urals. A slightly younger, sparse fauna is known from Paj-Khoj. Over most of the Ural border north of the South Urals there was a further development of first a Ceratopyge biofacies, then an eastern Asaphid biofacies, together with more siliciclastic input to the lithofacies and with fewer asaphids than in Baltoscandia. In the South Urals there was a development in the Darriwilian of a Cheirurid biofacies following the Ceratopyge biofacies. By contrast, the shelf part of the South China Plate shows a development of fifteen biofacies distinguished on the genus level, and the number of species for each biofacies is notably small. The major difference in the pattern of distribution of the biofacies probably reflects the faunal development in rather different climatic conditions, suggesting that the Yangtze block is supposedly positioned rather distant from Baltica, but still close enough to share genera inhabiting the outer shelf.

  18. The Life History of Flabellula baltica Smirnov (Gymnamoebae, Rhizopoda): Adaptations to a Spatially and Temporally Heterogeneous Environment

    DEFF Research Database (Denmark)

    Fenchel, Tom

    2010-01-01

    The polymorphic life history of the marine naked amoeba Flabellula baltica was studied. It can be interpreted in terms of adaptations to an environment that is patchy in time and space and it represents trade-off between longevity during starvation and the ability to initiate multiplication soon ...

  19. Hyperextension in the Caledonian margin of Baltica and its bearing on the structural and metamorphic evolution of Scandinavian Caledonides (Invited)

    Science.gov (United States)

    Andersen, T. B.

    2013-12-01

    The Scandinavian segment (~2000 km) of the Caledonian-Appalachian orogen formed by a head-on collision of Baltica and Laurentia. The collision followed rapid (>10 cm/yr) convergence, subduction and closure of the Iapetus Ocean in the Ordovician to the Middle Silurian. The collision culminated in a Himalayan type continental collision at 430 Ma, after which the continental subduction/convergence continued for 20 Myr. The terminal stage was characterized by syn- and post-orogenic extension and exhumation, which produced a template used in opening of the present-day Norwegian Sea. The Scandian collision produced a 'layer-cake' tectono-stratigraphy, but correlation of individual nappe units along strike is not trivial. The vestiges of the Iapetus can, however, be traced along the entire Scandinavian Peninsula and constitute the Iapetus suture. Rocks of assumed Laurentian origin structurally overlie the suture. The outboard units underwent several orogenic events that pre-date the Scandian collision and which took place outboard of Baltica. These will not be discussed further here. The Caledonian passive margin of Baltica was very wide, consisting of non-volcanic hyperextended segments as well as passive volcanic margin domains. Basement-cover pairs, in places with mafic dyke-swarms constitute most of these units. The Baltican and assumed Baltican units below the suture have evidence of diachronous and relatively locally developed pre-Scandian deformation and metamorphic events. In S. Norway large basement-cover units are separated by a melange with numerous solitary mantle peridotites and a number of detrital serpentinites. The melange can be traced along strike across S. Norway. Locally, an island-type ';Celtic' fauna is preserved in detrital serpentinite. Some mantle rocks were structurally emplaced, exhumed, eroded and juxtaposed with continental clastics and crust before the Early Ordovician. The melange was recently interpreted to represent an oceanic to

  20. Paludisphaera borealis gen. nov., sp. nov., a hydrolytic planctomycete from northern wetlands, and proposal of Isosphaeraceae fam. nov.

    Science.gov (United States)

    Kulichevskaya, Irina S; Ivanova, Anastasia A; Suzina, Natalia E; Rijpstra, W Irene C; Sinninghe Damsté, Jaap S; Dedysh, Svetlana N

    2016-02-01

    Two isolates of aerobic, budding, pink-pigmented bacteria, designated strains PX4 T and PT1, were isolated from a boreal Sphagnum peat bog and a forested tundra wetland. Cells of these strains were non-motile spheres that occurred singly or in short chains. Novel isolates were capable of growth at pH values between 3.5 and 6.5 (optimum at pH 5.0-5.5) and at temperatures between 6 and 30 °C (optimum at 15-25 °C). Most sugars and a number of polysaccharides including pectin, xylan, lichenin and Phytagel were used as growth substrates. The major fatty acids were C 16 : 0 , C 18 : 1 ω9 and C 18 : 0 ; the major polar lipids were phosphocholine and trimethylornithine. The quinone was menaquinone-6, and the G+C content of the DNA was 66 mol%. Strains PX4 T and PT1 were members of the order Planctomycetales and displayed 93-94 % 16S rRNA gene sequence similarity to Aquisphaera giovannonii , 91-92 % to species of the genus Singulisphaera and 90-91 % to Isosphaera pallida . The two novel strains, however, differed from members of these genera by cell morphology, substrate utilization pattern and a number of physiological characteristics. Based on these data, the novel isolates should be considered as representing a novel genus and species of planctomycetes, for which the name Paludisphaera borealis gen. nov., sp. nov., is proposed. The type strain is PX4 T ( = DSM 28747 T  = VKM B-2904 T ). We also suggest the establishment of a novel family, Isosphaeraceae fam. nov., to accommodate stalk-free planctomycetes with spherical cells, which can be assembled in short chains, long filaments or shapeless aggregates. This family includes the genera Isosphaera, Aquisphaera, Singulisphaera and Paludisphaera .

  1. Identification of Shewanella baltica as the most important H2S-producing species during iced storage of danish marine fish

    DEFF Research Database (Denmark)

    Vogel, Birte Fonnesbech; Venkateswaran, K.; Satomi, M.

    2005-01-01

    are important in fish spoilage. More than 500 H2S-producing strains were isolated from iced stored marine fish (cod, plaice, and flounder) caught in the Baltic Sea during winter or summer time. All strains were identified as Shewanella species by phenotypic tests. Different Shewanella species were present...... unchanged (i.e., trimethylamine-N-oxide reduction and H2S production); however, the main H2S-producing organism was identified as S. baltica....

  2. Paleomagnetic data for Siberia and Baltica in the context of testing some geodynamic models of the formation of the Central Asian Mobile Belt

    Science.gov (United States)

    Shatsillo, A. V.; Kuznetsov, N. B.; Dronov, A. V.

    2017-09-01

    The synthesis of the paleomagnetic data for the Siberian (Siberia) and East European (Baltica) platforms shows that since the Early Paleozoic they could have experienced coherent movements as a part of consolidated continental agglomeration (a composite continent), which also includes the Arctida continent. Based on the paleomagnetic data, the relative positions of the Siberia and Baltica during the Ordovician is reconstructed, and a series of paleogeographical reconstructions describing the drift of the composite continent is suggested. The results of the lithologic-facial analysis of the sedimentation settings within the Ordovician basins of the Siberian and East European platforms and paleoclimatic markers are consistent with the suggested configuration and paleogeographical position of the composite continent. The suggested reconstructions and the ages of detrital zircons from the Early Paleozoic complexes of the platform margins and some objects of the Central Asian Mobile Belt (CAMB) reasonably well agree with the hypothesis (Sengör et al., 1993) which interprets the formation of the structure of CAMB Paleozoides as a result of the evolution of the island arc stretching along the margins of Siberia and Baltica.

  3. Uptake and loss of 134Cs and 60Co by the Baltic bivalve Macoma Baltica under laboratory conditions

    International Nuclear Information System (INIS)

    Evans, S.

    1982-01-01

    In order to predict the radiological impact on man via harvestable sea food products, it is essential to make a critical evaluation of the transfer routes and the rates on which radionuclides are transferred through the aquatic food chains. In the Baltic, the bivalve Macoma Baltica comprises a main food item for fish species of commercial interest, such as flounder. The accumulation and release of Cs-134 and Co-60 by Macoma was experimentally investigated. The nuclides were added to the water and the activity content of the bivalves was determined at regular intervals. The uptake was quite rapid, 40 per cent (Cs) and 55 per cent (Co) respectively of the final steady state was obtained after 24 hours. The subsequent release was rapid as well, 50 per cent (Cs) and 40 per cent (Co) respectively of the accumulated activity was lost within 6 days. The experiments demonstrated that the major intake route following short-term releases of activity will be from the water column. The close connection between activity in water and organism can thus be used for predictive purposes without the complication of radionuclide uptake from contaminated sediments. (Author)

  4. The 1st EMBO workshop on PVC bacteria-Planctomycetes-Verrucomicrobia-Chlamydiae superphylum: exceptions to the bacterial definition?

    Science.gov (United States)

    Devos, Damien P; Jogler, Christian; Fuerst, John A

    2013-10-01

    The PVC superphylum is a phylogenetically supported collection of various related bacterial phyla that comprise unusual characteristics and traits. The 'PVC' abbreviation derives from Planctomycetes, Verrucomicrobia and Chlamydiae as members of this superphylum, while additional bacterial phyla are related. There has recently been increasing and exciting interest in the cell biology, physiology and ecology of members of this superphylum, including evolutionary implications of the complex cell organization of some species. It is timely that international researchers in the PVC superphylum field met to discuss these developments. The first meeting entirely dedicated to those bacteria, the EMBO workshop "PVC superphylum: Exceptions to the bacterial definition" was held at the Heidelberg University to catalyze the formation of a vital scientific community supporting PVC-bacterial research. More than 45 investigators from more than 20 countries (PIs, senior scientists and students) attended the meeting and produced a great starting point for future collaborative research. This Special Issue will focus on the EMBO-PVC meeting. This Perspective briefly summarizes the history of PVC-research, focusing on the key findings and provides a brief summary of the meeting with a focus on the major questions that arose during discussion and that might influence the research in the years to come.

  5. Singulisphaera rosea sp. nov., a planctomycete from acidic Sphagnum peat, and emended description of the genus Singulisphaera.

    Science.gov (United States)

    Kulichevskaya, Irina S; Detkova, Ekaterina N; Bodelier, Paul L E; Rijpstra, W Irene C; Damsté, Jaap S Sinninghe; Dedysh, Svetlana N

    2012-01-01

    An aerobic, pink-pigmented, budding bacterium, designated strain S26(T), was isolated from an acidic Sphagnum peat bog of north-western Russia. Cells were non-motile and spherical, occurring singly, in pairs or in short chains, and were able to attach to surfaces by means of a holdfast material. Strain S26(T) was a moderately acidophilic, mesophilic organism capable of growth at pH 3.2-7.1 (optimum at pH 4.8-5.0) and at 4-33 °C (optimum at 20-26 °C). Most sugars, several organic acids and polyalcohols were the preferred growth substrates. The major fatty acids were C(16:0), C(18:1)ω9c and C(18:2)ω6c,12c. The major neutral lipids were n-C(31:9) hydrocarbon and squalene; the polar lipids were phosphatidylglycerol, phosphatidylcholine and components with an unknown structure. The DNA G+C content of strain S26(T) was 62.2 mol%. 16S rRNA gene sequence analysis showed that strain S26(T) is a member of the order Planctomycetales. Among taxonomically characterized representatives of this order, highest levels of 16S rRNA gene sequence similarity (95.1-95.2%) were observed with strains of the non-filamentous, peat-inhabiting planctomycete Singulisphaera acidiphila. Strain S26(T) could be differentiated from Singulisphaera acidiphila based on pigmentation, significant differences in substrate utilization patterns, greater tolerance of acidic conditions and the presence of C(16:1)ω9c. Based on the data presented, strain S26(T) is considered to represent a novel species of the genus Singulisphaera, for which the name Singulisphaera rosea sp. nov. is proposed; the type strain is S26(T) (=DSM 23044(T)=VKM B-2599(T)).

  6. Proteins Related to the Type I Secretion System Are Associated with Secondary SecA_DEAD Domain Proteins in Some Species of Planctomycetes, Verrucomicrobia, Proteobacteria, Nitrospirae and Chlorobi.

    Directory of Open Access Journals (Sweden)

    Olga K Kamneva

    Full Text Available A number of bacteria belonging to the PVC (Planctomycetes-Verrucomicrobia-Chlamydiae super-phylum contain unusual ribosome-bearing intracellular membranes. The evolutionary origins and functions of these membranes are unknown. Some proteins putatively associated with the presence of intracellular membranes in PVC bacteria contain signal peptides. Signal peptides mark proteins for translocation across the cytoplasmic membrane in prokaryotes, and the membrane of the endoplasmic reticulum in eukaryotes, by highly conserved Sec machinery. This suggests that proteins might be targeted to intracellular membranes in PVC bacteria via the Sec pathway. Here, we show that canonical signal peptides are significantly over-represented in proteins preferentially present in PVC bacteria possessing intracellular membranes, indicating involvement of Sec translocase in their cellular targeting. We also characterized Sec proteins using comparative genomics approaches, focusing on the PVC super-phylum. While we were unable to detect unique changes in Sec proteins conserved among membrane-bearing PVC species, we identified (1 SecA ATPase domain re-arrangements in some Planctomycetes, and (2 secondary SecA_DEAD domain proteins in the genomes of some Planctomycetes, Verrucomicrobia, Proteobacteria, Nitrospirae and Chlorobi. This is the first report of potentially duplicated SecA in Gram-negative bacteria. The phylogenetic distribution of secondary SecA_DEAD domain proteins suggests that the presence of these proteins is not related to the occurrence of PVC endomembranes. Further genomic analysis showed that secondary SecA_DEAD domain proteins are located within genomic neighborhoods that also encode three proteins possessing domains specific for the Type I secretion system.

  7. Rail Baltica tuleb : reisiterminalide arhitektuurivõistlused Tallinnas ja Pärnus = Rail Baltic is coming : Arhitecture competitions for passenger rail terminals in Tallinn and Pärnu / Andres Lindemann

    Index Scriptorium Estoniae

    Lindemann, Andres

    2015-01-01

    2014.a. lõpus lõppesid arhitektuurivõistlused Tallinnas Ülemistele ja Pärnus Papiniidu piirkonda plaanitavatele Rail Baltica reisiterminalidele. Artiklis on antud põgus ülevaade võitnud töödest

  8. Identification of Shewanella baltica as the most important H2S-producing species during iced storage of Danish marine fish.

    Science.gov (United States)

    Fonnesbech Vogel, Birte; Venkateswaran, Kasthuri; Satomi, Masataka; Gram, Lone

    2005-11-01

    Shewanella putrefaciens has been considered the main spoilage bacteria of low-temperature stored marine seafood. However, psychrotropic Shewanella have been reclassified during recent years, and the purpose of the present study was to determine whether any of the new Shewanella species are important in fish spoilage. More than 500 H2S-producing strains were isolated from iced stored marine fish (cod, plaice, and flounder) caught in the Baltic Sea during winter or summer time. All strains were identified as Shewanella species by phenotypic tests. Different Shewanella species were present on newly caught fish. During the warm summer months the mesophilic human pathogenic S. algae dominated the H2S-producing bacterial population. After iced storage, a shift in the Shewanella species was found, and most of the H2S-producing strains were identified as S. baltica. The 16S rRNA gene sequence analysis confirmed the identification of these two major groups. Several isolates could only be identified to the genus Shewanella level and were separated into two subgroups with low (44%) and high (47%) G+C mol%. The low G+C% group was isolated during winter months, whereas the high G+C% group was isolated on fish caught during summer and only during the first few days of iced storage. Phenotypically, these strains were different from the type strains of S. putrefaciens, S. oneidensis, S. colwelliana, and S. affinis, but the high G+C% group clustered close to S. colwelliana by 16S rRNA gene sequence comparison. The low G+C% group may constitute a new species. S. baltica, and the low G+C% group of Shewanella spp. strains grew well in cod juice at 0 degrees C, but three high G+C Shewanella spp. were unable to grow at 0 degrees C. In conclusion, the spoilage reactions of iced Danish marine fish remain unchanged (i.e., trimethylamine-N-oxide reduction and H2S production); however, the main H2S-producing organism was identified as S. baltica.

  9. Paleomagnetism of Devonian dykes in the northern Kola Peninsula and its bearing on the apparent polar wander path of Baltica in the Precambrian

    Science.gov (United States)

    Veselovskiy, Roman V.; Bazhenov, Mikhail L.; Arzamastsev, Andrey A.

    2016-04-01

    Mafic dykes and large alkaline and carbonatite intrusions of Middle-Late Devonian age are widespread on the Kola Peninsula in NE Fennoscandia. These magmatic rocks are well characterized with petrographic, geochemical and geochronological data but no paleomagnetic results have been reported yet. We studied dolerite dykes from the northern part of the Peninsula and isolated three paleomagnetic components in these rocks. A low-temperature component is aligned along the present-day field, while a major constituent of natural remanent magnetization is an intermediate-temperature component (Decl. = 79.6°, Inc. = 78.5°, α95 = 5,9°, N = 17 sites) that is present in most Devonian dykes but is found in some baked metamorphic rocks and Proterozoic dykes too. Finally, a primary Devonian component could be reliably isolated from two dykes only. Rock-magnetic studies point to presumably primary low-Ti titanomagnetite and/or pure magnetite as the main remanence carriers but also reveal alteration of the primary minerals and the formation of new magnetic phases. The directions of a major component differ from the Middle Paleozoic reference data for Baltica but closely match those for the 190 ± 10 Ma interval recalculated from the apparent polar wander path of the craton. We assume that this Early Jurassic component is a low-temperature overprint of chemical origin. The main impact of the new results is not to mid-Paleozoic or Early Mesozoic times but to much older epochs. Analysis of paleomagnetic data shows that the directionally similar remanences are present in objects with the ages ranging from 500 Ma to 2 Ga over entire Fennoscandia. Hence we argue that an Early Jurassic remagnetization is of regional extent but cannot link it to a certain process and a certain tectonic event. If true, this hypothesis necessitates a major revision of the APWP for Baltica over a wide time interval.

  10. ORF Alignment: NC_005027 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_005027 gi|32477023 >1t06A 1 191 9 220 1e-24 ... ref|NP_870017.1| probable DNA alkylation... repair enzyme [Rhodopirellula baltica SH 1] ... emb|CAD79170.1| probable DNA alkylation repair

  11. The structure of a novel thermophilic esterase from the Planctomycetes species, Thermogutta terrifontis reveals an open active site due to a minimal ‘cap’ domain.

    Directory of Open Access Journals (Sweden)

    Jennifer Ann Littlechild

    2015-11-01

    Full Text Available A carboxyl esterase (TtEst2 has been identified in a novel thermophilic bacterium, Thermogutta terrifontis from the phylum Planctomycetes and has been cloned and over-expressed in Escherichia coli. The enzyme has been characterised biochemically and shown to have activity towards small p-nitrophenyl (pNP carboxylic esters with optimal activity for pNP-acetate. The enzyme shows moderate thermostability retaining 75% activity after incubation for 30 minutes at 70°C. The crystal structures have been determined for the native TtEst2 and its complexes with the carboxylic acid products propionate, butyrate and valerate. TtEst2 differs from most enzymes of the α/β-hydrolase family 3 as it lacks the majority of the ‘cap’ domain and its active site cavity is exposed to the solvent. The bound ligands have allowed the identification of the carboxyl pocket in the enzyme active site. Comparison of TtEst2 with structurally related enzymes has given insight into how differences in their substrate preference can be rationalised based upon the properties of their active site pockets.

  12. Kinetics of biofilm formation and desiccation survival of Listeria monocytogenes in single and dual species biofilms with Pseudomonas fluorescens, Serratia proteamaculans or Shewanella baltica on food-grade stainless steel surfaces.

    Science.gov (United States)

    Daneshvar Alavi, Hessam Edin; Truelstrup Hansen, Lisbeth

    2013-01-01

    This study investigated the dynamics of static biofilm formation (100% RH, 15 °C, 48-72 h) and desiccation survival (43% RH, 15 °C, 21 days) of Listeria monocytogenes, in dual species biofilms with the common spoilage bacteria, Pseudomonas fluorescens, Serratia proteamaculans and Shewanella baltica, on the surface of food grade stainless steel. The Gram-negative bacteria reduced the maximum biofilm population of L. monocytogenes in dual species biofilms and increased its inactivation during desiccation. However, due to the higher desiccation resistance of Listeria relative to P. fluorescens and S. baltica, the pathogen survived in greater final numbers. In contrast, S. proteamaculans outcompeted the pathogen during the biofilm formation and exhibited similar desiccation survival, causing the N21 days of Serratia to be ca 3 Log10(CFU cm(-2)) greater than that of Listeria in the dual species biofilm. Microscopy revealed biofilm morphologies with variable amounts of exopolymeric substance and the presence of separate microcolonies. Under these simulated food plant conditions, the fate of L. monocytogenes during formation of mixed biofilms and desiccation depended on the implicit characteristics of the co-cultured bacterium.

  13. Fimbriiglobus ruber gen. nov., sp. nov., a Gemmata-like planctomycete from Sphagnum peat bog and the proposal of Gemmataceae fam. nov.

    Science.gov (United States)

    Kulichevskaya, Irina S; Ivanova, Anastasia A; Baulina, Olga I; Rijpstra, W Irene C; Sinninghe Damsté, Jaap S; Dedysh, Svetlana N

    2017-02-01

    An aerobic, budding, dark pink to red-pigmented bacterium was isolated from an acidic boreal Sphagnum peat bog and designated strain SP5T. Cells of this strain were non-motile spheres that were uniformly covered with crateriform pits and fimbria, and tended to form aggregates during growth in liquid media. Strain SP5T was capable of growth between pH 4.0 and pH 6.8 (optimum at pH 5.5-6.0) and at temperatures between 10 and 30 °C (optimum at 20-25 °C). The preferred growth substrates were sugars and some heteropolysaccharides. The major fatty acids were C20 : 1ω9c, C16 : 1ω9c and C16 : 0, and the major polar lipid was trimethylornithine. Cells contained also significant amounts of bound (ω-1)OH-C30 : 1 fatty acid. The quinone was menaquinone-6, and the G+C content of the DNA was 60.7 mol%. Strain SP5T was a member of the order Planctomycetales and belonged to the phylogenetic lineage defined by the genus Gemmata. It displayed 88 and 89 % 16S rRNA gene sequence similarity to Gemmata obscuriglobusUQM 2246T and 'Gemmata massiliana' IIL30, 89 % to Zavarzinella formosa A10T and 86 % to Telmatocola sphagniphila SP2T. However, strain SP5T differed from members of these genera by cell morphology, substrate utilization pattern and fatty acid composition. Based on these data, the novel isolate should be considered as representing a novel species of a new genus of planctomycetes, for which the name Fimbriiglobus ruber gen. nov., sp. nov, is proposed. The type strain is SP5T (=LMG 29572T=VKM B-3045T). We also suggest the establishment of a novel family, Gemmataceaefam. nov., which includes the phylogenetically related genera Gemmata, Zavarzinella, Telmatocola and Fimbriiglobus.

  14. Regina Baltica runs aground, none injured

    Index Scriptorium Estoniae

    2005-01-01

    Tallinki laev sõitis 27. septembri õhtul Kapellskäri lähedal madalikule, kust pääses omal jõul poole kahe paiku liikuma, reisijad kannatada ei saanud. Õnnetuse põhjuseks oli elektrihäire, mille tõttu muutus laev juhitamatuks

  15. Dicty_cDB: AFK338 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available AF (Link to library) AFK338 (Link to dictyBase) - - - - AFK338P (Link to Original s...ite) AFK338F 659 AFK338Z 221 AFK338P 880 - - Show AFK338 Library AF (Link to library) Clone ID AFK338 (Link to dic...01175_2502( CP001175 |pid:none) Listeria monocytogenes HCC23, c... 40 0.099 AY714838_16( AY714838 |pid:none) Unculture...A sequence. 44 3.0 1 AE006080 |AE006080.1 Pasteurella multocida PM70 section 47 o... 0.003 BX294148_242( BX294148 |pid:none) Rhodopirellula baltica SH 1 comp... 44 0.005 CP000910_1528( CP00091

  16. A new Late Ordovician erratic anthaspidellid sponge (Porifera) originating from Baltica

    NARCIS (Netherlands)

    Rhebergen, F.

    2014-01-01

    The new anthaspidellid taxon Brevaspidella dispersa is erected for specimens recovered from the Late Ordovician sponge assemblages of the island of Gotland, Sweden and the Dutch-German border region. In the latter area, they are collected from Early Pleistocene fluvial deposits of the Baltic River

  17. Alleged cnidarian Sphenothallus in the Late Ordovician of Baltica, its mineral composition and microstructure

    Directory of Open Access Journals (Sweden)

    Olev Vinn

    2015-12-01

    Full Text Available Sphenothallus is a problematic fossil with possible cnidarian affinities. Two species of Sphenothallus, S. aff. longissimus and S. kukersianus, occur in the normal marine sediments of the Late Ordovician of Estonia. S. longissimus is more common than S. kukersianus and has a range from early Sandbian to middle Katian. Sphenothallus had a wide paleo-biogeographic distribution in the Late Ordovician. The tubes of Sphenothallus are composed of lamellae with a homo-geneous microstructure. The homogeneous microstructure could represent a diagenetic fabric, based on the similarity to diagenetic structures in Torellella (Cnidaria?, Hyolithelminthes. Tubes of Sphenothallus have an apatitic composition, but one tube contains lamellae of diagenetic calcite within the apatitic structure. Sphenothallus presumably had origi-nally biomineralized apatitic tubes. Different lattice parameters of the apatite indicate that biomineralization systems of phosphatic cnidarians Sphenothallus and Conularia sp. may have been different.

  18. MCDA and Risk Analysis in Transport Infrastructure Appraisals: the Rail Baltica Case

    DEFF Research Database (Denmark)

    Ambrasaite, Inga; Barfod, Michael Bruhn; Salling, Kim Bang

    2011-01-01

    This paper sets out a decision support system (DSS), COSIMA, involving the combination of cost-benefit analysis and multicriteria decision analysis (MCDA) for transport infrastructure appraisals embracing both economic and strategic impacts. However, some shortcomings appear in the methodology re...

  19. "Baltica und Seltene Drucke" in der Akademischen Bibliothek der Universität Tallinn / Helje Kannik

    Index Scriptorium Estoniae

    Kannik, Helje-Laine

    2010-01-01

    Tallinna Ülikooli Akadeemilise Raamatukogu Baltika ja haruldaste raamatute osakonna kogust, eesti retrospektiivse rahvusbibliograafia koostamisest, eesti vanaraamatu kohta ilmunud bibliograafiatest ja kajastumisest andmebaasides

  20. Zavarzinella formosa gen. nov., sp. nov., a novel stalked, Gemmata-like planctomycete from a Siberian peat bog

    NARCIS (Netherlands)

    Kulichevskaya, I.S.; Baulina, O.I.; Bodelier, P.L.E.; Rijpstra, W.I.C.; Sinninghe Damsté, J.S.; Dedysh, S.N.

    2009-01-01

    An aerobic, pink-pigmented, budding and rosette-forming bacterium was isolated from an acidic Sphagnum peat bog and designated strain A10T. The 16S rRNA gene sequence analysis showed that strain A10T was a member of the order Planctomycetales and belonged to a phylogenetic lineage defined by the

  1. Singulisphaera rosea sp. nov., a planctomycete from acidic Sphagnum peat, and emended description of the genus Singulisphaera

    NARCIS (Netherlands)

    Kulichevskaya, I.S.; Detkova, E.N.; Bodelier, P.L.E.; Rijpstra, W.I.C.; Sinninghe Damsté, J.S.; Dedysh, S.N.

    2012-01-01

    A novel species, Singulisphaera rosea sp. nov., is proposed for aerobic, pink-pigmented, budding bacterium isolated from an acidic Sphagnum peat bog of northwestern Russia. This bacterium, designated strain S26T, has non-motile, spherical cells that occur singly, in pairs or in short chains and

  2. The Sorgenfrei-Tornquist Zone as the mantle edge of Baltica lithosphere: new evidence from three-dimensional seismic anisotropy

    Czech Academy of Sciences Publication Activity Database

    Babuška, Vladislav; Plomerová, Jaroslava

    2004-01-01

    Roč. 16, č. 5 (2004), s. 243-249 ISSN 0954-4879 R&D Projects: GA AV ČR KSK3012103; GA ČR GA205/04/0748; GA AV ČR IAA3012405 Keywords : seismic experiment TOR * Trans-European Suture Zone * seismic anisotropy Subject RIV: DC - Siesmology, Volcanology, Earth Structure Impact factor: 2.059, year: 2004

  3. The effect of algae diets (Skeletonema costatum and Rhodomonas baltica) on the biochemical composition and sensory characteristics of Pacific cupped oysters (Crassostrea gigas) during land-based refinement

    NARCIS (Netherlands)

    Houcke, van Jasper; Medina, Isabel; Maehre, Hanne K.; Cornet, Josiane; Cardinal, Mireille; Linssen, Jozef; Luten, Joop

    2017-01-01

    Oyster refinement, a common practice in France, is aimed at increasing the weight of oyster tissue and influencing the taste properties of the refined oysters. Refinement usually takes place in land-based systems where the oysters are fed with relatively high concentrations of microalgae. In this

  4. Environmental consequence analyses of fish farm emissions related to different scales and exemplified by data from the Baltic--a review.

    Science.gov (United States)

    Gyllenhammar, Andreas; Håkanson, Lars

    2005-08-01

    The aim of this work is to review studies to evaluate how emissions from fish cage farms cause eutrophication effects in marine environments. The focus is on four different scales: (i) the conditions at the site of the farm, (ii) the local scale related to the coastal area where the farm is situated, (iii) the regional scale encompassing many coastal areas and (iv) the international scale including several regional coastal areas. The aim is to evaluate the role of nutrient emissions from fish farms in a general way, but all selected examples come from the Baltic Sea. An important part of this evaluation concerns the method to define the boundaries of a given coastal area. If this is done arbitrarily, one would obtain arbitrary results in the environmental consequence analysis. In this work, the boundary lines between the coast and the sea are drawn using GIS methods (geographical information systems) according to the topographical bottleneck method, which opens a way to determine many fundamental characteristics in the context of mass balance calculations. In mass balance modelling, the fluxes from the fish farm should be compared to other fluxes to, within and from coastal areas. Results collected in this study show that: (1) at the smallest scale (impact areas of fish cage farm often corresponds to the size of a "football field" (50-100 m) if the annual fish production is about 50 ton, (2) at the local scale (1 ha to 100 km2), there exists a simple load diagram (effect-load-sensitivity) to relate the environmental response and effects from a specific load from a fish cage farm. This makes it possible to obtain a first estimate of the maximum allowable fish production in a specific coastal area, (3) at the regional scale (100-10,000 km2), it is possible to create negative nutrient fluxes, i.e., use fish farming as a method to reduce the nutrient loading to the sea. The breaking point is to use more than about 1.1 g wet weight regionally caught wild fish per gram feed for the cultivated fish, and (4) at the international scale (>10,000 km2) related to the Baltic Proper, the contribution from fish farms to the overall nutrient fluxes are very small. We have also given two case-studies at the local scale where the impact of the fish farm emissions are greatest and the idea is to identify coastal areas unsuitable and suitable for fish cage farms and the reasons why. It should also be stressed that the results presented here are exemplified using emissions from fish farms, but that the underlying principles to evaluate the ecosystem effects of nutrient discharges from point source emissions are valid in a wider and more general perspective.

  5. Taanlased pidasid Pärnut läbivat Rail Balticat kalleimaks / Raavo Raadik

    Index Scriptorium Estoniae

    Raadik, Raavo

    2007-01-01

    Taani konsultatsioonifirma COWI tutvustas uuringut, milles analüüsiti Balti riike Euroopaga ühendava raudtee Rail Baltica majanduslikku tasuvust ning selle loomiseks vajalike investeeringute mahtu. Kaart: Rail Baltica võimalik teekond Eestis

  6. Doroga do jevroporoga / Mihhail Tuzhikov

    Index Scriptorium Estoniae

    Tuzhikov, Mihhail

    2003-01-01

    Ülevaade investeeringutest maanteede remonti Eestis, Lätis, Leedus, samuti projektidest Via Baltica ja Via-Hanseatica. Tabel: Võrdlevad andmed Baltimaade ja Soome teedest. Diagrammid: Investeeringute jagunemine Baltimaades projektis Via Baltica 1996-2006

  7. Timetable set for new transport development / Michael West

    Index Scriptorium Estoniae

    West, Michael

    2003-01-01

    Kuna Rail Baltica ja Via Baltica projektid on stagneerunud, oodatakse uuelt, multimodaalselt transpordikoridorilt (maanteed, raudteed, sadamad) mitmekülgsemaid võimalusi ühendamaks Baltimaid Poola ja Euroopa Liidu liikmesriikidega

  8. Anaerobic ammonium oxidation by marine and freshwater planctomycete-like bacteria RID B-8834-2011 RID B-5428-2008 RID C-3269-2011 RID D-1875-2009

    DEFF Research Database (Denmark)

    Jetten, MSM; Sliekers, O.; Kuypers, M.

    2003-01-01

    , and contributed substantially to the loss of fixed nitrogen. All three species contain a unique organelle-the anammoxosome-in their cytoplasm. The anammoxosome contains the hydrazine/hydroxylamine oxidoreductase enzyme, and is thus the site of anammox catabolism. The anammoxosome is surrounded by a very dense...

  9. Herderi instituudist Marburgis, eesti kunstiajaloost ja "Eesti kunsti ajaloost" / Krista Kodres

    Index Scriptorium Estoniae

    Kodres, Krista, 1957-

    2001-01-01

    Herderi instituudist, mida sealt leiab Eesti uurija (Baltica-kogu, pildiarhiiv, fotokogud, kaardikogu). Eesti kunstiteaduse olukorrast, perspektiivist, akadeemiliste kohtade vähesusest, probleemidest "Eesti kunsti ajaloo" kirjutamisel.

  10. Transport "guru" Augulis speaks before thinking

    Index Scriptorium Estoniae

    2011-01-01

    Rail Baltica projekti kõrvale on Lätis kerkinud Riia-Moskva vahelise kiirema rongiliini ehitamise projekt. Euroopa Komisjoni transpordivoliniku Siim Kallase sõnul on Rail Baltica ühendus tähtsam ning Moskva liini arendamine ei saa Euroopa Liidult rahastust

  11. Draft Genome of Scalindua rubra, Obtained from the Interface Above the Discovery Deep Brine in the Red Sea, Sheds Light on Potential Salt Adaptation Strategies in Anammox Bacteria

    NARCIS (Netherlands)

    Speth, Daan R.; Lagkouvardos, Ilias; Wang, Yong; Qian, Pei Yuan; Dutilh, Bas E.|info:eu-repo/dai/nl/304546313; Jetten, Mike S M

    2017-01-01

    Several recent studies have indicated that members of the phylum Planctomycetes are abundantly present at the brine-seawater interface (BSI) above multiple brine pools in the Red Sea. Planctomycetes include bacteria capable of anaerobic ammonium oxidation (anammox). Here, we investigated the

  12. Draft Genome of Scalindua rubra, Obtained from the Interface Above the Discovery Deep Brine in the Red Sea, Sheds Light on Potential Salt Adaptation Strategies in Anammox Bacteria

    NARCIS (Netherlands)

    Speth, Daan R.; Lagkouvardos, Ilias; Wang, Yong; Qian, Pei Yuan; Dutilh, Bas E.; Jetten, M.S.M.

    2017-01-01

    Several recent studies have indicated that members of the phylum Planctomycetes are abundantly present at the brine-seawater interface (BSI) above multiple brine pools in the Red Sea. Planctomycetes include bacteria capable of anaerobic ammonium oxidation (anammox). Here, we investigated the

  13. The East Greenland Caledonides from the viewpoint of Receiver Functions, gravity and topography data

    DEFF Research Database (Denmark)

    Schiffer, Christian; Balling, N.; Jacobsen, B. H.

    The topography and crustal structure of the Caledonides were shaped by various events, including the Caledonian orogeny, lithospheric extensional collapse, continental breakup and erosional processes. Before the closure of the Iapetus Ocean (480 Ma), convergence of Laurentia, Baltica and Avalonia...

  14. Concerts & Opera

    Index Scriptorium Estoniae

    2006-01-01

    Kammerorkestri Kremerata Baltica kontserdid: 19. apr. Londonis LSO St Lukesis, 21. apr. Oxfordis Sheldonian Theatre'is, 17. apr. Aldeburghis, 20. apr. Manchesteris Bridgewater Hallis, 23. apr. Wales Millennium Centre'is, 22. apr. Edinburghis Usher Hallis

  15. Gidon Kremer ja Tatjana Grindenko : vana arm ei roosteta! / Tatjana Grindenko ; interv. Aleksandra Moorast

    Index Scriptorium Estoniae

    Grindenko, Tatjana

    2007-01-01

    Viiuldajatest Gidon Kremerist ja Tatjana Grindenkost. Kontserdist Tallinna Polütehnilise Instituudi aulas 30 aasta eest. Kontserdist "Jubilate: Gidon Kremer 60 ja Kremerata Baltica 10" 11. veebr. Estonia kontserdisaalis

  16. Muusika hiilgus ja pahupool Grammy peegelduses / Immo Mihkelson

    Index Scriptorium Estoniae

    Mihkelson, Immo, 1959-

    2002-01-01

    Los Angeleses toimunud 44. Grammyde jagamisest 101 kategoorias. Parema kammeransambli esituse kategoorias pärjati võitjaks Gido Kremer ja Kremerata Baltica uus plaat "After Mozart". Muusikaauhindade valikloetelu

  17. Arte näitab filmi Anu Talist / Immo Mihkelson

    Index Scriptorium Estoniae

    Mihkelson, Immo, 1959-

    2008-01-01

    24. veebruaril esilinastub telekanalil Arte Saksa portreefilm Eesti dirigendist "Maestra Baltica: Anu Tali dirigiert baltische Musik" (režissöörid Daniel Finkernagel, Alexander Lück). Lisatud info kultuurikanali Arte kohta

  18. Rootsi rangus kimbutab Tallinkit lisanõuetega / Lauri Linnamäe

    Index Scriptorium Estoniae

    Linnamäe, Lauri

    2007-01-01

    Rootsi mereinspektorid leidsid puudusi veekindlate uste elektrisüsteemides Tallinki laevadel Regina Baltica ja Vana Tallinn ning Viking Line'i Mariellal, kirjutab Rootsi meedia. Vt. samas: Galaxy vahetab lippu

  19. Mark Raidpere portreefotod Kielis

    Index Scriptorium Estoniae

    1999-01-01

    Kieli Linnagaleriis avatud 2. Ars Baltica fototriennaalil 'Can You Hear Me?' esindab Eestit Mark Raidpere seeriaga 'Portreed 1998'. Näituse Eesti-poolne kuraator Anu Liivak, kataloogiteksti kirjutas Anders Härm. Tuntumaid osalejaid triennaalil Wolfgang Tillmans

  20. Juhan Parts : "Ma ei tea, kas Pärnu linnale on vaja "munspaad"" / Juhan Parts ; interv. Kalev Vilgats

    Index Scriptorium Estoniae

    Parts, Juhan, 1966-

    2007-01-01

    Majandus- ja kommunikatsiooniminister Juhan Parts vastab oma visiidil Pärnusse nii Pärnu ettevõtlust, linna eduvalemit, kohalikku transpordiühendust, Rail Baltica projekti ning Pärnu lennujaama puudutavatele küsimustele. Lisa: CV

  1. Tallinna-Berliini raudteeprojekt valmimas / Toivo Tänavsuu

    Index Scriptorium Estoniae

    Tänavsuu, Toivo

    2002-01-01

    Saksa konsultatsioonifirmas PLANCO Consulting GmbH on valmimas Tallinna-Berliini kiirraudteeprojekti Rail Baltica eeluuring. Majandus- ja kommunikatsiooniministeeriumi peaspetsialisti Rein Lõokese kommentaare. Kaart. Poole ööpäevaga Berliini

  2. [Darius Staliūnas. Making Russians : meaning and practice of russification in Lithuania and Belarus after 1863

    Index Scriptorium Estoniae

    Woodworth, Bradley D., 1963-

    2011-01-01

    Arvustus: Darius Staliūnas. Making Russians. Meaning and practice of russification in Lithuania and Belarus after 1863. On the boundary of two worlds: identity, freedom, and moral imagination in the Baltica, 11. (Amsterdam : Rodopi, 2007)

  3. New Releases

    Index Scriptorium Estoniae

    2005-01-01

    Heliplaatidest: Giya Kancheli "In l'istesso tempo" (plaadil ka Kremerata Baltica), Various Cpsrs "Op. arias" (laulab Miliza Korjus), Various Cpsrs "Ob con Forca" (dirigeerib Arvo Volmer), "Anu Tali. Rahmaninov. Sibelius. Tüür"

  4. Varsti põrutab rong saja kahekümnega Riiga / Juhan Parts ; interv. Nils Niitra

    Index Scriptorium Estoniae

    Parts, Juhan, 1966-

    2007-01-01

    Majandus- ja kommunikatsiooniminister vastab küsimustele, mis puudutavad Tallinn-Tartu maantee ehitust, Rail Baltica rajamist, rahvusvahelist reisi- ja kaubarongiühendust, Tartu lennujaama investeeringuid ja doteerimist, Ahhaa teaduskeskuse rahastamist

  5. Pärnu linn toetab kultuurikavasid 4,5 miljoni krooniga

    Index Scriptorium Estoniae

    2007-01-01

    Toetuste saajateks ka muusikaüritused: David Oistrahhi festival, laste- ja noorte muusikafestival "Muusikamoos", MTÜ Suupilliklubi Piccolo, Pärnu Ooperipäevad, rahvusvaheline folkloorifestival "Baltica 2007"

  6. Fassaadi viimistlusvead kinni nii teadmatuses kui ka hoolimatuses / Eneken Laasme

    Index Scriptorium Estoniae

    Laasme, Eneken

    2006-01-01

    Viimistlusvigade tagajärjeks on hoone konstruktiivse osa lagunemine ning sise- ja välisseinte hallitus. Kommenteerivad SIA Caparol Baltica Eesti filiaali juhataja Jaan Vikat ja Heiki Tuisk OÜ Värvikeskuste Grupist

  7. Cruziana traces from the Late Silurian (Pridoli carbonate shelf of Saaremaa, Estonia

    Directory of Open Access Journals (Sweden)

    Olev Vinn

    2014-05-01

    Full Text Available Late Pridoli Cruziana traces have recently been found in carbonate shelf sediments of the Ohesaare Formation on Saaremaa Island, Estonia. Cruziana isp. is interpreted here as a locomotory trace (repichnia of an arthropod, possibly a trilobite. Cruziana traces previously known from the Silurian of Baltica differ from Cruziana isp., indicating that the diversity of Cruziana traces in the late Silurian of Baltica was higher than previously thought.

  8. Uudised : Kremerile Dresdenist Saeculum. Plink Plonk 2007

    Index Scriptorium Estoniae

    2007-01-01

    Viiuldaja Gidon Kremer pälvis Dresdeni muusikafestivali tänavuse elutööpreemia Saeculum (25 000 eurot) oma interpreeditegevuse ja kammerorkestri Kremerata Baltica rajamise eest. Kremerata Baltica kontserdil Semperoperis pidas pidukõne näitleja Bruno Ganz. Preemia on seni saanud dirigent Kurt Masur, koreograaf John Neumeier ja ooperilavastaja Joachim Herz. Muusikafestivalist Plink Plonk 21. juulil Tartu laululava muruplatsil

  9. Influence of Wastewater Discharge on the Metabolic Potential of the Microbial Community in River Sediments

    KAUST Repository

    Li, Dong; Sharp, Jonathan O.; Drewes, Jorg

    2015-01-01

    , sulfur, purine and pyrimidine metabolisms, as well as restriction–modification systems. More diverse bacterial phyla were associated with upstream and deep downstream sediments, mainly including Actinobacteria, Planctomycetes, and Firmicutes. In contrast

  10. Long hard road from Nuna to Rodinia

    Science.gov (United States)

    Pisarevsky, Sergei

    2014-05-01

    The popular concept of supercontinental cycles suggests the existence of at least two Precambrian supercontinents, referred to as Nuna (or Columbia) and Rodinia. The times of their assembly and breakup are debated, as are their constituents and configurations. The recent compilation of paleomagnetic data supported by the geological evidence suggests that Nuna have broken up at ca. 1450-1380 Ma by separation of the Australia-Mawson continent from western Laurentia. The recent robust paleomagnetic pole from 1210 Ma mafic dykes in Western Australia provides an additional evidence of wide separation of these continents by the time of the dykes' emplacement. On the other hand, there is the evidence that Laurentia and Baltica have been rigidly connected with present Scandinavia facing East Greenland until after 1270 Ma, when they broke up. Baltica then moved c.1000 km south and rotated clockwise 95° with respect to Laurentia by 1000 Ma and two continents recombined again with the Scandinavian margin of Baltica facing Scottish terranes of the Laurentian affinity, Rockall Bank and southeast Greenland. However, the published model of the simple fan-like opening of the Asgard Sea Between Laurentia and Baltica is somewhat hampered by the recent 1120 Ma paleomagnetic pole from Finland, which suggests a more complicated drift of Baltica with respect to Laurentia. There are also reasons to suggest that a large part of Nuna, which included Laurentia and Siberia has been incorporated into Rodinia after 1000 Ma. The c. 1300-1000 Ma Apparent Polar Wander Paths for Laurentia, Baltica, Australia, Amazonia and India are significantly different in their lengths and shapes suggesting relative movements of these continents with respect to each other. There is still not enough reliable published late Mesoproterozoic - early Neoproterozoic paleomagnetic data to make the unequivocal paleogeographic reconstructions for this time interval. However, it is unlikely that a large supercontinent

  11. Deeply concealed half-graben at the SW margin of the East European Craton (SE Poland) — Evidence for Neoproterozoic rifting prior to the break-up of Rodinia

    OpenAIRE

    P. Krzywiec; P. Poprawa; M. Mikołajczak; S. Mazur; M. Malinowski

    2018-01-01

    Baltica was one of continents formed as a result of Rodinia break-up 850–550 Ma. It was separated from Amazonia(?) by the Tornquist Ocean, the opening of which was preceded by Neoproterozoic extension in a network of continental rifts. Some of these rifts were subsequently aborted whereas the Tornquist Rift gave rise to splitting of Rodinia and formation of the Tornquist Ocean. The results of 1-D subsidence analysis at the fossil passive margin of Baltica provided insight in the timing and ki...

  12. Upper mantle and crustal structure of the East Greenland Caledonides

    DEFF Research Database (Denmark)

    Schiffer, Christian; Balling, N.; Jacobsen, B. H.

    The East Greenland and Scandinavian Caledonides once formed a major coherent mountain range, as a consequence of the collision of the continents of Laurentia and Baltica. The crustal and upper mantle structure was furthermore influenced by several geodynamic processes leading to the formation of ...

  13. Summer festivals 2008 : European Festivals

    Index Scriptorium Estoniae

    2008-01-01

    Bergeni Rahvusvahelisest Festivalist võtab 3. ja 4. juunil osa ka Eesti Rahvusmeeskoor (vt. www.fib.no). Rheingau Muusikafestivalil 28. ja 29. mail dirigeerib Paavo Järvi, 23. aug. esineb kammerorkester Kremerata Baltica (vt. www.rheingau-musik-festival.de), Verbier Festivalil (18. juuli- 3. aug) dirigeerib Paavo Järvi (vt. verbierfestival.com)

  14. European festivals. The best events worldwide

    Index Scriptorium Estoniae

    2007-01-01

    Eesti Filharmoonia Kammerkoor esinemas 23. maist 5. juunini toimuval Bergeni rahvusvahelisel festivalil. Paavo Järvi dirigeerimas 23. ja 24. juunil ning kammerorkester Kremerata Baltica esinemas 24. juulil Rheingau muusikafestivalil. Eesti Filharmoonia Kammerkoor esinemas 3. mail Oxfordi Sheldonian Theatre's (esitusel ka Arvo Pärdi muusika)

  15. Sustainable national transport planning: Managing multiple objectives and criteria

    DEFF Research Database (Denmark)

    Jensen, Anders Vestergaard; Salling, Kim Bang; Leleur, Steen

    not included in the CBA. One important part of the assessment is the selection of criteria to be included and this aspect will be examined by an appraisal study of the Rail Baltica corridor. In the study various alternatives are appraised with an explicit consideration of each alternative’s sustainability...... performance....

  16. Notes on the genus Sordaria in Spain. Sordaria elongatispora, a new coprophilous species (Pyrenomycetes)

    OpenAIRE

    Barrasa, J.M.; Lundqvist, N.; Moreno, G.

    1986-01-01

    Sordaria elongatispora Barrasa, Lundq. & Moreno is proposed as a new species, characterized by its large, narrow spores. It is compared with related taxa and a key is given to the four known, narrow-spored species of the genus, three of which occur in Spain: S. baltica Lundq., S. elongatispora, and S. papillata Urríes.

  17. Notes on the genus Sordaria in Spain. Sordaria elongatispora, a new coprophilous species (Pyrenomycetes)

    NARCIS (Netherlands)

    Barrasa, J.M.; Lundqvist, N.; Moreno, G.

    1986-01-01

    Sordaria elongatispora Barrasa, Lundq. & Moreno is proposed as a new species, characterized by its large, narrow spores. It is compared with related taxa and a key is given to the four known, narrow-spored species of the genus, three of which occur in Spain: S. baltica Lundq., S. elongatispora, and

  18. Eesti võimalused Soome lahe kasvukolmnurgas / Aare-Maldus Uustalu

    Index Scriptorium Estoniae

    Uustalu, Aare-Maldus, 1935-

    2005-01-01

    Euroopa Komisjoni ekspert logistika, transpordi ja regionaalökonoomika alal, TTÜ Tallinna Kolledzhi dotsent 2002. aasta alguses käivitatud Soome lahe kasvukolmnurga projektist, Eesti majanduse arenguperspektiivist projekti raames ning Eesti riigiametnike ükskõiksusest projekti suhtes. Via Baltica lisakoridoride projekti Via Islands ideest

  19. [Stat-kyrka-samhälle : Den stormaktstida samhällsordningen i Sverige och Östersjöpinserna] / Enn Küng

    Index Scriptorium Estoniae

    Küng, Enn, 1963-

    2002-01-01

    Arvustus: Stat-kyrka-samhälle : Den stormaktstida samhällsordningen i Sverige och Östersjöpinserna. (Acta Universitatis Stockholmiensis Studia Baltica Stockholmiensa, 21). Stockholm, 2000. Stockholmi Ülikooli Balti Uuringute Keskuse teaduslik väljaanne "Riik-kirik-ühiskond" Rootsi suurriigi provintsipoliitikast Eesti- ja Liivimaal 16.-17. sajandil

  20. Näost näkku / Maaretta Jaukkuri ; ülevaate koostas Tõnu Tammets

    Index Scriptorium Estoniae

    Jaukkuri, Maaretta

    1992-01-01

    Programmi "Ars Baltica" raames toimunud Läänemeremaade kujutava kunsti näitus "Näost näkku" ("Face to face") Kieli Kunstihallis 6. okt. - 10. nov. 1991. Eestit esindas Raul Rajangu. Mõtteid näitusekataloogi eessõnast

  1. Maavanema avaldus surus linnavõimu kaitsesse / Eno-Gerrit Link

    Index Scriptorium Estoniae

    Link, Eno-Gerrit

    2008-01-01

    Pärnu maavanem Toomas Kivimägi kritiseeris linnavalitsust Via Baltica Pärnu ümbersõidu projekti venimise pärast. Linnapea Mart Viisitamm ei pea avaldust põhjendatuks. Vt. samas lk. 15: Mart Viisitamm. Demokraatia või diktatuur - selles on küsimus

  2. Päästjatele tuli mullu tuhat väljakutset / Eno-Gerrit Link

    Index Scriptorium Estoniae

    Link, Eno-Gerrit

    2006-01-01

    Pärnumaa päästeteenistus sai 2005. a. kõige rohkem väljakutseid Pärnusse ning Via Baltica äärde jäävatesse Pärnumaa valdadesse ja Vändrasse. Kaart: Pärnumaa päästeteenistuste väljasõidud omavalitsustesse 2005

  3. Balti kultuurifestival Pariisis / Kristi Hinsberg

    Index Scriptorium Estoniae

    Hinsberg, Kristi

    2008-01-01

    1.-14. oktoobrini Pariisis toimunud Balti kultuurifestivalist "Semaines Baltes a Paris" (Balti nädalad Pariisis), kus tutvustati prantslastele balti muusikat, filme ja nüüdiskunsti. Pianist Andres Paasi, kes fesivalil Trio Baltica koosseisus üles astus, muljeid

  4. Augustis on Tallinna galeriides võimust võtnud soomlased / Anne Vetik

    Index Scriptorium Estoniae

    Vetik, Anne

    2007-01-01

    Krista Launoneni maalinäitus "Kasvun paika/Time to Grow Up" Draakoni galeriis. Panu Ruotsalo, Matti Reivi ja Roy Hopiavuori näitus "The Baltic Sea Delegation" ArtDepoos. Ars Baltica fotokunsti triennaal "Don't Worry, Ge Curious!" Kumu Kunstimuuseumis

  5. Iz Berlina v Tampere za neskolko tshasov? / Helga Balode

    Index Scriptorium Estoniae

    Balode, Helga

    2002-01-01

    Rail Baltica raudtee, mis hakkab reisi- ja kaubaronge teenindama marsruudil Tallinn-Varssavi, läheb maksma miljardeid kroone. Kommenteerivad Soome transpordi- ja kommunikatsiooniministeeriumi nõunik Kai-Peter Mattson, Läti sideministeeriumi raudteeosakonnajuhataja Janis Veidmanis ja Eesti raudteeameti peadirektor Oleg Epner

  6. Baltimaad 1900-1914 / Jaanus Arukaevu

    Index Scriptorium Estoniae

    Arukaevu, Jaanus

    1992-01-01

    Rets.: The Baltic Countries 1900-1914 : proceedings from the 9th conference on baltic studies in Scandinavia, Stockholm, June 3-6, 1987. Ed. Aleksander Loit. (Acta Universitatis Stockholmiensis. Studia Baltica Stockholmiensia 5:1-2). Uppsala, 1990Red terror in Estonia 1918-1919 : sources and major problems. Lk. 96

  7. Burrowing and avoidance behaviour in marine organisms exposed to pesticide-contaminated sediment

    DEFF Research Database (Denmark)

    Møhlenberg, Flemming; Kiørboe, Thomas

    1983-01-01

    Behavioural effects of marine sediment contaminated with pesticides (6000 ppm parathion, 200 ppm methyl parathion, 200 ppm malathion) were studied in a number of marine organisms in laboratory tests and in situ. The burrowing behaviour in Macoma baltica, Cerastoderma edule, Abra alba, Nereis...

  8. Estonija mozhet ostatsja bez uzkoi kolei / Jelizaveta Gavrilova

    Index Scriptorium Estoniae

    Gavrilova, Jelizaveta

    2005-01-01

    Poola-Leedu-Läti-Eesti raudteeprojekt Rail Baltica on lülitatud Euroopa Komisjoni transpordi prioriteetide hulka. Eesti probleemiks on kujunenud madal koostöövõime infrastruktuuride valduse küsimuses riigi ja erafirma Eesti Raudtee vahel

  9. Anu Tali : enda elust filmi vaadata ei ole väga lihtne / Jaanus Kulli

    Index Scriptorium Estoniae

    Kulli, Jaanus, 1955-

    2008-01-01

    Dirigent Anu Tali elust ja tööst rääkivat filmi "Maestra Baltica : Anu Tali dirigiert baltische Musik" (režissöörid Daniel Finkernagel ja Alexander Lück) näitab telekanal Arte. Noor dirigent kommenteerib

  10. Dicty_cDB: Contig-U15071-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 753_861( CP000753 |pid:none) Shewanella baltica OS185, comple... 42 0.057 EU682994_1( EU682994 |pid:none) Francisella noatun...g... 42 0.057 FJ217169_1( FJ217169 |pid:none) Francisella noatunensis subsp. ori... 42 0.057 BA000012_917( B

  11. Growth and metabolism of Anammox Bacteria

    NARCIS (Netherlands)

    Van der Star, W.R.L.

    2008-01-01

    The anoxic ammonium oxidation (anammox) process is the conversion of nitrite and ammonium under anoxic conditions- to form dinitrogen gas. The process is performed by deep-branching Planctomycetes. The startup of the first full-scale anammox reactor in the world is described in Chapter 2. The

  12. Metagenomic analysis of bacterial diversity of Siloam hot water ...

    African Journals Online (AJOL)

    The bacterial diversity of Siloam hot water spring was determined using 454 pyrosequencing of two 16S rRNA variable regions V1-3 and V4-7. Analysis of the community DNA revealed that the phyla Proteobacteria, Cyanobacteria, Bacteriodetes, Planctomycetes, Firmicutes, Chloroflexi and Verrucomicrobia were the most ...

  13. Cell biology of anaerobic ammonium-oxidizing bacteria

    NARCIS (Netherlands)

    Niftrik, L.A.M.P. van

    2008-01-01

    Anammox bacteria perform anaerobic ammonium oxidation to dinitrogen gas and belong to the phylum Planctomycetes. Whereas most Prokaryotes consist of one compartment, the cytoplasm bounded by the cytoplasmic membrane and cell wall, the species within this phylum are compartmentalized by intracellular

  14. The anammoxosome: an intracytoplasmic compartment in anammox bacteria

    NARCIS (Netherlands)

    Niftrik, L.A.M.P. van; Fuerst, J.A.; Damste, J.S.S.; Kuenen, J.G.; Jetten, M.S.M.; Strous, M.

    2004-01-01

    Anammox bacteria belong to the phylum Planctomycetes and perform anaerobic ammonium oxidation (anammox); they oxidize ammonium with nitrite as the electron acceptor to yield dinitrogen gas. The anammox reaction takes place inside the anammoxosome: an intracytoplasmic compartment bounded by a single

  15. The anammoxosome : An intracytoplasmic compartment in anammox bacteria

    NARCIS (Netherlands)

    Sinninghe Damsté, J.S.; Niftrik, L.A. van; Fuerst, J.A.; Kuenen, J.G.; Jetten, M.S.M.; Strous, M.

    2004-01-01

    Anammox bacteria belong to the phylum Planctomycetes and perform anaerobic ammonium oxidation (anammox); they oxidize ammonium with nitrite as the electron acceptor to yield dinitrogen gas. The anammox reaction takes place inside the anammoxosome: an intracytoplasmic compartment bounded by a single

  16. Telmatocola sphagniphila

    NARCIS (Netherlands)

    Kulichevskaya, I.S.; Serkebaeva, Y.M.; Kim, Y.; Rijpstra, W.I.C.; Sinninghe Damsté, J.S.; Liesack, W.; Dedysh, S.N.

    2012-01-01

    Members of the phylum Planctomycetes are common inhabitants of northern wetlands. We used barcoded pyrosequencing to survey bacterial diversity in an acidic (pH 4.0) Sphagnum peat sampled from the peat bog Obukhovskoye, European North Russia. A total of 21189 bacterial 16S rRNA gene sequences were

  17. Cornulitids (tubeworms) from the Late Ordovician Hirnantia fauna of Morocco

    Science.gov (United States)

    Gutiérrez-Marco, Juan Carlos; Vinn, Olev

    2018-01-01

    Two species of cornulitids, Cornulites gondwanensis sp. nov. and C. aff. shallochensis Reed are described from the Hirnantian of Morocco, within an assemblage representative of the Hirnantia brachiopod fauna occurring near the Ordovician South Pole. The dominance of aggregated and solitary free forms could be explained by particular sedimentary environments preceding the Hirnantian glaciation and the latest Ordovician Extinction Event. The diversity of cornulitids in the Late Ordovician of Gondwana and related terranes was relatively low, and less diverse than the cornulitids of Laurentia and Baltica. Hirnantian cornulitids from Morocco do not resemble Late Ordovician cornulitids of Baltica and Laurentia. Moroccan cornulitids seem to be closely allied to some older Gondwanan cornulitids, especially Sardinian ones. They resemble species described from the Late Ordovician and Llandovery of Scotland suggesting a palaeobiogeographic link.

  18. Devonian paleomagnetism of the North Tien Shan: Implications for the middle-Late Paleozoic paleogeography of Eurasia

    Science.gov (United States)

    Levashova, Natalia M.; Mikolaichuk, Alexander V.; McCausland, Philip J. A.; Bazhenov, Mikhail L.; Van der Voo, Rob

    2007-05-01

    The Ural-Mongol belt (UMB), between Siberia, Baltica and Tarim, is widely recognized as the locus of Asia's main growth during the Paleozoic, but its evolution remains highly controversial, as illustrated by the disparate paleogeographic models published in the last decade. One of the largest tectonic units of the UMB is the Kokchetav-North Tien Shan Domain (KNTD) that stretches from Tarim in the south nearly to the West Siberian Basin. The KNTD comprises several Precambrian microcontinents and numerous remnants of Early Paleozoic island arcs, marginal basins and accretionary complexes. In Late Ordovician time, all these structures had amalgamated into a single contiguous domain. Its paleogeographic position is of crucial importance for elucidating the Paleozoic evolution of the UMB in general and of the Urals in particular. The Aral Formation, located in Kyrgyzstan in the southern part of the KNTD, consists of a thick Upper Devonian (Frasnian) basalt-andesite sequence. Paleomagnetic data show a dual-polarity characteristic component (Dec/Inc = 286° / + 56°, α95 = 9°, k = 21, N = 15 sites). The primary origin of this magnetization is confirmed by a positive test on intraformational conglomerates. We combine this result with other Paleozoic data from the KNTD and show its latitudinal motion from the Late Ordovician to the end of the Paleozoic. The observed paleolatitudes are found to agree well with the values extrapolated from Baltica to a common reference point (42.5°N, 73°E) in our sampling area for the entire interval; hence coherent motion of the KNTD and Baltica is strongly indicated for most of the Paleozoic. This finding contradicts most published models of the UMB evolution, where the KNTD is separated from Baltica by a rather wide Ural Ocean containing one or more major plate boundaries. An exception is the model of Şengör and Natal'in [A.M.C. Şengör, B.A. Natal'in, Paleotectonics of Asia: fragments of a synthesis, in: A. Yin and M. Harrison (eds

  19. The oldest ascocerid cephalopod from the Silurian of Estonia and notes on the biogeography of the order Ascocerida (class Cephalopoda

    Directory of Open Access Journals (Sweden)

    Martina Aubrechtova

    2016-05-01

    Full Text Available The early Palaeozoic order Ascocerida is a group of morphologically unique and rare cephalopods known from the Ordovician and Silurian rocks of Avalonia, Baltica, Laurentia and Perunica. The limited Estonian record of Silurian ascocerids is complemented with a specimen from the Pähkla locality (Island of Saaremaa; Paadla Regional Stage, Ludlow Series representing the stratigraphically oldest known occurrence of ascocerids in the Silurian of Estonia. The strata that were formerly exposed in Pähkla are likely correlated to the Hemse Group of the Island of Gotland (Sweden having a remarkable record of ascocerids. The appearance of Silurian ascocerids in Estonia is confined to a time interval when the group had the highest species diversity and the widest geographic dispersion, reaching also outside Baltica for the first time.

  20. Evolution of the Altaid tectonic collage and Palaeozoic crustal growth in Eurasia

    Science.gov (United States)

    Şengör, A. M. C.; Natal'in, B. A.; Burtman, V. S.

    1993-07-01

    A new tectonic model, postulating the growth of giant subduction-accretion complexes along a single magmatic arc now found contorted between Siberia and Baltica, shows that Asia grew by 5.3 million square kilometres during the Palaeozoic era. Half of this growth may have occurred by the addition of juvenile crust newly extracted from the mantle, supporting models of considerable continental growth continuing throughout the Phanerozoic eon.

  1. Kohastumus eluks vee ääres / Laura Kuusk

    Index Scriptorium Estoniae

    Kuusk, Laura, 1982-

    2007-01-01

    4. "Ars Baltica" fototriennaal Kumu Kunstimuuseumis kuni 30. IX. Tellervo Kalleineni ja Oliver Kochta-Kalleineni, Alexander Vaindorfi, Coloneli (Thierry Geoffroy) ja Khaled D. Ramadani, Kaspars Goba, Tanja Nellemann Poulseni, Katrin Teesi, Anu Pennaneni, Petra Baueri, Talleiv Taro Manumi (sünd. 1968 Jaapanis, elab Norras), Olga Tshernõsheva, Kristina Inciuraite, Julita Wojciki, Sven Johne, Anna Baumgarti, Arturas Valiauga ja duo J&K (Janne Schäfer, Kristine Agergaard) töödest

  2. Studies on woloszynskioid dinoflagellates IV: the genus Biecheleria gen. nov

    DEFF Research Database (Denmark)

    Moestrup, Øjvind; Lindberg, Karin; Daugbjerg, Niels

    2009-01-01

    in the dinoflagellates. Biecheleria also comprises the brackish water species Biecheleria baltica sp. nov. (presently identified as Woloszynskia halophila) and the marine species Biecheleria natalensis (syn. Gymnodinium natalense). Gymnodinium halophilum described in 1952 by B. Biecheler but apparently not subsequently...... refound, is transferred to Biecheleria. The Suessiaceae further includes the marine species Protodinium simplex, described by Lohmann in 1908 but shortly afterwards (1921) transferred to Gymnodinium by Kofoid and Swezy and subsequently known as Gymnodinium simplex. It only distantly related to Gymnodinium...

  3. Rong viib autod ohutult rööbastel Euroopasse / Mirko Ojakivi

    Index Scriptorium Estoniae

    Ojakivi, Mirko

    2007-01-01

    Helsingi-Rovaniemi reisirongi külge on haagitud autotreiler reisijate autodega. Edelaraudtee juhi Kalvi Pukka väitel on selline idee liikvel olnud ka Edelaraudtees, kuid niisugune teenus õigustab end, kui linnadevaheline kaugus on umbes 600 km. Rail Baltica valmimisel on mõeldav, et rongiga Lätti või Leetu sõites saab kaasa võtta ka auto. Lisa: Rongi autotreilerid

  4. The Cambrian to Devonian odyssey of the Brabant Massif within Avalonia: A review with new zircon ages, geochemistry, Sm-Nd isotopes, stratigraphy and palaeogeography

    Science.gov (United States)

    Linnemann, Ulf; Herbosch, Alain; Liégeois, Jean-Paul; Pin, Christian; Gärtner, Andreas; Hofmann, Mandy

    2012-05-01

    This study provides an up-to-date and comprehensive review of the Early Palaeozoic evolution of the Brabant Massif belonging to the Anglo-Brabant Deformation Belt. Situated at the southeastern side of Avalonia microplate, it is the only well-known part of the northern passive margin of the Rheic Ocean. The Cambrian-Silurian sedimentary pile is > 13 km thick, with > 9 km for the Cambrian only. The unraveling of this continuous registration reflects the successive rifting and drifting of Avalonia from the Gondwana mainland, followed by soft-collisional processes with Baltica and finally the formation of Laurussia. Based on recently established detailed stratigraphy, sedimentology and basin development, on U-Pb LA-ICP-MS analyses of igneous and detrital zircon grains along with geochemical data including Sm-Nd isotopes, a new geodynamic and palaeogeographic evolution is proposed. Brabant Megasequence 1 (lower Cambrian to lowermost Ordovician, > 9 km thick) represents an embayment of the peri-Gondwanan rift from which the Rheic Ocean has evolved. Detrital zircon ages demonstrate that the Brabant is a typical peri-Gondwanan terrane with a major Pan-African (Neoproterozoic age) and a mixed West African and Amazonian source (Palaeoproterozoic, Archaean and some Mesoproterozoic age). The transition towards the Avalonia drifting is marked by an unconformity and a short volcanic episode. The northward drift of Avalonia towards Baltica is recorded by the Megasequence 2 (Middle to Upper Ordovician, 1.3 km thick). The source for Mesoproterozoic zircons vanished, as the result of the Rheic Ocean opening and the isolation from Amazonian sources. The transition to Megasequence 3 is marked by a drastic change in palaeobathymetry and an important (sub)volcanic episode during a tectonic instability period (460-430 Ma), reflecting the Avalonia-Baltica soft docking as also shown by the reappearance of Mesoproterozoic detrital zircons, typical of Baltica. Unradiogenic Nd isotope

  5. A comparative assessment of the role of anoxia during the Cambrian SPICE event

    Science.gov (United States)

    LeRoy, M.; Gill, B. C.; Sperling, E. A.

    2017-12-01

    The Cambrian SPICE (Steptoean Positive Carbon Isotope Excursion) is recognized as a major oceanographic event recorded in globally-distributed stratigraphic sections as positive isotopic excursions in marine carbonates (δ13Ccarb), organic matter (δ13Corg), sulfate (δ34SCAS) and pyrite (δ34Spy). A proposed mechanism for these observed isotopic trends is that a transient increase in the areal extent of anoxic conditions within the oceans fostered enhanced burial of organic carbon and pyrite. However, direct sedimentary (e.g., abundant black shale) and geochemical (e.g., redox proxy) evidence for such a shift is scant. While the antiquity of this event is likely responsible for loss of much of this evidence, through destruction by tectonic processes, a number of stratigraphic successions suitable for investigating this hypothesis exist. Here we explore the relationship between anoxia and the SPICE using previously published and novel data generated from core material from three sedimentary basins distributed along the margins of the Iapetus Ocean. The units studied are: the Nolichucky Formation of eastern Laurentia, the Alum Shale of Baltica, and the Outwoods Shale of Avalonia. Our iron speciation data indicate consistently oxic conditions prior to the SPICE along Laurentia, while Avalonia was oxic with intervals of anoxia, and Baltica was persistently anoxic. With the initiation of the SPICE, anoxic conditions intensified in Laurentia and Avalonia and continued to persist in Baltica. This redox shift was coupled with a sharp rise in δ34Spy at all three locations. Average total organic carbon (TOC) showed little change in relation to the SPICE at the Laurentia location ( 0.15 wt%), but showed an increase in conjunction with the excursion in both the Avalonia ( 1 to 1.5 wt%) and Baltica ( 8 to 12 wt%) sections. Large differences in nutrient availability and sedimentation rates are likely responsible for the between-site disparity in TOC, while overall, anoxia

  6. Diatom stratigraphy and long-term dissolved silica concentrations in the Baltic Sea

    Science.gov (United States)

    Olli, Kalle; Clarke, Annemarie; Danielsson, Åsa; Aigars, Juris; Conley, Daniel J.; Tamminen, Timo

    2008-10-01

    In many parts of the world coastal waters with anthropogenic eutrophication have experienced a gradual depletion of dissolved silica (DSi) stocks. This could put pressure on spring bloom diatom populations, e.g. by limiting the intensity of blooms or by causing shifts in species composition. In addition, eutrophication driven enhanced diatom growth is responsible for the redistribution of DSi from the water phase to the sediments, and changes in the growth conditions may be reflected in the sediment diatom stratigraphy. To test for changes in diatom communities we have analyzed four sediment cores from the Baltic Sea covering approximately the last 100 years. The sediment cores originate from the western Gulf of Finland, the Kattegat, the Baltic Proper and the Gulf of Riga. Three out of the four cores reveal only minor changes in composition of diatom assemblages, while the Gulf of Riga core contains major changes, occurring after the second World War. This area is set apart from the other Baltic Sea basins by a high frequency of low after spring bloom DSi concentrations (< 2 µmol L - 1 ) during a relatively well defined time period from 1991-1998. In 1991 to 1993 a rapid decline of DSi spring concentrations and winter stocks (down to 5 µmol L - 1 ) in the Gulf was preceded by exceptionally intense diatom spring blooms dominated by the heavily silicified species Thalassiosira baltica (1991-1992; up to 5.5 mg ww L - 1 ). T. baltica has been the principal spring bloom diatom in the Gulf of Riga since records began in 1975. DSi consumption and biomass yield experiments with cultured T. baltica suggest that intense blooms can potentially exhaust the DSi stock of the water column and exceed the annual Si dissolution in the Gulf of Riga. The phytoplankton time series reveals another exceptional T. baltica bloom period in 1981-1983 (up to 8 mg L - 1 ), which, however, took place before the regular DSi measurements. These periods may be reflected in the conspicuous

  7. Short-and long-term effects of ammonia and nitrite on the anammox process

    International Nuclear Information System (INIS)

    Fernandez, I.; Campos, J. L.; Mosquera-Corral, A.; Mendez, R.

    2009-01-01

    Auto trophic anaerobic ammonium oxidation (Anammox) process is a feasible alternative to treat industrial wastewater with high ammonia concentration but low content of organic matter. In this process ammonium and nitrite are used by Planctomycete-type bacteria under anoxic conditions to generate nitrogen gas. Both substrates can exert inhibitory effects on the process, causing the decrease of the specific activity of the biomass and the loss of the performance and stability of reactors. (Author)

  8. North European Transect

    Science.gov (United States)

    Korja, Annakaisa; Heikkinen, Pekka J.; Roslov, Yuri; Ivanova, Nina; Verba, Marc; Sakoulina, Tamara

    2010-05-01

    A nearly continuous, 3600 km long, NE-running North European Transect (NET) is combined from the existing deep seismic reflection data sets in the Baltic Sea (BABEL, 1600 km), Northern Finland (FIRE 4-4A, 580 km) and Barents Sea (1-AR, 1440 km;). The reflective image of the deep crust is highly dependent on the thickness of the sedimentary cover. The cover is few hundred meters in the Baltic sea, few tens of meters in the land areas and few kilometers in the Barents Sea area. In the Barents Sea area, the seismic image is dominated by the layered structure of the sedimentary basins and the middle and lower crust are poorly imaged. Therefore the Moho boundary in the Barents Sea has been determined from wide-angle reflections. Geologically the transect covers the transition from Phanerozoic Europe to Precambrian Europe and back to the Phanerozoic Barents Sea Shelf. It displays how Northern Europe grew around Baltica in several tectonic episodes involving the formation and destruction of Columbia/Hudsonland, Rodinia and Pangea supercontinents. The paleo plateboundaries are traversed by subvertical transparent zones suggesting transpressional and trantensional environments. The BABEL lines image how the core of Baltica was formed by sequential accretion of microcontinents and arc terranes at the old continental margin during the Svecofennian Orogeny ~1.9-1.8 Ga .When Baltica joined the Columbia supercontinent, new terranes were added to its southern edge in the Sveocbaltic Orogeny (~1.8 Ga). During the dispersal of the Columbia, the Baltic Sea failed rift was formed, rapakivi granitoids were intruded and sedimentary basins were developed. An extended plate margin structure has been imposed on the Rodinian (Sveconorwegian) and Pangean additions (Variscan-Caledonian). Major crustal thinning takes place along a series of subvertical faults across the Trans-European Suture Zone marking the transition from Phanerozoic to Proterozoic Europe. The FIRE lines in Northen Finland

  9. Fennoscandia in the Phanerozoic: Paleogeodynamic Reconstructions Based on the New Paleomagnetic and Geochronological Data from the Kola Magmatic Province (kola Peninsula, Russia)

    Science.gov (United States)

    Veselovskiy, R. V.; Arzamastsev, A. A.

    2013-12-01

    During last four years we studied more than 100 dolerite and alkaline dykes, which are widely spread on the Kola Peninsula and belong to the Devonian magmatic province. Within the scope of our researches some of these dykes have been dated and their precise isotopic ages (Ar/Ar, Sm-Nd, Rb-Sr) lie in the range of 390-360 Ma (Veselovskiy et al., 2013). The age of other sampled dykes can be considered as Devonian due to similarity of their paleomagnetic, geochemical and petrological characteristics to the dated ones. Paleomagnetic directions have been obtained from more than 80 dykes. Almost all dykes yielded (a) a low-temperature component that is aligned along the present-day field and is likely of viscous origin; (b) a well defined dual-polarity intermediate-temperature component with steep eastward directions that accounts for a main part of the NRM and often decays to the origin on orthogonal plots; and (c) a dual-polarity high-temperature component with shallow inclinations and ENE declinations of presumed primary origin. The presence of the primary high-temperature component makes us possible to calculate preliminary Baltica's paleomagnetic pole for the Middle-Late Devonian. In view of the obtained microprobe data we believe that intermediate component is a result of unknown hydrothermal process, which age can be estimated from the comparison of corresponding paleomagnetic pole with the Baltica's APWP as Jurassic. We believe that both mentioned episodes of endogenous activity within the large stable craton were connected with plume-lithospheric interaction in the Devonian and Jurassic. In this presentation we use the obtained paleomagnetic, petrological and geochronological data to determine the paleogeography of Baltica in the Devonian and Jurassic times and to find its position within the global paleotectonic and geodynamic reconstructions. This study was funded by grants RFBR # 12-05-00216, 13-05-12021, 13-05-12030 and grant MK-3383.2012.5.

  10. Arsukibacterium ikkense gen. nov., sp. nov, a novel alkaliphilic, enzyme-producing gamma-Proteobacterium isolated from a cold and alkaline environment in Greenland.

    Science.gov (United States)

    Schmidt, Mariane; Priemé, Anders; Stougaard, Peter

    2007-04-01

    A novel aerobic, Gram-negative, non-pigmented bacterium, GCM72(T), was isolated from the alkaline, low-saline ikaite columns in the Ikka Fjord, SW Greenland. Strain GCM72(T) is a motile, non-pigmented, amylase- and protease-producing, oxidase-positive, and catalase-negative bacterium, showing optimal growth at pH 9.2-10.0, at 15 degrees C, and at 3% (w/v) NaCl. Major fatty acids were C(12:0) 3-OH (12.2+/-0.1%), C(16:00) (18.0+/-0.1%), C(18:1)omega7c (10.7+/-0.5%), and summed feature 3 comprising C(16:1)omega7c and/or iso-C(15:0) 2-OH (36.3+/-0.7%). Phylogenetic analysis based on 16S rRNA gene sequences showed that isolate GCM72(T) was most closely related to Rheinheimera baltica and Alishewanella fetalis of the gamma-Proteobacteria with a 93% sequence similarity to both. The G+C content of DNA isolated from GCM72(T) was 49.9mol% and DNA-DNA hybridization between GCM72T and R. baltica was 9.5%. Fatty acid analysis and G+C content supports a relationship primarily to R. baltica, but several different features, such as a negative catalase-response and optimal growth at low temperature and high pH, together with the large phylogenetic distance and low DNA similarity to its closest relatives, lead us to propose a new genus, Arsukibacterium, gen. nov., with the new species Arsukibacterium ikkense sp. nov. (type strain is GCM72(T)).

  11. Rhodonellum psychrophilum gen. nov., sp. nov., a novel psychrophilic and alkaliphilic bacterium of the phylum Bacteroidetes isolated from Greenland.

    Science.gov (United States)

    Schmidt, Mariane; Priemé, Anders; Stougaard, Peter

    2006-12-01

    A novel alkaliphilic and psychrophilic bacterium was isolated from the cold and alkaline ikaite tufa columns of the Ikka Fjord in south-west Greenland. According to 16S rRNA gene sequence analysis, strain GCM71(T) belonged to the family 'Flexibacteraceae' in the phylum Bacteroidetes. Strain GCM71(T), together with five related isolates from ikaite columns, formed a separate cluster with 86-93 % gene sequence similarity to their closest relative, Belliella baltica. The G+C content of the DNA from strain GCM71(T) was 43.1 mol%, whereas that of B. baltica was reported to be 35 mol%. DNA-DNA hybridization between strain GCM71(T) and B. baltica was 9.5 %. The strain was red pigmented, Gram-negative, strictly aerobic with non-motile, rod-shaped cells. The optimal growth conditions for strain GCM71(T) were pH 9.2-10.0, 5 degrees C and 0.6 % NaCl. The fatty acid profile of the novel strain was dominated by branched and unsaturated fatty acids (90-97 %), with a high abundance of iso-C(17 : 1)omega9c (17.5 %), iso-C(17 : 0) 3-OH (17.5 %) and summed feature 3, comprising iso-C(15 : 0) 2-OH and/or C(16 : 1)omega7c (12.6 %). Phylogenetic, chemotaxonomic and physiological characteristics showed that the novel strain could not be affiliated to any known genus. A new genus, Rhodonellum gen. nov., is proposed to accommodate the novel strain. Strain GCM71(T) (=DSM 17998(T)=LMG 23454(T)) is proposed as the type strain of the type species, Rhodonellum psychrophilum sp. nov.

  12. From a collage of microplates to stable continental crust - an example from Precambrian Europe

    Science.gov (United States)

    Korja, Annakaisa

    2013-04-01

    Svecofennian orogen (2.0-1.7 Ga) comprises the oldest undispersed orogenic belt on Baltica and Eurasian plate. Svecofennian orogenic belt evolved from a series of short-lived terrane accretions around Baltica's Archean nucleus during the formation of the Precambrian Nuna supercontinent. Geological and geophysical datasets indicate W-SW growth of Baltica with NE-ward dipping subduction zones. The data suggest a long-lived retreating subduction system in the southwestern parts whereas in the northern and central parts the northeasterly transport of continental fragments or microplates towards the continental nucleus is also documented. The geotectonic environment resembles that of the early stages of the Alpine-Himalayan or Indonesian orogenic system, in which dispersed continental fragments, arcs and microplates have been attached to the Eurasian plate margin. Thus the Svecofennian orogeny can be viewed as proxy for the initial stages of an internal orogenic system. Svecofennian orogeny is a Paleoproterozoic analogue of an evolved orogenic system where terrane accretion is followed by lateral spreading or collapse induced by change in the plate architecture. The exposed parts are composed of granitoid intrusions as well as highly deformed supracrustal units. Supracrustal rocks have been metamorphosed in LP-HT conditions in either paleo-lower-upper crust or paleo-upper-middle crust. Large scale seismic reflection profiles (BABEL and FIRE) across Baltica image the crust as a collage of terranes suggesting that the bedrock has been formed and thickened in sequential accretions. The profiles also image three fold layering of the thickened crust (>55 km) to transect old terrane boundaries, suggesting that the over-thickened bedrock structures have been rearranged in post-collisional spreading and/or collapse processes. The middle crust displays typical large scale flow structures: herringbone and anticlinal ramps, rooted onto large scale listric surfaces also suggestive

  13. Gravity signals from the lithosphere in the Central European Basin System

    Science.gov (United States)

    Yegorova, T.; Bayer, U.; Thybo, H.; Maystrenko, Y.; Scheck-Wenderoth, M.; Lyngsie, S. B.

    2007-01-01

    We study the gravity signals from different depth levels in the lithosphere of the Central European Basin System (CEBS). The major elements of the CEBS are the Northern and Southern Permian Basins which include the Norwegian-Danish Basin (NDB), the North-German Basin (NGB) and the Polish Trough (PT). An up to 10 km thick sedimentary cover of Mesozoic-Cenozoic sediments, hides the gravity signal from below the basin and masks the heterogeneous structure of the consolidated crust, which is assumed to be composed of domains that were accreted during the Paleozoic amalgamation of Europe. We performed a three-dimensional (3D) gravity backstripping to investigate the structure of the lithosphere below the CEBS. Residual anomalies are derived by removing the effect of sediments down to the base of Permian from the observed field. In order to correct for the influence of large salt structures, lateral density variations are incorporated. These sediment-free anomalies are interpreted to reflect Moho relief and density heterogeneities in the crystalline crust and uppermost mantle. The gravity effect of the Moho relief compensates to a large extent the effect of the sediments in the CEBS and in the North Sea. Removal of the effects of large-scale crustal inhomogeneities shows a clear expression of the Variscan arc system at the southern part of the study area and the old crust of Baltica further north-east. The remaining residual anomalies (after stripping off the effects of sediments, Moho topography and large-scale crustal heterogeneities) reveal long wavelength anomalies, which are caused mainly by density variations in the upper mantle, though gravity influence from the lower crust cannot be ruled out. They indicate that the three main subbasins of the CEBS originated on different lithospheric domains. The PT originated on a thick, strong and dense lithosphere of the Baltica type. The NDB was formed on a weakened Baltica low-density lithosphere formed during the Sveco

  14. The fate of lipids during development and cold-storage of eggs in the laboratory-reared calanoid copepod, Acartia tonsa Dana, and in response to different algal diets

    DEFF Research Database (Denmark)

    Støttrup, Josianne; Bell, J.G.; Sargent, J.R.

    1999-01-01

    : the cryptophyte Rhodomonas baltica, the haptophyte Isochrysis galbana clone T- iso, the diatom Thalassiosira weissflogii and the dinoflagellate Heterocapsa triquetra. Further, the effect of cold storage of eggs on the lipid composition of the newly hatched nauplii was examined. During development, the fatty acid...... composition changes from a tendency towards high levels of long-chain polyunsaturated fatty acids in the early developmental stages towards a tendency to accumulate more saturated and monounsaturated fatty acids in the later developmental stages. However, the content and composition of polyunsaturated fatty...

  15. Die Frage der Menschenrechte in Estland, Lettland und Litauen / V. Stanley Vardys

    Index Scriptorium Estoniae

    Vardys, Vytas Stanley, 1924-1993

    1984-01-01

    Varem avaldatud: Acta Baltica : liber annalis Instituti Baltici. Vol. 22. - Königstein im Taunus, 1982, lk. 181-209, korrigeeritud ja täiendatud lk. 162-164. - Lisa: Der baltische Appell von 1979 (Balti apell - Eest, Läti ja Leedu kodanike märgukiri, mis sisaldas nõuet avalikustada Molotovi-Ribbentropi pakt koos oma salaprotokollidega, kuulutada pakt kehtetuks selle allakirjutamise momendist peale ja taastada Balti riikide iseseisvus, avalikustati 23. aug. 1979) ; Offener Brief aus der Estnischen SSR (Avalik kiri Eest NSV-st, nn. 40 kiri, 28. okt. 1980)

  16. Igor Stromajer / Igor Stromajer ; interv. Tilman Baumgärtel

    Index Scriptorium Estoniae

    Stromajer, Igor

    2006-01-01

    Sloveeni kunstnikust Igor Stromajerist (sünd. 1967) ja tema loomingust. I. Stromajer võitis 1997. a. Hamburgi Kunstihalle korraldatud võrgukunsti võistluse "Extension" tööga "0.html". Tema domeeni www.intima.org ülespandud tööd kuuluvad parima disainiga võrgukunsti näidete hulka. I. Stromajer on loonud WAP-kunsti mobiiltelefonidele, lavastanud Interneti-performance'eid. I. Stromajer 1999. a. tehtud meiliintervjuus oma töödest, pikemalt võrguprojektist "b.ALT.ica", võrgukunsti tulevikust

  17. Il Teatro Shakespeariano di Danzica. L'Alato / Gdansk Shakespearian Theatre. The Winged

    OpenAIRE

    Renato Rizzi

    2014-01-01

    Il 23 aprile, giorno della nascita e della morte di William Shakespeare, è stato inaugurato il tetto apribile del nuovo Teatro Elisabettiano, che sarà inaugurato il prossimo settembre a Danzica. L'evento diventa l'occasione per celebrare allo stesso tempo le potenze plastiche del simbolo, che, disseminate nella metafisica dei luoghi (e della memoria), guidano le forze alla 'forma' e i valori e gli ideali che hanno sostenuto il tormentato processo storico della città baltica e della nazione p...

  18. Influence of algal diet on feeding and egg-production of the calanoid copepod Acartia tonsa Dana

    DEFF Research Database (Denmark)

    Støttrup, Josianne; Jensen, Johanne

    1990-01-01

    Threshold concentration, retention efficiency and egg-production in the calanoid copepod Acartia tonsa Dana were examined using the algal species Isochrysis galbana clone T-iso, Dunalietta tertiolecta Butcher, Rhodomonas baltica Karsten, Ditylum brightwellii Grunow and Thalassiosira weissflogii...... Grun. Feeding and egg-production in A. tonsa was shown to be influenced by the size, quantity and quality of the food particles. The small I. galbana (4.8 μm) were inefficiently retained by A. tonsa and maximum ingestion rates on this species were first obtained at algal concentrations s> 1 μg C · ml−1...

  19. Close Link Between Harmful Cyanobacterial Dominance and Associated Bacterioplankton in a Tropical Eutrophic Reservoir

    Directory of Open Access Journals (Sweden)

    Iame A. Guedes

    2018-03-01

    Full Text Available Cyanobacteria tend to become the dominant phytoplankton component in eutrophic freshwater environments during warmer seasons. However, general observations of cyanobacterial adaptive advantages in these circumstances are insufficient to explain the prevalence of one species over another in a bloom period, which may be related to particular strategies and interactions with other components of the plankton community. In this study, we present an integrative view of a mixed cyanobacterial bloom occurring during a warm, rainy period in a tropical hydropower reservoir. We used high-throughput sequencing to follow temporal shifts in the dominance of cyanobacterial genera and shifts in the associated heterotrophic bacteria community. The bloom occurred during late spring-summer and included two distinct periods. The first period corresponded to Microcystis aeruginosa complex (MAC dominance with a contribution from Dolichospermum circinale; this pattern coincided with high water retention time and low transparency. The second period corresponded to Cylindrospermopsis raciborskii and Synechococcus spp. dominance, and the reservoir presented lower water retention time and higher water transparency. The major bacterial phyla were primarily Cyanobacteria and Proteobacteria, followed by Actinobacteria, Bacteroidetes, Verrucomicrobia, and Planctomycetes. Temporal shifts in the dominance of cyanobacterial genera were not only associated with physical features of the water but also with shifts in the associated heterotrophic bacteria. The MAC bloom was associated with a high abundance of Bacteroidetes, particularly Cytophagales. In the second bloom period, Planctomycetes increased in relative abundance, five Planctomycetes OTUs were positively correlated with Synechococcus or C. raciborskii OTUs. Our results suggest specific interactions of the main cyanobacterial genera with certain groups of the heterotrophic bacterial community. Thus, considering biotic

  20. Platystrophia (Orthida and new related Ordovician and Early Silurian brachiopod genera

    Directory of Open Access Journals (Sweden)

    Harper, David A. T.

    2007-03-01

    Full Text Available More than 150 Ordovician and Early Silurian brachiopod species have been assigned to the genus Platystrophia King, 1850 mainly on the basis of their Spirifer-like shell exteriors. King’s concept of the genus was based on Platystrophia biforata King, which is not conspecific with Terebratulites biforatus Schlotheim, traditionally regarded as the type species of Platystrophia. Porambonites costatus Pander, 1830 is formally proposed as the type species of the genus to replace P. biforata; the latter is considered to be a nomen dubium. In our revised diagnosis, Platystrophia is restricted to a group of Arenig to upper Caradoc species from Baltica and Avalonia, whereas the Ashgill and lower Silurian taxa of these regions, hitherto assigned to Platystrophia, are placed in the new genus Neoplatystrophia. Platystrophia ponderosa Foerste, 1909 from the Upper Ordovician of North America is proposed as the type species of a new genus Vinlandostrophia. Two new species, Platystrophia baltica and Platystrophia pogrebovi from the Llanvirn–Caradoc of the East Baltic are also described.

  1. Paleomagnetic study of 1765 Ma dyke swarm from the Singhbhum Craton: Implications to the paleogeography of India

    Science.gov (United States)

    Shankar, Ravi; Srinivasa Sarma, D.; Ramesh Babu, N.; Parashuramulu, V.

    2018-05-01

    We report the first key paleopole as a result of paleomagnetic study on a precisely dated 1765.3 ± 1.0 Ma WNW-ESE trending dyke swarm from Singhbhum Craton. This pole has been used in this study to propose the paleogeographic reconstruction of India with Baltica Craton and North China Craton. Incremental alternating field (AF) and thermal demagnetization, isolated high coercivity components with north to north-westerly declination and shallow negative inclination from 9 sampling sites which are representing different individual dykes. The primary origin of the ChRM is supported by the positive baked contact test. The WNW-ESE trending dykes yield a mean paleomagnetic direction with a declination = 329.2° and an inclination = -22.8° (k = 31.6; α95 = 9.3°). The positive bake contact test proves the primary nature of remanence. The pole position of Singhbhum Craton at 1765 Ma is 45°N, 311°E (dp = 5.2 and dm = 9.9). Paleogeographic reconstruction at ca. 1770 Ma, supported by geological, tectonic and metallogenic evidences indicate that the Baltica Craton and India linkage can be stable for at least ∼370 Ma (∼1770-1400 Ma). There is also reasonable evidence in support of India-North China Craton spatial proximity at ∼1770 Ma.

  2. Tectonic regimes in the Baltic Shield during the last 1200 Ma - A review

    International Nuclear Information System (INIS)

    Larsson, S.Aa.; Tullborg, E.L. and

    1993-11-01

    This report is a review about tectonic regimes in the Baltic (Fennoscandian) Shield from the Sveconorwegian (1.2 Ga ago) to the present. It also covers what is known about palaeostress during this period, which was chosen to include both orogenic and anorogenic events. A summery is given in table form, and a litho-stratigraphic map of Baltica including adjacent sea areas is enclosed. Plate movements are the ultimate reason for stress build-up in the crust. It is concluded that continental drift and rotation velocity have changed during the Earth's history. Periods of convergence and collision between continents are succeeded by periods of continental break-up. The different stress regimes, which prevailed during fracturing, produced specific fracture patterns on different scales. These fractures were reactivated during later favourable stress regimes. Within the next 100 000 years the stress situation of the Baltica crust will not change, except for the effects imposed by the growth and melting of an ice cover. 214 refs

  3. Short-term variation of nutritive and metabolic parameters in Temora longicornis females (Crustacea, Copepoda) as a response to diet shift and starvation

    Science.gov (United States)

    Kreibich, Tobias; Saborowski, Reinhard; Hagen, Wilhelm; Niehoff, Barbara

    2008-09-01

    Changes in fatty acid patterns, digestive and metabolic enzyme activities and egg production rates (EPR) were studied in the small calanoid copepod Temora longicornis. Female copepods were collected in spring 2005 off Helgoland (North Sea). In the laboratory one group of copepods was fed with the cryptophycean Rhodomonas baltica for a period of 3 days. Another group of copepods was maintained without food. According to the fatty acid patterns, animals from the field were feeding on a more detrital, animal-based and to a minor extent to a diatom-based diet. Under laboratory conditions, females rapidly accumulated fatty acids such as 18:4 (n-3), 18:3 (n-3) and 18:2 (n-6) which are specific of R. baltica. Diatom-specific fatty acids such as 16:1 (n-7) were strongly reduced. In fed animals the activities of digestive and metabolic enzymes remained constant and egg production rates were highest on day 2. Starving animals, in contrast, showed significantly reduced faecal pellet production and EPR. Proteolytic enzyme activity decreased rapidly within 24 h and remained at a low level until the end of the experiment. Citrate synthase decreased continuously as well. T. longicornis rapidly reacts to dietary changes and food depletion. It has limited energy stores and, thus, strongly depends on continuous food supply.

  4. Subduction and exhumation of a continental margin in the Scandinavian Caledonides: Insights from ultrahigh pressure metamorphism, late orogenic basins and 3D numerical modelling

    Science.gov (United States)

    Cuthbert, Simon

    2017-04-01

    The Scandinavian Caledonides (SC) represents a plate collision zone of Himalayan style and scale. Three fundamental characteristics of this orogen are: (1) early foreland-directed, tectonic transport and stacking of nappes; (2) late, wholesale reversal of tectonic transport; (3) ultrahigh pressure metamorphism of felsic crust derived from the underthrusting plate at several levels in the orogenic wedge and below the main thrust surface, indicating subduction of continental crust into the mantle. The significance of this for crustal evolution is the profound remodeling of continental crust, direct geochemical interaction of such crust and the mantle and the opening of accommodation space trapping large volumes of clastic detritus within the orogen. The orogenic wedge of the SC was derived from the upper crust of the Baltica continental margin (a hyper-extended passive margin), plus terranes derived from an assemblage of outboard arcs and intra-oceanic basins and, at the highest structural level, elements of the Laurentian margin. Nappe emplacement was driven by Scandian ( 430Ma) collision of Baltica with Laurentia, but emerging Middle Ordovician ages for diamond-facies metamorphism for the most outboard (or rifted) elements of Baltica suggest prior collision with an arc or microcontinent. Nappes derived from Baltica continental crust were subducted, in some cases to depths sufficient to form diamond. These then detached from the upper part of the down-going plate along major thrust faults, at which time they ceased to descend and possibly rose along the subduction channel. Subduction of the remaining continental margin continued below these nappes, possibly driven by slab-pull of the previously subducted Iapetus oceanic lithosphere and metamorphic densification of subducted felsic continental margin. 3D numerical modelling based upon a Caledonide-like plate scenario shows that if a continental corner or promontory enters the subduction zone, the continental margin

  5. Draft Genome of Scalindua rubra, Obtained from the Interface Above the Discovery Deep Brine in the Red Sea, Sheds Light on Potential Salt Adaptation Strategies in Anammox Bacteria.

    Science.gov (United States)

    Speth, Daan R; Lagkouvardos, Ilias; Wang, Yong; Qian, Pei-Yuan; Dutilh, Bas E; Jetten, Mike S M

    2017-07-01

    Several recent studies have indicated that members of the phylum Planctomycetes are abundantly present at the brine-seawater interface (BSI) above multiple brine pools in the Red Sea. Planctomycetes include bacteria capable of anaerobic ammonium oxidation (anammox). Here, we investigated the possibility of anammox at BSI sites using metagenomic shotgun sequencing of DNA obtained from the BSI above the Discovery Deep brine pool. Analysis of sequencing reads matching the 16S rRNA and hzsA genes confirmed presence of anammox bacteria of the genus Scalindua. Phylogenetic analysis of the 16S rRNA gene indicated that this Scalindua sp. belongs to a distinct group, separate from the anammox bacteria in the seawater column, that contains mostly sequences retrieved from high-salt environments. Using coverage- and composition-based binning, we extracted and assembled the draft genome of the dominant anammox bacterium. Comparative genomic analysis indicated that this Scalindua species uses compatible solutes for osmoadaptation, in contrast to other marine anammox bacteria that likely use a salt-in strategy. We propose the name Candidatus Scalindua rubra for this novel species, alluding to its discovery in the Red Sea.

  6. Role of primary substrate composition on microbial community structure and function and trace organic chemical attenuation in managed aquifer recharge systems

    KAUST Repository

    Li, Dong

    2014-03-26

    This study was performed to reveal the microbial community characteristics in simulated managed aquifer recharge (MAR), a natural water treatment system, under different concentrations and compositions of biodegradable dissolved organic carbon (BDOC) and further link these to the biotransformation of emerging trace organic chemicals (TOrCs). Two pairs of soil-column setups were established in the laboratory receiving synthetic feed solutions composed of different peptone/humic acid ratios and concentrations. Higher BDOC concentration resulted in lower microbial community diversity and higher relative abundance of Betaproteobacteria. Decreasing the peptone/humic acid ratio resulted in higher diversity of the community and higher relative abundances of Firmicutes, Planctomycetes, and Actinobacteria. The metabolic capabilities of microbiome involved in xenobiotics biodegradation were significantly promoted under lower BDOC concentration and higher humic acid content. Cytochrome P450 genes were also more abundant under these primary substrate conditions. Lower peptone/humic acid ratios also promoted the attenuation of most TOrCs. These results suggest that the primary substrate characterized by a more refractory character could increase the relative abundances of Firmicutes, Planctomycetes, and Actinobacteria, as well as associated cytochrome P450 genes, all of which should play important roles in the biotransformation of TOrCs in this natural treatment system. © 2014 Springer-Verlag.

  7. [Analysis of the bacterial community developing in the course of Sphagnum moss decomposition].

    Science.gov (United States)

    Kulichevskaia, I S; Belova, S E; Kevbrin, V V; Dedysh, S N; Zavarzin, G A

    2007-01-01

    Slow degradation of organic matter in acidic Sphagnum peat bogs suggests a limited activity of organotrophic microorganisms. Monitoring of the Sphagnum debris decomposition in a laboratory simulation experiment showed that this process was accompanied by a shift in the water color to brownish due to accumulation of humic substances and by the development of a specific bacterial community with a density of 2.4 x 10(7) cells ml(-1). About half of these organisms are metabolically active and detectable with rRNA-specific oligonucleotide probes. Molecular identification of the components of this microbial community showed the numerical dominance of bacteria affiliated with the phyla Alphaproteobacteria, Actinobacteria, and Phanctomycetes. The population sizes of Firmicutes and Bacteroidetes, which are believed to be the main agents of bacterially-mediated decomposition in eutrophic wetlands, were low. The numbers of planctomycetes increased at the final stage of Sphagnum decomposition. The representative isolates of Alphaproteobacteria were able to utilize galacturonic acid, the only low-molecular-weight organic compound detected in the water samples; the representatives of Planctomycetes were able to decompose some heteropolysaccharides, which points to the possible functional role of these groups of microorganisms in the community under study. Thus, the composition of the bacterial community responsible for Sphagnum decomposition in acidic and low-mineral oligotrophic conditions seems to be fundamentally different from that of the bacterial community which decomposes plant debris in eutrophic ecosystems at neutral pH.

  8. Sphagnum mosses harbour highly specific bacterial diversity during their whole lifecycle.

    Science.gov (United States)

    Bragina, Anastasia; Berg, Christian; Cardinale, Massimiliano; Shcherbakov, Andrey; Chebotar, Vladimir; Berg, Gabriele

    2012-04-01

    Knowledge about Sphagnum-associated microbial communities, their structure and their origin is important to understand and maintain climate-relevant Sphagnum-dominated bog ecosystems. We studied bacterial communities of two cosmopolitan Sphagnum species, which are well adapted to different abiotic parameters (Sphagnum magellanicum, which are strongly acidic and ombrotrophic, and Sphagnum fallax, which are weakly acidic and mesotrophic), in three Alpine bogs in Austria by a multifaceted approach. Great differences between bacterial fingerprints of both Sphagna were found independently from the site. This remarkable specificity was confirmed by a cloning and a deep sequencing approach. Besides the common Alphaproteobacteria, we found a discriminative spectrum of bacteria; although Gammaproteobacteria dominated S. magellanicum, S. fallax was mainly colonised by Verrucomicrobia and Planctomycetes. Using this information for fluorescent in situ hybridisation analyses, corresponding colonisation patterns for Alphaproteobacteria and Planctomycetes were detected. Bacterial colonies were found in high abundances inside the dead big hyalocytes, but they were always connected with the living chlorocytes. Using multivariate statistical analysis, the abiotic factors nutrient richness and pH were identified to modulate the composition of Sphagnum-specific bacterial communities. Interestingly, we found that the immense bacterial diversity was transferred via the sporophyte to the gametophyte, which can explain the high specificity of Sphagnum-associated bacteria over long distances. In contrast to higher plants, which acquire their bacteria mainly from the environment, mosses as the phylogenetically oldest land plants maintain their bacterial diversity within the whole lifecycle.

  9. Anammox biofilm in activated sludge swine wastewater treatment plants.

    Science.gov (United States)

    Suto, Ryu; Ishimoto, Chikako; Chikyu, Mikio; Aihara, Yoshito; Matsumoto, Toshimi; Uenishi, Hirohide; Yasuda, Tomoko; Fukumoto, Yasuyuki; Waki, Miyoko

    2017-01-01

    We investigated anammox with a focus on biofilm in 10 wastewater treatment plants (WWTPs) that use activated sludge treatment of swine wastewater. In three plants, we found red biofilms in aeration tanks or final sedimentation tanks. The biofilm had higher anammox 16S rRNA gene copy numbers (up to 1.35 × 10 12 copies/g-VSS) and higher anammox activity (up to 295 μmoL/g-ignition loss/h) than suspended solids in the same tank. Pyrosequencing analysis revealed that Planctomycetes accounted for up to 17.7% of total reads in the biofilm. Most of them were related to Candidatus Brocadia or Ca. Jettenia. The highest copy number and the highest proportion of Planctomycetes were comparable to those of enriched anammox sludge. Thus, swine WWTPs that use activated sludge treatment can fortuitously acquire anammox biofilm. Thus, concentrated anammox can be detected by focusing on red biofilm. Copyright © 2016 Elsevier Ltd. All rights reserved.

  10. Nuclear Pore-Like Structures in a Compartmentalized Bacterium.

    Directory of Open Access Journals (Sweden)

    Evgeny Sagulenko

    Full Text Available Planctomycetes are distinguished from other Bacteria by compartmentalization of cells via internal membranes, interpretation of which has been subject to recent debate regarding potential relations to Gram-negative cell structure. In our interpretation of the available data, the planctomycete Gemmata obscuriglobus contains a nuclear body compartment, and thus possesses a type of cell organization with parallels to the eukaryote nucleus. Here we show that pore-like structures occur in internal membranes of G.obscuriglobus and that they have elements structurally similar to eukaryote nuclear pores, including a basket, ring-spoke structure, and eight-fold rotational symmetry. Bioinformatic analysis of proteomic data reveals that some of the G. obscuriglobus proteins associated with pore-containing membranes possess structural domains found in eukaryote nuclear pore complexes. Moreover, immunogold labelling demonstrates localization of one such protein, containing a β-propeller domain, specifically to the G. obscuriglobus pore-like structures. Finding bacterial pores within internal cell membranes and with structural similarities to eukaryote nuclear pore complexes raises the dual possibilities of either hitherto undetected homology or stunning evolutionary convergence.

  11. Role of primary substrate composition on microbial community structure and function and trace organic chemical attenuation in managed aquifer recharge systems.

    Science.gov (United States)

    Li, Dong; Alidina, Mazahirali; Drewes, Jörg E

    2014-06-01

    This study was performed to reveal the microbial community characteristics in simulated managed aquifer recharge (MAR), a natural water treatment system, under different concentrations and compositions of biodegradable dissolved organic carbon (BDOC) and further link these to the biotransformation of emerging trace organic chemicals (TOrCs). Two pairs of soil-column setups were established in the laboratory receiving synthetic feed solutions composed of different peptone/humic acid ratios and concentrations. Higher BDOC concentration resulted in lower microbial community diversity and higher relative abundance of Betaproteobacteria. Decreasing the peptone/humic acid ratio resulted in higher diversity of the community and higher relative abundances of Firmicutes, Planctomycetes, and Actinobacteria. The metabolic capabilities of microbiome involved in xenobiotics biodegradation were significantly promoted under lower BDOC concentration and higher humic acid content. Cytochrome P450 genes were also more abundant under these primary substrate conditions. Lower peptone/humic acid ratios also promoted the attenuation of most TOrCs. These results suggest that the primary substrate characterized by a more refractory character could increase the relative abundances of Firmicutes, Planctomycetes, and Actinobacteria, as well as associated cytochrome P450 genes, all of which should play important roles in the biotransformation of TOrCs in this natural treatment system.

  12. Bacterial diversity and community structure in lettuce soil are shifted by cultivation time

    Science.gov (United States)

    Liu, Yiqian; Chang, Qing; Guo, Xu; Yi, Xinxin

    2017-08-01

    Compared with cereal production, vegetable production usually requires a greater degree of management and larger input of nutrients and irrigation, but these systems are not sustainable in the long term. This study aimed to what extent lettuce determine the bacterial community composition in the soil, during lettuce cultivation, pesticides and fertilizers were not apply to soil. Soil samples were collected from depths of 0-20cm and 20-40cm. A highthroughput sequencing approach was employed to investigate bacterial communities in lettuce-cultivated soil samples in a time-dependent manner. The dominant bacteria in the lettuce soil samples were mainly Proteobacteria, Actinobacteria, Chloroflexi, Nitrospirae, Firmicutes, Acidobacteria, Bacteroidetes, Verrucomicrobia, Planctomycetes, Gemmatimo nadetes, Cyanobacteria. Proteobacteria was the most abundant phylum in the 6 soil samples. The relative abundance of Acidobacteria, Firmicutes, Bacteroidetes, Verrucomicrobia and Cyanobacteria decreased through time of lettuce cultivation, but the relative abundance of Proteobacteria, Actinobacteria, Gemmatimonadetes, Chloroflexi, Planctomycetes and Nitrospirae increased over time. In the 0-20cm depth group and the 20-40cm depth soil, a similar pattern was observed that the percentage number of only shared OTUs between the early and late stage was lower than that between the early and middle stage soil, the result showed that lettuce growth can affect structure of soil bacterial communities.

  13. Macrozoobenthic recolonization of the littoral and the soft bottom after an oil spill

    International Nuclear Information System (INIS)

    Lax, H.J.; Vainio, T.

    1988-01-01

    Two years after the Eira oil spill the oil concentration in the water had returned to its background level (0.5 ug/l) in the open sea areas. On the polluted shores (depth 0.1- 0.5 m) higher concentrations (2.3 ug/l) occurred occasionaly. No clear effects related to the oil spill were noticed on the dominating soft bottom species (Macoma baltica, Pontoporeia affinis). Among the other soft bottom species the crustacean Corophium volutator showed its lowest density immediately after the spill, becoming more and more abundant during the following two years. The effect of the oil spill on the littoral fauna could still be noticed two years after the spill. The crustacean Gammarus duebeni avoided its natural habitat (uppermost littoral zone). Lymnaea palustris showed and increased mortality immediately after the oil spill but recolonized the polluted shores a normal distribution

  14. Food size spectra, ingestion and growth of the copepod Acartia tonsa during development: implications for the determination of copepod production

    DEFF Research Database (Denmark)

    Berggren, U.; Hansen, B.; Kiørboe, Thomas

    1988-01-01

    Clearance rates on different sizes of spherically shaped algae were determined in uni-algal experiments for all developmental stages (NII through adult) of the copepodAcartia tonsa, and used to construct food size spectra. Growth and developmental rates were determined at 7 food levels (0 to 1 500...... g C l-1 ofRhodomonas baltica). The lower size limit for particle capture was between 2 and 4 m for all developmental stages. Optimum particle size and upper size limit increased during development from 7 m and 10 to 14 m for NII to NIII to 14 to 70 m and 250 m for adults, respectively. When food...... size spectra were normalized (percent of maximum clearance in a particular stage versus particle diameter/prosome length) they resembled log-normal distributions with near constant width (variance). Optimum, relative particle sizes corresponded to 2 to 5% of prosome length independent of developmental...

  15. IDENTIFIKASI BAKTERI DARI IKAN TONGKOL (Euthynnus affinis YANG DIPERDAGANGKAN DI PASAR IKAN KEDONGANAN BALI

    Directory of Open Access Journals (Sweden)

    Gusti Ayu Dianti Violentina

    2016-06-01

    Full Text Available Ikan tongkol (Euthynnus affinis merupakan ikan konsumsi yang disukai masyarakat.Pengetahuan tentang bakteri yang ditemukan pada tubuh ikan ini sangat penting untuk tujuan kesehatan masyarakat dan kajian biologi ikan.  Penelitian ini bertujuan untuk mengidentifikasi bakteri yang berasosiasi dengan ikan tersebut.Bakteri dari usus ikan diambil secara aseptis dan ditumbuhkan pada Blood Agar dan Nutrient Broth. DNA total dari kultur agar cair diisolasi dengan chelax, gen 16S RNA diamplifikasi dengan PCR menggunakan primer universal dengan produk sekitar 1300 bp. Produk PCR dirunut dengan metode Big-Dye termination. Hasilnya disepadankan dan dianalisis dengan MEGA 6.0. Pada penelitian ini, 14 spesies bakteri yang memiliki > 99% kesamaan dengan data GenBankteridentifikasi, yaitu Photobacterium leiognathi, Uruburuella testudinis, Aeromonas molluscorum, Psychrobacter celer, Psychrobacer faecalis, Acinetobacter johnsonii, Vibrio gallicus, Bacillus megaterium, Vagococcus fessus, Shewanella baltica, Shewanella algae, Rothia nasimurium, Myroides phaeus dan Yersinia ruckeri. Peran bakteribakteri tersebut dalam biologi ikan dan kesehatan masyarakat perlu dikaji lebih lanjut.

  16. Muusika : Kremer tuleb üllatama. Bartokiga Pariisis. Raimo Kangro CD kiitvad arvustused. Festivalikorraldajad ühendavad jõud. EOÜ kolmas tegevusaasta. Jüri Pärg 50 aastat laval. Harri Vasar 75. Ernesaksa nimelised stipendiumid / Heili Vaus-Tamm

    Index Scriptorium Estoniae

    Vaus-Tamm, Heili, 1961-

    2001-01-01

    Tartus ja Tallinnas annab kontserte Gidon Kremer ja tema orkester Kremerata Baltica. 30.XI toimus Pariisis Liszti saalis HonEst Quintette debüütkontsert, kus kanti ette Bela Bartoki kammerloomingut. Saksa muusikaajakirjad Fono Forum ning Piano News arvustavad Raimo Kangro hiljuti välja antud CDd. 11.XII kohtusid kultuuriministeeriumis süvamuusikafestivalide korraldajad. 7.XII tuli EMA orelisaalis kokku Eesti Orelisõprade Ühingu aastakoosolek, juhatuse esimees A.-P. Lattik. Jüri Pärg märkis soolokontserdiga 25.XII Estonia talveaias oma 70. sünnipäeva ja 50 lava-aastat. Estonia talveaias meenutatukse Harri Vasarat, kes saanuks 75. aastaseks. 15.XII antakse TÜ aulas traditsioonilisel jõulukontserdil üle tänavused Gustav Ernesaksa nimelised stipendiumid.

  17. Recirculating aquaculture system for high density production of the calanoid copepod Acartia tonsa (Dana)

    DEFF Research Database (Denmark)

    Vu, Minh Thi Thuy; Øie, Gunvor; Reinertsen, Helge

    2013-01-01

    The calanoid copepod Acartia tonsa (Dana) is one of the most promising copepod species for marine larviculture. This species has a wide tolerance to temperature and salinity, small size, can produce resting eggs. All their nauplii, copepodites and adults can be use as excellent feeds for marine...... capacity. A. tonsa fed the unicellular algae Rhodomonas baltica were registered for four weeks in triplicate 50 L tanks in each system. Water quality parameters were recorded daily for temperature, oxygen, pH, salinity, particles and every five days for nitrogenous waste and bacteria through...... the similar survival, growth, and reproduction, yet the nauplii developed into copepodites faster in RAS (110h) compared to FTAS (158h). This can be an indication for the potential for culturing or maintaining A. tonsa nauplii and early copepodite stages at higher densities before feeding larvae of marine...

  18. Properties and development of the middle European Lithospere: Reality and Ideas

    Directory of Open Access Journals (Sweden)

    Miloš Suk

    2007-01-01

    Full Text Available The structure of the middle European lithosphere is extra-ordinary complicated by a combination of the shield type (Baltica the organic type (European Cadomiles, Hercyniles and Alpides and the basin types (Po and Pannonian basins lithosphere. The geological and geophysical data on its structure, age distribution of temperature and pressures and on the plate movements in its geological development inspire some loubts about the correctness of the theories exploining the relations of the parts by subduction processes only. For example, the long distance autonomous movements deduced from paleomagnetic data can be explained by an expansion of the continental crust and the anomalous properties or tne basins are explainable by the beginning of the origin of a new intracontinental rift zone.

  19. Dicty_cDB: Contig-U11706-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available one) Shewanella baltica OS195, complet... 37 1.1 AJ875406_1( AJ875406 |pid:none) Candida intermedia mRNA for...none) Leishmania major strain Friedlin... 35 4.3 AD2736( AD2736 ) MFS permease [imported] - Agrobacterium tumefacie..... 36 3.0 8 ( ER451042 ) 1092963849549 Global-Ocean-Sampling_GS-35-01-01-1... 34 3.2 3 ( AC115626 ) Homo sapie...J956921 ) 1093018976377 Global-Ocean-Sampling_GS-30-02-01-1... 38 0.13 2 ( EJ412209 ) 1093012157126 Global-Ocean-Sampli...6 0.33 2 ( EK421366 ) 1095515508395 Global-Ocean-Sampling_GS-31-01-01-1... 42 0.48 2 ( AM430719 ) Vitis vini

  20. Root zone of a continental rift

    DEFF Research Database (Denmark)

    Kirsch, Moritz; Svenningsen, Olaf

    2016-01-01

    melt are considered to account for the compositional range exhibited by the KIC igneous rocks. U/Pb SIMS geochronological data from zircon rims yield an emplacement age of 578 ± 9 Ma. The KIC is thus younger and more depleted than coeval mafic rocks found in the Seve Nappe, and is interpreted...... to represent a high-level magma plumbing system in a late-stage continental rift. The composition and volume of rift-related igneous rocks in the Seve Nappes are inconsistent with a mantle plume origin, but are thought to record progressive lithospheric thinning and increasing involvement of an asthenospheric......Mafic magmatic rocks formed between ca. 615 and 560 Ma along the Neoproterozoic margins of Baltica and Laurentia are classically attributed to continental rifting heralding the opening of the Iapetus Ocean. We report new data for the Kebnekaise Intrusive Complex (KIC) exposed in the Seve Nappes...

  1. Fontibacter flavus gen. nov., sp. nov., a member of the family 'Cyclobacteriaceae', isolated from a hot spring.

    Science.gov (United States)

    Kämpfer, Peter; Young, Chiu-Chung; Chen, Wen-Ming; Rekha, P D; Fallschissel, Kerstin; Lodders, Nicole; Chou, Jui-Hsing; Shen, Fo-Ting; Frischmann, Alexa; Busse, Hans-Jürgen; Arun, A B

    2010-09-01

    The taxonomic position of a bright orange-pigmented bacterial strain, designated CC-GZM-130(T), isolated from a water sample of the Guan-zing-ling hot spring, southern Taiwan, was studied. The strain was able to grow on nutrient agar at 25-40 degrees C and in the presence of 1-3 % (w/v) NaCl. Comparative analyses of the 16S rRNA gene sequence showed that the isolate was grouped in the vicinity of the genus Aquiflexum with the highest sequence similarity of 92.1 % to the type strain of Aquiflexum balticum, followed by sequence similarities of 92.0, 91.6 and 91.5 % to the type strains of Algoriphagus ornithinivorans, Algoriphagus hitonicola and Belliella baltica, respectively. The polyamine pattern showed that the major compound was sym-homospermidine. The quinone system was menaquinone MK-7. The polar lipid profile was composed predominantly of phosphatidylethanolamine, three polar lipids and one aminolipid. Minor amounts of other lipids were also detectable. The main characteristics of the fatty acid profiles of strain CC-GZM-130(T), B. baltica and Aquiflexum balticum were similar, with iso-C(15 : 0), iso-C(17 : 1)ω 9c and iso-C(17 : 0) 3-OH as the major fatty acids, but some qualitative and quantitative differences were observed. The DNA G+C content of the novel strain was 53.2 mol%. The isolate clearly differed genotypically and phenotypically from representatives of the most closely related genera. On the basis of these differences, a novel species in a new genus, Fontibacter flavus gen. nov., sp. nov., is proposed with CC-GZM-130(T) (=CCUG 57694(T)=CCM 7650(T)) as the type strain of the type species.

  2. An autochthonous Avalonian basement source for the latest Ordovician Brenton Pluton in the Meguma terrane of Nova Scotia: U-Pb-Hf isotopic constraints and paleogeographic implications

    Science.gov (United States)

    Duncan Keppie, J.; Gregory Shellnutt, J.; Dostal, Jaroslav; Fraser Keppie, D.

    2018-04-01

    The Ediacaran-Ordovician Meguma Supergroup was thrust over Avalonia basement prior to the intrusion of post-Acadian, ca. 370 Ma, S-type granitic batholiths. This has led to two main hypotheses regarding the original location of the Meguma terrane, a continental rise prism bordering either NW Africa or Avalonia. On the other hand, the pre-Acadian, ca. 440 Ma Brenton pluton has yielded the following U/Pb LA-ICP-MS zircon data: (1) 448 ± 3 Ma population peak inferred to be the intrusive age and (2) ca. 550 and 700 Ma inherited ages common to both Avalonia and NW Africa. In contrast, Hf isotopic analyses of zircon yielded model ages ranging from 814 to 1127 Ma with most between 940 and 1040 Ma: such ages are typical of Avalonia and not NW Africa. The ages of the inherited zircons found within the Brenton pluton suggest that it was probably derived by partial melting of sub-Meguma, mid-crustal Avalonian rocks, upon which the Meguma Supergroup was deposited. Although Avalonia is commonly included in the peri-Gondwanan terranes off NW Africa or Amazonia, paleomagnetic data, faunal provinciality, and Hf data suggest that, during the Ediacaran-Early Cambrian, it was an island chain lying near the tropics (ca. 20-30 °S) and was possibly a continuation of the Bolshezemel volcanic arc accreted to northern Baltica during the Ediacaran Timanide orogenesis. This is consistent with the similar derital zircon population in the Ediacaran-Cambrian Meguma Supergroup and the Dividal Group in northeastern Baltica.

  3. Lower Cambrian-Ediacaran Paleogeography and True Polar Wander with New Paleomagnetic Constraints from West African Craton

    Science.gov (United States)

    Robert, B.; Besse, J.; Blein, O.; Greff-Lefftz, M.; Baudin, T.; Fernando, L.; Meslouh, S.; Belbadaoui, M.

    2014-12-01

    Paleomagnetic data from Laurentia and Baltica continents suggest fast large oscillations of the virtual geomagnetic poles (VGP) from high to low latitudes during the Ediacaran (635-542 Ma). These data are interpreted in the literature either as oscillations of the Earth magnetic dipole between polar and equatorial positions, or as True Polar Wander (TPW), implying a very fast tumbling of continents and perhaps, of whole Earth. In this study, we try to test these hypotheses by bringing new paleomagnetic data on volcanic series from another continent, the West African Craton (WAC). We have sampled well dated pyroclastic and lava flows from the Ouarzazate and Taroudant groups in the Anti-Atlas, (Morocco). 480 samples from 105 sites were thermally demagnetized in our laboratory. Our preliminary results highlight two major groups of directions, mainly carried by hematite, magnetite also contributing sometimes to the magnetization. The first group consists of a dual polarity high inclination direction that may represent the original magnetization. The observed paleolatitude is compatible with that predicted by the lower Cambrian-Ediacaran apparent polar wander path (APWP) of Gondwana, assuming that the WAC was already accreted to Gondwana at this age. Nevertheless, a complete agreement between our pole and the APWP needs a local rotation of around 80° on a vertical axis. The second group displays a single polarity direction, with a shallow inclination and a south-east declination. This direction is close to the expected direction derived from the Permo-Carboniferous segment of the Gondwana APWP, and may represent a remagnetization acquired during the Kiaman reversed polarity superchron. Our preliminary paleomagnetic results thus display large changes in the VGP position, as also evidenced by others on Baltica and Laurentia. However, their interpretation does not favor TPW episodes or equatorial Earth magnetic dipole during the lower Cambrian-Ediacaran periods, but

  4. [Prokaryote diversity in water environment of land-ocean ecotone of Zhuhai City].

    Science.gov (United States)

    Huang, Xiao-Lan; Chen, Jian-Yao; Zhou, Shi-Ning; Xie, Li-Chun; Fu, Cong-Sheng

    2010-02-01

    By constructing 16S rDNA clone library with PCR-RFLP, the prokaryote diversity in the seawater and groundwater of land-ocean ecotone of Zhuhai City was investigated, and the similarity and cluster analyses were implemented with the database of the sequences in Genbank. In the seawater, Proteobacteria was dominant, followed by Archaeon, Gemmatimonadetes, Candidate division OP3 and OP8, and Planctomycetes, etc.; while in the groundwater, Archaeon was dominant, followed by Proteobacteria, Sphingobacteria, Candidate division OP3, Actinobacterium, and Pseudomonas. The dominant taxa in the groundwater had high similarity to the unculturable groups of marine microorganisms. Large amount of bacteria capable of degrading organic matter and purifying water body existed in the groundwater, suggesting that after long-term evolution, the land-ocean ecotone of Zhuhai City had the characteristics of both land and ocean.

  5. Long-term nickel exposure altered the bacterial community composition but not diversity in two contrasting agricultural soils.

    Science.gov (United States)

    Li, Jing; Hu, Hang-Wei; Ma, Yi-Bing; Wang, Jun-Tao; Liu, Yu-Rong; He, Ji-Zheng

    2015-07-01

    Nickel pollution imposes deleterious effects on soil ecosystem. The responses of soil microorganisms to long-term nickel pollution under field conditions remain largely unknown. Here, we used high-throughput sequencing to elucidate the impacts of long-term nickel pollution on soil bacterial communities in two contrasting agricultural soils. Our results found that the soil microbial biomass carbon consistently decreased along the nickel gradients in both soils. Nickel pollution selectively favored or impeded the prevalence of several dominant bacterial guilds, in particular, Actinobacteria showed tolerance, while Acidobacteria and Planctomycetes displayed sensitivity. Despite the apparent shifts in the bacterial community composition, no clear tendency in the bacterial diversity and abundance was identified along the nickel gradients in either soil. Collectively, we provide evidence that long-term nickel pollution shifted the soil bacterial communities, resulting in the decrease of microbial biomass although the bacterial diversity was not significantly changed.

  6. Rhizospheric metagenome of the terrestrial mangrove fern Acrostichum from Indian Sunderbans

    Directory of Open Access Journals (Sweden)

    Sayak Ganguli

    2017-12-01

    Full Text Available This study reports the analyses of the rhizospheric microbiome of the terrestrial mangrove fern Acrostichum aureum Linn. from the Indian Sunderbans. Samples were collected using standard protocols and 16S rRNA gene V3–V4 region amplicon sequencing was performed to identify the microbial communities prevalent in the rhizosphere. A total of 1,931,252 quality checked reads were assembled into 204,818 contigs and were analysed using QIIME to reveal the abundance of Proteobacteria, Acidobacteria and Planctomycetes. The data is available at the NCBI - Sequence Read Archive with accession number: SRX2660456. This is the first report of the rhizospheric microbiome belonging to a fern species.

  7. [Phylogenetic diversity of microorganisms associated with the deep-water sponge Baikalospongia intermedia].

    Science.gov (United States)

    Kalyzhnaya, O V; Itskovich, V B

    2014-07-01

    The diversity of bacteria associated with deep-water sponge Baikalospongia intermedia was evaluated by sequence analysis of 16S rRNA genes from two sponge samples collected in Lake Baikal from depths of 550 and 1204 m. A total of 64 operational taxonomic units, belonging to nine bacterial phyla, Proteobacteria (classes Alphaproteobacteria,. Betaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria), Actinobacteria, Planctomycetes, Cloroflexi, Verrucomicrobia, Acidobacteria, Chlorobi, and Nitrospirae, including candidate phylum WS5, were identified. Phylogenetic analysis showed that the examined communities contained phylotypes exhibiting homology to uncultured bacteria from different lake ecosystems, freshwater sediments, soil and geological formations. Moreover, a number of phylotypes were relative to psychrophilic, methane-oxidizing, sulfate-reducing bacteria, and to microorganisms resistant to the influence of heavy metals. It seems likely that the unusual habitation conditions of deep-water sponges contribute to the taxonomic diversity of associated bacteria and have an influence on the presence of functionally important microorganisms in bacterial communities.

  8. Prokaryotic communities differ along a geothermal soil photic gradient.

    Science.gov (United States)

    Meadow, James F; Zabinski, Catherine A

    2013-01-01

    Geothermal influenced soils exert unique physical and chemical limitations on resident microbial communities but have received little attention in microbial ecology research. These environments offer a model system in which to investigate microbial community heterogeneity and a range of soil ecological concepts. We conducted a 16S bar-coded pyrosequencing survey of the prokaryotic communities in a diatomaceous geothermal soil system and compared communities across soil types and along a conspicuous photic depth gradient. We found significant differences between the communities of the two different soils and also predictable differences between samples taken at different depths. Additionally, we targeted three ecologically relevant bacterial phyla, Cyanobacteria, Planctomycetes, and Verrucomicrobia, for clade-wise comparisons with these variables and found strong differences in their abundances, consistent with the autecology of these groups.

  9. A comparative study of composting the solid fraction of dairy manure with or without bulking material: Performance and microbial community dynamics.

    Science.gov (United States)

    Zhong, Xiao-Zhong; Ma, Shi-Chun; Wang, Shi-Peng; Wang, Ting-Ting; Sun, Zhao-Yong; Tang, Yue-Qin; Deng, Yu; Kida, Kenji

    2018-01-01

    The present study compared the development of various physicochemical properties and the composition of microbial communities involved in the composting process in the solid fraction of dairy manure (SFDM) with a sawdust-regulated SFDM (RDM). The changes in several primary physicochemical properties were similar in the two composting processes, and both resulted in mature end-products within 48days. The bacterial communities in both composting processes primarily comprised Proteobacteria and Bacteroidetes. Firmicutes were predominant in the thermophilic phase, whereas Chloroflexi, Planctomycetes, and Nitrospirae were more abundant in the final mature phase. Furthermore, the succession of bacteria in both groups proceeded in a similar pattern, suggesting that the effects of the bulking material on bacterial dynamics were minor. These results demonstrate the feasibility of composting using only the SFDM, reflected by the evolution of physicochemical properties and the microbial communities involved in the composting process. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. Multiple approaches to characterize the microbial community in a thermophilic anaerobic digester running on swine manure: a case study.

    Science.gov (United States)

    Tuan, Nguyen Ngoc; Chang, Yi-Chia; Yu, Chang-Ping; Huang, Shir-Ly

    2014-01-01

    In this study, the first survey of microbial community in thermophilic anaerobic digester using swine manure as sole feedstock was performed by multiple approaches including denaturing gradient gel electrophoresis (DGGE), clone library and pyrosequencing techniques. The integrated analysis of 21 DGGE bands, 126 clones and 8506 pyrosequencing read sequences revealed that Clostridia from the phylum Firmicutes account for the most dominant Bacteria. In addition, our analysis also identified additional taxa that were missed by the previous researches, including members of the bacterial phyla Synergistetes, Planctomycetes, Armatimonadetes, Chloroflexi and Nitrospira which might also play a role in thermophilic anaerobic digester. Most archaeal 16S rRNA sequences could be assigned to the order Methanobacteriales instead of Methanomicrobiales comparing to previous studies. In addition, this study reported that the member of Methanothermobacter genus was firstly found in thermophilic anaerobic digester. Copyright © 2014 Elsevier GmbH. All rights reserved.

  11. Performance and diversity of polyvinyl alcohol-degrading bacteria under aerobic and anaerobic conditions.

    Science.gov (United States)

    Huang, Jianping; Yang, Shisu; Zhang, Siqi

    2016-11-01

    To compare the degradation performance and biodiversity of a polyvinyl alcohol-degrading microbial community under aerobic and anaerobic conditions. An anaerobic-aerobic bioreactor was operated to degrade polyvinyl alcohol (PVA) in simulated wastewater. The degradation performance of the bioreactor during sludge cultivation and the microbial communities in each reactor were compared. Both anaerobic and aerobic bioreactors demonstrated high chemical oxygen demand removal efficiencies of 87.5 and 83.6 %, respectively. Results of 16S rDNA sequencing indicated that Proteobacteria dominated in both reactors and that the microbial community structures varied significantly under different operating conditions. Both reactors obviously differed in bacterial diversity from the phyla Planctomycetes, Chlamydiae, Bacteroidetes, and Chloroflexi. Betaproteobacteria and Alphaproteobacteria dominated, respectively, in the anaerobic and aerobic reactors. The anaerobic-aerobic system is suitable for PVA wastewater treatment, and the microbial genetic analysis may serve as a reference for PVA biodegradation.

  12. Bacterial reduction of mercury in the high arctic

    DEFF Research Database (Denmark)

    Møller, Annette Klæstrup

    than the rare phyla, suggesting that the ecological success of a bacterial phylum depends on the diversity rather than the dominance of a few genera. The most dominant phyla included Proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria and Firmicutes in the snow and Proteobacteria......, Bacteroidetes, Actinobacteria and Planctomycetes in freshwater. The bacteria identified in this study both included phylotypes commonly found in cold environments as well as rare phylotypes. During the time of sampling atmospheric ozone measurements and total Hg measurements in the snow indicated......, Firmicutes, Actinobacteria, and Bacteriodetes. It was found that 25% of the isolates resistant to Hg also reduced HgII to Hg0, although there was no correlation between level of resistance, ability to reduce HgII, and taxonomic group. An estimation of the potential bacterial reduction of HgII in snow...

  13. Meta-omic signatures of microbial metal and nitrogen cycling in marine oxygen minimum zones

    Directory of Open Access Journals (Sweden)

    Jennifer B. Glass

    2015-09-01

    Full Text Available Iron (Fe and copper (Cu are essential cofactors for microbial metalloenzymes, but little is known about the metalloenyzme inventory of anaerobic marine microbial communities despite their importance to the nitrogen cycle. We compared dissolved O2, NO3-, NO2-, Fe and Cu concentrations with nucleic acid sequences encoding Fe and Cu-binding proteins in 21 metagenomes and 9 metatranscriptomes from Eastern Tropical North and South Pacific oxygen minimum zones and 7 metagenomes from the Bermuda Atlantic Time-series Station. Dissolved Fe concentrations increased sharply at upper oxic-anoxic transition zones, with the highest Fe:Cu molar ratio (1.8 occurring at the anoxic core of the Eastern Tropical North Pacific oxygen minimum zone and matching the predicted maximum ratio based on data from diverse ocean sites. The relative abundance of genes encoding Fe-binding proteins was negatively correlated with O2, driven by significant increases in genes encoding Fe-proteins involved in dissimilatory nitrogen metabolisms under anoxia. Transcripts encoding cytochrome c oxidase, the Fe- and Cu-containing terminal reductase in aerobic respiration, were positively correlated with O2 content. A comparison of the taxonomy of genes encoding Fe- and Cu-binding vs. bulk proteins in OMZs revealed that Planctomycetes represented a higher percentage of Fe genes while Thaumarchaeota represented a higher percentage of Cu genes, particularly at oxyclines. These results are broadly consistent with higher relative abundance of genes encoding Fe-proteins in the genome of a marine planctomycete vs. higher relative abundance of genes encoding Cu-proteins in the genome of a marine thaumarchaeote. These findings highlight the importance of metalloenzymes for microbial processes in oxygen minimum zones and suggest preferential Cu use in oxic habitats with Cu > Fe vs. preferential Fe use in anoxic niches with Fe > Cu.

  14. Assessing biosynthetic potential of agricultural groundwater through metagenomic sequencing: A diverse anammox community dominates nitrate-rich groundwater.

    Directory of Open Access Journals (Sweden)

    William B Ludington

    Full Text Available Climate change produces extremes in both temperature and precipitation causing increased drought severity and increased reliance on groundwater resources. Agricultural practices, which rely on groundwater, are sensitive to but also sources of contaminants, including nitrate. How agricultural contamination drives groundwater geochemistry through microbial metabolism is poorly understood.On an active cow dairy in the Central Valley of California, we sampled groundwater from three wells at depths of 4.3 m (two wells and 100 m (one well below ground surface (bgs as well as an effluent surface water lagoon that fertilizes surrounding corn fields. We analyzed the samples for concentrations of solutes, heavy metals, and USDA pathogenic bacteria of the Escherichia coli and Enterococcus groups as part of a long term groundwater monitoring study. Whole metagenome shotgun sequencing and assembly revealed taxonomic composition and metabolic potential of the community.Elevated nitrate and dissolved organic carbon occurred at 4.3m but not at 100m bgs. Metagenomics confirmed chemical observations and revealed several Planctomycete genomes, including a new Brocadiaceae lineage and a likely Planctomycetes OM190, as well novel diversity and high abundance of nano-prokaryotes from the Candidate Phyla Radiation (CPR, the Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaea (DPANN and the Thaumarchaeota, Aigarchaeota, Crenarchaeota, Korarchaeota (TACK superphyla. Pathway analysis suggests community interactions based on complimentary primary metabolic pathways and abundant secondary metabolite operons encoding antimicrobials and quorum sensing systems.The metagenomes show strong resemblance to activated sludge communities from a nitrogen removal reactor at a wastewater treatment plant, suggesting that natural bioremediation occurs through microbial metabolism. Elevated nitrate and rich secondary metabolite biosynthetic capacity suggest

  15. Evolutionary gradient of predicted nuclear localization signals (NLS)-bearing proteins in genomes of family Planctomycetaceae.

    Science.gov (United States)

    Guo, Min; Yang, Ruifu; Huang, Chen; Liao, Qiwen; Fan, Guangyi; Sun, Chenghang; Lee, Simon Ming-Yuen

    2017-04-04

    The nuclear envelope is considered a key classification marker that distinguishes prokaryotes from eukaryotes. However, this marker does not apply to the family Planctomycetaceae, which has intracellular spaces divided by lipidic intracytoplasmic membranes (ICMs). Nuclear localization signal (NLS), a short stretch of amino acid sequence, destines to transport proteins from cytoplasm into nucleus, and is also associated with the development of nuclear envelope. We attempted to investigate the NLS motifs in Planctomycetaceae genomes to demonstrate the potential molecular transition in the development of intracellular membrane system. In this study, we identified NLS-like motifs that have the same amino acid compositions as experimentally identified NLSs in genomes of 11 representative species of family Planctomycetaceae. A total of 15 NLS types and 170 NLS-bearing proteins were detected in the 11 strains. To determine the molecular transformation, we compared NLS-bearing protein abundances in the 11 representative Planctomycetaceae genomes with them in genomes of 16 taxonomically varied microorganisms: nine bacteria, two archaea and five fungi. In the 27 strains, 29 NLS types and 1101 NLS-bearing proteins were identified, principal component analysis showed a significant transitional gradient from bacteria to Planctomycetaceae to fungi on their NLS-bearing protein abundance profiles. Then, we clustered the 993 non-redundant NLS-bearing proteins into 181 families and annotated their involved metabolic pathways. Afterwards, we aligned the ten types of NLS motifs from the 13 families containing NLS-bearing proteins among bacteria, Planctomycetaceae or fungi, considering their diversity, length and origin. A transition towards increased complexity from non-planctomycete bacteria to Planctomycetaceae to archaea and fungi was detected based on the complexity of the 10 types of NLS-like motifs in the 13 NLS-bearing proteins families. The results of this study reveal that

  16. Soil microbiome responses to the short-term effects of Amazonian deforestation.

    Science.gov (United States)

    Navarrete, Acacio A; Tsai, Siu M; Mendes, Lucas W; Faust, Karoline; de Hollander, Mattias; Cassman, Noriko A; Raes, Jeroen; van Veen, Johannes A; Kuramae, Eiko E

    2015-05-01

    Slash-and-burn clearing of forest typically results in increase in soil nutrient availability. However, the impact of these nutrients on the soil microbiome is not known. Using next generation sequencing of 16S rRNA gene and shotgun metagenomic DNA, we compared the structure and the potential functions of bacterial community in forest soils to deforested soils in the Amazon region and related the differences to soil chemical factors. Deforestation decreased soil organic matter content and factors linked to soil acidity and raised soil pH, base saturation and exchangeable bases. Concomitant to expected changes in soil chemical factors, we observed an increase in the alpha diversity of the bacterial microbiota and relative abundances of putative copiotrophic bacteria such as Actinomycetales and a decrease in the relative abundances of bacterial taxa such as Chlamydiae, Planctomycetes and Verrucomicrobia in the deforested soils. We did not observe an increase in genes related to microbial nutrient metabolism in deforested soils. However, we did observe changes in community functions such as increases in DNA repair, protein processing, modification, degradation and folding functions, and these functions might reflect adaptation to changes in soil characteristics due to forest clear-cutting and burning. In addition, there were changes in the composition of the bacterial groups associated with metabolism-related functions. Co-occurrence microbial network analysis identified distinct phylogenetic patterns for forest and deforested soils and suggested relationships between Planctomycetes and aluminium content, and Actinobacteria and nitrogen sources in Amazon soils. The results support taxonomic and functional adaptations in the soil bacterial community following deforestation. We hypothesize that these microbial adaptations may serve as a buffer to drastic changes in soil fertility after slash-and-burning deforestation in the Amazon region. © 2015 John Wiley & Sons Ltd.

  17. Diversity and abundance of the bacterial community of the red Macroalga Porphyra umbilicalis: did bacterial farmers produce macroalgae?

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    Lilibeth N Miranda

    Full Text Available Macroalgae harbor microbial communities whose bacterial biodiversity remains largely uncharacterized. The goals of this study were 1 to examine the composition of the bacterial community associated with Porphyra umbilicalis Kützing from Schoodic Point, ME, 2 determine whether there are seasonal trends in species diversity but a core group of bacteria that are always present, and 3 to determine how the microbial community associated with a laboratory strain (P.um.1 established in the presence of antibiotics has changed. P. umbilicalis blades (n = 5, fall 2010; n = 5, winter 2011; n = 2, clonal P.um.1 were analyzed by pyrosequencing over two variable regions of the 16 S rDNA (V5-V6 and V8; 147,880 total reads. The bacterial taxa present were classified at an 80% confidence threshold into eight phyla (Bacteroidetes, Proteobacteria, Planctomycetes, Chloroflexi, Actinobacteria, Deinococcus-Thermus, Firmicutes, and the candidate division TM7. The Bacteroidetes comprised the majority of bacterial sequences on both field and lab blades, but the Proteobacteria (Alphaproteobacteria, Gammaproteobacteria were also abundant. Sphingobacteria (Bacteroidetes and Flavobacteria (Bacteroidetes had inverse abundances on natural versus P.um.1 blades. Bacterial communities were richer and more diverse on blades sampled in fall compared to winter. Significant differences were observed between microbial communities among all three groups of blades examined. Only two OTUs were found on all 12 blades, and only one of these, belonging to the Saprospiraceae (Bacteroidetes, was abundant. Lewinella (as 66 OTUs was found on all field blades and was the most abundant genus. Bacteria from the Bacteroidetes, Proteobacteria and Planctomycetes that are known to digest the galactan sulfates of red algal cell walls were well-represented. Some of these taxa likely provide essential morphogenetic and beneficial nutritive factors to P. umbilicalis and may have had

  18. Differences between the rhizosphere microbiome of Beta vulgaris ssp. maritima - ancestor of all beet crops - and modern sugar beets

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    Christin eZachow

    2014-08-01

    Full Text Available The structure and function of the plant microbiome is driven by plant species and prevailing environmental conditions. Effectuated by breeding efforts, modern crops diverge genetically and phenotypically from their wild relatives but little is known about consequences for the associated microbiota. Therefore, we studied bacterial rhizosphere communities associated with the wild beet B. vulgaris ssp. maritima grown in their natural habitat soil from coastal drift lines (CS and modern sugar beets (Beta vulgaris ssp. vulgaris cultivated in CS and potting soil (PS under greenhouse conditions. Analysis of 16S rRNA gene fingerprints and pyrosequencing-based amplicon libraries revealed plant genotype- and soil-specific microbiomes. Wild beet plants harbor distinct operational taxonomic units (OTUs and a more diverse bacterial community than the domesticated sugar beet plants. Although the rhizospheres of both plant genotypes were dominated by Proteobacteria and Planctomycetes, 47.4% of dominant OTUs were additionally detected in the wild beet rhizosphere. Analysis of the cultivable fraction confirmed these plant genotype-specific differences at functional level. The proportion of isolates displayed in vitro activity against phytopathogens was lower for wild beet (≤45.8% than for sugar beet (≤57.5%. Conversely, active isolates from the wild beet exhibited stronger ability to cope with abiotic stresses. From all samples, active isolates of Stenotrophomonas rhizophila were frequently identified. In addition, soil type-specific impacts on the composition of bacterial communities were found: Acidobacteria, Chloroflexi, and Planctomycetes were only detected in plants cultivated in CS; whereas Bacteroidetes and Proteobacteria dominated in PS. Overall, in comparison to modern sugar beets, wild beets were associated with taxonomically and functionally distinct microbiomes.

  19. Controls of late Palaeozoic and Mesozoic extension in the British Isles: evidence from seismic reflection data in the Central North Sea

    Science.gov (United States)

    Smith, K.; Cameron, T. D. J.

    2009-04-01

    Controls of late Palaeozoic and Mesozoic extension in the British Isles: evidence from seismic reflection data in the Central North Sea. Kevin Smith (1) and Don Cameron (2) (1) British Geological Survey, Murchison House, West Mains Road, Edinburgh, EH9 3LA. (ksm@bgs.ac.uk). (2) British Geological Survey, 376 Gilmerton Road, Edinburgh, EH17 7QS. In the area of the British Isles during the late Devonian and early Carboniferous, the oblique convergence of Laurentia and Gondwana imposed a torque on the adjoining terranes of Baltica and Avalonia. Their resulting clockwise rotation was accommodated by widely distributed N-S extension in the intervening zones previously formed by Caledonian and Acadian convergence. South of Laurentia and Baltica, late Palaeozoic extension was focused (1) at terrane margins, (2) in areas of limited Caledonian-Acadian plutonism, and (3) in places where the western (Iapetus) and eastern (Tornquist) convergence zones intersect at a high angle. One of these latter areas lies in Central England immediately north of the Midland Microcraton (part of Eastern Avalonia), where thermal subsidence associated with early Carboniferous extension gave rise to the late Carboniferous Pennine Basin. Interpretation of an extensive set of 3D and 2D long-offset seismic reflection data suggests that a similar area of enhanced extension at a fold belt intersection lies to north of the Mid North Sea High in the middle of the Central North Sea. Variscan uplift and inversion of the late Palaeozoic basins began to predominate in mid-Carboniferous times as final amalgamation of all the different terranes to form Pangaea curtailed the initial episode of extension and thermal subsidence. This change in the tectonic regime was associated with the onset of tholeiitic volcanism within the convergence zones, and was followed by localised extension during the earliest Permian. Evidence obtained from seismic interpretation of the deep structure of the UK sector of the Central

  20. Geology of the Severnaya Zemlya Archipelago and the North Kara Terrane in the Russian high Arctic

    Science.gov (United States)

    Lorenz, Henning; Männik, Peep; Gee, David; Proskurnin, Vasilij

    2008-05-01

    The Severnaya Zemlya Archipelago is located at 80°N near the continental shelf break, between the Kara and Laptev seas. Sedimentary successions of Neoproterozoic and Palaeozoic age dominate the bedrock geology. Together with Northern Tajmyr, Severnaya Zemlya constitutes the main land areas of the North Kara Terrane (NKT), which is inferred here to have been a part of the Timanide margin of Baltica, i.e. an integral part of Baltica at least since the Vendian. Vendian turbidites derived from the Timanide Orogen are inferred to have been deposited on Neoproterozoic greenschist facies, granite-intruded basement. Shallow-water siliclastic deposition in the Early to Mid-Cambrian was followed by highly organic-rich shales in the Late Cambrian and influx of more turbidites. An episode of folding, the Kan’on River deformation, separates these formations from the overlying Tremadocian conglomerates and sandstones. In the Early Ordovician, rift-related magmatic rocks accompanied the deposition of variegated marls, sandstones, carbonates and evaporites. Dark shales and gypsiferous limestones characterise the Mid-Ordovician. Late Ordovician quartz-sandstones mark a hiatus, followed by carbonate rocks that extend up into and through most of the Silurian. The latter give way upwards into Old Red Sandstones, which are inferred to have been deposited in a Caledonian foreland basin. Deformation, reaching the area in the latest Devonian or earliest Carboniferous and referred to as the Severnaya Zemlya episode, is thought to be Caledonian-related. The dominating E-vergent structure was controlled by décollement zones in Ordovician evaporite-bearing strata; detachment folds and thrusts developed in the west and were apparently impeded by a barrier of Ordovician igneous rocks in the east. Below the décollement zones, the Neoproterozoic to Early Ordovician succession was deformed into open to close folds. The exposed strata in the lower structural level have been juxtaposed with

  1. Crustal structure and evolution of the Arctic Caledonides: Results from controlled-source seismology

    Science.gov (United States)

    Aarseth, Iselin; Mjelde, Rolf; Breivik, Asbjørn Johan; Minakov, Alexander; Faleide, Jan Inge; Flueh, Ernst; Huismans, Ritske S.

    2017-10-01

    The continuation of the Caledonides into the Barents Sea has long been a subject of discussion, and two major orientations of the Caledonian deformation fronts have been suggested: NNW-SSE striking and NE-SW striking. A regional NW-SE oriented ocean bottom seismic profile across the western Barents Sea was acquired in 2014. In this paper we map the crust and upper mantle structure along this profile in order to discriminate between different interpretations of Caledonian structural trends and orientation of rift basins in the western Barents Sea. Modeling of P-wave travel times has been done using a ray-tracing method, and combined with gravity modeling. The results show high P-wave velocities (4 km/s) close to the seafloor, as well as localized sub-horizontal high velocity zones (6.0 km/s and 6.9 km/s) at shallow depths which are interpreted as magmatic sills. Refractions from the top of the crystalline basement together with reflections from the Moho give basement velocities from 6.0 km/s at the top to 6.7 km/s at the base of the crust. P-wave travel time modeling of the OBS profile indicate an eastwards increase in velocities from 6.4 km/s to 6.7 km/s at the base of the crystalline crust, and the western part of the profile is characterized by a higher seismic reflectivity than the eastern part. This change in seismic character is consistent with observations from vintage reflection seismic data and is interpreted as a Caledonian suture extending through the Barents Sea, separating Barentsia and Baltica. Local deepening of Moho (from 27 km to 33 km depth) creates ;root structures; that can be linked to the Caledonian compressional deformation or a suture zone imprinted in the lower crust. Our model supports a separate NE-SW Caledonian trend extending into the central Barents Sea, branching off from the northerly trending Svalbard Caledonides, implying the existence of Barentsia as an independent microcontinent between Laurentia and Baltica.

  2. Dinoflagelados em diversos habitats e hidroperíodos na zona costeira do sul do Brasil Dinoflagellates in different habitats and hydroperiods on the coast of southern Brazil

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    Luciana de Souza Cardoso

    2007-06-01

    Full Text Available Informações sobre a riqueza, densidade, diversidade e distribuição de dinoflagelados em habitats aquáticos (lagoas abertas e fechadas, canais, açudes e áreas úmidas, em relação aos períodos de águas altas e baixas, são apresentadas. O estudo baseou-se em amostragens realizadas em 23 pontos, localizados nas margens leste (área da Lagoa do Casamento e oeste (área do Butiazal de Tapes da laguna dos Patos, no ano de 2003. Foram identificados 11 táxons, cuja distribuição teve maior homogeneidade no período de águas altas. Durinskia baltica (Levander Carty & Cox foi o único táxon cuja distribuição não se alterou pelo hidroperíodo. Peridinium gatunense Nygaard foi uma espécie indicadora de águas altas e P. umbonatum Stein foi indicadora de habitats associados à área do Butiazal de Tapes. Esta área mostrou ter mais alta diversidade de Dinophyceae em relação à área da Lagoa do Casamento, independente do hidroperíodo, refletindo a maior diversidade e especificidade de habitats aquáticos. O tipo de habitat influenciou significativamente (pData on richness, density, diversity and distribution of dinoflagellates in aquatic habitats (open and closed lagoons, channels, reservoirs and wetlands during high and low water periods are presented. The study was based on 23 point samples, located on the eastern (Lagoa do Casamento area and western (Butiazal de Tapes area shores of Laguna dos Patos, in 2003. Eleven taxa were identified; taxon distribution was more homogeneous during the high-water period. Durinskia baltica (Levander Carty & Cox was the only taxon whose distribution was the same for both hydroperiods. Peridinium gatunense Nygaard was a high-water indicator species and P. umbonatum Stein was an indicator of habitats associated with the Butiazal de Tapes area. This area had higher Dinophyceae diversity than the Lagoa do Casamento area, regardless of hydroperiod, due to the higher diversity and specificity of aquatic

  3. Avalonian crustal controls on basin evolution: implications for the Mesozoic basins of the southern North Sea

    Science.gov (United States)

    Smit, Jeroen; van Wees, Jan-Diederik; Cloetingh, Sierd

    2015-04-01

    Little is known of the Southern North Sea Basin's (SNSB) Pre-Permian basement due to a lack of outcrop and cores. The nature and structure of the East Avalonian crust and lithosphere remain even less constrained in the absence of deep seismic (refraction) lines. However, various studies have hinted at the importance of the Reactivation of the Early Carboniferous fault network during each consecutive Mesozoic and Cenozoic tectonic phase, demonstrating the key role of weak zones from the Early Carboniferous structural grain in partitioning of structural deformation and vertical basin motions at various scales. Although the older basin history and the basement attract increasing attention, the Pre-Permian tectonics of the SNSB remains little studied with most attention focused on the Permian and younger history. The strong dispersal of existing constraints requires a comprehensive study from Denmark to the UK, i.e. the East Avalonian microplate, bordered by the Variscan Rheïc suture, the Atlantic and Baltica. Based on an extensive literature study and the reinterpretation of publicly available data, linking constraints from the crust and mantle to stratigraphic-sedimentological information, we complement the map of Early Carboniferous rifting of East Avalonia and propose a new tectonic scenario. From the reinterpretation of the boundary between Avalonia and Baltica we propose a new outline for the Avalonian microplate with implications for the tectonics of the North German Basin. Furthermore, we highlight the nature and extent of the major crustal/lithospheric domains with contrasting structural behaviour and the major boundaries that separate them. Results shed light on the effects of long lived differences in crustal fabric that are responsible for spatial heterogeneity in stress and strain magnitudes and zonations of fracturing, burial history and temperature history. The geomechanical control of large crustal-scale fault structures will provide the constraints

  4. Deeply concealed half-graben at the SW margin of the East European Craton (SE Poland — Evidence for Neoproterozoic rifting prior to the break-up of Rodinia

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    P. Krzywiec

    2018-01-01

    Full Text Available Baltica was one of continents formed as a result of Rodinia break-up 850–550 Ma. It was separated from Amazonia(? by the Tornquist Ocean, the opening of which was preceded by Neoproterozoic extension in a network of continental rifts. Some of these rifts were subsequently aborted whereas the Tornquist Rift gave rise to splitting of Rodinia and formation of the Tornquist Ocean. The results of 1-D subsidence analysis at the fossil passive margin of Baltica provided insight in the timing and kinematics of continental rifting that led to break-up of Rodinia. Rifting was associated with Neoproterozoic syn-rift subsidence accompanied by deposition of continental coarse-grained sediments and emplacement of continental basalts. Transition from a syn-rift to post-rift phase in the latest Ediacaran to earliest early Cambrian was concomitant with deposition of continental conglomerates and arkoses, laterally passing into mudstones. An extensional scenario of the break-up of Rodinia along the Tornquist Rift is based on the character of tectonic subsidence curves, evolution of syn-rift and post-rift depocenters in time, as well as geochemistry and geochronology of the syn-rift volcanics. It is additionally reinforced by the high-quality deep seismic reflection data from SE Poland, located above the SW edge of the East European Craton. The seismic data allowed for identification of a deeply buried (11–18 km, well-preserved extensional half-graben, developed in the Palaeoproterozoic crystalline basement and filled with a Neoproterozoic syn-rift volcano-sedimentary succession. The results of depth-to-basement study based on integration of seismic and gravity data show the distribution of local NE–SW elongated Neoproterozoic depocenters within the SW slope of the East European Craton. Furthermore, they document the rapid south-eastwards thickness increase of the Neoproterozoic succession towards the NW–SE oriented craton margin. This provides evidence

  5. Allelopathic effects of microcystin-LR on the germination, growth and metabolism of five charophyte species and a submerged angiosperm.

    Science.gov (United States)

    Rojo, Carmen; Segura, Matilde; Cortés, Francisco; Rodrigo, María A

    2013-11-15

    Microcystins (MCs) are produced by cyanobacteria in aquatic environments and adversely affect macrophytes at very high concentrations. However, the effects of MC on macrophytes at concentrations of environmental relevance are largely unknown. The main objective of this study was to analyze the allelopathic effects of MC-LR at natural concentrations (1, 8 and 16 μg MC-LR/L) on five charophyte species (Chara aspera, C. baltica, C. hispida, C. vulgaris and Nitella hyalina) and the angiosperm Myriophyllum spicatum. Macrophyte specimens were obtained from a restored area located in Albufera de València Natural Park, a protected coastal Mediterranean wetland. Two different experiments were conducted involving (i) the addition of MC-LR to natural sediment to evaluate its effects on seed germination and (ii) the addition of MC-LR to water cultures of macrophytes to evaluate its effects on growth and metabolic functions. In water, the MC-LR concentration decreased by 84% in two weeks; the loss was not significant in sediment. The first seedlings (all C. hispida) emerged from the wetland sediment following a delay of a few days in the presence of MC-LR. The germination rates in 8 and 16 μg MC-LR/L treatments were 44% and 11% of that occurring in the absence of MC, but these differences disappeared over time. The final density was 6-7 germlings/dm(3). Final germling length was unaffected by MC-LR. Rotifers (Lecane spp.) emerging from the natural sediment during the experiment were favored by MC-LR; the opposite pattern was observed in the cladoceran Daphnia magna. The growth rates of C. vulgaris, C. baltica and N. hyalina were unaffected by MC exposure, whereas those of C. hispida and C. aspera were reduced in the MC treatments relative to the control treatment. The concentration of chlorophyll-a and the in vivo net photosynthetic rate were lower in the presence of MC-LR, even at the lowest concentration, for all of the characeans tested. M. spicatum was sensitive to the

  6. NEW PALEOMAGNETIC DATA ON THE SILURIAN AND DEVONIAN SEDIMENTARY ROCKS FROM PODOLIA, SW UKRAINE, AND KINEMATICS OF THE EAST EUROPEAN PLATFORM IN THE MIDDLE PALEOZOIC

    Directory of Open Access Journals (Sweden)

    V. G. Bakhmutov

    2014-01-01

    Full Text Available Paleomagnetic data are the priority source of information for global paleotectonic reconstructions representing horizontal movements of the crustal blocks. Upon receipt of new paleomagnetic data, kinematic models of the East European platform in the Paleozoic are regularly revised and improved. The article presents results of the paleomagnetic study of sedimentary gray-colored and red beds of the Silurian and Lower Devonian sequences located in the Dniester river basin, Podolia region, SW Ukraine. The study covered 17 outcrops that are stratigraphically correlated with the Wenlock, Ludlow, Pridoli states of the Sillurian and the Lochkovian stage of the Devon. Over 400 samples of grey limestone, argillite, dolomite, red limestone and sandstone were analyzed, and two components of natural remnant magnetization (NRM were revealed. The first component with SSW declination and negative inclination is revealed in the majority of the samples during AF- and T-magnetic cleaning. Its pole positions, that are calculated separately for each series, are trending to the Permian segment of the apparent polar wander path (APWP published by Torsvik et al. [2012] for Baltica / Stable Europe. Considering its chemical origin, this NRM component is related to formation of authigenic minerals due to rock remagnetization. The second component is revealed only in some samples taken from the red beds (during thermal demagnetization in the range of unblocking temperatures from 590 to 690 °С and in few samples of grey limestone (in AF fields from 30 to 70 mT or in the range of unblocking temperatures from 300 to 460 °С. This component has SW declination and positive inclination, goes to the origin of coordinates of the diagrams, and has all the indicators of primary magnetization of sediments. Calculated positions of the poles (0 ºS and 329 ºE for grey limestone of the Tiverskaya series, 2.3 °S and 338.4 °E for red beds of the Dniestrovskaya series, etc. are well

  7. Surface wave tomography across the Sorgenfrei-Tornquist Zone, SW Scandinavia, using ambient noise and earthquake data

    Science.gov (United States)

    Köhler, Andreas; Maupin, Valérie; Balling, Niels

    2015-10-01

    We produce a S-wave velocity model of the crust and upper mantle around the Sorgenfrei-Tornquist Zone, southern Scandinavia, by analysing ambient seismic noise and earthquake recordings on temporary and permanent regional network stations. In a first step, we perform tomographical inversion of surface wave dispersion data from seismic noise to obtain Rayleigh and Love wave phase-velocity maps from 3 to about 30 s period. Local dispersion curves are then combined with regionally averaged surface wave velocities from earthquake data measured between 15 and about 100 s period. Dispersion curves are jointly inverted for a 3-D model of the S-wave velocity and radial velocity anisotropy by using a combined Monte Carlo and linearized inversion approach. Results reveal significant crustal as well as uppermost mantle velocity variations at all depth levels. Upper crustal structural variations are mainly controlled by the thick sedimentary Danish Basin with both low S-wave velocities and high anisotropy. Despite of the known limited capability of surface wave inversion to constrain interface depths and model parameter trade-offs, obtained Moho depths are in good agreement with previous studies in the region. Marked crustal thinning is clearly revealed beneath the Danish Basin with a narrow transition to the thicker crust in Swedish shield areas. Despite very different crustal and morphological structures, Denmark and southern Norway both have similar well-defined upper-mantle low-velocity zones, interpreted as asthenosphere, starting a depth of about 100 km. Compared with southern Sweden, showing high upper-mantle velocities, characteristic for shields, velocities are reduced by 0.30-0.40 km s-1 (6-8 per cent) at the depth levels of 140-200 km and radial anisotropy of 2-4 per cent is observed. Our study confirms the importance of the Sorgenfrei-Tornquist Zone, as a very deep structural boundary, separating old, thick, cratonic Baltica lithosphere in southern Sweden from

  8. PALEOMAGNETISM OF SILURIAN AND DEVONIAN VOLCANICS FROM THE CHINGIZ ISLAND ARC, KAZAKHSTAN, AND ITS BEARING ON TECTONIC EVOLUTION OF THE URAL-MONGOL BELT

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    Natalia M. Levashova

    2011-01-01

    Full Text Available The tectonic and paleogeographic evolution of the Ural-Mongol belt between the cratons of Baltica, Siberia, and Tarim is the key to the formation of the Eurasian supercontinent during Paleozoic time, but the views on this complicated process remain very disparate and sometimes controversial. Three volcanic formations of the Middle Silurian, LowertoMiddle Devonian and Middle Devonian age from the southwestern boundary of the Chingiz Range (NE Kazakhstan yields what are interpreted as primary paleomagnetic directions that help clarify the evolution of the belt. A singlepolarity characteristic component in midSilurian andesites yields a positive intraformational conglomerate test, whereas dualpolarity prefolding components are isolated from the two Devonian collections. These new data were evaluated together with previously published paleomagnetic results from Paleozoic rocks in the Chingiz Range, and allow us to establish with confidence the hemisphere in which the area was located at a given time. We conclude that NE Kazakhstan was steadily moving northward crossing the equator in Silurian time. These new paleomagnetic data from the Chingiz range also agree with and reinforce the hypothesis that the strongly curved volcanic belts of Kazakhstan underwent oroclinal bending between Middle Devonian and Late Carboniferous time. A comparison of the Chingiz paleolatitudes with those of Siberia shows similarities between the northward motion and rotational history of the Chingiz unit and those of Siberia, which imposes important constraints on the evolving paleogeography of the Ural-Mongol belt.

  9. Lactic Acid Bacteria Selection for Biopreservation as a Part of Hurdle Technology Approach Applied on Seafood

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    Norman Wiernasz

    2017-05-01

    Full Text Available As fragile food commodities, microbial, and organoleptic qualities of fishery and seafood can quickly deteriorate. In this context, microbial quality and security improvement during the whole food processing chain (from catch to plate, using hurdle technology, a combination of mild preserving technologies such as biopreservation, modified atmosphere packaging, and superchilling, are of great interest. As natural flora and antimicrobial metabolites producers, lactic acid bacteria (LAB are commonly studied for food biopreservation. Thirty-five LAB known to possess interesting antimicrobial activity were selected for their potential application as bioprotective agents as a part of hurdle technology applied to fishery products. The selection approach was based on seven criteria including antimicrobial activity, alteration potential, tolerance to chitosan coating, and superchilling process, cross inhibition, biogenic amines production (histamine, tyramine, and antibiotics resistance. Antimicrobial activity was assessed against six common spoiling bacteria in fishery products (Shewanella baltica, Photobacterium phosphoreum, Brochothrix thermosphacta, Lactobacillus sakei, Hafnia alvei, Serratia proteamaculans and one pathogenic bacterium (Listeria monocytogenes in co-culture inhibitory assays miniaturized in 96-well microtiter plates. Antimicrobial activity and spoilage evaluation, both performed in cod and salmon juice, highlighted the existence of sensory signatures and inhibition profiles, which seem to be species related. Finally, six LAB with no unusual antibiotics resistance profile nor histamine production ability were selected as bioprotective agents for further in situ inhibitory assays in cod and salmon based products, alone or in combination with other hurdles (chitosan, modified atmosphere packing, and superchilling.

  10. U-Pb geochronology and paleomagnetism of the Neoproterozoic St Simeon dolerite dykes, Quebec: an eastern Laurentian perspective of Ediacaran Rodinia breakup

    Science.gov (United States)

    Pisarevsky, Sergei; Murphy, Brendan; Hamilton, Mike; Söderlund, Ulf; Hodych, Joseph

    2013-04-01

    The St Simeon (SS) mafic dykes (150 km NE of Quebec City) are now dated at 548 ± 1 Ma (U-Pb; baddeleyite). This age is similar to a published LA-ICPMS zircon age of 550 ± 7 Ma for the Mt. St-Anselme (MS) basalts, which supports previous inferences of (i) a genetic relationship between them, (ii) the pene-contemporaneity of OIB-type mafic magmatism in East Laurentia and (iii) the existence of two late Ediacaran plumes that attended the final breakup of Rodinia and opening of the Iapetus Ocean and Tornquist Sea. Both the SS dykes and the MS basalts were sampled for paleomagnetic study. The paleomagnetic pole for SS is similar to the previously published pole for coeval basalts (Skinner Cove, SC) from Newfoundland. Unlike SC, the St Simeon pole represents rocks which are unambiguously coherent tectonically with the Laurentian Craton. This new pole is also coeval with high quality poles from the Winter Coast (Baltica) and provides paleomagnetic constraints on the history of the final breakup of Rodinia and opening of Eastern Iapetus and Tornquist Sea.

  11. New paleomagnetic data from Siberia: Non-uniformitarian geomagnetic field around the Proterozoic-Phanerozoic boundary?

    Science.gov (United States)

    Pavlov, V.; Shatsillo, A.; Kouznetsov, N.; Gazieva, E.

    2017-12-01

    There is a range of evidence, mainly from sedimentary and volcanic rocks of the Laurentia and Baltica cratons, that argue for the anomalous character of the Ediacaran-Early Cambrian paleomagnetic record. This feature could be linked either to some peculiarities of the paleomagnetic record itself or to some unusual geophysical event that would have taken place around the Proterozoic-Phanerozoic boundary (e.g., true polar wander or nonuniformitarian geomagnetic field behavior). In the latter case, the traces of this event should be observed in Ediacaran-Early Cambrian rocks anywhere there is a possibility to observe a primary paleomagnetic signal. In previous work, we reported results that suggested an anomalous paleomagnetic record in Siberian Ediacaran-Lower Cambrian rocks. Here we present new Siberian data that indicate a very high geomagnetic reversal frequency during this period and the coexistence of two very different paleomagnetic directions. We speculate that these features could be due either to a near-equatorial geomagnetic dipole during the polarity transitions or to alternation between axial and near equatorial dipoles not directly linked with polarity reversals.

  12. Il Teatro Shakespeariano di Danzica. L'Alato / Gdansk Shakespearian Theatre. The Winged

    Directory of Open Access Journals (Sweden)

    Renato Rizzi

    2014-05-01

    Full Text Available Il 23 aprile, giorno della nascita e della morte di William Shakespeare, è stato inaugurato il tetto apribile del nuovo Teatro Elisabettiano, che sarà inaugurato il prossimo settembre a Danzica. L'evento diventa l'occasione per celebrare allo stesso tempo le potenze plastiche del simbolo, che, disseminate nella metafisica dei luoghi (e della memoria, guidano le forze alla 'forma' e i valori e gli ideali che hanno sostenuto il tormentato processo storico della città baltica e della nazione polacca. / On 23 April, the date of the birth and death of William Shakespeare, the openable roof of the new Elizabethan Theatre in Gdańsk was inaugurated, with an official ceremony for the latter to come in September. The event became an opportunity to celebrate both the plastic powers of the symbol, which, scattered through the metaphysics of places (and memory, guide the forces to 'form' as well as the values and ideals that have sustained the tormented historical process of this Baltic city and the Polish nation as a whole.

  13. Solar PAR and UVR modify the community composition and photosynthetic activity of sea ice algae.

    Science.gov (United States)

    Enberg, Sara; Piiparinen, Jonna; Majaneva, Markus; Vähätalo, Anssi V; Autio, Riitta; Rintala, Janne-Markus

    2015-10-01

    The effects of increased photosynthetically active radiation (PAR) and ultraviolet radiation (UVR) on species diversity, biomass and photosynthetic activity were studied in fast ice algal communities. The experimental set-up consisted of nine 1.44 m(2) squares with three treatments: untreated with natural snow cover (UNT), snow-free (PAR + UVR) and snow-free ice covered with a UV screen (PAR). The total algal biomass, dominated by diatoms and dinoflagellates, increased in all treatments during the experiment. However, the smaller biomass growth in the top 10-cm layer of the PAR + UVR treatment compared with the PAR treatment indicated the negative effect of UVR. Scrippsiella complex (mainly Scrippsiella hangoei, Biecheleria baltica and Gymnodinium corollarium) showed UV sensitivity in the top 5-cm layer, whereas Heterocapsa arctica ssp. frigida and green algae showed sensitivity to both PAR and UVR. The photosynthetic activity was highest in the top 5-cm layer of the PAR treatment, where the biomass of the pennate diatom Nitzschia frigida increased, indicating the UV sensitivity of this species. This study shows that UVR is one of the controlling factors of algal communities in Baltic Sea ice, and that increased availability of PAR together with UVR exclusion can cause changes in algal biomass, photosynthetic activity and community composition. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  14. Marine environment status assessment based on macrophytobenthic plants as bio-indicators of heavy metals pollution.

    Science.gov (United States)

    Zalewska, Tamara; Danowska, Beata

    2017-05-15

    The main aim of study was to develop the environmental quality standards (EQS MP ) for selected heavy metals: Pb, Cd, Hg and Ni bioaccumulated in the tissues of marine macrophytobenthic plants: Chara baltica, Cladophora spp., Coccotylus truncatus, Furcellaria lumbricalis, Polysiphonia fucoides, Stuckenia pectinata and Zanichellia palustris, collected in designated areas of the southern Baltic Sea in period 2008-2015. The calculated concentration ratios (CR), which attained very high values: 10 4 Lkg -1 for lead, 10 3 Lkg -1 for nickel and mercury and even 10 5 Lkg -1 for cadmium formed the basis for the determination of EQS MP values. The EQS MP values were: 26mgkg -1 d.w. for Pb, 33mgkg -1 d.w. for Cd, 32mgkg -1 d.w. for Ni and 0.4mgkg -1 d.w. for Hg. The application of macrophytobenthic plants as bioindicators in marine environment status assessment of certain areas of the Baltic Sea is also described in the paper. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. Direct Effects of Microalgae and Protists on Herring (Clupea harengus Yolk Sac Larvae.

    Directory of Open Access Journals (Sweden)

    Björn Illing

    Full Text Available This study investigated effects of microalgae (Rhodomonas baltica and heterotrophic protists (Oxyrrhis marina on the daily growth, activity, condition and feeding success of Atlantic herring (Clupea harengus larvae from hatch, through the end of the endogenous (yolk sac period. Yolk sac larvae were reared in the presence and absence of microplankton and, each day, groups of larvae were provided access to copepods. Larvae reared with microalgae and protists exhibited precocious (2 days earlier and ≥ 60% increased feeding incidence on copepods compared to larvae reared in only seawater (SW. In the absence and presence of microalgae and protists, life span and growth trajectories of yolk sac larvae were similar and digestive enzyme activity (trypsin and nutritional condition (RNA-DNA ratio markedly declined in all larvae directly after yolk sac depletion. Thus, microplankton promoted early feeding but was not sufficient to alter life span and growth during the yolk sac phase. Given the importance of early feeding, field programs should place greater emphasis on the protozooplankton-ichthyoplankton link to better understand match-mismatch dynamics and bottom-up drivers of year class success in marine fish.

  16. Stratigraphical distribution of the Ordovician conodont Erraticodon Dzik in Argentina

    Science.gov (United States)

    Heredia, S.; Carlorosi, J.; Mestre, A.; Soria, T.

    2013-08-01

    Three different species of the Ordovician genus Erraticodon Dzik are described and illustrated. Erraticodon patu Cooper is reported from the Lower-Midde Ordovician strata of the Acoite and Alto del Cóndor formations. E. cf. Erraticodon balticus and Erraticodon hexianensis from Middle Ordovician carbonate deposits of the San Juan Formation are analyzed and compared to specimens of these species from Australia, China, Newfoundland, and Baltica. E. patu and E. hexianensis are recorded for first time in the San Juan Formation of Precordillera. The elements of E. cf. E. balticus resemble closely E. balticus Dzik but lack the important denticle on the posterior process of the S elements. An evaluation of the stratigraphic occurrences of these species relative to those of key Lower and Middle Ordovician conodont species such as Trapezognathus diprion Lindström, Oepikodus intermedius Serpagli, Baltoniodus triangularis (Lindström), Baltoniodus navis Lindström, Yangtzeplacognathus crassus (Chen and Zhang) and Eoplacognathus pseudoplanus (Viira) indicates they value for biostratigraphic correlation.

  17. Marine environment status assessment based on macrophytobenthic plants as bio-indicators of heavy metals pollution

    International Nuclear Information System (INIS)

    Zalewska, Tamara; Danowska, Beata

    2017-01-01

    The main aim of study was to develop the environmental quality standards (EQS MP ) for selected heavy metals: Pb, Cd, Hg and Ni bioaccumulated in the tissues of marine macrophytobenthic plants: Chara baltica, Cladophora spp., Coccotylus truncatus, Furcellaria lumbricalis, Polysiphonia fucoides, Stuckenia pectinata and Zanichellia palustris, collected in designated areas of the southern Baltic Sea in period 2008–2015. The calculated concentration ratios (CR), which attained very high values: 10 4 L kg −1 for lead, 10 3 L kg −1 for nickel and mercury and even 10 5 L kg −1 for cadmium formed the basis for the determination of EQS MP values. The EQS MP values were: 26 mg kg −1 d.w. for Pb, 33 mg kg −1 d.w. for Cd, 32 mg kg −1 d.w. for Ni and 0.4 mg kg −1 d.w. for Hg. The application of macrophytobenthic plants as bioindicators in marine environment status assessment of certain areas of the Baltic Sea is also described in the paper. - Highlights: • Macrophytobenthic plants were applied as a bioindicators for heavy metals pollution assessment. • The environmental quality standards for Pb, Cd, Ni, Hg in macrophytobenthic plants were evaluated. • The marine environment status assessment method based on bioindicators was proposed.

  18. Two-stage pretreatment of excess sludge for electricity generation in microbial fuel cell.

    Science.gov (United States)

    Zhang, Yi; Zhao, Yang-Guo; Guo, Liang; Gao, Mengchun

    2018-01-12

    Thermophiles hydrolysis and acidogens fermentation were sequentially adopted to pretreat excess sludge for microbial fuel cell (MFC) electricity production. The results indicated that MFC fed with the thermophiles-acidogens pretreated sludge (MFC AB), reached a higher removal of ammonia nitrogen than the MFC fed with the heating hydrolysis and acidogens fermentation pretreated sludge (MFC NB). However, compared with the MFC AB, MFC NB presented a better performance for removal of soluble chemical oxygen demand (SCOD) (90.08%) and protein (82.42%). As for the electricity production, MFC NB obtained higher voltage of 0.632 V and maximum power density with 1.05 W/m 3 while MFC AB reached maximum voltage of 0.373 V and maximum power density of 0.58 W/m 3 . Bacterial 16S rRNA-based molecular microbial techniques showed that microbial communities on both MFC anode biofilms was diverse and different. The cooperation of fermentation bacteria and electricigen Shewanella baltica in the MFC NB may have contributed towards the improvement of electricity generation.

  19. Direct Effects of Microalgae and Protists on Herring (Clupea harengus) Yolk Sac Larvae.

    Science.gov (United States)

    Illing, Björn; Moyano, Marta; Niemax, Jan; Peck, Myron A

    2015-01-01

    This study investigated effects of microalgae (Rhodomonas baltica) and heterotrophic protists (Oxyrrhis marina) on the daily growth, activity, condition and feeding success of Atlantic herring (Clupea harengus) larvae from hatch, through the end of the endogenous (yolk sac) period. Yolk sac larvae were reared in the presence and absence of microplankton and, each day, groups of larvae were provided access to copepods. Larvae reared with microalgae and protists exhibited precocious (2 days earlier) and ≥ 60% increased feeding incidence on copepods compared to larvae reared in only seawater (SW). In the absence and presence of microalgae and protists, life span and growth trajectories of yolk sac larvae were similar and digestive enzyme activity (trypsin) and nutritional condition (RNA-DNA ratio) markedly declined in all larvae directly after yolk sac depletion. Thus, microplankton promoted early feeding but was not sufficient to alter life span and growth during the yolk sac phase. Given the importance of early feeding, field programs should place greater emphasis on the protozooplankton-ichthyoplankton link to better understand match-mismatch dynamics and bottom-up drivers of year class success in marine fish.

  20. Life-cycle, ultrastructure, and phylogeny of Parvilucifera corolla sp. nov. (Alveolata, Perkinsozoa), a parasitoid of dinoflagellates.

    Science.gov (United States)

    Reñé, Albert; Alacid, Elisabet; Figueroa, Rosa Isabel; Rodríguez, Francisco; Garcés, Esther

    2017-04-01

    Recent studies of marine protists have revealed parasites to be key components of marine communities. Here we describe a new species of the parasitoid genus Parvilucifera that was observed infecting the dinoflagellate Durinskia baltica in salt marshes of the Catalan coast (NW Mediterranean). In parallel, the same species was detected after the incubation of seawater from the Canary Islands (Lanzarote, NE Atlantic). The successful isolation of strains from both localities allowed description of the life cycle, ultrastructure, and phylogeny of the species. Its infection mechanism consists of a free-living zoospore that penetrates a dinoflagellate cell. The resulting trophont gradually degrades the dinoflagellate cytoplasm while growing in size. Once the host is consumed, schizogony of the parasitoid yields a sporocyte. After cytokinesis is complete, the newly formed zoospores are released into the environment and are ready to infect new host cells. A distinguishing feature of the species is the radial arrangement of its zoospores around the central area of the sporocyte during their formation. The species shows a close morphological similarity with other species of the genus, including P. infectans, P. sinerae, and P. rostrata. Copyright © 2016 Elsevier GmbH. All rights reserved.

  1. Bringing Western-standard service stations to the Baltic countries

    International Nuclear Information System (INIS)

    Pesonen, H.

    1992-01-01

    Neste is the only Western oil company so far to have established a service station presence in the Baltic, with the exception of Norway's Statoil, which has one outlet near Tallinn Airport. Neste has an important logistical advantage compared to other companies in this respect as its two Finnish refineries are ideally located for supplying the region with high-quality petroleum products. Neste's first joint venture in the Baltic, Traffic Service, based in Estonia, was set up with Eesti Kutus in 1988 and opened its first service station in 1990. Other joint ventures are now up and running in Latvia, Lithuania, Poland, and St. Petersburg. A total of 10 - 15 stations, the majority strategically located along the route of the Via Baltica, are expected to be operational by the end of this year. The Neste network comprises a combination of new outlets and refurbished older stations that have been modernized to bring them up to Western standards. These offer a comprehensive range of fuels, lubricants, spare parts, and accessories, as well as food, confectionery, and coffee shop services. Some stations also offer repair and car wash facilities. Adapting to the transition from a communist economy to a Western, capitalist one has not been easy for the Baltic countries, and has inevitably created difficulties for companies like Neste, in areas such as legislation covering land ownership. Neste's joint ventures have also encountered difficulties in instilling the Western approach to business efficiency, and customer service in a workforce used to the Soviet retail system

  2. Late Ordovician palaeogeography and the positions of the Kazakh terranes through analysis of their brachiopod faunas

    Science.gov (United States)

    Popov, Leonid E.; Cocks, Robin M.

    2017-09-01

    Detailed biogeographical and biofacies analyses of the Late Ordovician brachiopod faunas with 160 genera, grouped into 94 faunas from individual lithotectonic units within the Kazakh Orogen strongly support an archipelago model for that time in that area. The Kazakh island arcs and microcontinents within several separate clusters were located in the tropics on both sides of the Equator. Key units, from which the Late Ordovician faunas are now well known, include the Boshchekul, Chingiz-Tarbagatai, and Chu-Ili terranes. The development of brachiopod biogeography within the nearly ten million year time span of the Late Ordovician from about 458 to 443 Ma (Sandbian, Katian, and Hirnantian), is supported by much new data, including our revised identifications from the Kazakh Orogen and elsewhere. The Kazakh archipelago was west of the Australasian segment of the Gondwana Supercontinent, and relatively near the Tarim, South China and North China continents, apart from the Atashu-Zhamshi Microcontinent, which probably occupied a relatively isolated position on the south-western margin of the archipelago. Distinct faunal signatures indicate that the Kazakh terranes were far away from Baltica and Siberia throughout the Ordovician. Although some earlier terranes had joined each other before the Middle Ordovician, the amalgamation of Kazakh terranes into the single continent of Kazakhstania by the end of the Ordovician is very unlikely. The Late Ordovician brachiopods from the other continents are also compared with the Kazakh faunas and global provincialisation statistically determined.

  3. Pyrosequencing-based assessment of the bacteria diversity in surface and subsurface peat layers of a northern wetland, with focus on poorly studied phyla and candidate divisions.

    Science.gov (United States)

    Serkebaeva, Yulia M; Kim, Yongkyu; Liesack, Werner; Dedysh, Svetlana N

    2013-01-01

    Northern peatlands play a key role in the global carbon and water budget, but the bacterial diversity in these ecosystems remains poorly described. Here, we compared the bacterial community composition in the surface (0-5 cm depth) and subsurface (45-50 cm) peat layers of an acidic (pH 4.0) Sphagnum-dominated wetland, using pyrosequencing of 16S rRNA genes. The denoised sequences (37,229 reads, average length ∼430 bp) were affiliated with 27 bacterial phyla and corresponded to 1,269 operational taxonomic units (OTUs) determined at 97% sequence identity. Abundant OTUs were affiliated with the Acidobacteria (35.5±2.4% and 39.2±1.2% of all classified sequences in surface and subsurface peat, respectively), Alphaproteobacteria (15.9±1.7% and 25.8±1.4%), Actinobacteria (9.5±2.0% and 10.7±0.5%), Verrucomicrobia (8.5±1.4% and 0.6±0.2%), Planctomycetes (5.8±0.4% and 9.7±0.6%), Deltaproteobacteria (7.1±0.4% and 4.4%±0.3%), and Gammaproteobacteria (6.6±0.4% and 2.1±0.1%). The taxonomic patterns of the abundant OTUs were uniform across all the subsamples taken from each peat layer. In contrast, the taxonomic patterns of rare OTUs were different from those of the abundant OTUs and varied greatly among subsamples, in both surface and subsurface peat. In addition to the bacterial taxa listed above, rare OTUs represented the following groups: Armatimonadetes, Bacteroidetes, Chlamydia, Chloroflexi, Cyanobacteria, Elusimicrobia, Fibrobacteres, Firmicutes, Gemmatimonadetes, Spirochaetes, AD3, WS1, WS4, WS5, WYO, OD1, OP3, BRC1, TM6, TM7, WPS-2, and FCPU426. OTU richness was notably higher in the surface layer (882 OTUs) than in the anoxic subsurface peat (483 OTUs), with only 96 OTUs common to both data sets. Most members of poorly studied phyla, such as the Acidobacteria, Verrucomicrobia, Planctomycetes and the candidate division TM6, showed a clear preference for growth in either oxic or anoxic conditions. Apparently, the bacterial communities in surface and

  4. Targeting Unknowns Just Underfoot: Microbial Ecology and Community Genomics of C Cycling in Soil Informed and Enabled with DNA-SIP

    Science.gov (United States)

    Pepe-Ranney, C. P.; Campbell, A.; Buckley, D. H.

    2015-12-01

    Microorganisms drive biogeochemical cycles and because soil is a large global carbon (C) reservoir (soil contains more C than plants and the atmosphere combined), soil microorganisms are important players in the global C-cycle. Frustratingly, however, many soil microorganisms resist cultivation and soil communities are astoundingly complex. This makes soil microbiology difficult to study and without a solid understanding of soil microbial ecology, models of soil C feedbacks to climate change are under-informed. Stable isotope probing (SIP) is a useful approach for establishing identity-function connections in microbial communities but has been challenging to employ in soil due to the inadequate resolution of microbial community fingerprinting techniques. High throughput DNA sequencing improves SIP resolving power transforming it into a powerful tool for studying the soil C cycle. We conducted a DNA-SIP experiment to track flow of xylose-C, a labile component of plant biomass, and cellulose-C, the most abundant global biopolymer, through a soil microbial community. We could track 13C into microbial DNA even when added 13C amounted to less than 5% of native C and found Spartobacteria, Chloroflexi, and Planctomycetes taxa were among those that assimilated 13C cellulose. These lineages are cosmopolitan in soil but little is known of their ecophysiology. By profiling SSU rRNA genes across entire DNA-SIP density gradients, we assessed relative DNA atom % 13C per taxon in 13C treatments and found cellulose degraders exhibited signal consistent with a specialist lifestyle with respect to C preference. Further, DNA-SIP enriches DNA of targeted microorganisms (Verrucomicrobia cellulose degraders were enriched by nearly two orders of magnitude) and this enriched DNA can serve as template for community genomics. We produced draft genomes from soil cellulose degraders including microorganisms belonging to Verrucomicrobia, Chloroflexi, and Planctomycetes from SIP enriched DNA

  5. The Evolution of Sterol Biosynthesis in Bacteria: In Situ Fluorescence Localization of Sterols in the Nucleoid Bacterium Gemmata obscuriglobus

    Science.gov (United States)

    Budin, M.; Jorgenson, T. L.; Pearson, A.

    2004-12-01

    The biosynthesis of sterols is generally regarded as a eukaryotic process. The first enzymatic step in the production of sterols requires molecular oxygen. Therefore, both the origin of eukaryotes and the evolution of sterol biosynthesis were thought to postdate the rise of oxygen in earth's atmosphere, until Brocks et al. discovered steranes in rocks aged 2.7 Ga (1). Many prokaryotes produce hopanoids, sterol-like compounds that are synthesized from the common precursor squalene without the use of molecular oxygen. However, a few bacterial taxa are also known to produce sterols, suggesting this pathway could precede the rise of oxygen (2, 3). Recently, we discovered the shortest sterol-producing biosynthetic pathway known to date in the bacterium Gemmata obscuriglobus (4). Using genomic searches, we found that Gemmata has the enzymes necessary for synthesis of sterols, and lipid analyses showed that the sterols produced are lanosterol and its isomer parkeol. Gemmata is a member of the Planctomycetes, an unusual group of bacteria, all of the known species of which contain intracellular compartmentalization. Among the Planctomycetes, Gemmata uniquely is the only prokaryote known to contain a double-membrane-bounded nuclear body (5). Since sterols usually are found in eukaryotes, and Gemmata has a eukaryote-like nuclear organelle, we investigated the location of the sterols within Gemmata to postulate whether they play a role in stabilization of the nuclear membrane and control of genomic organization. We used the sterol-specific fluorescent dye Filipin III in conjunction with fluorescent dyes for internal and external cellular membranes in order to determine whether the sterols are located in the nuclear body membrane, external membrane, or both. We found that sterols in Gemmata are concentrated in the internal membrane, implying that they function in maintaining this unusual cellular component. It is notable that Gemmata also produce hopanoids, suggesting that they

  6. Bacterial Diversity in Bentonites, Engineered Barrier for Deep Geological Disposal of Radioactive Wastes.

    Science.gov (United States)

    Lopez-Fernandez, Margarita; Cherkouk, Andrea; Vilchez-Vargas, Ramiro; Jauregui, Ruy; Pieper, Dietmar; Boon, Nico; Sanchez-Castro, Ivan; Merroun, Mohamed L

    2015-11-01

    The long-term disposal of radioactive wastes in a deep geological repository is the accepted international solution for the treatment and management of these special residues. The microbial community of the selected host rocks and engineered barriers for the deep geological repository may affect the performance and the safety of the radioactive waste disposal. In this work, the bacterial population of bentonite formations of Almeria (Spain), selected as a reference material for bentonite-engineered barriers in the disposal of radioactive wastes, was studied. 16S ribosomal RNA (rRNA) gene-based approaches were used to study the bacterial community of the bentonite samples by traditional clone libraries and Illumina sequencing. Using both techniques, the bacterial diversity analysis revealed similar results, with phylotypes belonging to 14 different bacterial phyla: Acidobacteria, Actinobacteria, Armatimonadetes, Bacteroidetes, Chloroflexi, Cyanobacteria, Deinococcus-Thermus, Firmicutes, Gemmatimonadetes, Planctomycetes, Proteobacteria, Nitrospirae, Verrucomicrobia and an unknown phylum. The dominant groups of the community were represented by Proteobacteria and Bacteroidetes. A high diversity was found in three of the studied samples. However, two samples were less diverse and dominated by Betaproteobacteria.

  7. Biogeographical distribution and diversity of bacterial communities in surface sediments of the South China Sea.

    Science.gov (United States)

    Li, Tao; Wang, Peng

    2013-05-01

    This paper aims at an investigation of the features of bacterial communities in surface sediments of the South China Sea (SCS). In particular, biogeographical distribution patterns and the phylogenetic diversity of bacteria found in sediments collected from a coral reef platform, a continental slope, and a deep-sea basin were determined. Bacterial diversity was measured by an observation of 16S rRNA genes, and 18 phylogenetic groups were identified in the bacterial clone library. Planctomycetes, Deltaproteobacteria, candidate division OP11, and Alphaproteobacteria made up the majority of the bacteria in the samples, with their mean bacterial clones being 16%, 15%, 12%, and 9%, respectively. By comparison, the bacterial communities found in the SCS surface sediments were significantly different from other previously observed deep-sea bacterial communities. This research also emphasizes the fact that geographical factors have an impact on the biogeographical distribution patterns of bacterial communities. For instance, canonical correspondence analyses illustrated that the percentage of sand weight and water depth are important factors affecting the bacterial community composition. Therefore, this study highlights the importance of adequately determining the relationship between geographical factors and the distribution of bacteria in the world's seas and oceans.

  8. Microbial community composition and functions are resilient to metal pollution along two forest soil gradients.

    Science.gov (United States)

    Azarbad, Hamed; Niklińska, Maria; Laskowski, Ryszard; van Straalen, Nico M; van Gestel, Cornelis A M; Zhou, Jizhong; He, Zhili; Wen, Chongqing; Röling, Wilfred F M

    2015-01-01

    Despite the global importance of forests, it is virtually unknown how their soil microbial communities adapt at the phylogenetic and functional level to long-term metal pollution. Studying 12 sites located along two distinct gradients of metal pollution in Southern Poland revealed that functional potential and diversity (assessed using GeoChip 4.2) were highly similar across the gradients despite drastically diverging metal contamination levels. Metal pollution level did, however, significantly impact bacterial community structure (as shown by MiSeq Illumina sequencing of 16S rRNA genes), but not bacterial taxon richness and community composition. Metal pollution caused changes in the relative abundance of specific bacterial taxa, including Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Planctomycetes and Proteobacteria. Also, a group of metal-resistance genes showed significant correlations with metal concentrations in soil. Our study showed that microbial communities are resilient to metal pollution; despite differences in community structure, no clear impact of metal pollution levels on overall functional diversity was observed. While screens of phylogenetic marker genes, such as 16S rRNA genes, provide only limited insight into resilience mechanisms, analysis of specific functional genes, e.g. involved in metal resistance, appears to be a more promising strategy. © FEMS 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  9. Pyrosequencing reveals the microbial communities in the Red Sea sponge Carteriospongia foliascens and their impressive shifts in abnormal tissues.

    Science.gov (United States)

    Gao, Zhao-Ming; Wang, Yong; Lee, On On; Tian, Ren-Mao; Wong, Yue Him; Bougouffa, Salim; Batang, Zenon; Al-Suwailem, Abdulaziz; Lafi, Feras F; Bajic, Vladimir B; Qian, Pei-Yuan

    2014-10-01

    Abnormality and disease in sponges have been widely reported, yet how sponge-associated microbes respond correspondingly remains inconclusive. Here, individuals of the sponge Carteriospongia foliascens under abnormal status were collected from the Rabigh Bay along the Red Sea coast. Microbial communities in both healthy and abnormal sponge tissues and adjacent seawater were compared to check the influences of these abnormalities on sponge-associated microbes. In healthy tissues, we revealed low microbial diversity with less than 100 operational taxonomic units (OTUs) per sample. Cyanobacteria, affiliated mainly with the sponge-specific species "Candidatus Synechococcus spongiarum," were the dominant bacteria, followed by Bacteroidetes and Proteobacteria. Intraspecies dynamics of microbial communities in healthy tissues were observed among sponge individuals, and potential anoxygenic phototrophic bacteria were found. In comparison with healthy tissues and the adjacent seawater, abnormal tissues showed dramatic increase in microbial diversity and decrease in the abundance of sponge-specific microbial clusters. The dominated cyanobacterial species Candidatus Synechococcus spongiarum decreased and shifted to unspecific cyanobacterial clades. OTUs that showed high similarity to sequences derived from diseased corals, such as Leptolyngbya sp., were found to be abundant in abnormal tissues. Heterotrophic Planctomycetes were also specifically enriched in abnormal tissues. Overall, we revealed the microbial communities of the cyanobacteria-rich sponge, C. foliascens, and their impressive shifts under abnormality.

  10. Lettuce and rhizosphere microbiome responses to growth promoting Pseudomonas species under field conditions.

    Science.gov (United States)

    Cipriano, Matheus A P; Lupatini, Manoeli; Lopes-Santos, Lucilene; da Silva, Márcio J; Roesch, Luiz F W; Destéfano, Suzete A L; Freitas, Sueli S; Kuramae, Eiko E

    2016-12-01

    Plant growth promoting rhizobacteria are well described and recommended for several crops worldwide. However, one of the most common problems in research into them is the difficulty in obtaining reproducible results. Furthermore, few studies have evaluated plant growth promotion and soil microbial community composition resulting from bacterial inoculation under field conditions. Here we evaluated the effect of 54 Pseudomonas strains on lettuce (Lactuca sativa) growth. The 12 most promising strains were phylogenetically and physiologically characterized for plant growth-promoting traits, including phosphate solubilization, hormone production and antagonism to pathogen compounds, and their effect on plant growth under farm field conditions. Additionally, the impact of beneficial strains on the rhizospheric bacterial community was evaluated for inoculated plants. The strains IAC-RBcr4 and IAC-RBru1, with different plant growth promoting traits, improved lettuce plant biomass yields up to 30%. These two strains also impacted rhizosphere bacterial groups including Isosphaera and Pirellula (phylum Planctomycetes) and Acidothermus, Pseudolabrys and Singusphaera (phylum Actinobacteria). This is the first study to demonstrate consistent results for the effects of Pseudomonas strains on lettuce growth promotion for seedlings and plants grown under tropical field conditions. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  11. Influence of Wastewater Discharge on the Metabolic Potential of the Microbial Community in River Sediments.

    Science.gov (United States)

    Li, Dong; Sharp, Jonathan O; Drewes, Jörg E

    2016-01-01

    To reveal the variation of microbial community functions during water filtration process in river sediments, which has been utilized widely in natural water treatment systems, this study investigates the influence of municipal wastewater discharge to streams on the phylotype and metabolic potential of the microbiome in upstream and particularly various depths of downstream river sediments. Cluster analyses based on both microbial phylogenetic and functional data collectively revealed that shallow upstream sediments grouped with those from deeper subsurface downstream regions. These sediment samples were distinct from those found in shallow downstream sediments. Functional genes associated with carbohydrate, xenobiotic, and certain amino acid metabolisms were overrepresented in upstream and deep downstream samples. In contrast, the more immediate contact with wastewater discharge in shallow downstream samples resulted in an increase in the relative abundance of genes associated with nitrogen, sulfur, purine and pyrimidine metabolisms, as well as restriction-modification systems. More diverse bacterial phyla were associated with upstream and deep downstream sediments, mainly including Actinobacteria, Planctomycetes, and Firmicutes. In contrast, in shallow downstream sediments, genera affiliated with Betaproteobacteria and Gammaproteobacteria were enriched with putative functions that included ammonia and sulfur oxidation, polyphosphate accumulation, and methylotrophic bacteria. Collectively, these results highlight the enhanced capabilities of microbial communities residing in deeper stream sediments for the transformation of water contaminants and thus provide a foundation for better design of natural water treatment systems to further improve the removal of contaminants.

  12. Metagenomic identification of bacterioplankton taxa and pathways involved in microcystin degradation in lake erie.

    Directory of Open Access Journals (Sweden)

    Xiaozhen Mou

    Full Text Available Cyanobacterial harmful blooms (CyanoHABs that produce microcystins are appearing in an increasing number of freshwater ecosystems worldwide, damaging quality of water for use by human and aquatic life. Heterotrophic bacteria assemblages are thought to be important in transforming and detoxifying microcystins in natural environments. However, little is known about their taxonomic composition or pathways involved in the process. To address this knowledge gap, we compared the metagenomes of Lake Erie free-living bacterioplankton assemblages in laboratory microcosms amended with microcystins relative to unamended controls. A diverse array of bacterial phyla were responsive to elevated supply of microcystins, including Acidobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, Proteobacteria of the alpha, beta, gamma, delta and epsilon subdivisions and Verrucomicrobia. At more detailed taxonomic levels, Methylophilales (mainly in genus Methylotenera and Burkholderiales (mainly in genera Bordetella, Burkholderia, Cupriavidus, Polaromonas, Ralstonia, Polynucleobacter and Variovorax of Betaproteobacteria were suggested to be more important in microcystin degradation than Sphingomonadales of Alphaproteobacteria. The latter taxa were previously thought to be major microcystin degraders. Homologs to known microcystin-degrading genes (mlr were not overrepresented in microcystin-amended metagenomes, indicating that Lake Erie bacterioplankton might employ alternative genes and/or pathways in microcystin degradation. Genes for xenobiotic metabolism were overrepresented in microcystin-amended microcosms, suggesting they are important in bacterial degradation of microcystin, a phenomenon that has been identified previously only in eukaryotic systems.

  13. Bacterial community composition of South China Sea sediments through pyrosequencing-based analysis of 16S rRNA genes.

    Science.gov (United States)

    Zhu, Daochen; Tanabe, Shoko-Hosoi; Yang, Chong; Zhang, Weimin; Sun, Jianzhong

    2013-01-01

    Subseafloor sediments accumulate large amounts of organic and inorganic materials that contain a highly diverse microbial ecosystem. The aim of this study was to survey the bacterial community of subseafloor sediments from the South China Sea. Pyrosequencing of over 265,000 amplicons of the V3 hypervariable region of the 16S ribosomal RNA gene was performed on 16 sediment samples collected from multiple locations in the northern region of the South China Sea from depths ranging from 35 to 4000 m. A total of 9,726 operational taxonomic units (OTUs; between 695 and 2819 unique OTUs per sample) at 97% sequence similarity level were generated. In total, 40 bacterial phyla including 22 formally described phyla and 18 candidate phyla, with Proteobacteria, Firmicutes, Planctomycetes, Actinobacteria and Chloroflexi being most diverse, were identified. The most abundant phylotype, accounting for 42.6% of all sequences, belonged to Gammaproteobacteria, which possessed absolute predominance in the samples analyzed. Among the 18 candidate phyla, 12 were found for the first time in the South China Sea. This study provided a novel insight into the composition of bacterial communities of the South China Sea subseafloor. Furthermore, abundances and community similarity analysis showed that the compositions of the bacterial communities are very similar at phylum level at different depths from 35-4000 m.

  14. Microbial diversity in the hydrate-containing and -free surface sediments in the Shenhu area, South China Sea

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    Lu Jiao

    2015-07-01

    Full Text Available Microbial diversity in the hydrate-containing (sites SH3B and SH7B and -free (sites SH1B, SH5B, SH5C sediments collected from the Shenhu area of the South China Sea (SCS was investigated using 16S rRNA gene phylogenetic analysis. The phylogenetic results indicate difference in microbial communities between hydrate-containing and -free sediments. At the gas hydrate-containing sites, bacterial communities were dominated by Deltaproteobacteria (30.5%, and archaeal communities were dominated by Miscellaneous Crenarchaeotic Group (33.8%; In contrast, Planctomycetes was the major group (43.9% in bacterial communities, while Marine Benthic Group-D (MBG-D (32.4% took up the largest proportion in the archaeal communities. Moreover, the microbial communities have characteristics different from those in other hydrate-related sediments around the world, indicating that the presence of hydrates can affect the microbial distribution. In addition, the microbial community composition in the studied sediments has its own uniqueness, which may result from co-effect of geochemical characteristics and presence/absence of hydrate.

  15. Comparative bacterial community analysis in relatively pristine and anthropogenically influenced mangrove ecosystems on the Red Sea.

    Science.gov (United States)

    Ullah, Riaz; Yasir, Muhammad; Khan, Imran; Bibi, Fehmida; Sohrab, Sayed Sartaj; Al-Ansari, Ahmed; Al-Abbasi, Fahad; Al-Sofyani, Abdulmohsin A; Daur, Ihsanullah; Lee, Seon-Woo; Azhar, Esam I

    2017-08-01

    Mangrove habitats are ecologically important ecosystems that are under severe pressure worldwide because of environmental changes and human activities. In this study, 16S rRNA gene amplicon deep-sequencing was used to compare bacterial communities in Red Sea mangrove ecosystems at anthropogenically influenced coastal sites with those at a relatively pristine island site. In total, 32 phyla were identified from the mangrove rhizospheres, with Proteobacteria predominating at each of the studied sites; however, the relative abundance was significantly decreased at the coastal sites (Mastorah, MG-MS; Ar-Rayis, MG-AR) compared with the pristine island site near Dhahban (MG-DBI). The phyla Actinobacteria, Firmicutes, Acidobacteria, Chloroflexi, Spirochetes, and Planctomycetes were present at a relative abundance of >1% at the MG-MS and MG-AR sites, but their concentration was <1% at the MG-DBI site. A total of 1659 operational taxonomic units (OTUs) were identified at the species level, and approximately 945 OTUs were shared across the different sampling sites. Multivariate principal coordinate data analysis separated the MG-DBI site from the MG-AR and MG-MS cluster. Specific bacterial taxa were enriched at each location, and in particular, the genera Pseudoalteromonas and Cobetia were predominantly identified in the MG-DBI site compared with the anthropogenically influenced coastal sites.

  16. Bioprospecting Red Sea Coastal Ecosystems for Culturable Microorganisms and Their Antimicrobial Potential.

    Science.gov (United States)

    Al-Amoudi, Soha; Essack, Magbubah; Simões, Marta F; Bougouffa, Salim; Soloviev, Irina; Archer, John A C; Lafi, Feras F; Bajic, Vladimir B

    2016-09-10

    Microorganisms that inhabit unchartered unique soil such as in the highly saline and hot Red Sea lagoons on the Saudi Arabian coastline, represent untapped sources of potentially new bioactive compounds. In this study, a culture-dependent approach was applied to three types of sediments: mangrove mud (MN), microbial mat (MM), and barren soil (BS), collected from Rabigh harbor lagoon (RHL) and Al-Kharrar lagoon (AKL). The isolated bacteria were evaluated for their potential to produce bioactive compounds. The phylogenetic characterization of 251 bacterial isolates based on the 16S rRNA gene sequencing, supported their assignment to five different phyla: Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, and Planctomycetes. Fifteen putative novel species were identified based on a 16S rRNA gene sequence similarity to other strain sequences in the NCBI database, being ≤98%. We demonstrate that 49 of the 251 isolates exhibit the potential to produce antimicrobial compounds. Additionally, at least one type of biosynthetic gene sequence, responsible for the synthesis of secondary metabolites, was recovered from 25 of the 49 isolates. Moreover, 10 of the isolates had a growth inhibition effect towards Staphylococcus aureus, Salmonella typhimurium and Pseudomonas syringae. We report the previously unknown antimicrobial activity of B. borstelensis, P. dendritiformis and M. salipaludis against all three indicator pathogens. Our study demonstrates the evidence of diverse cultured microbes associated with the Red Sea harbor/lagoon environments and their potential to produce antimicrobial compounds.

  17. Bacterial community evolutions driven by organic matter and powder activated carbon in simultaneous anammox and denitrification (SAD) process.

    Science.gov (United States)

    Ge, Cheng-Hao; Sun, Na; Kang, Qi; Ren, Long-Fei; Ahmad, Hafiz Adeel; Ni, Shou-Qing; Wang, Zhibin

    2018-03-01

    A distinct shift of bacterial community driven by organic matter (OM) and powder activated carbon (PAC) was discovered in the simultaneous anammox and denitrification (SAD) process which was operated in an anti-fouling submerged anaerobic membrane bio-reactor. Based on anammox performance, optimal OM dose (50 mg/L) was advised to start up SAD process successfully. The results of qPCR and high throughput sequencing analysis indicated that OM played a key role in microbial community evolutions, impelling denitrifiers to challenge anammox's dominance. The addition of PAC not only mitigated the membrane fouling, but also stimulated the enrichment of denitrifiers, accounting for the predominant phylum changing from Planctomycetes to Proteobacteria in SAD process. Functional genes forecasts based on KEGG database and COG database showed that the expressions of full denitrification functional genes were highly promoted in R C , which demonstrated the enhanced full denitrification pathway driven by OM and PAC under low COD/N value (0.11). Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Impact of land-use change and soil organic carbon quality on microbial diversity in soils across Europe.

    Science.gov (United States)

    Szoboszlay, Márton; Dohrmann, Anja B; Poeplau, Christopher; Don, Axel; Tebbe, Christoph C

    2017-12-01

    Land-use and their change have dramatic consequences for above-ground biodiversity, but their impact on soil microbial communities is poorly understood. In this study, soils from 19 European sites representing conversion of croplands to grasslands or forests and of grasslands to croplands or forests were characterized for microbial abundance and bacterial diversity. The abundance of Bacteria and Fungi but not Archaea responded to land-use change. Site was the major determinant of the soil bacterial community structure, explaining 32% of the variation in 16S rRNA gene diversity. While the quantity of soil organic carbon (SOC) only explained 5% of the variation, SOC when differentiated by its quality could explain 22%. This was similar to the impact of soil pH (21%) and higher than that of land-use type (15%). Croplands had the highest bacterial diversity. Converting croplands to grassland caused an increase of Verrucomicrobia; croplands to forest increased Rhizobiales but decreased Bacteroidetes and Nitrospirae; and grasslands to cropland increased Gemmatimonadetes but decreased Verrucomicrobia and Planctomycetes. Network analysis identified associations between particular SOC fractions and specific bacterial taxa. We conclude that land-use-related effects on soil microorganisms can be consistently observed across a continental scale. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  19. [Bacterial anaerobic ammonia oxidation (Anammox) in the marine nitrogen cycle--a review].

    Science.gov (United States)

    Hong, Yiguo; Li, Meng; Gu, Jidong

    2009-03-01

    Anaerobic ammonium oxidation (Anammox) is a microbial oxidation process of ammonium, with nitrite as the electron acceptor and dinitrogen gas as the main product, and is performed by a clade of deeply branched Planctomycetes, which possess an intracytoplasmic membrane-bounded organelle, the anammoxosome, for the Anammox process. The wide distribution of Anammox bacteria in different natural environments has been greatly modified the traditional view of biogeochemical cycling of nitrogen, in which microbial denitrifier is considered as the only organism to respire nitrate and nitrite to produce nitric and nitrous oxides, and eventually nitrogen gas. More evidences indicate that Anammox is responsible for the production of more than 50% of oceanic N2 and plays an important role in global nitrogen cycling. Moreover, due to the close relationship between nitrogen and carbon cycling, it is anticipated that Anammox process might also affect the concentration of CO2 in the atmosphere, and influence the global climate change. In addition, the simultaneous transformation of nitrite and ammonium in wastewater treatment by Anammox would allow a 90% reduction in operational costs and provide a much more effective biotechnological process for wastewater treatment.

  20. Compositional profile of α / β-hydrolase fold proteins in mangrove soil metagenomes: prevalence of epoxide hydrolases and haloalkane dehalogenases in oil-contaminated sites.

    Science.gov (United States)

    Jiménez, Diego Javier; Dini-Andreote, Francisco; Ottoni, Júlia Ronzella; de Oliveira, Valéria Maia; van Elsas, Jan Dirk; Andreote, Fernando Dini

    2015-05-01

    The occurrence of genes encoding biotechnologically relevant α/β-hydrolases in mangrove soil microbial communities was assessed using data obtained by whole-metagenome sequencing of four mangroves areas, denoted BrMgv01 to BrMgv04, in São Paulo, Brazil. The sequences (215 Mb in total) were filtered based on local amino acid alignments against the Lipase Engineering Database. In total, 5923 unassembled sequences were affiliated with 30 different α/β-hydrolase fold superfamilies. The most abundant predicted proteins encompassed cytosolic hydrolases (abH08; ∼ 23%), microsomal hydrolases (abH09; ∼ 12%) and Moraxella lipase-like proteins (abH04 and abH01; mangroves BrMgv01-02-03. This suggested selection and putative involvement in local degradation/detoxification of the pollutants. Seven sequences that were annotated as genes for putative epoxide hydrolases and five for putative haloalkane dehalogenases were found in a fosmid library generated from BrMgv02 DNA. The latter enzymes were predicted to belong to Actinobacteria, Deinococcus-Thermus, Planctomycetes and Proteobacteria. Our integrated approach thus identified 12 genes (complete and/or partial) that may encode hitherto undescribed enzymes. The low amino acid identity (< 60%) with already-described genes opens perspectives for both production in an expression host and genetic screening of metagenomes. © 2014 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

  1. Compositional profile of α/β-hydrolase fold proteins in mangrove soil metagenomes: prevalence of epoxide hydrolases and haloalkane dehalogenases in oil-contaminated sites

    Science.gov (United States)

    Jiménez, Diego Javier; Dini-Andreote, Francisco; Ottoni, Júlia Ronzella; de Oliveira, Valéria Maia; van Elsas, Jan Dirk; Andreote, Fernando Dini

    2015-01-01

    The occurrence of genes encoding biotechnologically relevant α/β-hydrolases in mangrove soil microbial communities was assessed using data obtained by whole-metagenome sequencing of four mangroves areas, denoted BrMgv01 to BrMgv04, in São Paulo, Brazil. The sequences (215 Mb in total) were filtered based on local amino acid alignments against the Lipase Engineering Database. In total, 5923 unassembled sequences were affiliated with 30 different α/β-hydrolase fold superfamilies. The most abundant predicted proteins encompassed cytosolic hydrolases (abH08; ∼ 23%), microsomal hydrolases (abH09; ∼ 12%) and Moraxella lipase-like proteins (abH04 and abH01; mangroves BrMgv01-02-03. This suggested selection and putative involvement in local degradation/detoxification of the pollutants. Seven sequences that were annotated as genes for putative epoxide hydrolases and five for putative haloalkane dehalogenases were found in a fosmid library generated from BrMgv02 DNA. The latter enzymes were predicted to belong to Actinobacteria, Deinococcus-Thermus, Planctomycetes and Proteobacteria. Our integrated approach thus identified 12 genes (complete and/or partial) that may encode hitherto undescribed enzymes. The low amino acid identity (< 60%) with already-described genes opens perspectives for both production in an expression host and genetic screening of metagenomes. PMID:25171437

  2. Molecular Techniques Revealed Highly Diverse Microbial Communities in Natural Marine Biofilms on Polystyrene Dishes for Invertebrate Larval Settlement

    KAUST Repository

    Lee, On On

    2014-01-09

    Biofilm microbial communities play an important role in the larval settlement response of marine invertebrates. However, the underlying mechanism has yet to be resolved, mainly because of the uncertainties in characterizing members in the communities using traditional 16S rRNA gene-based molecular methods and in identifying the chemical signals involved. In this study, pyrosequencing was used to characterize the bacterial communities in intertidal and subtidal marine biofilms developed during two seasons. We revealed highly diverse biofilm bacterial communities that varied with season and tidal level. Over 3,000 operational taxonomic units with estimates of up to 8,000 species were recovered in a biofilm sample, which is by far the highest number recorded in subtropical marine biofilms. Nineteen phyla were found, of which Cyanobacteria and Proteobacteria were the most dominant one in the intertidal and subtidal biofilms, respectively. Apart from these, Actinobacteria, Bacteroidetes, and Planctomycetes were the major groups recovered in both intertidal and subtidal biofilms, although their relative abundance varied among samples. Full-length 16S rRNA gene clone libraries were constructed for the four biofilm samples and showed similar bacterial compositions at the phylum level to those revealed by pyrosequencing. Laboratory assays confirmed that cyrids of the barnacle Balanus amphitrite preferred to settle on the intertidal rather than subtidal biofilms. This preference was independent of the biofilm bacterial density or biomass but was probably related to the biofilm community structure, particularly, the Proteobacterial and Cyanobacterial groups. © 2014 Springer Science+Business Media New York.

  3. Searching for convergent evolution in manganese superoxidase dismutase using hydrophobic cluster analysis

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    Heng Xiang

    2014-06-01

    Full Text Available There are numerous examples of convergent evolution in nature. Major ecological adaptations such as flight, loss of limbs in vertebrates, pesticide resistance, adaptation to a parasitic way of life, etc., have all evolved more than once, as seen by their analogous functions in separate taxa. But what about protein evolution? Does the environment have a strong enough influence on intracellular processes that enzymes and other functional proteins play, to evolve similar functional roles separately in different organisms? Manganese Superoxide Dismutase (MnSOD is a manganesedependant metallo-enzyme which plays a crucial role in protecting cells from anti-oxidative stress by eliminating reactive (superoxide oxygen species. It is a ubiquitous housekeeping enzyme found in nearly all organisms. In this study we compare phylogenies based on MnSOD protein sequences to those based on scores from Hydrophobic Cluster Analysis (HCA. We calculated HCA similarity values for each pair of taxa to obtain a pair-wise distance matrix. A UPGMA tree based on the HCA distance matrix and a common tree based on the primary protein sequence for MnSOD was constructed. Differences between these two trees within animals, enterobacteriaceae, planctomycetes and cyanobacteria are presented and cited as possible examples of convergence. We note that several residue changes result in changes in hydrophobicity at positions which apparently are under the effect of positive selection.

  4. Phylogenetic analysis of a microbialite-forming microbial mat from a hypersaline lake of the Kiritimati atoll, Central Pacific.

    Science.gov (United States)

    Schneider, Dominik; Arp, Gernot; Reimer, Andreas; Reitner, Joachim; Daniel, Rolf

    2013-01-01

    On the Kiritimati atoll, several lakes exhibit microbial mat-formation under different hydrochemical conditions. Some of these lakes trigger microbialite formation such as Lake 21, which is an evaporitic, hypersaline lake (salinity of approximately 170‰). Lake 21 is completely covered with a thick multilayered microbial mat. This mat is associated with the formation of decimeter-thick highly porous microbialites, which are composed of aragonite and gypsum crystals. We assessed the bacterial and archaeal community composition and its alteration along the vertical stratification by large-scale analysis of 16S rRNA gene sequences of the nine different mat layers. The surface layers are dominated by aerobic, phototrophic, and halotolerant microbes. The bacterial community of these layers harbored Cyanobacteria (Halothece cluster), which were accompanied with known phototrophic members of the Bacteroidetes and Alphaproteobacteria. In deeper anaerobic layers more diverse communities than in the upper layers were present. The deeper layers were dominated by Spirochaetes, sulfate-reducing bacteria (Deltaproteobacteria), Chloroflexi (Anaerolineae and Caldilineae), purple non-sulfur bacteria (Alphaproteobacteria), purple sulfur bacteria (Chromatiales), anaerobic Bacteroidetes (Marinilabiacae), Nitrospirae (OPB95), Planctomycetes and several candidate divisions. The archaeal community, including numerous uncultured taxonomic lineages, generally changed from Euryarchaeota (mainly Halobacteria and Thermoplasmata) to uncultured members of the Thaumarchaeota (mainly Marine Benthic Group B) with increasing depth.

  5. Phylogenetic analysis of a microbialite-forming microbial mat from a hypersaline lake of the Kiritimati atoll, Central Pacific.

    Directory of Open Access Journals (Sweden)

    Dominik Schneider

    Full Text Available On the Kiritimati atoll, several lakes exhibit microbial mat-formation under different hydrochemical conditions. Some of these lakes trigger microbialite formation such as Lake 21, which is an evaporitic, hypersaline lake (salinity of approximately 170‰. Lake 21 is completely covered with a thick multilayered microbial mat. This mat is associated with the formation of decimeter-thick highly porous microbialites, which are composed of aragonite and gypsum crystals. We assessed the bacterial and archaeal community composition and its alteration along the vertical stratification by large-scale analysis of 16S rRNA gene sequences of the nine different mat layers. The surface layers are dominated by aerobic, phototrophic, and halotolerant microbes. The bacterial community of these layers harbored Cyanobacteria (Halothece cluster, which were accompanied with known phototrophic members of the Bacteroidetes and Alphaproteobacteria. In deeper anaerobic layers more diverse communities than in the upper layers were present. The deeper layers were dominated by Spirochaetes, sulfate-reducing bacteria (Deltaproteobacteria, Chloroflexi (Anaerolineae and Caldilineae, purple non-sulfur bacteria (Alphaproteobacteria, purple sulfur bacteria (Chromatiales, anaerobic Bacteroidetes (Marinilabiacae, Nitrospirae (OPB95, Planctomycetes and several candidate divisions. The archaeal community, including numerous uncultured taxonomic lineages, generally changed from Euryarchaeota (mainly Halobacteria and Thermoplasmata to uncultured members of the Thaumarchaeota (mainly Marine Benthic Group B with increasing depth.

  6. Think big--giant genes in bacteria.

    Science.gov (United States)

    Reva, Oleg; Tümmler, Burkhard

    2008-03-01

    Long genes should be rare in archaea and eubacteria because of the demanding costs of time and resources for protein production. The search in 580 sequenced prokaryotic genomes, however, revealed 0.2% of all genes to be longer than 5 kb (absolute number: 3732 genes). Eighty giant bacterial genes of more than 20 kb in length were identified in 47 taxa that belong to the phyla Thermotogae (1), Chlorobi (3), Planctomycetes (1), Cyanobacteria (2), Firmicutes (7), Actinobacteria (9), Proteobacteria (23) or Euryarchaeota (1) (number of taxa in brackets). Giant genes are strain-specific, differ in their tetranucleotide usage from the bulk genome and occur preferentially in non-pathogenic environmental bacteria. The two longest bacterial genes known to date were detected in the green sulfur bacterium Chlorobium chlorochromatii CaD3 encoding proteins of 36 806 and 20 647 amino acids, being surpassed in length only by the human titin coding sequence. More than 90% of bacterial giant genes either encode a surface protein or a polyketide/non-ribosomal peptide synthetase. Most surface proteins are acidic, threonine-rich, lack cystein and harbour multiple amino acid repeats. Giant proteins increase bacterial fitness by the production of either weapons towards or shields against animate competitors or hostile environments.

  7. Bioprospecting Red Sea Coastal Ecosystems for Culturable Microorganisms and Their Antimicrobial Potential

    KAUST Repository

    Al Amoudi, Soha; Essack, Magbubah; Simoes, Marta; Bougouffa, Salim; Soloviev, Irina; Archer, John A.C.; Lafi, Feras Fawzi; Bajic, Vladimir B.

    2016-01-01

    Microorganisms that inhabit unchartered unique soil such as in the highly saline and hot Red Sea lagoons on the Saudi Arabian coastline, represent untapped sources of potentially new bioactive compounds. In this study, a culture-dependent approach was applied to three types of sediments: mangrove mud (MN), microbial mat (MM), and barren soil (BS), collected from Rabigh harbor lagoon (RHL) and Al-Kharrar lagoon (AKL). The isolated bacteria were evaluated for their potential to produce bioactive compounds. The phylogenetic characterization of 251 bacterial isolates based on the 16S rRNA gene sequencing, supported their assignment to five different phyla: Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, and Planctomycetes. Fifteen putative novel species were identified based on a 16S rRNA gene sequence similarity to other strain sequences in the NCBI database, being ≤98%. We demonstrate that 49 of the 251 isolates exhibit the potential to produce antimicrobial compounds. Additionally, at least one type of biosynthetic gene sequence, responsible for the synthesis of secondary metabolites, was recovered from 25 of the 49 isolates. Moreover, 10 of the isolates had a growth inhibition effect towards Staphylococcus aureus, Salmonella typhimurium and Pseudomonas syringae. We report the previously unknown antimicrobial activity of B. borstelensis, P. dendritiformis and M. salipaludis against all three indicator pathogens. Our study demonstrates the evidence of diverse cultured microbes associated with the Red Sea harbor/lagoon environments and their potential to produce antimicrobial compounds.

  8. Microbial Diversity in Cerrado Biome (Neotropical Savanna Soils.

    Directory of Open Access Journals (Sweden)

    Alinne Pereira de Castro

    Full Text Available The Cerrado, the largest savanna region in South America, is located in central Brazil. Cerrado physiognomies, which range from savanna grasslands to forest formations, combined with the highly weathered, acidic clay Cerrado soils form a unique ecoregion. In this study, high-throughput sequencing of ribosomal RNA genes was combined with shotgun metagenomic analysis to explore the taxonomic composition and potential functions of soil microbial communities in four different vegetation physiognomies during both dry and rainy seasons. Our results showed that changes in bacterial, archaeal, and fungal community structures in cerrado denso, cerrado sensu stricto, campo sujo, and gallery forest soils strongly correlated with seasonal patterns of soil water uptake. The relative abundance of AD3, WPS-2, Planctomycetes, Thermoprotei, and Glomeromycota typically decreased in the rainy season, whereas the relative abundance of Proteobacteria and Ascomycota increased. In addition, analysis of shotgun metagenomic data revealed a significant increase in the relative abundance of genes associated with iron acquisition and metabolism, dormancy, and sporulation during the dry season, and an increase in the relative abundance of genes related to respiration and DNA and protein metabolism during the rainy season. These gene functional categories are associated with adaptation to water stress. Our results further the understanding of how tropical savanna soil microbial communities may be influenced by vegetation covering and temporal variations in soil moisture.

  9. Methanotrophic community dynamics in a seasonally anoxic fjord: Saanich Inlet, British Columbia

    Directory of Open Access Journals (Sweden)

    Mónica Torres-Beltrán

    2016-12-01

    Full Text Available Marine oxygen minimum zones (OMZs play disproportionate roles in nutrient and climate active trace gas cycling including nitrous oxide and methane, in the ocean. OMZs are currently expanding due to climate change making it increasingly important to identify microbial controls on trace gas cycling at the individual, population and community levels. Here we present a two-year survey of the microbial community along seasonal redox gradients in Saanich Inlet focused on identifying microbial agents driving methane oxidation. Although methanotrophs were rare, we identified three uncultivated groups affiliated with particulate methane monooxygenase (pMMO encoding phylogenetic groups (OPU, and methanotrophic symbionts as primary drivers of methane oxidation in Saanich Inlet. Distribution and activity patterns for these three groups were consistent with niche partitioning that became increasingly resolved during water column stratification. Moreover co-occurrence analysis combined with multi-level indicator species analysis revealed significant correlations between operational taxonomic units affiliated with Methylophaga, Methylophilales, SAR324, Verrucomicrobia, and Planctomycetes with OPUs and methanotrophic symbiont groups. Taken together these observations shed new light on the composition, dynamics, and potential interspecific interactions of microbes associated with CH4 cycling in the Saanich Inlet water column, provide a baseline for comparison between coastal and open ocean OMZs and support the potential role of OPUs, and methanotrophic symbiont groups as a widely distributed pelagic sink for CH4 along continental margins.

  10. Effects of iron and calcium carbonate on contaminant removal efficiencies and microbial communities in integrated wastewater treatment systems.

    Science.gov (United States)

    Zhao, Zhimiao; Song, Xinshan; Zhang, Yinjiang; Zhao, Yufeng; Wang, Bodi; Wang, Yuhui

    2017-12-01

    In the paper, we explored the influences of different dosages of iron and calcium carbonate on contaminant removal efficiencies and microbial communities in algal ponds combined with constructed wetlands. After 1-year operation of treatment systems, based on the high-throughput pyrosequencing analysis of microbial communities, the optimal operating conditions were obtained as follows: the ACW10 system with Fe 3+ (5.6 mg L -1 ), iron powder (2.8 mg L -1 ), and CaCO 3 powder (0.2 mg L -1 ) in influent as the adjusting agents, initial phosphorus source (PO 4 3- ) in influent, the ratio of nitrogen to phosphorus (N/P) of 30 in influent, and hydraulic retention time (HRT) of 1 day. Total nitrogen (TN) removal efficiency and total phosphorus (TP) removal efficiency were improved significantly. The hydrolysis of CaCO 3 promoted the physicochemical precipitation in contaminant removal. Meanwhile, Fe 3+ and iron powder produced Fe 2+ , which improved contaminant removal. Iron ion improved the diversity, distribution, and metabolic functions of microbial communities in integrated treatment systems. In the treatment ACW10, the dominant phylum in the microbial community was PLANCTOMYCETES, which positively promoted nitrogen removal. After 5 consecutive treatments in ACW10, contaminant removal efficiencies for TN and TP respectively reached 80.6% and 57.3% and total iron concentration in effluent was 0.042 mg L -1 . Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. High-throughput profiling of microbial community structures in an ANAMMOX-UASB reactor treating high-strength wastewater.

    Science.gov (United States)

    Cao, Shenbin; Du, Rui; Li, Baikun; Ren, Nanqi; Peng, Yongzhen

    2016-07-01

    In this study, the microbial community structure was assessed in an anaerobic ammonium oxidation-upflow anaerobic sludge blanket (ANAMMOX-UASB) reactor treating high-strength wastewater (approximately 700 mg N L(-1) in total nitrogen) by employing Illumina high-throughput sequencing analysis. The reactor was started up and reached a steady state in 26 days by seeding mature ANAMMOX granules, and a high nitrogen removal rate (NRR) of 2.96 kg N m(-3) day(-1) was obtained at 13.2∼17.6 °C. Results revealed that the abundance of ANAMMOX bacteria increased during the operation, though it occupied a low proportion in the system. The phylum Planctomycetes was only 8.39 % on day 148 and Candidatus Brocadia was identified as the dominant ANAMMOX species with a percentage of 2.70 %. The phylum of Chloroflexi, Bacteroidetes, and Proteobacteria constituted a percentage up to 70 % in the community, of which the Chloroflexi and Bacteroidetes were likely to be related to the sludge granulation. In addition, it was found that heterotrophic denitrifying bacteria of Denitratisoma belonging to Proteobacteria phylum occupied a large proportion (22.1∼23.58 %), which was likely caused by the bacteria lysis and decay with the internal carbon source production. The SEM images also showed that plenty of other microorganisms existed in the ANAMMOX-UASB reactor.

  12. Microbial monitoring of ammonia removal in a UASB reactor treating pre-digested chicken manure with anaerobic granular inoculum.

    Science.gov (United States)

    Yangin-Gomec, Cigdem; Pekyavas, Goksen; Sapmaz, Tugba; Aydin, Sevcan; Ince, Bahar; Akyol, Çağrı; Ince, Orhan

    2017-10-01

    Performance and microbial community dynamics in an upflow anaerobic sludge bed (UASB) reactor coupled with anaerobic ammonium oxidizing (Anammox) treating diluted chicken manure digestate (Total ammonia nitrogen; TAN=123±10mg/L) were investigated for a 120-d operating period in the presence of anaerobic granular inoculum. Maximum TAN removal efficiency reached to above 80% with as low as 20mg/L TAN concentrations in the effluent. Moreover, total COD (tCOD) with 807±215mg/L in the influent was removed by 60-80%. High-throughput sequencing revealed that Proteobacteria, Actinobacteria, and Firmicutes were dominant phyla followed by Euryarchaeota and Bacteroidetes. The relative abundance of Planctomycetes significantly increased from 4% to 8-9% during the late days of the operation with decreased tCOD concentration, which indicated a more optimum condition to favor ammonia removal through anammox route. There was also significant association between the hzsA gene and ammonia removal in the UASB reactor. Copyright © 2017 Elsevier Ltd. All rights reserved.

  13. Effect of organic matter strength on anammox for modified greenhouse turtle breeding wastewater treatment.

    Science.gov (United States)

    Chen, Chongjun; Huang, Xiaoxiao; Lei, Chenxiao; Zhang, Tian C; Wu, Weixiang

    2013-11-01

    Anaerobic ammonium-N removal from modified greenhouse turtle breeding wastewater with different chemical oxygen demand (COD) strengths (194.0-577.8 mg L(-1)) at relatively fixed C/N ratios (≈ 2) was investigated using a lab-scale up-flow anaerobic sludge blanket (UASB) anammox reactor. During the entire experiment, the total nitrogen (TN) removal efficiency was about 85% or higher, while the average COD removal efficiency was around 56.5 ± 7.9%. Based on the nitrogen and carbon balance, the nitrogen removal contribution was 79.6 ± 4.2% for anammox, 12.7 ± 3.0% for denitrification+denitritation and 7.7 ± 4.9% for other mechanisms. Denaturing gradient gel electrophoresis (DGGE) analyses revealed that Planctomycete, Proteobacteria and Chloroflexi bacteria were coexisted in the reactor. Anammox was always dominant when the reactor was fed with different COD concentrations, which indicated the stability of the anammox process with the coexistence of the denitrification process in treating greenhouse turtle breeding wastewater. Copyright © 2013 Elsevier Ltd. All rights reserved.

  14. [Effect of Elodea nuttallii-immobilized Nitrogen Cycling Bacteria on Nitrogen Removal Mechanism in an Inflow River, Gonghu Bay].

    Science.gov (United States)

    Han, Hua-yang; Li, Zheng-kui; Wang, Hao; Zhu, Qian

    2016-04-15

    Undisturbed sediment cores and surface water from Qinshui River in Gonghu Bay were collected to carry out a simulation experiment in our laboratory. The remediation effect of Elodea nuttallii-Immobilized Nitrogen Cycling Bacteria (INCB) was applied in the polluted inflow river. The denitrification rate, ANAMMOX rate and nitrogen microorganism diversity were measured by ¹⁵N isotope pairing technology and high-throughput sequencing technology based on 16S rRNA. The TN, NH₄⁺-N, NO₃⁻-N concentrations were reduced by 72.03%, 46.67% and 76.65% in the treatment with addition of Elodea nuttallii and INCB in our laboratory experiment. Meanwhile, denitrification bacteria and ANAMMOX bacteria had synergistic effect with each other. The denitrification and ANAMMOX rates were increased by 165 µmol (m² · h)⁻¹ and 269.7 µmol · (m² · h)⁻¹, respectively. The diversities of denitrification and ANAMMOX bacteria also increased in our experiment. From the level of major phylum, Proteobacteria, Planctomycetes, Acidobbacteria and Bacteroidetes all increased significantly. The results showed that the Elodea nuttallii-INCB assemblage technology could increase the bio-diversity of nitrogen cycling bacteria and promote the ability of nitrogen removal in Qinshui River.

  15. Seeking key microorganisms for enhancing methane production in anaerobic digestion of waste sewage sludge.

    Science.gov (United States)

    Mustapha, Nurul Asyifah; Hu, Anyi; Yu, Chang-Ping; Sharuddin, Siti Suhailah; Ramli, Norhayati; Shirai, Yoshihito; Maeda, Toshinari

    2018-04-25

    Efficient approaches for the utilization of waste sewage sludge have been widely studied. One of them is to use it for the bioenergy production, specifically methane gas which is well-known to be driven by complex bacterial interactions during the anaerobic digestion process. Therefore, it is important to understand not only microorganisms for producing methane but also those for controlling or regulating the process. In this study, azithromycin analogs belonging to macrolide, ketolide, and lincosamide groups were applied to investigate the mechanisms and dynamics of bacterial community in waste sewage sludge for methane production. The stages of anaerobic digestion process were evaluated by measuring the production of intermediate substrates, such as protease activity, organic acids, the quantification of bacteria and archaea, and its community dynamics. All azithromycin analogs used in this study achieved a high methane production compared to the control sample without any antibiotic due to the efficient hydrolysis process and the presence of important fermentative bacteria and archaea responsible in the methanogenesis stage. The key microorganisms contributing to the methane production may be Clostridia, Cladilinea, Planctomycetes, and Alphaproteobacteria as an accelerator whereas Nitrosomonadaceae and Nitrospiraceae may be suppressors for methane production. In conclusion, the utilization of antibiotic analogs of macrolide, ketolide, and lincosamide groups has a promising ability in finding the essential microorganisms and improving the methane production using waste sewage sludge.

  16. [Microbial community in nitrogen cycle of aquaculture water of the Pearl River Delta].

    Science.gov (United States)

    Cai, Xiaolong; Luo, Jianfei; Lin, Weitie; Tian, Guoliang

    2012-05-04

    In order to study the characteristic of nitrogen transport, the community structure and diversity of related microorganisms in aquaculture water of the Pearl River Delta. We established an artificial aquaculture ecosystem to study the microbial community of 15N-stable isotope probing (15N-SIP) labeled nitrogen transport microorganisms. The 15N-labeled DNA was separated by CsCl-ethidium bromide density gradient centrifugation, and was used to construct 16S rRNA gene clone libraries of bacteria and archaea. Phylogenetic analysis shows that 19 Operational Taxonomic Units (OTUs) from bacterial library were clustered in Proteobacteria and Planctomycetes. Proteobacteria (99.2%) was the dominant group, mainly consisted of Comamonas (15.7%), Nitrosomonas (12.4%), Enterobacteriaceae (11.5%) and Nitrobacter (11.5%). From archaeal library 9 OTUs were divided into 3 phyla: Thaumarchaeota, Crenarchaeota and Euryarchaeota. We successfully elucidated the microbial community of nitrogen transport microorganisms in aquaculture water of Pearl River Delta by using 15N-SIP. The data of the community will provide essential information for isolating nitrogen degrading microorganism, and provide scientific basis for creating a healthy aquaculture environment.

  17. Bacterial community involved in the nitrogen cycle in a down-flow sponge-based trickling filter treating UASB effluent.

    Science.gov (United States)

    Mac Conell, E F A; Almeida, P G S; Martins, K E L; Araújo, J C; Chernicharo, C A L

    2015-01-01

    The bacterial community composition of a down-flow sponge-based trickling filter treating upflow anaerobic sludge blanket (UASB) effluent was investigated by pyrosequencing. Bacterial community composition considerably changed along the reactor and over the operational period. The dominant phyla detected were Proteobacteria, Verrucomicrobia, and Planctomycetes. The abundance of denitrifiers decreased from the top to the bottom and it was consistent with the organic matter concentration gradients. At lower loadings (organic and nitrogen loading rates), the abundance of anammox bacteria was higher than that of the ammonium-oxidizing bacteria in the upper portion of the reactor, suggesting that aerobic and anaerobic ammonium oxidation occurred. Nitrification occurred in all the compartments, while anammox bacteria prominently appeared even in the presence of high organic carbon to ammonia ratios (around 1.0-2.0 gCOD gN(-1)). The results suggest that denitrifiers, nitrifiers, and anammox bacteria coexisted in the reactor; thus, different metabolic pathways were involved in ammonium removal in the post-UASB reactor sponge-based.

  18. Cultivation Versus Molecular Analysis of Banana (Musa sp.) Shoot-Tip Tissue Reveals Enormous Diversity of Normally Uncultivable Endophytic Bacteria.

    Science.gov (United States)

    Thomas, Pious; Sekhar, Aparna Chandra

    2017-05-01

    The interior of plants constitutes a unique environment for microorganisms with various organisms inhabiting as endophytes. Unlike subterranean plant parts, aboveground parts are relatively less explored for endophytic microbial diversity. We employed a combination of cultivation and molecular approaches to study the endophytic bacterial diversity in banana shoot-tips. Cultivable bacteria from 20 sucker shoot-tips of cv. Grand Naine included 37 strains under 16 genera and three phyla (Proteobacteria, Actinobacteria, Firmicutes). 16S rRNA gene-ribotyping approach on 799f and 1492r PCR-amplicons to avoid plant organelle sequences was ineffective showing limited bacterial diversity. 16S rRNA metagene profiling targeting the V3-V4 hypervariable region after filtering out the chloroplast (74.2 %), mitochondrial (22.9 %), and unknown sequences (1.1 %) revealed enormous bacterial diversity. Proteobacteria formed the predominant phylum (64 %) succeeded by Firmicutes (12.1 %), Actinobacteria (9.5 %), Bacteroidetes (6.4 %), Planctomycetes, Cyanobacteria, and minor shares (banana shoot-tips (20 phyla, 46 classes) with about 2.6 % of the deciphered 269 genera and 1.5 % of the 656 observed species from the same source of shoot-tips attained through cultivation. The predominant genera included several agriculturally important bacteria. The study reveals an immense ecosystem of endophytic bacteria in banana shoot tissues endorsing the earlier documentation of intracellular "Cytobacts" and "Peribacts" with possible roles in plant holobiome and hologenome.

  19. Microbial and viral-like rhodopsins present in coastal marine sediments from four polar and subpolar regions

    Energy Technology Data Exchange (ETDEWEB)

    López, José L.; Golemba, Marcelo; Hernández, Edgardo; Lozada, Mariana; Dionisi, Hebe; Jansson, Janet K.; Carroll, Jolynn; Lundgren, Leif; Sjöling, Sara; Mac Cormack, Walter P.; Sobecky, Patricia

    2016-11-03

    Rhodopsins are broadly distributed. In this work, we analyzed 23 metagenomes corresponding to marine sediment samples from four regions that share cold climate conditions (Norway; Sweden; Argentina and Antarctica). In order to investigate the genes evolution of viral rhodopsins, an initial set of 6224 bacterial rhodopsin sequences according to COG5524 were retrieved from the 23 metagenomes. After selection by the presence of transmembrane domains and alignment, 123 viral (51) and non-viral (72) sequences (>50 amino acids) were finally included in further analysis. Viral rhodopsin genes were homologs of Phaeocystis globosa virus and Organic lake Phycodnavirus. Non-viral microbial rhodopsin genes were ascribed to Bacteroidetes, Planctomycetes, Firmicutes, Actinobacteria, Cyanobacteria, Proteobacteria, Deinococcus-Thermus and Cryptophyta and Fungi. A rescreening using Blastp, using as queries the viral sequences previously described, retrieved 30 sequences (>100 amino acids). Phylogeographic analysis revealed a geographical clustering of the sequences affiliated to the viral group. This clustering was not observed for the microbial non-viral sequences. The phylogenetic reconstruction allowed us to propose the existence of a putative ancestor of viral rhodopsin genes related to Actinobacteria and Chloroflexi. This is the first report about the existence of a phylogeographic association of the viral rhodopsin sequences from marine sediments.

  20. Bioprospecting Red Sea Coastal Ecosystems for Culturable Microorganisms and Their Antimicrobial Potential

    KAUST Repository

    Al Amoudi, Soha

    2016-09-10

    Microorganisms that inhabit unchartered unique soil such as in the highly saline and hot Red Sea lagoons on the Saudi Arabian coastline, represent untapped sources of potentially new bioactive compounds. In this study, a culture-dependent approach was applied to three types of sediments: mangrove mud (MN), microbial mat (MM), and barren soil (BS), collected from Rabigh harbor lagoon (RHL) and Al-Kharrar lagoon (AKL). The isolated bacteria were evaluated for their potential to produce bioactive compounds. The phylogenetic characterization of 251 bacterial isolates based on the 16S rRNA gene sequencing, supported their assignment to five different phyla: Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, and Planctomycetes. Fifteen putative novel species were identified based on a 16S rRNA gene sequence similarity to other strain sequences in the NCBI database, being ≤98%. We demonstrate that 49 of the 251 isolates exhibit the potential to produce antimicrobial compounds. Additionally, at least one type of biosynthetic gene sequence, responsible for the synthesis of secondary metabolites, was recovered from 25 of the 49 isolates. Moreover, 10 of the isolates had a growth inhibition effect towards Staphylococcus aureus, Salmonella typhimurium and Pseudomonas syringae. We report the previously unknown antimicrobial activity of B. borstelensis, P. dendritiformis and M. salipaludis against all three indicator pathogens. Our study demonstrates the evidence of diverse cultured microbes associated with the Red Sea harbor/lagoon environments and their potential to produce antimicrobial compounds.

  1. Molecular assessment of the bacterial community associated with Cassava (Manihot esculenta Crantz) cultivation in Cameroon.

    Science.gov (United States)

    Sarr, Papa Saliou; Sugiyama, Akifumi; Begoude, Aime Didier Boyogueno; Yazaki, Kazufumi; Araki, Shigeru; Nawata, Eiji

    2017-04-01

    Bacterial communities play an important role in nutrient cycles and plant development. Their distribution and activity may depend on location and environmental heterogeneity. This study characterized soil bacterial communities in cassava fields of Eastern (Andom) and Southern (Bityili) Cameroon using molecular tools. In both sites, two improved varieties (TMS-96/1414; TMS-92/0326) and a local variety (Local) were grown in a randomized block design. Composite bulk soils were collected at 10months after planting from cassava plots. The 16S rDNA region was amplified, MiSeq was performed and sequence data analyzed. The same 17 bacterial phyla were present in both Andom and Bityili, while Chlorobi and Deinococcus-Thermus were only specific to Andom. The phyla Proteobacteria, Planctomycetes, Actinobacteria and Acidobacteria were dominant. Although both sites shared similar phyla, the principal coordinate analysis revealed significant variations in their composition, suggesting that the functions of the bacteria in nutrients cycling are likely to differ between Andom and Bityili. Cassava yields were generally higher in Andom which also displayed a higher diversity of bacterial communities. This study provides useful information on the composition of bacterial communities in cassava fields in two agro-ecologies of Cameroon. It constitutes to our knowledge the first report describing soil bacterial communities in association with cassava growth in the country, using molecular tools. Copyright © 2017 Elsevier GmbH. All rights reserved.

  2. Diversity rankings among bacterial lineages in soil.

    Science.gov (United States)

    Youssef, Noha H; Elshahed, Mostafa S

    2009-03-01

    We used rarefaction curve analysis and diversity ordering-based approaches to rank the 11 most frequently encountered bacterial lineages in soil according to diversity in 5 previously reported 16S rRNA gene clone libraries derived from agricultural, undisturbed tall grass prairie and forest soils (n=26,140, 28 328, 31 818, 13 001 and 53 533). The Planctomycetes, Firmicutes and the delta-Proteobacteria were consistently ranked among the most diverse lineages in all data sets, whereas the Verrucomicrobia, Gemmatimonadetes and beta-Proteobacteria were consistently ranked among the least diverse. On the other hand, the rankings of alpha-Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes and Chloroflexi varied widely in different soil clone libraries. In general, lineages exhibiting largest differences in diversity rankings also exhibited the largest difference in relative abundance in the data sets examined. Within these lineages, a positive correlation between relative abundance and diversity was observed within the Acidobacteria, Actinobacteria and Chloroflexi, and a negative diversity-abundance correlation was observed within the Bacteroidetes. The ecological and evolutionary implications of these results are discussed.

  3. Composition and variation of sediment bacterial and nirS-harboring bacterial communities at representative sites of the Bohai Gulf coastal zone, China.

    Science.gov (United States)

    Guan, Xiangyu; Zhu, Lingling; Li, Youxun; Xie, Yuxuan; Zhao, Mingzhang; Luo, Ximing

    2014-04-01

    With rapid urbanization, anthropogenic activities are increasingly influencing the natural environment of the Bohai Bay. In this study, the composition and variation of bacterial and nirS-harboring bacterial communities in the coastal zone sediments of the Bohai Gulf were analyzed using PCR-based clone libraries. A total of 95 genera were detected in the bacterial communities, with Proteobacteria (72.1 %), Acidobacteria (10.5 %), Firmicutes (1.7 %), Bacteroidetes (1.4 %), Chloroflexi (0.7 %) and Planctomycetes (0.7 %) being the dominated phyla. The NirS sequences were divided into nine Clusters (A-I). Canonical correlation analysis showed that the bacterial or denitrifying communities were correlated with different environmental factors, such as total organic carbon, total nitrogen, ammonium, sulfate, etc. Furthermore, bacterial communities' composition and diversity are influenced by oil exploration, sewage discharge and other anthropogenic activities in the coastal area of the Bohai Sea. Thus, this study provided useful information on further research on regional or global environmental control and restore.

  4. Exploring the dynamics of bacterial community composition in soil: the pan-bacteriome approach.

    Science.gov (United States)

    Bacci, Giovanni; Ceccherini, Maria Teresa; Bani, Alessia; Bazzicalupo, Marco; Castaldini, Maurizio; Galardini, Marco; Giovannetti, Luciana; Mocali, Stefano; Pastorelli, Roberta; Pantani, Ottorino Luca; Arfaioli, Paola; Pietramellara, Giacomo; Viti, Carlo; Nannipieri, Paolo; Mengoni, Alessio

    2015-03-01

    We performed a longitudinal study (repeated observations of the same sample over time) to investigate both the composition and structure of temporal changes of bacterial community composition in soil mesocosms, subjected to three different treatments (water and 5 or 25 mg kg(-1) of dried soil Cd(2+)). By analogy with the pan genome concept, we identified a core bacteriome and an accessory bacteriome. Resident taxa were assigned to the core bacteriome, while occasional taxa were assigned to the accessory bacteriome. Core and accessory bacteriome represented roughly 35 and 50 % of the taxa detected, respectively, and were characterized by different taxonomic signatures from phylum to genus level while 15 % of the taxa were found to be unique to a particular sample. In particular, the core bacteriome was characterized by higher abundance of members of Planctomycetes, Actinobacteria, Verrucomicrobia and Acidobacteria, while the accessory bacteriome included more members of Firmicutes, Clamydiae and Proteobacteria, suggesting potentially different responses to environmental changes of members from these phyla. We conclude that the pan-bacteriome model may be a useful approach to gain insight for modeling bacterial community structure and inferring different abilities of bacteria taxa.

  5. Prokaryotic diversity, distribution, and insights into their role in biogeochemical cycling in marine basalts

    Energy Technology Data Exchange (ETDEWEB)

    Mason, Olivia U.; Di Meo-Savoie, Carol A.; Van Nostrand, Joy D.; Zhou, Jizhong; Fisk, Martin R.; Giovannoni, Stephen J.

    2008-09-30

    We used molecular techniques to analyze basalts of varying ages that were collected from the East Pacific Rise, 9 oN, from the rift axis of the Juan de Fuca Ridge, and from neighboring seamounts. Cluster analysis of 16S rDNA Terminal Restriction Fragment Polymorphism data revealed that basalt endoliths are distinct from seawater and that communities clustered, to some degree, based on the age of the host rock. This age-based clustering suggests that alteration processes may affect community structure. Cloning and sequencing of bacterial and archaeal 16S rRNA genes revealed twelve different phyla and sub-phyla associated with basalts. These include the Gemmatimonadetes, Nitrospirae, the candidate phylum SBR1093 in the c, andin the Archaea Marine Benthic Group B, none of which have been previously reported in basalts. We delineated novel ocean crust clades in the gamma-Proteobacteria, Planctomycetes, and Actinobacteria that are composed entirely of basalt associated microflora, and may represent basalt ecotypes. Finally, microarray analysis of functional genes in basalt revealed that genes coding for previously unreported processes such as carbon fixation, methane-oxidation, methanogenesis, and nitrogen fixation are present, suggesting that basalts harbor previously unrecognized metabolic diversity. These novel processes could exert a profound influence on ocean chemistry.

  6. Comprehensive in silico prediction and analysis of chlamydial outer membrane proteins reflects evolution and life style of the Chlamydiae

    Directory of Open Access Journals (Sweden)

    Myers Garry

    2009-12-01

    Full Text Available Abstract Background Chlamydiae are obligate intracellular bacteria comprising some of the most important bacterial pathogens of animals and humans. Although chlamydial outer membrane proteins play a key role for attachment to and entry into host cells, only few have been described so far. We developed a comprehensive, multiphasic in silico approach, including the calculation of clusters of orthologues, to predict outer membrane proteins using conservative criteria. We tested this approach using Escherichia coli (positive control and Bacillus subtilis (negative control, and applied it to five chlamydial species; Chlamydia trachomatis, Chlamydia muridarum, Chlamydia (a.k.a. Chlamydophila pneumoniae, Chlamydia (a.k.a. Chlamydophila caviae, and Protochlamydia amoebophila. Results In total, 312 chlamydial outer membrane proteins and lipoproteins in 88 orthologous clusters were identified, including 238 proteins not previously recognized to be located in the outer membrane. Analysis of their taxonomic distribution revealed an evolutionary conservation among Chlamydiae, Verrucomicrobia, Lentisphaerae and Planctomycetes as well as lifestyle-dependent conservation of the chlamydial outer membrane protein composition. Conclusion This analysis suggested a correlation between the outer membrane protein composition and the host range of chlamydiae and revealed a common set of outer membrane proteins shared by these intracellular bacteria. The collection of predicted chlamydial outer membrane proteins is available at the online database pCOMP http://www.microbial-ecology.net/pcomp and might provide future guidance in the quest for anti-chlamydial vaccines.

  7. Bacterial communities in sediment of a Mediterranean marine protected area.

    Science.gov (United States)

    Catania, Valentina; Sarà, Gianluca; Settanni, Luca; Quatrini, Paola

    2017-04-01

    Biodiversity is crucial in preservation of ecosystems, and bacterial communities play an indispensable role for the functioning of marine ecosystems. The Mediterranean marine protected area (MPA) "Capo Gallo-Isola delle Femmine" was instituted to preserve marine biodiversity. The bacterial diversity associated with MPA sediment was compared with that from sediment of an adjacent harbour exposed to intense nautical traffic. The MPA sediment showed higher diversity with respect to the impacted site. A 16S rDNA clone library of the MPA sediment allowed the identification of 7 phyla: Proteobacteria (78%), Firmicutes (11%), Acidobacteria (3%), Actinobacteria (3%), Bacteroidetes (2%), Planctomycetes (2%), and Cyanobacteria (1%). Analysis of the hydrocarbon (HC)-degrading bacteria was performed using enrichment cultures. Most of the MPA sediment isolates were affiliated with Gram-positive G+C rich bacteria, whereas the majority of taxa in the harbour sediment clustered with Alpha- and Gammaproteobacteria; no Gram-positive HC degraders were isolated from the harbour sediment. Our results show that protection probably has an influence on bacterial diversity, and suggest the importance of monitoring the effects of protection at microbial level as well. This study creates a baseline of data that can be used to assess changes over time in bacterial communities associated with a Mediterranean MPA.

  8. Different organic loading rates on the biogas production during the anaerobic digestion of rice straw: A pilot study.

    Science.gov (United States)

    Zhou, Jun; Yang, Jun; Yu, Qing; Yong, Xiaoyu; Xie, Xinxin; Zhang, Lijuan; Wei, Ping; Jia, Honghua

    2017-11-01

    The aim of this work was to investigate the mesophilic methane fermentation of rice straw at different organic loading rates (OLRs) in a 300m 3 bioreactor. It was found that biogas production increased when the OLR was below 2.00kg VS substrate /(m 3 ·d). The average volumetric biogas production reached 0.86m 3 /(m 3 ·d) at an OLR of 2.00kg VS substrate /(m 3 ·d). Biogas production rate was 323m 3 /t dry rice straw over the whole process. The pH, chemical oxygen demand, volatile fatty acid, and NH 4 + -N concentrations were all in optimal range at different OLRs. High-throughput sequencing analysis indicated that Firmicutes, Fibrobacteres, and Spirochaetes predominated in straw samples. Chloroflexi, Proteobacteria, and Planctomycetes were more abundant in the slurry. The hydrogenotrophic pathway was the main biochemical pathway of methanogenesis in the reactor. This study provides new information regarding the OLR and the differences in the spatial distribution of specific microbiota in a rice straw biogas plant. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. Active Microbial Communities Inhabit Sulphate-Methane Interphase in Deep Bedrock Fracture Fluids in Olkiluoto, Finland

    Directory of Open Access Journals (Sweden)

    Malin Bomberg

    2015-01-01

    Full Text Available Active microbial communities of deep crystalline bedrock fracture water were investigated from seven different boreholes in Olkiluoto (Western Finland using bacterial and archaeal 16S rRNA, dsrB, and mcrA gene transcript targeted 454 pyrosequencing. Over a depth range of 296–798 m below ground surface the microbial communities changed according to depth, salinity gradient, and sulphate and methane concentrations. The highest bacterial diversity was observed in the sulphate-methane mixing zone (SMMZ at 250–350 m depth, whereas archaeal diversity was highest in the lowest boundaries of the SMMZ. Sulphide-oxidizing ε-proteobacteria (Sulfurimonas sp. dominated in the SMMZ and γ-proteobacteria (Pseudomonas spp. below the SMMZ. The active archaeal communities consisted mostly of ANME-2D and Thermoplasmatales groups, although Methermicoccaceae, Methanobacteriaceae, and Thermoplasmatales (SAGMEG, TMG were more common at 415–559 m depth. Typical indicator microorganisms for sulphate-methane transition zones in marine sediments, such as ANME-1 archaea, α-, β- and δ-proteobacteria, JS1, Actinomycetes, Planctomycetes, Chloroflexi, and MBGB Crenarchaeota were detected at specific depths. DsrB genes were most numerous and most actively transcribed in the SMMZ while the mcrA gene concentration was highest in the deep methane rich groundwater. Our results demonstrate that active and highly diverse but sparse and stratified microbial communities inhabit the Fennoscandian deep bedrock ecosystems.

  10. Bacterial community diversity of the deep-sea octocoral Paramuricea placomus

    Directory of Open Access Journals (Sweden)

    Christina A. Kellogg

    2016-09-01

    Full Text Available Compared to tropical corals, much less is known about deep-sea coral biology and ecology. Although the microbial communities of some deep-sea corals have been described, this is the first study to characterize the bacterial community associated with the deep-sea octocoral, Paramuricea placomus. Samples from five colonies of P. placomus were collected from Baltimore Canyon (379–382 m depth in the Atlantic Ocean off the east coast of the United States of America. DNA was extracted from the coral samples and 16S rRNA gene amplicons were pyrosequenced using V4-V5 primers. Three samples sequenced deeply (>4,000 sequences each and were further analyzed. The dominant microbial phylum was Proteobacteria, but other major phyla included Firmicutes and Planctomycetes. A conserved community of bacterial taxa held in common across the three P. placomus colonies was identified, comprising 68–90% of the total bacterial community depending on the coral individual. The bacterial community of P. placomus does not appear to include the genus Endozoicomonas, which has been found previously to be the dominant bacterial associate in several temperate and tropical gorgonians. Inferred functionality suggests the possibility of nitrogen cycling by the core bacterial community.

  11. Stratification of Diversity and Activity of Methanogenic and Methanotrophic Microorganisms in a Nitrogen-Fertilized Italian Paddy Soil

    Directory of Open Access Journals (Sweden)

    Annika Vaksmaa

    2017-11-01

    Full Text Available Paddy fields are important ecosystems, as rice is the primary food source for about half of the world’s population. Paddy fields are impacted by nitrogen fertilization and are a major anthropogenic source of methane. Microbial diversity and methane metabolism were investigated in the upper 60 cm of a paddy soil by qPCR, 16S rRNA gene amplicon sequencing and anoxic 13C-CH4 turnover with a suite of electron acceptors. The bacterial community consisted mainly of Acidobacteria, Chloroflexi, Proteobacteria, Planctomycetes, and Actinobacteria. Among archaea, Euryarchaeota and Bathyarchaeota dominated over Thaumarchaeota in the upper 30 cm of the soil. Bathyarchaeota constituted up to 45% of the total archaeal reads in the top 5 cm. In the methanogenic community, Methanosaeta were generally more abundant than the versatile Methanosarcina. The measured maximum methane production rate was 444 nmol gdwh-1, and the maximum rates of nitrate-, nitrite-, and iron-dependent anaerobic oxidation of methane (AOM were 57 nmol, 55 nmol, and 56 nmol gdwh-1, respectively, at different depths. qPCR revealed a higher abundance of ‘Candidatus Methanoperedens nitroreducens’ than methanotrophic NC10 phylum bacteria at all depths, except at 60 cm. These results demonstrate that there is substantial potential for AOM in fertilized paddy fields, with ‘Candidatus Methanoperedens nitroreducens’ archaea as a potential important contributor.

  12. Bacterial community composition of South China Sea sediments through pyrosequencing-based analysis of 16S rRNA genes.

    Directory of Open Access Journals (Sweden)

    Daochen Zhu

    Full Text Available BACKGROUND: Subseafloor sediments accumulate large amounts of organic and inorganic materials that contain a highly diverse microbial ecosystem. The aim of this study was to survey the bacterial community of subseafloor sediments from the South China Sea. METHODOLOGY/PRINCIPAL FINDINGS: Pyrosequencing of over 265,000 amplicons of the V3 hypervariable region of the 16S ribosomal RNA gene was performed on 16 sediment samples collected from multiple locations in the northern region of the South China Sea from depths ranging from 35 to 4000 m. A total of 9,726 operational taxonomic units (OTUs; between 695 and 2819 unique OTUs per sample at 97% sequence similarity level were generated. In total, 40 bacterial phyla including 22 formally described phyla and 18 candidate phyla, with Proteobacteria, Firmicutes, Planctomycetes, Actinobacteria and Chloroflexi being most diverse, were identified. The most abundant phylotype, accounting for 42.6% of all sequences, belonged to Gammaproteobacteria, which possessed absolute predominance in the samples analyzed. Among the 18 candidate phyla, 12 were found for the first time in the South China Sea. CONCLUSIONS: This study provided a novel insight into the composition of bacterial communities of the South China Sea subseafloor. Furthermore, abundances and community similarity analysis showed that the compositions of the bacterial communities are very similar at phylum level at different depths from 35-4000 m.

  13. The candidate phylum Poribacteria by single-cell genomics: new insights into phylogeny, cell-compartmentation, eukaryote-like repeat proteins, and other genomic features.

    Directory of Open Access Journals (Sweden)

    Janine Kamke

    Full Text Available The candidate phylum Poribacteria is one of the most dominant and widespread members of the microbial communities residing within marine sponges. Cell compartmentalization had been postulated along with their discovery about a decade ago and their phylogenetic association to the Planctomycetes, Verrucomicrobia, Chlamydiae superphylum was proposed soon thereafter. In the present study we revised these features based on genomic data obtained from six poribacterial single cells. We propose that Poribacteria form a distinct monophyletic phylum contiguous to the PVC superphylum together with other candidate phyla. Our genomic analyses supported the possibility of cell compartmentalization in form of bacterial microcompartments. Further analyses of eukaryote-like protein domains stressed the importance of such proteins with features including tetratricopeptide repeats, leucin rich repeats as well as low density lipoproteins receptor repeats, the latter of which are reported here for the first time from a sponge symbiont. Finally, examining the most abundant protein domain family on poribacterial genomes revealed diverse phyH family proteins, some of which may be related to dissolved organic posphorus uptake.

  14. Biliary Microbiota, Gallstone Disease and Infection with Opisthorchis felineus.

    Directory of Open Access Journals (Sweden)

    Irina V Saltykova

    2016-07-01

    Full Text Available There is increasing interest in the microbiome of the hepatobiliary system. This study investigated the influence of infection with the fish-borne liver fluke, Opisthorchis felineus on the biliary microbiome of residents of the Tomsk region of western Siberia.Samples of bile were provided by 56 study participants, half of who were infected with O. felineus, and all of who were diagnosed with gallstone disease. The microbiota of the bile was investigated using high throughput, Illumina-based sequencing targeting the prokaryotic 16S rRNA gene. About 2,797, discrete phylotypes of prokaryotes were detected. At the level of phylum, bile from participants with opisthorchiasis showed greater numbers of Synergistetes, Spirochaetes, Planctomycetes, TM7 and Verrucomicrobia. Numbers of > 20 phylotypes differed in bile of the O. felineus-infected compared to non-infected participants, including presence of species of the genera Mycoplana, Cellulosimicrobium, Microlunatus and Phycicoccus, and the Archaeans genus, Halogeometricum, and increased numbers of Selenomonas, Bacteroides, Rothia, Leptotrichia, Lactobacillus, Treponema and Klebsiella.Overall, infection with the liver fluke O. felineus modified the biliary microbiome, increasing abundance of bacterial and archaeal phylotypes.

  15. Microbial Community Structure of Deep-sea Hydrothermal Vents on the Ultraslow Spreading Southwest Indian Ridge

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    Jian Ding

    2017-06-01

    Full Text Available Southwest Indian Ridge (SWIR is a typical oceanic ultraslow spreading ridge with intensive hydrothermal activities. The microbial communities in hydrothermal fields including primary producers to support the entire ecosystem by utilizing geochemical energy generated from rock-seawater interactions. Here we have examined the microbial community structures on four hydrothermal vents from SWIR, representing distinct characteristics in terms of temperature, pH and metal compositions, by using Illumina sequencing of the 16S small subunit ribosomal RNA (rRNA genes, to correlate bacterial and archaeal populations with the nature of the vents influenced by ultraslow spreading features. Epsilon-, Gamma-, Alpha-, and Deltaproteobacteria and members of the phylum Bacteroidetes and Planctomycetes, as well as Thaumarchaeota, Woesearchaeota, and Euryarchaeota were dominant in all the samples. Both bacterial and archaeal community structures showed distinguished patterns compared to those in the fast-spreading East Pacific Ridge or the slow-spreading Mid-Atlantic Ridge as previously reported. Furthermore, within SWIR, the microbial communities are highly correlated with the local temperatures. For example, the sulfur-oxidizing bacteria were dominant within bacteria from low-temperature vents, but were not represented as the dominating group recovered from high temperature (over 300°C venting chimneys in SWIR. Meanwhile, Thaumarchaeota, the ammonium oxidizing archaea, only showed high relative abundance of amplicons in the vents with high-temperature in SWIR. These findings provide insights on the microbial community in ultraslow spreading hydrothermal fields, and therefore assist us in the understanding of geochemical cycling therein.

  16. Influence of Wastewater Discharge on the Metabolic Potential of the Microbial Community in River Sediments

    KAUST Repository

    Li, Dong

    2015-09-24

    To reveal the variation of microbial community functions during water filtration process in river sediments, which has been utilized widely in natural water treatment systems, this study investigates the influence of municipal wastewater discharge to streams on the phylotype and metabolic potential of the microbiome in upstream and particularly various depths of downstream river sediments. Cluster analyses based on both microbial phylogenetic and functional data collectively revealed that shallow upstream sediments grouped with those from deeper subsurface downstream regions. These sediment samples were distinct from those found in shallow downstream sediments. Functional genes associated with carbohydrate, xenobiotic, and certain amino acid metabolisms were overrepresented in upstream and deep downstream samples. In contrast, the more immediate contact with wastewater discharge in shallow downstream samples resulted in an increase in the relative abundance of genes associated with nitrogen, sulfur, purine and pyrimidine metabolisms, as well as restriction–modification systems. More diverse bacterial phyla were associated with upstream and deep downstream sediments, mainly including Actinobacteria, Planctomycetes, and Firmicutes. In contrast, in shallow downstream sediments, genera affiliated with Betaproteobacteria and Gammaproteobacteria were enriched with putative functions that included ammonia and sulfur oxidation, polyphosphate accumulation, and methylotrophic bacteria. Collectively, these results highlight the enhanced capabilities of microbial communities residing in deeper stream sediments for the transformation of water contaminants and thus provide a foundation for better design of natural water treatment systems to further improve the removal of contaminants. © 2015, Springer Science+Business Media New York.

  17. Bacterial Community Diversity of Oil-Contaminated Soils Assessed by High Throughput Sequencing of 16S rRNA Genes

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    Mu Peng

    2015-09-01

    Full Text Available Soil bacteria play a major role in ecological and biodegradable function processes in oil-contaminated soils. Here, we assessed the bacterial diversity and changes therein in oil-contaminated soils exposed to different periods of oil pollution using 454 pyrosequencing of 16S rRNA genes. No less than 24,953 valid reads and 6246 operational taxonomic units (OTUs were obtained from all five studied samples. OTU richness was relatively higher in contaminated soils than clean samples. Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Planctomycetes and Proteobacteria were the dominant phyla among all the soil samples. The heatmap plot depicted the relative percentage of each bacterial family within each sample and clustered five samples into two groups. For the samples, bacteria in the soils varied at different periods of oil exposure. The oil pollution exerted strong selective pressure to propagate many potentially petroleum degrading bacteria. Redundancy analysis (RDA indicated that organic matter was the highest determinant factor for explaining the variations in community compositions. This suggests that compared to clean soils, oil-polluted soils support more diverse bacterial communities and soil bacterial community shifts were mainly controlled by organic matter and exposure time. These results provide some useful information for bioremediation of petroleum contaminated soil in the future.

  18. Bacterial Community Diversity of Oil-Contaminated Soils Assessed by High Throughput Sequencing of 16S rRNA Genes.

    Science.gov (United States)

    Peng, Mu; Zi, Xiaoxue; Wang, Qiuyu

    2015-09-24

    Soil bacteria play a major role in ecological and biodegradable function processes in oil-contaminated soils. Here, we assessed the bacterial diversity and changes therein in oil-contaminated soils exposed to different periods of oil pollution using 454 pyrosequencing of 16S rRNA genes. No less than 24,953 valid reads and 6246 operational taxonomic units (OTUs) were obtained from all five studied samples. OTU richness was relatively higher in contaminated soils than clean samples. Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Planctomycetes and Proteobacteria were the dominant phyla among all the soil samples. The heatmap plot depicted the relative percentage of each bacterial family within each sample and clustered five samples into two groups. For the samples, bacteria in the soils varied at different periods of oil exposure. The oil pollution exerted strong selective pressure to propagate many potentially petroleum degrading bacteria. Redundancy analysis (RDA) indicated that organic matter was the highest determinant factor for explaining the variations in community compositions. This suggests that compared to clean soils, oil-polluted soils support more diverse bacterial communities and soil bacterial community shifts were mainly controlled by organic matter and exposure time. These results provide some useful information for bioremediation of petroleum contaminated soil in the future.

  19. Start-Up and Aeration Strategies for a Completely Autotrophic Nitrogen Removal Process in an SBR

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    Xiaoling Zhang

    2017-01-01

    Full Text Available The start-up and performance of the completely autotrophic nitrogen removal via nitrite (CANON process were examined in a sequencing batch reactor (SBR with intermittent aeration. Initially, partial nitrification was established, and then the DO concentration was lowered further, surplus water in the SBR with high nitrite was replaced with tap water, and continuous aeration mode was turned into intermittent aeration mode, while the removal of total nitrogen was still weak. However, the total nitrogen (TN removal efficiency and nitrogen removal loading reached 83.07% and 0.422 kgN/(m3·d, respectively, 14 days after inoculating 0.15 g of CANON biofilm biomass into the SBR. The aggregates formed in SBR were the mixture of activated sludge and granular sludge; the volume ratio of floc and granular sludge was 7 : 3. DNA analysis showed that Planctomycetes-like anammox bacteria and Nitrosomonas-like aerobic ammonium oxidization bacteria were dominant bacteria in the reactor. The influence of aeration strategies on CANON process was investigated using batch tests. The result showed that the strategy of alternating aeration (1 h and nonaeration (1 h was optimum, which can obtain almost the same TN removal efficiency as continuous aeration while reducing the energy consumption, inhibiting the activity of NOB, and enhancing the activity of AAOB.

  20. The Paradigms They Are a-Changin': past, present and future of PVC bacteria research.

    Science.gov (United States)

    Rivas-Marín, Elena; Devos, Damien P

    2018-06-01

    These are exciting times for PVC researchers! The PVC superphylum is composed of the bacterial phyla Planctomycetes, Verrucomicrobia, Chlamydiae (those three founders giving it its name), Lentisphaerae and Kirimatiellaeota as well as some uncultured candidate phyla, such as the Candidatus Omnitrophica (previously known as OP3). Despite early debates, most of the disagreements that surround this group of bacteria have been recently resolved. In this article, we review the history of the study of PVC bacteria, with a particular focus on the misinterpretations that emerged early in the field and their resolution. We begin with a historical perspective that describes the relevant facts of PVC research from the early times when they were not yet termed PVC. Those were controversial times and we refer to them as the "discovery age" of the field. We continue by describing new discoveries due to novel techniques and data that combined with the reinterpretations of old ones have contributed to solve most of the discordances and we refer to these times as the "illumination age" of PVC research. We follow by arguing that we are just entering the "golden age" of PVC research and that the future of this growing community is looking bright. We finish by suggesting a few of the directions that PVC researches might take in the future.

  1. Ribosome reinitiation at leader peptides increases translation of bacterial proteins.

    Science.gov (United States)

    Korolev, Semen A; Zverkov, Oleg A; Seliverstov, Alexandr V; Lyubetsky, Vassily A

    2016-04-16

    Short leader genes usually do not encode stable proteins, although their importance in expression control of bacterial genomes is widely accepted. Such genes are often involved in the control of attenuation regulation. However, the abundance of leader genes suggests that their role in bacteria is not limited to regulation. Specifically, we hypothesize that leader genes increase the expression of protein-coding (structural) genes via ribosome reinitiation at the leader peptide in the case of a short distance between the stop codon of the leader gene and the start codon of the structural gene. For instance, in Actinobacteria, the frequency of leader genes at a distance of 10-11 bp is about 70 % higher than the mean frequency within the 1 to 65 bp range; and it gradually decreases as the range grows longer. A pronounced peak of this frequency-distance relationship is also observed in Proteobacteria, Bacteroidetes, Spirochaetales, Acidobacteria, the Deinococcus-Thermus group, and Planctomycetes. In contrast, this peak falls to the distance of 15-16 bp and is not very pronounced in Firmicutes; and no such peak is observed in cyanobacteria and tenericutes. Generally, this peak is typical for many bacteria. Some leader genes located close to a structural gene probably play a regulatory role as well.

  2. Characterization of bovine ruminal epithelial bacterial communities using 16S rRNA sequencing, PCR-DGGE, and qRT-PCR analysis.

    Science.gov (United States)

    Li, Meiju; Zhou, Mi; Adamowicz, Elizabeth; Basarab, John A; Guan, Le Luo

    2012-02-24

    Currently, knowledge regarding the ecology and function of bacteria attached to the epithelial tissue of the rumen wall is limited. In this study, the diversity of the bacterial community attached to the rumen epithelial tissue was compared to the rumen content bacterial community using 16S rRNA gene sequencing, PCR-DGGE, and qRT-PCR analysis. Sequence analysis of 2785 randomly selected clones from six 16S rDNA (∼1.4kb) libraries showed that the community structures of three rumen content libraries clustered together and were separated from the rumen tissue libraries. The diversity index of each library revealed that ruminal content bacterial communities (4.12/4.42/4.88) were higher than ruminal tissue communities (2.90/2.73/3.23), based on 97% similarity. The phylum Firmicutes was predominant in the ruminal tissue communities, while the phylum Bacteroidetes was predominant in the ruminal content communities. The phyla Fibrobacteres, Planctomycetes, and Verrucomicrobia were only detected in the ruminal content communities. PCR-DGGE analysis of the bacterial profiles of the rumen content and ruminal epithelial tissue samples from 22 steers further confirmed that there is a distinct bacterial community that inhibits the rumen epithelium. The distinctive epimural bacterial communities suggest that Firmicutes, together with other epithelial-specific species, may have additional functions other than food digestion. Copyright © 2011 Elsevier B.V. All rights reserved.

  3. Substrate type and free ammonia determine bacterial community structure in full-scale mesophilic anaerobic digesters treating cattle or swine manure

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    Jiabao eLi

    2015-11-01

    Full Text Available The microbial-mediated anaerobic digestion (AD process represents an efficient biological process for the treatment of organic waste along with biogas harvest. Currently, the key factors structuring bacterial communities and the potential core and unique bacterial populations in manure anaerobic digesters are not completely elucidated yet. In this study, we collected sludge samples from 20 full-scale anaerobic digesters treating cattle or swine manure, and investigated the variations of bacterial community compositions using high-throughput 16S rRNA amplicon sequencing. Clustering and correlation analysis suggested that substrate type and free ammonia (FA play key roles in determining the bacterial community structure. The COD: NH4+-N (C:N ratio of substrate and FA were the most important available operational parameters correlating to the bacterial communities in cattle and swine manure digesters, respectively. The bacterial populations in all of the digesters were dominated by phylum Firmicutes, followed by Bacteroidetes, Proteobacteria and Chloroflexi. Increased FA content selected Firmicutes, suggesting that they probably play more important roles under high FA content. Syntrophic metabolism by Proteobacteria, Chloroflexi, Synergistetes and Planctomycetes are likely inhibited when FA content is high. Despite the different manure substrates, operational conditions and geographical locations of digesters, core bacterial communities were identified. The core communities were best characterized by phylum Firmicutes, wherein Clostridium predominated overwhelmingly. Substrate-unique and abundant communities may reflect the properties of manure substrate and operational conditions. These findings extend our current understanding of the bacterial assembly in full-scale manure anaerobic digesters.

  4. Substrate Type and Free Ammonia Determine Bacterial Community Structure in Full-Scale Mesophilic Anaerobic Digesters Treating Cattle or Swine Manure.

    Science.gov (United States)

    Li, Jiabao; Rui, Junpeng; Yao, Minjie; Zhang, Shiheng; Yan, Xuefeng; Wang, Yuanpeng; Yan, Zhiying; Li, Xiangzhen

    2015-01-01

    The microbial-mediated anaerobic digestion (AD) process represents an efficient biological process for the treatment of organic waste along with biogas harvest. Currently, the key factors structuring bacterial communities and the potential core and unique bacterial populations in manure anaerobic digesters are not completely elucidated yet. In this study, we collected sludge samples from 20 full-scale anaerobic digesters treating cattle or swine manure, and investigated the variations of bacterial community compositions using high-throughput 16S rRNA amplicon sequencing. Clustering and correlation analysis suggested that substrate type and free ammonia (FA) play key roles in determining the bacterial community structure. The COD: [Formula: see text] (C:N) ratio of substrate and FA were the most important available operational parameters correlating to the bacterial communities in cattle and swine manure digesters, respectively. The bacterial populations in all of the digesters were dominated by phylum Firmicutes, followed by Bacteroidetes, Proteobacteria and Chloroflexi. Increased FA content selected Firmicutes, suggesting that they probably play more important roles under high FA content. Syntrophic metabolism by Proteobacteria, Chloroflexi, Synergistetes and Planctomycetes are likely inhibited when FA content is high. Despite the different manure substrates, operational conditions and geographical locations of digesters, core bacterial communities were identified. The core communities were best characterized by phylum Firmicutes, wherein Clostridium predominated overwhelmingly. Substrate-unique and abundant communities may reflect the properties of manure substrate and operational conditions. These findings extend our current understanding of the bacterial assembly in full-scale manure anaerobic digesters.

  5. Phylogenetic Study of the Evolution of PEP-Carboxykinase

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    Sanjukta Aich

    2007-01-01

    Full Text Available Phosphoenolpyruvate carboxykinase (PCK is the key enzyme to initiate the gluconeogenic pathway in vertebrates, yeast, plants and most bacteria. Nucleotide specificity divided all PCKs into two groups. All the eukaryotic mammalian and most archaeal PCKs are GTP-specifi c. Bacterial and fungal PCKs can be ATP-or GTP-specific but all plant PCKs are ATPspecific. Amino acid sequence alignment of PCK enzymes shows that the nucleotide binding sites are somewhat conserved within each class with few exceptions that do not have any clear ATP- or GTP-specific binding motif. Although the active site residues are mostly conserved in all PCKs, not much significant sequence homology persists between ATP- and GTPdependent PCK enzymes. There is only one planctomycetes PCK enzyme (from Cadidatus Kuenenia stuttgartiensis that shows sequence homology with both ATP-and GTP-dependent PCKs. Phylogenetic studies have been performed to understand the evolutionary relationship of various PCKs from different sources. Based on this study a flowchart of the evolution of PCK has been proposed.

  6. Stromatolites on the rise in peat-bound karstic wetlands.

    Science.gov (United States)

    Proemse, Bernadette C; Eberhard, Rolan S; Sharples, Chris; Bowman, John P; Richards, Karen; Comfort, Michael; Barmuta, Leon A

    2017-11-13

    Stromatolites are the oldest evidence for life on Earth, but modern living examples are rare and predominantly occur in shallow marine or (hyper-) saline lacustrine environments, subject to exotic physico-chemical conditions. Here we report the discovery of living freshwater stromatolites in cool-temperate karstic wetlands in the Giblin River catchment of the UNESCO-listed Tasmanian Wilderness World Heritage Area, Australia. These stromatolites colonize the slopes of karstic spring mounds which create mildly alkaline (pH of 7.0-7.9) enclaves within an otherwise uniformly acidic organosol terrain. The freshwater emerging from the springs is Ca-HCO 3 dominated and water temperatures show no evidence of geothermal heating. Using 16 S rRNA gene clone library analysis we revealed that the bacterial community is dominated by Cyanobacteria, Alphaproteobacteria and an unusually high proportion of Chloroflexi, followed by Armatimonadetes and Planctomycetes, and is therefore unique compared to other living examples. Macroinvertebrates are sparse and snails in particular are disadvantaged by the development of debilitating accumulations of carbonate on their shells, corroborating evidence that stromatolites flourish under conditions where predation by metazoans is suppressed. Our findings constitute a novel habitat for stromatolites because cool-temperate freshwater wetlands are not a conventional stromatolite niche, suggesting that stromatolites may be more common than previously thought.

  7. Microbial community characterization of ozone-biofiltration systems in drinking water and potable reuse applications.

    Science.gov (United States)

    Gerrity, Daniel; Arnold, Mayara; Dickenson, Eric; Moser, Duane; Sackett, Joshua D; Wert, Eric C

    2018-05-15

    Microbial community structure in the ozone-biofiltration systems of two drinking water and two wastewater treatment facilities was characterized using 16S rRNA gene sequencing. Collectively, these datasets enabled comparisons by facility, water type (drinking water, wastewater), pre-oxidation (ozonation, chlorination), media type (anthracite, activated carbon), media depth, and backwash dynamics. Proteobacteria was the most abundant phylum in drinking water filters, whereas Bacteroidetes, Chloroflexi, Firmicutes, and Planctomycetes were differentially abundant in wastewater filters. A positive correlation was observed between media depth and relative abundance of Cyanobacteria in drinking water filters, but there was only a slight increase in one alpha diversity metric with depth in the wastewater filters. Media type had a significant effect on beta but not alpha diversity in drinking water and wastewater filters. Pre-ozonation caused a significant decrease in alpha diversity in the wastewater filters, but the effect on beta diversity was not statistically significant. An evaluation of backwash dynamics resulted in two notable observations: (1) endosymbionts such as Neochlamydia and Legionella increased in relative abundance following backwashing and (2) nitrogen-fixing Bradyrhizobium dominated the microbial community in wastewater filters operated with infrequent backwashing. Bradyrhizobium is known to generate extracellular polymeric substances (EPS), which may adversely impact biofilter performance and effluent water quality. These findings have important implications for public health and the operation and resiliency of biofiltration systems. Copyright © 2018 Elsevier Ltd. All rights reserved.

  8. Enrichment of anammox bacteria fro marine environment for the construction of a bioremediation reactor

    Energy Technology Data Exchange (ETDEWEB)

    Nakajima, Jun; Sakka, Makiko; Kimura, Tetsuya; Sakka, Kazuo [Mie Univ., Tsu (Japan). Graduate School of Bioresources; Furukawa, Kenji [Kumamoto Univ. (Japan). Dept. of Civil Engineering and Architecture

    2008-01-15

    In the global ocean nitrogen cycle, the anaerobic ammonium-oxidizing (anammox) process is recognized as important. In this study, we established an enrichment culture of marine anammox bacteria (MAB) in a column-type reactor. The reactor, which included a porous polyester non-woven fabric that had been placed at the sea floor in advance for enrichment, was continuously fed with NH{sub 4}Cl and NaNO{sub 2} for more than 1 year. Anammox activity in the MAB reactor was confirmed by {sup 15}N tracer analysis using {sup 15}NH{sub 4}Cl and Na{sup 14}NO{sub 2}. We identified two 16S rRNA genes in the amplified DNA fragments derived from MAB, which were highly homologous with those from Candidatus ''Scalindua wagneri'' and an uncultured planctomycete clone. Fluorescence in situ hybridization analysis using an anammox-specific probe also confirmed that MAB predominated in the reactor. To our knowledge, this is the first report on the establishment of an enrichment culture of anammox bacteria from the marine environment using a continuous culture system. (orig.)

  9. Electricity generation using chocolate industry wastewater and its treatment in activated sludge based microbial fuel cell and analysis of developed microbial community in the anode chamber.

    Science.gov (United States)

    Patil, Sunil A; Surakasi, Venkata Prasad; Koul, Sandeep; Ijmulwar, Shrikant; Vivek, Amar; Shouche, Y S; Kapadnis, B P

    2009-11-01

    Feasibility of using chocolate industry wastewater as a substrate for electricity generation using activated sludge as a source of microorganisms was investigated in two-chambered microbial fuel cell. The maximum current generated with membrane and salt bridge MFCs was 3.02 and 2.3 A/m(2), respectively, at 100 ohms external resistance, whereas the maximum current generated in glucose powered MFC was 3.1 A/m(2). The use of chocolate industry wastewater in cathode chamber was promising with 4.1 mA current output. Significant reduction in COD, BOD, total solids and total dissolved solids of wastewater by 75%, 65%, 68%, 50%, respectively, indicated effective wastewater treatment in batch experiments. The 16S rDNA analysis of anode biofilm and suspended cells revealed predominance of beta-Proteobacteria clones with 50.6% followed by unclassified bacteria (9.9%), alpha-Proteobacteria (9.1%), other Proteobacteria (9%), Planctomycetes (5.8%), Firmicutes (4.9%), Nitrospora (3.3%), Spirochaetes (3.3%), Bacteroides (2.4%) and gamma-Proteobacteria (0.8%). Diverse bacterial groups represented as members of the anode chamber community.

  10. Pyrosequencing Reveals the Microbial Communities in the Red Sea Sponge Carteriospongia foliascens and Their Impressive Shifts in Abnormal Tissues

    KAUST Repository

    Gao, Zhaoming

    2014-04-24

    Abnormality and disease in sponges have been widely reported, yet how sponge-associated microbes respond correspondingly remains inconclusive. Here, individuals of the sponge Carteriospongia foliascens under abnormal status were collected from the Rabigh Bay along the Red Sea coast. Microbial communities in both healthy and abnormal sponge tissues and adjacent seawater were compared to check the influences of these abnormalities on sponge-associated microbes. In healthy tissues, we revealed low microbial diversity with less than 100 operational taxonomic units (OTUs) per sample. Cyanobacteria, affiliated mainly with the sponge-specific species “Candidatus Synechococcus spongiarum,” were the dominant bacteria, followed by Bacteroidetes and Proteobacteria. Intraspecies dynamics of microbial communities in healthy tissues were observed among sponge individuals, and potential anoxygenic phototrophic bacteria were found. In comparison with healthy tissues and the adjacent seawater, abnormal tissues showed dramatic increase in microbial diversity and decrease in the abundance of sponge-specific microbial clusters. The dominated cyanobacterial species Candidatus Synechococcus spongiarum decreased and shifted to unspecific cyanobacterial clades. OTUs that showed high similarity to sequences derived from diseased corals, such as Leptolyngbya sp., were found to be abundant in abnormal tissues. Heterotrophic Planctomycetes were also specifically enriched in abnormal tissues. Overall, we revealed the microbial communities of the cyanobacteria-rich sponge, C. foliascens, and their impressive shifts under abnormality.

  11. Functional and genomic analyses of alpha-solenoid proteins.

    Science.gov (United States)

    Fournier, David; Palidwor, Gareth A; Shcherbinin, Sergey; Szengel, Angelika; Schaefer, Martin H; Perez-Iratxeta, Carol; Andrade-Navarro, Miguel A

    2013-01-01

    Alpha-solenoids are flexible protein structural domains formed by ensembles of alpha-helical repeats (Armadillo and HEAT repeats among others). While homology can be used to detect many of these repeats, some alpha-solenoids have very little sequence homology to proteins of known structure and we expect that many remain undetected. We previously developed a method for detection of alpha-helical repeats based on a neural network trained on a dataset of protein structures. Here we improved the detection algorithm and updated the training dataset using recently solved structures of alpha-solenoids. Unexpectedly, we identified occurrences of alpha-solenoids in solved protein structures that escaped attention, for example within the core of the catalytic subunit of PI3KC. Our results expand the current set of known alpha-solenoids. Application of our tool to the protein universe allowed us to detect their significant enrichment in proteins interacting with many proteins, confirming that alpha-solenoids are generally involved in protein-protein interactions. We then studied the taxonomic distribution of alpha-solenoids to discuss an evolutionary scenario for the emergence of this type of domain, speculating that alpha-solenoids have emerged in multiple taxa in independent events by convergent evolution. We observe a higher rate of alpha-solenoids in eukaryotic genomes and in some prokaryotic families, such as Cyanobacteria and Planctomycetes, which could be associated to increased cellular complexity. The method is available at http://cbdm.mdc-berlin.de/~ard2/.

  12. Characterizing bacterial communities in tilapia pond surface sediment and their responses to pond differences and temporal variations.

    Science.gov (United States)

    Fan, Limin; Barry, Kamira; Hu, Gengdong; Meng, Shunlong; Song, Chao; Qiu, Liping; Zheng, Yao; Wu, Wei; Qu, Jianhong; Chen, Jiazhang; Xu, Pao

    2017-01-01

    Bacterial community compositions in the surface sediment of tilapia ponds and their responses to pond characteristics or seasonal variations were investigated. For that, three ponds with different stocking densities were selected to collect the samples. And the method of Illumina high-throughput sequencing was used to amplify the bacterial 16S rRNA genes. A total of 662, 876 valid reads and 5649 operational taxonomic units were obtained. Further analysis showed that the dominant phyla in all three ponds were Proteobacteria, Bacteroidetes, Chloroflexi, and Acidobacteria. The phyla Planctomycetes, Firmicutes, Chlorobi, and Spirochaetae were also relatively abundant. Among the eight phyla, the abundances of only Proteobacteria, Bacteroidetes, Firmicutes, and Spirochaetae were affected by seasonal variations, while seven of these (with the exception of Acidobacteria) were affected by pond differences. A comprehensive analysis of the richness and diversity of the bacterial 16S rRNA gene, and of the similarity in bacterial community composition in sediment also showed that the communities in tilapia pond sediment were shaped more by pond differences than by seasonal variations. Linear discriminant analysis further indicated that the influences of pond characteristics on sediment bacterial communities might be related to feed coefficients and stocking densities of genetically improved farmed tilapia (GIFT).

  13. Bacterial Diversity Associated with Cinachyra cavernosa and Haliclona pigmentifera, Cohabiting Sponges in the Coral Reef Ecosystem of Gulf of Mannar, Southeast Coast of India.

    Directory of Open Access Journals (Sweden)

    C Jasmin

    Full Text Available Sponges are abundant, diverse and functionally important organisms of coral reef ecosystems. Sponge-associated microorganisms have been receiving greater attention because of their significant contribution to sponge biomass, biogeochemical cycles and biotechnological potentials. However, our understanding of the sponge microbiome is limited to a few species of sponges from restricted geographical locations. Here, we report for the first time the bacterial diversity of two cohabiting sponges, viz. Cinachyra cavernosa and Haliclona pigmentifera, as well as that in the ambient water from the coral reef ecosystems of the Gulf of Mannar, located along the southeast coast of India. Two hundred and fifty two clones in the 16S rRNA gene library of these sponges were grouped into eight distinct phyla, of which four belonged to the core group that are associated only with sponges. Phylogenetic analysis of the core bacteria showed close affinity to other sponge-associated bacteria from different geographical locations. γ-Proteobacteria, Chloroflexi, Planctomycetes and Deferribacter were the core groups in C. cavernosa while β and δ-Proteobacteria performed this role in H. pigmentifera. We observed greater OTU diversity for C. cavernosa (Hǀ 2.07 compared to H. pigmentifera (Hǀ 1.97. UniFrac analysis confirmed the difference in bacterial diversity of the two sponge species and also between the sponges and the reef water (p<0.001. The results of our study restate the existence of a host driven force in shaping the sponge microbiome.

  14. Standard filtration practices may significantly distort planktonic microbial diversity estimates

    Directory of Open Access Journals (Sweden)

    Cory Cruz Padilla

    2015-06-01

    Full Text Available Fractionation of biomass by filtration is a standard method for sampling planktonic microbes. It is unclear how the taxonomic composition of filtered biomass changes depending on sample volume. Using seawater from a marine oxygen minimum zone, we quantified the 16S rRNA gene composition of biomass on a prefilter (1.6 μm pore-size and a downstream 0.2 μm filter over sample volumes from 0.05 to 5 L. Significant community shifts occurred in both filter fractions, and were most dramatic in the prefilter community. Sequences matching Vibrionales decreased from ~40-60% of prefilter datasets at low volumes (0.05-0.5 L to less than 5% at higher volumes, while groups such at the Chromatiales and Thiohalorhabdales followed opposite trends, increasing from minor representation to become the dominant taxa at higher volumes. Groups often associated with marine particles, including members of the Deltaproteobacteria, Planctomycetes and Bacteroidetes, were among those showing the greatest increase with volume (4 to 27-fold. Taxon richness (97% similarity clusters also varied significantly with volume, and in opposing directions depending on filter fraction, highlighting potential biases in community complexity estimates. These data raise concerns for studies using filter fractionation for quantitative comparisons of aquatic microbial diversity, for example between free-living and particle-associated communities.

  15. Abundance and composition of indigenous bacterial communities in a multi-step biofiltration-based drinking water treatment plant.

    Science.gov (United States)

    Lautenschlager, Karin; Hwang, Chiachi; Ling, Fangqiong; Liu, Wen-Tso; Boon, Nico; Köster, Oliver; Egli, Thomas; Hammes, Frederik

    2014-10-01

    Indigenous bacterial communities are essential for biofiltration processes in drinking water treatment systems. In this study, we examined the microbial community composition and abundance of three different biofilter types (rapid sand, granular activated carbon, and slow sand filters) and their respective effluents in a full-scale, multi-step treatment plant (Zürich, CH). Detailed analysis of organic carbon degradation underpinned biodegradation as the primary function of the biofilter biomass. The biomass was present in concentrations ranging between 2-5 × 10(15) cells/m(3) in all filters but was phylogenetically, enzymatically and metabolically diverse. Based on 16S rRNA gene-based 454 pyrosequencing analysis for microbial community composition, similar microbial taxa (predominantly Proteobacteria, Planctomycetes, Acidobacteria, Bacteriodetes, Nitrospira and Chloroflexi) were present in all biofilters and in their respective effluents, but the ratio of microbial taxa was different in each filter type. This change was also reflected in the cluster analysis, which revealed a change of 50-60% in microbial community composition between the different filter types. This study documents the direct influence of the filter biomass on the microbial community composition of the final drinking water, particularly when the water is distributed without post-disinfection. The results provide new insights on the complexity of indigenous bacteria colonizing drinking water systems, especially in different biofilters of a multi-step treatment plant. Copyright © 2014 Elsevier Ltd. All rights reserved.

  16. The microbial community in a high-temperature enhanced biological phosphorus removal (EBPR process

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    Ying Hui Ong

    2016-01-01

    Full Text Available An enhanced biological phosphorus removal (EBPR process operated at a relatively high temperature, 28 °C, removed 85% carbon and 99% phosphorus from wastewater over a period of two years. This study investigated its microbial community through fluorescent in situ hybridization (FISH and clone library generation. Through FISH, considerably more Candidatus “Accumulibacter phosphatis” (Accumulibacter-polyphosphate accumulating organisms (PAOs than Candidatus ‘Competibacter phosphatis’ (Competibacter-glycogen accumulating organisms were detected in the reactor, at 36 and 7% of total bacterial population, respectively. A low ratio of Glycogen/Volatile Fatty Acid of 0.69 further indicated the dominance of PAOs in the reactor. From clone library generated, 26 operational taxonomy units were retrieved from the sludge and a diverse population was shown, comprising Proteobacteria (69.6%, Actinobacteria (13.7%, Bacteroidetes (9.8%, Firmicutes (2.94%, Planctomycetes (1.96%, and Acidobacteria (1.47%. Accumulibacter are the only recognized PAOs revealed by the clone library. Both the clone library and FISH results strongly suggest that Accumulibacter are the major PAOs responsible for the phosphorus removal in this long-term EBPR at relatively high temperature.

  17. Patterns of Bacterial and Archaeal Gene Expression through the Lower Amazon River

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    Satinsky, Brandon M.; Smith, Christa B.; Sharma, Shalabh; Ward, Nicholas D.; Krusche, Alex V.; Richey, Jeffrey E.; Yager, Patricia L.; Crump, Byron C.; Moran, Mary Ann

    2017-08-08

    Analysis of metatranscriptomic and metagenomic datasets from the lower reaches of the Amazon River between Obidos and the river mouth revealed microbial transcript and gene pools dominated by Actinobacteria, Thaumarchaeota, Bacteroidetes, Acidobacteria, Betaproteobacteria, and Planctomycetes. Three mainstem stations spanning a 625 km reach had similar gene expression patterns (transcripts gene copy-1) across a diverse suite of element cycling genes, but two tributary-influenced stations at the mouth of the Tapajos River and near the Tocantins River at Belem had distinct transcriptome composition and expression ratios, particularly for genes encoding light-related energy capture (higher) and iron acquisition and ammonia oxidation (lower). Environmental parameters that were useful predictors of gene expression ratios included concentrations of lignin phenols, suspended sediments, nitrate, phosphate, and particulate organic carbon and nitrogen. Similar to the gene expression data, these chemical properties reflected highly homogeneous mainstem stations punctuated by distinct tributary- influenced stations at Tapajos and Belem. Although heterotrophic processes were expected to dominate in the lower Amazon, transcripts from photosynthetic bacteria were abundant in tributary-influenced regions, and transcripts from Thaumarcheota taxa genetically capable of chemosynthetic ammonia oxidation accounted for up to 21% of the transcriptome at others. Based on regressions of transcript numbers against gene numbers, expression ratios of Thaumarchaeota populations were largely unchanged within the mainstem, suggesting a relatively minor role for gene regulation. These quantitative gene and transcript inventories detail a diverse array of energy acquisition strategies and metabolic capabilities for bacteria and archaea populations of the world’s largest river system.

  18. High-throughput sequencing reveals microbial communities in drinking water treatment sludge from six geographically distributed plants, including potentially toxic cyanobacteria and pathogens.

    Science.gov (United States)

    Xu, Hangzhou; Pei, Haiyan; Jin, Yan; Ma, Chunxia; Wang, Yuting; Sun, Jiongming; Li, Hongmin

    2018-04-10

    The microbial community structures of drinking water treatment sludge (DWTS) generated for raw water (RW) from different locations and with different source types - including river water, lake water and reservoir water -were investigated using high-throughput sequencing. Because the unit operations in the six DWTPs were similar, community composition in fresh sludge may be determined by microbial community in the corresponding RW. Although Proteobacteria, Cyanobacteria, Bacteroidetes, Firmicutes, Verrucomicrobia, and Planctomycetes were the dominant phyla among the six DWTS samples, no single phylum exhibited similar abundance across all the samples, owing to differences in total phosphorus, chemical oxygen demand, Al, Fe, and chloride in RW. Three genera of potentially toxic cyanobacteria (Planktothrix, Microcystis and Cylindrospermopsis), and four potential pathogens (Escherichia coli, Bacteroides ovatus, Prevotella copri and Rickettsia) were found in sludge samples. Because proliferation of potentially toxic cyanobacteria and Rickettsia in RW was mainly affected by nutrients, while growth of Escherichia coli, Bacteroides ovatus and Prevotella copri in RW may be influenced by Fe, control of nutrients and Fe in RW is essential to decrease toxic cyanobacteria and pathogens in DWTS. Copyright © 2018 Elsevier B.V. All rights reserved.

  19. Simultaneous enrichment of denitrifying anaerobic methane-oxidizing microorganisms and anammox bacteria in a hollow-fiber membrane biofilm reactor.

    Science.gov (United States)

    Ding, Zhao-Wei; Lu, Yong-Ze; Fu, Liang; Ding, Jing; Zeng, Raymond J

    2017-01-01

    In this study, the coculture system of denitrifying anaerobic methane oxidation (DAMO) microbes and anaerobic ammonium oxidation (anammox) bacteria was successfully enriched in a hollow-fiber membrane biofilm reactor (HfMBR) using freshwater sediment as the inoculum. The maximal removal rates of nitrate and ammonium were 78 mg N/L/day (131 mg N/m 2 /day) and 26 mg N/L/day (43 mg N/m 2 /day), respectively. Due to the high rate of methane mass transfer in HfMBR, the activity of DAMO archaea continued to increase during the enrichment period, indicating that HfMBR could be a powerful tool to enrich DAMO microorganisms. Effects of partial methane pressure, temperature, and pH on the cocultures were obvious. However, the microbial activity in HfMBR could be recovered quickly after the shock change of environmental factors. Furthermore, the result also found that DAMO bacteria likely had a stronger competitive advantage than anammox bacteria under the operating conditions in this study. High-throughput sequencing 16S rRNA genes illustrated that the dominant microbes were NC10, Euryarchaeota, Proteobacteria, Planctomycetes, and Chlorobi with relative abundance of 38.8, 26.2, 13.78, 6.2, and 3.6 %, respectively.

  20. The influence of Rickettsiologists on post-modern microbiology

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    Kalliopi eGeorgiades

    2011-10-01

    Full Text Available Many of the definitions in microbiology are factually false. We have revised the great denominations of microbiology and attempted to free microorganisms from the theories of the 20th century. The presence of compartmentation and a nucleoid in Planctomycetes clearly calls into question the accuracy of the definitions of eukaryotes and prokaryotes. Archaea are viewed as prokaryotes resembling bacteria. However, the name archaea, suggesting an archaic origin of lifestyle, is inconsistent with the actual history of this family. Viruses are defined as small, filterable infectious agents, but giant viruses challenge the size criteria used for the definition of a virus. Pathogenicity does not require the acquisition of virulence factors (except for toxins, and in many cases, gene loss seems to be implicated in the emergence of virulence. Species classification based on 16S rRNA is useless for taxonomic purposes of human pathogens, as a 2% divergence would classify all Rickettsiae within the same species and would not identify bacteria specialized for the infection of mammals. The use of metagenomics helps us to understand evolution and physiology by elucidating the structure, function and interactions of microbial communities, but it neglects the minority populations. Finally, the tree of life (TOL theory, as established by Darwin, no longer matches our current genomic knowledge because genomics has revealed the occurrence of de novo-created genes and the mosaic structure of genomes.

  1. Comparison of the rhizosphere bacterial communities of Zigongdongdou soybean and a high-methionine transgenic line of this cultivar.

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    Jingang Liang

    Full Text Available Previous studies have shown that methionine from root exudates affects the rhizosphere bacterial population involved in soil nitrogen fixation. A transgenic line of Zigongdongdou soybean cultivar (ZD91 that expresses Arabidopsis cystathionine γ-synthase resulting in an increased methionine production was examined for its influence to the rhizosphere bacterial population. Using 16S rRNA gene-based pyrosequencing analysis of the V4 region and DNA extracted from bacterial consortia collected from the rhizosphere of soybean plants grown in an agricultural field at the pod-setting stage, we characterized the populational structure of the bacterial community involved. In total, 87,267 sequences (approximately 10,908 per sample were analyzed. We found that Acidobacteria, Proteobacteria, Bacteroidetes, Actinobacteria, Chloroflexi, Planctomycetes, Gemmatimonadetes, Firmicutes, and Verrucomicrobia constitute the dominant taxonomic groups in either the ZD91 transgenic line or parental cultivar ZD, and that there was no statistically significant difference in the rhizosphere bacterial community structure between the two cultivars.

  2. Characterization of bacterial community structure in a hydrocarbon-contaminated tropical African soil.

    Science.gov (United States)

    Salam, Lateef B; Ilori, Mathew O; Amund, Olukayode O; LiiMien, Yee; Nojiri, Hideaki

    2018-04-01

    The bacterial community structure in a hydrocarbon-contaminated Mechanical Engineering Workshop (MWO) soil was deciphered using 16S rRNA gene clone library analysis. Four hundred and thirty-seven clones cutting across 13 bacterial phyla were recovered from the soil. The representative bacterial phyla identified from MWO soil are Proteobacteria, Bacteroidetes, Chloroflexi, Acidobacteria, Firmicutes, Actinobacteria, Verrucomicrobia, Planctomycetes, Ignavibacteriae, Spirochaetes, Chlamydiae, Candidatus Saccharibacteria and Parcubacteria. Proteobacteria is preponderant in the contaminated soil (51.2%) with all classes except Epsilonproteobacteria duly represented. Rarefaction analysis indicates 42%, 52% and 77% of the clone library is covered at the species, genus and family/class delineations with Shannon diversity (H') and Chao1 richness indices of 5.59 and 1126, respectively. A sizeable number of bacterial phylotypes in the clone library shared high similarities with strains previously described to be involved in hydrocarbon biodegradation. Novel uncultured genera were identified that have not been previously reported from tropical African soil to be associated with natural attenuation of hydrocarbon pollutants. This study establishes the involvement of a wide array of physiologically diverse bacterial groups in natural attenuation of hydrocarbon pollutants in soil.

  3. Urban-development-induced Changes in the Diversity and Composition of the Soil Bacterial Community in Beijing

    Science.gov (United States)

    Yan, Bing; Li, Junsheng; Xiao, Nengwen; Qi, Yue; Fu, Gang; Liu, Gaohui; Qiao, Mengping

    2016-12-01

    Numerous studies have implicated urbanization as a major cause of loss of biodiversity. Most of them have focused on plants and animals, even though soil microorganisms make up a large proportion of that biodiversity. However, it is unclear how the soil bacterial community is affected by urban development. Here, paired-end Illumina sequencing of the 16 S rRNA gene at V4 region was performed to study the soil microbial community across Beijing’s built-up area. Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, Gemmatimonadetes, Verrucomicrobia, Planctomycetes, and Chloroflexi were the dominant phyla in all samples, but the relative abundance of these phyla differed significantly across these concentric zones. The diversity and composition of the soil bacterial community were found to be closely correlated with soil pH. Variance partitioning analysis suggested that urban ring roads contributed 5.95% of the bacterial community variation, and soil environmental factors explained 17.65% of the variation. The results of the current work indicate that urban development can alter the composition and diversity of the soil microbial community, and showed pH to be a key factor in the shaping of the composition of the soil bacterial community. Urban development did have a strong impact on the bacterial community of urban soil in Beijing.

  4. Comparative metagenomic analysis of the microbial communities in the surroundings of Iheya north and Iheya ridge hydrothermal fields reveals insights into the survival strategy of microorganisms in deep-sea environments

    Science.gov (United States)

    Wang, Hai-liang; Sun, Li

    2018-04-01

    In this study, metagenomic analysis was performed to investigate the taxonomic compositions and metabolic profiles of the microbial communities inhabiting the sediments in the surroundings of Iheya North and Iheya Ridge hydrothermal fields. The microbial communities in four different samples were found to be dominated by bacteria and, to a much lesser extent, archaea belonging to the phyla Proteobacteria, Actinobacteria, Planctomycetes, Firmicutes, Deinococcus-Thermus, and Nitrospirae, which play important roles in the cycling of carbon, nitrogen, and sulfur. All four microbial communities (i) contained chemoautotrophs and heterotrophs, the former probably fixed CO2 via various carbon fixation pathways, and the latter may degrade organic matters using nitrate and sulfate as electron acceptors, (ii) exhibited an abundance of DNA repair genes and bacterial sulfur oxidation mediated by reverse sulfate reduction, and (iii) harbored bacteria and archaea involved in anaerobic methane oxidation via intra-aerobic denitrification and reverse methanogenesis, which were found for the first time in hydrothermal areas. Furthermore, genes involved in DNA repair, reductive acetyl-CoA pathway, and ammonia metabolism were possibly affected by distance to the vent fields. These findings facilitate our understanding of the strategies of the microbial communities to adapt to the environments in deep sea areas associated with hydrothermal vents.

  5. Unearthing the ecology of soil microorganisms using a high resolution DNA-SIP approach to explore cellulose and xylose metabolism in soil

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    Charles ePepe-Ranney

    2016-05-01

    Full Text Available We explored microbial contributions to decomposition using a sophisticated approach to DNA Stable Isotope Probing (SIP. Our experiment evaluated the dynamics and ecological characteristics of functionally defined microbial groups that metabolize labile and structural C in soils. We added to soil a complex amendment representing plant derived organic matter substituted with either 13C-xylose or 13C-cellulose to represent labile and structural C pools derived from abundant components of plant biomass. We found evidence for 13C-incorporation into DNA from 13C-xylose and 13C-cellulose in 49 and 63 operational taxonomic units (OTUs, respectively. The types of microorganisms that assimilated 13C in the 13C-xylose treatment changed over time being predominantly Firmicutes at day 1 followed by Bacteroidetes at day 3 and then Actinobacteria at day 7. These 13C-labeling dynamics suggest labile C traveled through different trophic levels. In contrast, microorganisms generally metabolized cellulose-C after 14 days and did not change to the same extent in phylogenetic composition over time. Microorganisms that metabolized cellulose-C belonged to poorly characterized but cosmopolitan soil lineages including Verrucomicrobia, Chloroflexi and Planctomycetes.

  6. Unraveling the biochemistry and provenance of pupylation: a prokaryotic analog of ubiquitination

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    Aravind L

    2008-11-01

    Full Text Available Abstract Recently Mycobacterium tuberculosis was shown to possess a novel protein modification, in which a small protein Pup is conjugated to the epsilon-amino groups of lysines in target proteins. Analogous to ubiquitin modification in eukaryotes, this remarkable modification recruits proteins for degradation via archaeal-type proteasomes found in mycobacteria and allied actinobacteria. While a mycobacterial protein named PafA was found to be required for this conjugation reaction, its biochemical mechanism has not been elucidated. Using sensitive sequence profile comparison methods we establish that the PafA family proteins are related to the γ-glutamyl-cysteine synthetase and glutamine synthetase. Hence, we predict that PafA is the Pup ligase, which catalyzes the ATP-dependent ligation of the terminal γ-carboxylate of glutamate to lysines, similar to the above enzymes. We further discovered that an ortholog of the eukaryotic PAC2 (e.g. cg2106 is often present in the vicinity of the actinobacterial Pup-proteasome gene neighborhoods and is likely to represent the ancestral proteasomal chaperone. Pup-conjugation is sporadically present outside the actinobacteria in certain lineages, such as verrucomicrobia, nitrospirae, deltaproteobacteria and planctomycetes, and in the latter two lineages it might modify membrane proteins. Reviewers This article was reviewed by M. Madan Babu and Andrei Osterman

  7. Microbial diversity and stratification of South Pacific abyssal marine sediments.

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    Durbin, Alan M; Teske, Andreas

    2011-12-01

    Abyssal marine sediments cover a large proportion of the ocean floor, but linkages between their microbial community structure and redox stratification have remained poorly constrained. This study compares the downcore gradients in microbial community composition to porewater oxygen and nitrate concentration profiles in an abyssal marine sediment column in the South Pacific Ocean. Archaeal 16S rRNA clone libraries showed a stratified archaeal community that changed from Marine Group I Archaea in the aerobic and nitrate-reducing upper sediment column towards deeply branching, uncultured crenarchaeotal and euryarchaeotal lineages in nitrate-depleted, anaerobic sediment horizons. Bacterial 16S rRNA clone libraries revealed a similar shift on the phylum and subphylum level within the bacteria, from a complex community of Alpha-, Gamma- and Deltaproteobacteria, Actinobacteria and Gemmatimonadetes in oxic surface sediments towards uncultured Chloroflexi and Planctomycetes in the anaerobic sediment column. The distinct stratification of largely uncultured bacterial and archaeal groups within the oxic and nitrate-reducing marine sediment column provides initial constraints for their microbial habitat preferences. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

  8. Biotechnological production of non-traditional beer

    Science.gov (United States)

    Parise, Adadi; Kovaleva, Elena G.; Glukhareva, Tatiana V.; Shatunova, Svetlana A.

    2017-09-01

    In the present study we brewed sorghum (pito) and low-alcoholic beer (LAB) utilizing Sacharomyces cerevisiae, Lactobacillus plantarum and Saccharomycodes ludwigii as starters, respectively, and characterized their quality parameters. Single infusion method of mashing was practiced. Physiochemical, sensory and antiradical properties of samples were determined. Pito was produced by pitching wort with S. cerevisae (single starter culture (SSC)) and S. cerevisae in combination with L. plantarum (mixed starter culture (MSC)). oBrix did not change over the next 24 hours for both cultures and began to decline, yet still it remain steady when the fermentation was over. After the end of fermentation, wort pitched with SSC showed lower oBrix (6.63±0.11), than the wort with MSC (6.73±0.20) and differ significantly (P < 0.05) with duration of the fermentation process. LAB also exhibited a decrease in oBrix from 12.2±0.12 to 8.04±0.01 at the end of the fermentation. Titratable acidity (TA) and pH remained constant after 24 hours of fermentation. TA began to increase from 0.73±0.02 to 1.04±0.02 and 0.73±0.02 to 1.07±0.02 for SSC and MSC, respectively. A decrease in pH from 4.33±0.20 to 3.86±0.15 and 4.33±0.20 to 4.2±0.1 was observed for SSC and MSC, respectively, during the rest of the fermentation period. A total of 22 volatile compounds including 11 esters, 3 alcohols and 8 acids, were identified in pito. Seven of these compounds were detected after the first fermentation (in green beer), whilst the rest (16 compounds) were distinguish after secondary fermentation. We also identified 8 volatiles in LAB, including 5 alcohols, 2 esters and 1 acid. Electron paramagnetic resonance spectroscopy of free radicals was used to determine the antiradical activity (AOA) of LAB in comparison with industrial alcoholic beverages (Baltica 7 from St Petersburg, Russia and Nectar beer from Bosnia-Herzegonia). LAB showed DPPH radical scavenging activity of 1.16 ×10-4 mol × equ (R2

  9. Algunos aspectos de la variabilidad de los oogonios en poblaciones actuales del género Chara (Charophyceae. Aplicación paleontológica

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    Pedrola, J.

    1986-10-01

    Full Text Available A critical revision of some useful taxonomic criteria in paleontology of Charophytes is carried Out. The results are based in four modern populations ((Chara aculeolata, Chara aff.baltica, Chara delicatula and Chara globularis and they permit to make some serious objections to these critera. The results are related with three principal aspects: the meaning of the absolute magnitudes of me girogonite, the behaviour of his joint variation and the morphological variability during the calcification process. In general, and for each one of the four populations, an absence of influence of the position of the girogonite over their measurements is observed. This doesn't happens when the verticil is considered as source of variation. These biometrical differences which are equivalent to some of those that has been used to distinguish fossil species, are not due to a process of progressive or heteregenous calcification in the secuence of verticils of me plant. Several arguments against the indiscriminate use of cocients between absolute magnitudes (e.g. the polarity index as detectors of systematic interest are showed. In the same way, some remarks to the use of the morphology of the spiral calcificated cells, the prominence of the basal pore and some aspects of the apex shape, as taxonomic criteria are made. All this are variable within the same plant when there are differents in the calcification degree of the girogonites.

    Se hace una revisión crítica de-algunos criterios taxonómicos de uso habitual en paleontología de carofitas. Sus resultados, basados en cuatro poblaciones actuales (Chara aculeolata, Chara aff.baltica, Chara delicatula y Chara globularis, permiten hacer algunas serias objeciones a estos criterios. Dichos resultados se relacionan con tres aspectos principales: el significado de las magnitudes absolutas del girogonito, el comportamiento de su variación conjunta y la variabilidad

  10. The tectonothermal evolution of the Venezuelan Caribbean Mountain System: 40Ar/39Ar age insights from a Rodinian-related rock, the Cordillera de la Costa and Margarita Island

    Science.gov (United States)

    Fournier, Herbert W.; Lee, James K. W.; Urbani, Franco; Grande, Sebastián

    2017-12-01

    The Caribbean Mountain System in Venezuela contains rocks formed at high-pressure/low-temperature (HP/LT) conditions by the Cretaceous-Paleocene oblique collision occurred between the Caribbean and South American plates and involving Rodinian-related blocks. 40Ar/39Ar dating of rocks from the Cordillera de la Costa and Margarita Island has constrained key pre- and syntectonothermal events associated with the emplacement of this system. In a Rodinian marble, two phlogopite crystals of different grain sizes yield plateau ages of 888 ± 4 Ma and 874 ± 4 Ma. These results are interpreted as cooling ages after a major anorthosite-mangerite-charnockite-granite-suite intrusion at 920 Ma related to the break-up of Rodinia along the Amazonian-Baltica collisional zone - the Putumayo Orogen. Current plate reconstructions during the Neoproterozoic and previous age results indicate a correlation between the anorthositic complexes located in northwestern Venezuela (Yumare Complex) and southern Norway (Rogaland Complex), suggesting a similar tectonic setting during orogenic relaxation along the Amazonian and Baltica suture. A temperature-time path based on calculated Ar-closure temperatures of phlogopite indicates rapid cooling of 14 ± 4 °C Ma-1 from 920 Ma to 888 Ma, and a very slow to almost isothermal cooling of 4 ± 2 °C Ma-1 from 888 Ma to 874 Ma. On Margarita Island, magnesiohornblende and (alumino) barroisite from HP/LT rocks and muscovite from a leucocratic rock that was intruded before the HP/LT event yield identical ages within error at c. 54-47 Ma, consistent with previous dating results across the island utilizing different isotopic systems. The close association of these rocks and the Manzanillo Shear Zone indicates a main pathway for Ca-rich, 40Ar-free and hot fluids that locally raised the ambient T of the already exhumed and juxtaposed rock units. These fluids crystallized new hornblende and muscovite and thermally reset barroisite. This fluid activity event

  11. The Öland limestone - A Swedish stone used for more than one thousand years

    Science.gov (United States)

    Schouenborg, Björn; Wickström, Linda; Mikaelsson, Jan

    2016-04-01

    The second largest island in Sweden is the home of the "Öland limestone", a condensed and bedded limestone whose origin dates back to Lower Ordovician, i.e. about 480 M years ago. Öland is a part of the palaeocontinent Baltica that, at the time, was situated at low latitudes with deposition of the calcareous sediments in a cool water environment. The limestone on Öland represents a proximal ramp tectonic setting, with the oldest sediments deposited in the west and younger sediments deposited towards east and southeast. Fluctuating sea-levels have created erosional hard grounds such as the Flowery sheet. These hardgrounds are recognised by their vivid colours and trace fossils, and can be traced all over Baltica, but is maybe best represented on Öland. Ordovician limestones are present in many places in Sweden, but it is the occurrence on Öland that is the most renowned in a building stone perspective. One reason for this is the favourable trading location, an island off the Swedish East coast in middle of the trading routes between the Baltic countries and the continent. Other reasons are the pleasant aesthetical values with numerous orthoceratites and other fossils. The limestones on Öland differ in colour. From the red varieties (with oxidized iron) to brownish and grey. The bedding is mostly in the cm-scale which easily enables very exploitable thickness of slabs. Every mm limestone represents about 1000 years of deposition. The limestone has most likely been used in a very crude way for many thousand years, but archaeological evidence of a more industrialized usage is just a little more than 1000 years. It is known from the literature that the first official Swedish king, Gustav Vasa (16th century), desired this stone. At the time it was called "Öland marble", and the king "imported" specialists to process it further at the Royal Stone workshop on northern Öland. Remnants of tools and working sites still remain in an outdoor museum. Export of the

  12. Modelling of Surface Fault Structures Based on Ground Magnetic Survey

    Science.gov (United States)

    Michels, A.; McEnroe, S. A.

    2017-12-01

    The island of Leka confines the exposure of the Leka Ophiolite Complex (LOC) which contains mantle and crustal rocks and provides a rare opportunity to study the magnetic properties and response of these formations. The LOC is comprised of five rock units: (1) harzburgite that is strongly deformed, shifting into an increasingly olivine-rich dunite (2) ultramafic cumulates with layers of olivine, chromite, clinopyroxene and orthopyroxene. These cumulates are overlain by (3) metagabbros, which are cut by (4) metabasaltic dykes and (5) pillow lavas (Furnes et al. 1988). Over the course of three field seasons a detailed ground-magnetic survey was made over the island covering all units of the LOC and collecting samples from 109 sites for magnetic measurements. NRM, susceptibility, density and hysteresis properties were measured. In total 66% of samples with a Q value > 1, suggests that the magnetic anomalies should include both induced and remanent components in the model.This Ophiolite originated from a suprasubduction zone near the coast of Laurentia (497±2 Ma), was obducted onto Laurentia (≈460 Ma) and then transferred to Baltica during the Caledonide Orogeny (≈430 Ma). The LOC was faulted, deformed and serpentinized during these events. The gabbro and ultramafic rocks are separated by a normal fault. The dominant magnetic anomaly that crosses the island correlates with this normal fault. There are a series of smaller scale faults that are parallel to this and some correspond to local highs that can be highlighted by a tilt derivative of the magnetic data. These fault boundaries which are well delineated by the distinct magnetic anomalies in both ground and aeromagnetic survey data are likely caused by increased amount of serpentinization of the ultramafic rocks in the fault areas.

  13. Aquiflexum balticum gen. nov., sp. nov., a novel marine bacterium of the Cytophaga-Flavobacterium-Bacteroides group isolated from surface water of the central Baltic Sea.

    Science.gov (United States)

    Brettar, Ingrid; Christen, Richard; Höfle, Manfred G

    2004-11-01

    A bacterial isolate from the Baltic Sea, BA160(T), was characterized for its physiological and biochemical features, fatty acid profile, G+C content and phylogenetic position based on 16S rRNA gene sequences. The strain was isolated from the surface water of the central Baltic Sea during the decay of a plankton bloom. Phylogenetic analyses of the 16S rRNA gene sequence revealed a clear affiliation with the family 'Flexibacteraceae', and showed the closest phylogenetic relationship with the species Belliella baltica and Cyclobacterium marinum. The G+C content of the DNA was 38.4 mol%. The strain was red-coloured due to carotenoids, Gram-negative, rod-shaped, and catalase- and oxidase-positive. Growth was observed at salinities from 0 to 6 %, with an optimum around 1.5 %. Temperature for growth ranged from 4 to 40 degrees C, with an optimum around 30 degrees C. The fatty acids were dominated by branched-chain fatty acids (>87 %), with a high abundance of iso-C(15 : 0) (23 %) and anteiso-C(15 : 0) (19 %). According to its morphology, physiology, fatty acid composition, G+C content and 16S rRNA gene sequence, strain BA160(T) is considered to represent a new genus of the family 'Flexibacteraceae'. Due to its aquatic origin, the name Aquiflexum balticum gen. nov, sp. nov. is suggested for the type species (type strain, BA160(T)=DSM 16537(T)=LMG 22565(T)=CIP 108445(T)) of the new genus.

  14. Twelve previously unknown phage genera are ubiquitous in global oceans.

    Science.gov (United States)

    Holmfeldt, Karin; Solonenko, Natalie; Shah, Manesh; Corrier, Kristen; Riemann, Lasse; Verberkmoes, Nathan C; Sullivan, Matthew B

    2013-07-30

    Viruses are fundamental to ecosystems ranging from oceans to humans, yet our ability to study them is bottlenecked by the lack of ecologically relevant isolates, resulting in "unknowns" dominating culture-independent surveys. Here we present genomes from 31 phages infecting multiple strains of the aquatic bacterium Cellulophaga baltica (Bacteroidetes) to provide data for an underrepresented and environmentally abundant bacterial lineage. Comparative genomics delineated 12 phage groups that (i) each represent a new genus, and (ii) represent one novel and four well-known viral families. This diversity contrasts the few well-studied marine phage systems, but parallels the diversity of phages infecting human-associated bacteria. Although all 12 Cellulophaga phages represent new genera, the podoviruses and icosahedral, nontailed ssDNA phages were exceptional, with genomes up to twice as large as those previously observed for each phage type. Structural novelty was also substantial, requiring experimental phage proteomics to identify 83% of the structural proteins. The presence of uncommon nucleotide metabolism genes in four genera likely underscores the importance of scavenging nutrient-rich molecules as previously seen for phages in marine environments. Metagenomic recruitment analyses suggest that these particular Cellulophaga phages are rare and may represent a first glimpse into the phage side of the rare biosphere. However, these analyses also revealed that these phage genera are widespread, occurring in 94% of 137 investigated metagenomes. Together, this diverse and novel collection of phages identifies a small but ubiquitous fraction of unknown marine viral diversity and provides numerous environmentally relevant phage-host systems for experimental hypothesis testing.

  15. APW path traced for the Guiana Shield (2070-1960 Ma) and Paleogeographic Implications: Paleomagnetic data from the 1.98-1.96 Ga Surumu Group (Northern Amazonian Craton)

    Science.gov (United States)

    Bispo-Santos, F.; Dagrella Filho, M. S.; Reis, N. J.; Trindade, R. I.

    2013-05-01

    Definition of continental paleogeography for times prior to formation of Columbia Supercontinent (1900-1850 Ma) is very complex, since amalgamation of some continental blocks of Earth was still in progress, as in the case of Laurentia, Baltica and Amazonian Craton. So, paleogeographic models proposed for this time are still very speculative and/or subjective. The use of the paleomagnetic technique tracing apparent polar wander (APW) paths for the various cratonic blocks can contribute to understand the continental amalgamation and breakup, especially for times where all created oceanic lithosphere was fully consumed. In this study, we present the paleomagnetic data obtained for samples collected from 39 sites from the well-dated 1980-1960 Ma (U-Pb) volcanic rocks belonging to the Surumu Group, cropping out in the northern Roraima State (Guiana Shield, Amazonian Craton). AF and thermal treatment revealed northwestern directions with moderate downward inclinations on samples from 20 out of the 39 analyzed sites. Site mean directions cluster around the mean, Dm = 298.6°; Im = 39.4° (N = 20; α95 = 10.1°), which yielded a key paleomagnetic pole (SG) for the Guiana Shield, located at 234.8°E, 27.4°N (A95 = 9.8°). Magnetic mineralogy experiments show that the magnetization of these rocks, probably of primary origin, is carried by magnetite and/or hematite. The SG pole contributes to a better fit of the APW path traced for Guiana Shield during the Paleoproterozoic (2070-1960 Ma). Comparison with the APW path traced for the West-Africa Craton for the same time interval suggests that these cratonic blocks were linked at 2000-1960 Ma ago, forming a paleogeography in which the Guri (Guiana Shield) and Sassandra (West-Africa Craton) shear zones were aligned as suggested in previous geologic models. KEYWORDS: Paleoproterozoic, Paleomagnetism, APWP, Amazonian Craton, Surumu Group.

  16. Geochronology of Zircon in Eclogite Reveals Imbrication of the Ultrahigh-Pressure Western Gneiss Region of Norway.

    Science.gov (United States)

    Young, D. J.; Kylander-Clark, A. R.; Root, D. B.

    2014-12-01

    Eclogite provides the only record of kinematic events at the deepest levels of orogens. Integrating the U-Pb geochronology and trace element chemistry of zircon in eclogite reveals the most complete view of the PTt history, yet low concentrations of uranium and zirconium and drier compositions that hinder zircon growth at peak conditions render it a challenging rocktype for this approach. The iconic Western Gneiss Region (WGR) in Norway is one of the largest terranes of deeply subducted continental rocks in the world, and contains many indicators of ultrahigh-pressure metamorphic conditions (P>2.8 GPa) that developed during the Siluro-Devonian Caledonian Orogeny. A metamorphic transition from amphibolite-facies to ultrahigh-pressure eclogite facies broadly coincides with a km-scale shear zone that underlies the majority of the WGR. A critical unknown is the timing of movement on this feature, which emplaced allochthonous units above the Baltica basement, but might also have accommodated late-orogenic exhumation of the WGR from mantle depths. We carried out laser ablation split-stream ICPMS (LASS) and selected multigrain TIMS analyses of zircons from eleven eclogites across the southern WGR, of which eight are located within or above the shear zone. LASS spots on polished grains mostly yield weakly discordant Proterozoic intrusive ages, and often minimal indication of a Caledonian (U)HP metamorphic overprint. Direct ablation into unpolished zircon reveals thin rims of Caledonian age in some cases. Overall, the dataset shows that all samples began zircon growth at approximately the same time (ca. 430-420 Ma). Eclogite from lower levels of the shear zone does not contain any dates younger than ca. 410 Ma, however, while eclogite from higher levels continued growth until ca. 400 Ma. We interpret this to result from thrusting of the WGR above cooler basement after 410 Ma, terminating new zircon crystallization within the shear zone but allowing limited further growth in

  17. Bringing Western-standard service stations to the Baltic countries. Neste palvelee Baltiassa laadulla ja varmuudella

    Energy Technology Data Exchange (ETDEWEB)

    Pesonen, H.

    1992-01-01

    Neste is the only Western oil company so far to have established a service station presence in the Baltic, with the exception of Norway's Statoil, which has one outlet near Tallinn Airport. Neste has an important logistical advantage compared to other companies in this respect as its two Finnish refineries are ideally located for supplying the region with high-quality petroleum products. Neste's first joint venture in the Baltic, Traffic Service, based in Estonia, was set up with Eesti Kutus in 1988 and opened its first service station in 1990. Other joint ventures are now up and running in Latvia, Lithuania, Poland, and St. Petersburg. A total of 10 - 15 stations, the majority strategically located along the route of the Via Baltica, are expected to be operational by the end of this year. The Neste network comprises a combination of new outlets and refurbished older stations that have been modernized to bring them up to Western standards. These offer a comprehensive range of fuels, lubricants, spare parts, and accessories, as well as food, confectionery, and coffee shop services. Some stations also offer repair and car wash facilities. Adapting to the transition from a communist economy to a Western, capitalist one has not been easy for the Baltic countries, and has inevitably created difficulties for companies like Neste, in areas such as legislation covering land ownership. Neste's joint ventures have also encountered difficulties in instilling the Western approach to business efficiency, and customer service in a workforce used to the Soviet retail system.

  18. Revision of Silurian vertebrate biozones and their correlation with the conodont succession

    Directory of Open Access Journals (Sweden)

    Tiiu Märss

    2013-11-01

    Full Text Available The first vertebrate-based subdivisions of Silurian strata were mainly drawn on material from outcrops in Britain and drill cores from the southern Baltic. Nearly twenty years ago the first vertebrate biozonal scheme was developed on the basis of vertebrate distribution in several continuous drill core sections in the northern Baltic. This paper presents a new scheme in which many new data on vertebrate distribution from the Baltica (Baltic region, NW Russia, Avalonia (southern Britain, eastern Canada, Laurentia (northern Canada, Greenland, Scotland and Kara (Arctic Russia palaeocontinents have been used. All the zones have been defined, and the geographical distribution and the reference stratum and locality for each zone have been given. The Llandovery part of the succession contains the Valyalepis crista, Loganellia aldridgei and L. scotica zones; the Wenlock part is represented by the Archipelepis bifurcata/Arch. turbinata, L. grossi, Overia adraini, L. einari and Paralogania martinssoni zones. The Par. martinssoni Zone continues in the Ludlow and is followed by the Phlebolepis ornata, Phl. elegans, Andreolepis hedei, Thelodus sculptilis and T. admirabilis zones. The last zone continues in the lower Přidoli and is followed by the Nostolepis gracilis, Poracanthodes punctatus and Trimerolepis timanica zones. The L. aldridgei and Arch. bifurcata zones are new, and the Arch. turbinata and O. adraini faunas have been raised from ‘faunal succession units’ to zones. The geographically widely distributed L. grossi Zone in the upper Sheinwoodian and the Par. martinssoni Zone in the upper Homerian–lowermost Gorstian allow the integration of regional successions into one Generalized Vertebrate Zonal Scheme. Possible correlations of conodont and vertebrate biozones, and gaps in sedimentation in the northern East Baltic Silurian sequence have been discussed, the most extensive hiatus being between the Paadla and Kuressaare stages.

  19. INTERMODAL TRANSPORT IN EUROPE - OPPORTUNITIES THROUGH INNOVATION

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    Norbert Wagener

    2014-12-01

    Full Text Available Background: Freight transport volume in ton-km in OECD countries will grow considerably up to 150 to 230 % in 2050 compared to 2010. Although the EU policy aims to shift 30% of road freight over 300 km to other modes such as rail or waterborne transport by 2030 the recent trends show a stable modal split of road at approx. 75%. Conventional intermodal transport on the major European routes has shown a steady but only limited organic growth through recent years. Therefore, new innovative concepts for intermodal transport and for the shift from road to rail are needed. Methods: Definitions of intermodal transport have been clarified and the development of combined transport in Europe and in Germany and Poland in particular has been analyzed on the basis of available data sources. New innovative concepts for intermodal transport have been identified on the basis of desk research, recent relevant projects (RETRACK, SCANDRIA, Rail Baltica and market intelligence. Results: The analysis leads to the conclusion that new innovative concepts in intermodal transport comprise new forms of organization as well as new technologies and new routes. The following three innovations to facilitate the shift from road to rail by intermodal transport are being introduced and discussed: multimodal operation of ocean carriers in maritime hinterland transportation, innovative handling technologies for non-crane able trainers and freight corridors for long distance intermodal transport within the TEN-T network and on the Europe-Asia corridor. Conclusions: Further accelerated growth in the shift from road to rail through intermodal transport requires new innovative concepts beyond the traditional combined transport in Western Europe. Three promising innovative concepts have been introduced. Further research is needed and should be focused on financial and economic appraisal as well as on the effectiveness of state intervention policies. 

  20. Marine bioearosol in the area of Gdańsk Bay

    Directory of Open Access Journals (Sweden)

    Małgorzata Michalska

    2011-03-01

    Full Text Available Formation of bioaerosol is an important process of mass and energy exchange between sea and atmosphere by means of droplets of marine dust. Studies on aerosol activity of the sea was developed in the last decades of the 20 th century. Those studies revealed that concentrations of bacteria in aerosol droplets were hundreds times higher than their concentrations in superficial parts of seawater. The research also proved that aerosol activity of the sea can influence the sanitary condition of the air, especially at the seacoast areas. Surveys of air structure in coastal regions were performed on the Tricity beaches as well as in Sobieszewo and Komary. Atmospheric air sampling stations in the marine zone were located on the Gulf of Gdansk at the Vistula river mouth. Air samples were collected from the front platform on the ship R/V Baltica at 4m above the sea surface. The air samples were collected by filtration method using Sartorius apparatus. Airborne microbes were deposited onto sterile gelatine Sartorius filters. All filters were exposed directly towards the oncoming wind. After sampling, the exposed filters were placed onto the agar media on Petri plates and incubated. All measurement results were depicted in (CFU/m3 i.e. colony forming units in 1 m3 of the examined air. Meteorological measurements included: temperature, humidity, wind speed and direction. The obtained results revealed that statistically significant trends were observed between the total number of bacteria or moulds and a season of sampling. The greatest number of microorganisms was noted in spring and autumn. Correlation analysis showed that statistically significant relationship exists between microbial abundance and the wind direction or speed and location of sampling site. Large quantities of fungal spores was detected in the areas of Gdynia and Gdansk - Brzeêno when south-west winds were blowing from the land. The highest number of bacteria were observed at the sampling

  1. Importance of a winter dinoflagellate-microflagellate bloom in the Patuxent River estuary

    Science.gov (United States)

    Sellner, K. G.; Lacouture, R. V.; Cibik, S. J.; Brindley, A.; Brownlee, S. G.

    1991-01-01

    A dense bloom of Katodinium rotundatum was observed in the Patuxent River estuary from December to February 1989. The dinoflagellate dominated phytoplankton densities reaching 10 8 cells l -1 and contributed up to 1900 μgC l -1 in near-surface depths. The bloom maintained a distinct patch extending over 10-25 km of the estuary or approximately one-third to one-half of the total estuary (salinities from 5-13 ppt) and was restricted to regions immediately upriver of the transition between the shallow upriver (3-4 m) and deeper lower estuary (10 m). Daily measurements collected in the primary bloom area at the same time each day in the study area indicated 80- and 120-fold variations in chlorophyll and cell densities from day to day. Densities of potential grazers in the region were high with rotifers, primarily Synchaeta baltica, reaching densities of 1000 l -1 in early winter, and the copepod Eurytemora affinis reaching levels exceeding 1·15 × 10 5 m -3 in February. Estimates of grazing pressure by these planktonic herbivores indicated substantial grazing losses for the bloom, with up to 67% of bloom biomass consumed day -1 in February. Nutrient concentrations and ratios of N/P during the bloom suggested potentially N-limited conditions; bloom demise was coincident with a shift to high N/P ratios and high river flows. These data as well as other historical data suggest that dinoflagellate blooms in the lower Patuxent River estuary could be the primary source of carbon to the system during the winter and supply a large reservoir of labile organic matter to planktonic secondary producers prior to annual spring diatom blooms in the region.

  2. More about the Ordovician–Silurian transition beds at Mirny Creek, Omulev Mountains, NE Russia: carbon isotopes and conodonts

    Directory of Open Access Journals (Sweden)

    Dimitri Kaljo

    2012-11-01

    Full Text Available Profound environmental and biodiversity changes take place in the Ordovician–Silurian boundary interval. The Mirny Creek and Neznakomka River bank sections discussed in this paper expose the upper Katian–lower Rhuddanian part of the boundary beds. The succession consists of carbonate rocks, partly with bioherms, alternating with argillaceous and siltstone packages that are well dated by graptolites. Microfossils are rare, especially in the Hirnantian, but conodonts provide some useful markers just below and above the Hirnantian stage boundaries. The Hirnantian δ13C trend in the Mirny Creek section is the stratigraphically longest described so far and it has a highly specific shape. The trend commenced at the first appearance datum of Normalograptus extraordinarius or slightly below this level. The main peak occurs near the middle of the N. persculptus Biozone. Samples from the Neznakomka River suggest a somewhat wider peak interval than at Mirny Creek. Detailed comparison of the Mirny and Stirnas (Latvia δ13C curves shows a general similarity despite great specific features of both trends. Correlation of the δ13C trends from China, Baltica and North America with that at Mirny Creek reveals a great variety of shapes of the carbon isotope curve. However, its rising limb commenced, if represented, everywhere close to the beginning of the N. extraordinarius Biozone or in terms of the Baltic succession, at the bottom of the Porkuni Regional Stage. Most likely a general shape of the HICE trend is pyramidal, which is peaking in the early N. persculptus Biochrone. Differences in the values and shape of an actual curve at different localities depend on local environmental conditions, sometimes modifying the global signal rather strongly.

  3. Engineering of EPA/DHA omega-3 fatty acid production by Lactococcus lactis subsp. cremoris MG1363.

    Science.gov (United States)

    Amiri-Jami, Mitra; Lapointe, Gisele; Griffiths, Mansel W

    2014-04-01

    Eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) have been shown to be of major importance in human health. Therefore, these essential polyunsaturated fatty acids have received considerable attention in both human and farm animal nutrition. Currently, fish and fish oils are the main dietary sources of EPA/DHA. To generate sustainable novel sources for EPA and DHA, the 35-kb EPA/DHA synthesis gene cluster was isolated from a marine bacterium, Shewanella baltica MAC1. To streamline the introduction of the genes into food-grade microorganisms such as lactic acid bacteria, unnecessary genes located upstream and downstream of the EPA/DHA gene cluster were deleted. Recombinant Escherichia coli harboring the 20-kb gene cluster produced 3.5- to 6.1-fold more EPA than those carrying the 35-kb DNA fragment coding for EPA/DHA synthesis. The 20-kb EPA/DHA gene cluster was cloned into a modified broad-host-range low copy number vector, pIL252m (4.7 kb, Ery) and expressed in Lactococcus lactis subsp. cremoris MG1363. Recombinant L. lactis produced DHA (1.35 ± 0.5 mg g(-1) cell dry weight) and EPA (0.12 ± 0.04 mg g(-1) cell dry weight). This is believed to be the first successful cloning and expression of EPA/DHA synthesis gene cluster in lactic acid bacteria. Our findings advance the future use of EPA/DHA-producing lactic acid bacteria in such applications as dairy starters, silage adjuncts, and animal feed supplements.

  4. In vitro antibacterial analysis of phenoloxidase reaction products from the sea cucumber Apostichopus japonicus.

    Science.gov (United States)

    Jiang, Jingwei; Zhou, Zunchun; Dong, Ying; Cong, Cong; Guan, Xiaoyan; Wang, Bai; Chen, Zhong; Jiang, Bei; Yang, Aifu; Gao, Shan; Sun, Hongjuan

    2014-08-01

    Three phenoloxidases (POs) of Apostichopus japonicus, AjPOs (AjPO1, AjPO2 and AjPO3), were partially purified from the coelomocytes with an electrophoretic method, and then employed for the in vitro antibacterial analysis. Using L-3,4-dihydroxyphenylalanine (L-DOPA) as a substrate, AjPO1 and AjPO2-derived compounds inhibited the growth of Vibrio splendidus and Staphylococcus aureus, while AjPO3-derived compounds only inhibited the growth of V. splendidus. When dopamine was used as a substrate, AjPO1 and AjPO3-derived compounds inhibited the growth of V. splendidus and Vibrio harveyi, while AjPO2-derived compounds only inhibited the growth of V. splendidus. Moreover, AjPO1-derived compounds showed stronger inhibition in V. harveyi than AjPO3-derived compounds did. However, all of the three AjPO reaction products showed no inhibitions on the growth of Pseudoalteromonas nigrifaciens, Shewanella baltica, Micrococcus lysodeikticus, Streptococcus dysgalactiae and Nocardiopsis sp. with L-DOPA or dopamine as a substrate. Scanning electron microscope (SEM) observation of V. harveyi treated by AjPOs and dopamine showed that AjPO1-derived compounds resulted in massive bacteriolysis, AjPO2-derived compounds caused no obvious alteration on bacterial morphology, and AjPO3-derived compounds increased the ratio of spheroidal bacteria. All these results suggested that AjPO reaction products derived by L-DOPA and dopamine had different but limited antibacterial spectrum, and the different antibacterial effects observed among three AjPOs resulted from the different reaction products generated by AjPOs with the same substrate. Copyright © 2014 Elsevier Ltd. All rights reserved.

  5. Testing the limits of Paleozoic chronostratigraphic correlation via high-resolution (13Ccarb) biochemostratigraphy across the Llandovery–Wenlock (Silurian) boundary: Is a unified Phanerozoic time scale achievable?

    Science.gov (United States)

    Cramer, Bradley D.; Loydell, David K.; Samtleben, Christian; Munnecke, Axel; Kaljo, Dimitri; Mannik, Peep; Martma, Tonu; Jeppsson, Lennart; Kleffner, Mark A.; Barrick, James E.; Johnson, Craig A.; Emsbo, Poul; Joachimski, Michael M.; Bickert, Torsten; Saltzman, Matthew R.

    2010-01-01

    The resolution and fidelity of global chronostratigraphic correlation are direct functions of the time period under consideration. By virtue of deep-ocean cores and astrochronology, the Cenozoic and Mesozoic time scales carry error bars of a few thousand years (k.y.) to a few hundred k.y. In contrast, most of the Paleozoic time scale carries error bars of plus or minus a few million years (m.y.), and chronostratigraphic control better than ??1 m.y. is considered "high resolution." The general lack of Paleozoic abyssal sediments and paucity of orbitally tuned Paleozoic data series combined with the relative incompleteness of the Paleozoic stratigraphic record have proven historically to be such an obstacle to intercontinental chronostratigraphic correlation that resolving the Paleozoic time scale to the level achieved during the Mesozoic and Cenozoic was viewed as impractical, impossible, or both. Here, we utilize integrated graptolite, conodont, and carbonate carbon isotope (??13Ccarb) data from three paleocontinents (Baltica, Avalonia, and Laurentia) to demonstrate chronostratigraphic control for upper Llando very through middle Wenlock (Telychian-Sheinwoodian, ~436-426 Ma) strata with a resolution of a few hundred k.y. The interval surrounding the base of the Wenlock Series can now be correlated globally with precision approaching 100 k.y., but some intervals (e.g., uppermost Telychian and upper Shein-woodian) are either yet to be studied in sufficient detail or do not show sufficient biologic speciation and/or extinction or carbon isotopic features to delineate such small time slices. Although producing such resolution during the Paleozoic presents an array of challenges unique to the era, we have begun to demonstrate that erecting a Paleozoic time scale comparable to that of younger eras is achievable. ?? 2010 Geological Society of America.

  6. Climate sensibility and stability of coastal dunes. Final report; Klimasensibilitaet und Stabiltaet nicht regenerierbarer Oekosysteme: Kuestenduenen. Schlussbericht

    Energy Technology Data Exchange (ETDEWEB)

    Handelmann, D.; Klittmann, T.; Badenhop, J.; Folger, M.

    2000-07-01

    Coastal dunes have an important function as unique habitats for plants and animals as well as natural barriers against storm tides. Thus, they are of special value for nature conservation and coastal defence issues. Facing their potential endangering due to accelerated climate change profound knowledge of stabilty of coastal dunes is essential. In this context the presented study deals with the impact of climate change on biogenic sand stabilization in coastal dunes, which have to be conceived as an ecosystemic process. Questions of climate affected reactions of organism groups involved in this process (plants, soil microflora, soil fauna) and alterations in soil structure were followed up. Within the scope of a 2-years-lasting field experiment conducted on the Eastfrisian Island Norderney the microclimate near the soil surface was modified by gauze covering, which was set up on field plots. (orig.) [German] In ihrer Funktion als Lebensraum fuer Pflanzen und Tiere sowie als natuerlicher Schutzwall bei Sturmfluten wird den Kuestenduenen eine wichtige Bedeutung im Natur- und Kuestenschutz beigemessen. Angesichts ihrer potentiellen Gefaehrdung durch einen beschleunigten Klimawandel ist ein fundierter Kenntnisstand zur Stabilitaet von Kuestenduenen von elementarem Interesse. Vor diesem Hintergrund befasst sich die vorliegende Studie mit dem Einfluss von Klimaaenderungen auf die biogene Sandstabilisierung in Kuestenduenen, die aufgrund des bestehenden organismischen Beziehungsgeflechtes als oekosystemarer Prozess aufzufassen ist. Dabei wurden Fragen nach klimaabhaengigen Reaktionen der an diesem Prozess beteiligten Organismengruppen (Pflanzen, Bodenmikroflora, Bodenfauna) und Veraenderungen des Bodengefueges bearbeitet. Im Rahmen eines 2-jaehrigen Freilandexperimentes auf der Ostfriesischen Insel Norderney wurde das bodennahe Mikroklima mittels einer Gazeueberspannung auf 4 m{sup 2} grossen und mit Strandhafer (Calammophila baltica) bepflanzten Parzellen experimentell

  7. Fault distribution in the Precambrian basement of South Norway

    Science.gov (United States)

    Gabrielsen, Roy H.; Nystuen, Johan Petter; Olesen, Odleiv

    2018-03-01

    Mapping of the structural pattern by remote sensing methods (Landsat, SPOT, aerial photography, potential field data) and field study of selected structural elements shows that the cratonic basement of South Norway is strongly affected by a regular lineament pattern that encompasses fault swarms of different orientation, age, style, attitude and frequency. Albeit counting numerous fault and fracture populations, the faults are not evenly distributed and N-S to NNE-SSW/NNW-SSE and NE-SE/ENE-WSW-systems are spatially dominant. N-S to NNW-SSE structures can be traced underneath the Caledonian nappes to the Western Gneiss Region in western and central South Norway, emphasizing their ancient roots. Dyke swarms of different ages are found within most of these zones. Also, the Østfold, Oslo-Trondheim and the Mandal-Molde lineament zones coincide with trends of Sveconorwegian post-collision granites. We conclude that the N-S-trend includes the most ancient structural elements, and that the trend can be traced back to the Proterozoic (Svecofennian and Sveconorwegian) orogenic events. Some of the faults may have been active in Neoproterozoic times as marginal faults of rift basins at the western margin of Baltica. Remnants of such fault activity have survived in the cores of many of the faults belonging to this system. The ancient systems of lineaments were passively overridden by the Caledonian fold-and-thrust system and remained mostly, but note entirely inactive throughout the Sub-Cambrian peneplanation and the Caledonian orogenic collapse in the Silurian-Devonian. The system was reactivated in extension from Carboniferous times, particularly in the Permian with the formation of the Oslo Rift and parts of it remain active to the Present, albeit by decreasing extension and fault activity.

  8. Large igneous provinces (LIPs) and carbonatites

    Science.gov (United States)

    Ernst, Richard E.; Bell, Keith

    2010-03-01

    There is increasing evidence that many carbonatites are linked both spatially and temporally with large igneous provinces (LIPs), i.e. high volume, short duration, intraplate-type, magmatic events consisting mainly of flood basalts and their plumbing systems (of dykes, sills and layered intrusions). Examples of LIP-carbonatite associations include: i. the 66 Ma Deccan flood basalt province associated with the Amba Dongar, Sarnu-Dandali (Barmer), and Mundwara carbonatites and associated alkali rocks, ii. the 130 Ma Paraná-Etendeka (e.g. Jacupiranga, Messum); iii. the 250 Ma Siberian LIP that includes a major alkaline province, Maimecha-Kotui with numerous carbonatites, iv. the ca. 370 Ma Kola Alkaline Province coeval with basaltic magmatism widespread in parts of the East European craton, and v. the 615-555 Ma CIMP (Central Iapetus Magmatic Province) of eastern Laurentia and western Baltica. In the Superior craton, Canada, a number of carbonatites are associated with the 1114-1085 Ma Keweenawan LIP and some are coeval with the pan-Superior 1880 Ma mafic-ultramafic magmatism. In addition, the Phalaborwa and Shiel carbonatites are associated with the 2055 Ma Bushveld event of the Kaapvaal craton. The frequency of this LIP-carbonatite association suggests that LIPs and carbonatites might be considered as different evolutionary ‘pathways’ in a single magmatic process/system. The isotopic mantle components FOZO, HIMU, EM1 but not DMM, along with primitive noble gas signatures in some carbonatites, suggest a sub-lithospheric mantle source for carbonatites, consistent with a plume/asthenospheric upwelling origin proposed for many LIPs.

  9. Endolithic microbial communities in carbonate precipitates from serpentinite-hosted hyperalkaline springs of the Voltri Massif (Ligurian Alps, Northern Italy).

    Science.gov (United States)

    Quéméneur, Marianne; Palvadeau, Alexandra; Postec, Anne; Monnin, Christophe; Chavagnac, Valérie; Ollivier, Bernard; Erauso, Gaël

    2015-09-01

    The Voltri Massif is an ophiolitic complex located in the Ligurian Alps close to the city of Genova (Northern Italy) where several springs discharge high pH (up to 11.7), low salinity waters produced by the active serpentinization of the ultramafic basement. Mixing of these hyperalkaline waters with the river waters along with the uptake of atmospheric carbon dioxide forms brownish carbonate precipitates covering the bedrock at the springs. Diverse archaeal and bacterial communities were detected in these carbonate precipitates using 454 pyrosequencing analyses of 16S ribosomal RNA (rRNA) genes. Archaeal communities were dominated by members of potential methane-producing and/or methane-oxidizing Methanobacteriales and Methanosarcinales (Euryarchaeota) together with ammonia-oxidizing Nitrososphaerales (Thaumarchaeota) similar to those found in other serpentinization-driven submarine and terrestrial ecosystems. Bacterial communities consisted of members of the Proteobacteria, Actinobacteria, Planctomycetes, Bacteroidetes, Chloroflexi, and Verrucomicrobia phyla, altogether accounting for 92.2% of total retrieved bacterial 16S rRNA gene sequences. Amongst Bacteria, potential chemolithotrophy was mainly associated with Alpha- and Betaproteobacteria classes, including nitrogen-fixing, methane-oxidizing or hydrogen-oxidizing representatives of the genera Azospirillum, Methylosinus, and Hydrogenophaga/'Serpentinomonas', respectively. Besides, potential chemoorganotrophy was attributed mainly to representatives of Actinobacteria and Planctomycetales phyla. The reported 16S rRNA gene data strongly suggested that hydrogen, methane, and nitrogen-based chemolithotrophy can sustain growth of the microbial communities inhabiting the carbonate precipitates in the hyperalkaline springs of the Voltri Massif, similarly to what was previously observed in other serpentinite-hosted ecosystems.

  10. Microbial diversity in hummock and hollow soils of three wetlands on the Qinghai-Tibetan Plateau revealed by 16S rRNA pyrosequencing.

    Directory of Open Access Journals (Sweden)

    Yongcui Deng

    Full Text Available The wetlands of the Qinghai-Tibetan Plateau are believed to play an important role in global nutrient cycling, but the composition and diversity of microorganisms in this ecosystem are poorly characterized. An understanding of the effects of geography and microtopography on microbial populations will provide clues to the underlying mechanisms that structure microbial communities. In this study, we used pyrosequencing-based analysis of 16S rRNA gene sequences to assess and compare the composition of soil microbial communities present in hummock and hollow soils from three wetlands (Dangxiong, Hongyuan and Maduo on the Qinghai-Tibetan Plateau, the world's highest plateau. A total of 36 bacterial phyla were detected. Proteobacteria (34.5% average relative abundance, Actinobacteria (17.3% and Bacteroidetes (11% had the highest relative abundances across all sites. Chloroflexi, Acidobacteria, Verrucomicrobia, Firmicutes, and Planctomycetes were also relatively abundant (1-10%. In addition, archaeal sequences belonging to Euryarchaea, Crenarchaea and Thaumarchaea were detected. Alphaproteobacteria sequences, especially of the order Rhodospirillales, were significantly more abundant in Maduo than Hongyuan and Dangxiong wetlands. Compared with Hongyuan soils, Dangxiong and Maduo had significantly higher relative abundances of Gammaproteobacteria sequences (mainly order Xanthomonadales. Hongyuan wetland had a relatively high abundance of methanogens (mainly genera Methanobacterium, Methanosarcina and Methanosaeta and methanotrophs (mainly Methylocystis compared with the other two wetlands. Principal coordinate analysis (PCoA indicated that the microbial community structure differed between locations and microtopographies and canonical correspondence analysis indicated an association between microbial community structure and soil properties or geography. These insights into the microbial community structure and the main controlling factors in wetlands of

  11. Microbial diversity in hummock and hollow soils of three wetlands on the Qinghai-Tibetan Plateau revealed by 16S rRNA pyrosequencing.

    Science.gov (United States)

    Deng, Yongcui; Cui, Xiaoyong; Hernández, Marcela; Dumont, Marc G

    2014-01-01

    The wetlands of the Qinghai-Tibetan Plateau are believed to play an important role in global nutrient cycling, but the composition and diversity of microorganisms in this ecosystem are poorly characterized. An understanding of the effects of geography and microtopography on microbial populations will provide clues to the underlying mechanisms that structure microbial communities. In this study, we used pyrosequencing-based analysis of 16S rRNA gene sequences to assess and compare the composition of soil microbial communities present in hummock and hollow soils from three wetlands (Dangxiong, Hongyuan and Maduo) on the Qinghai-Tibetan Plateau, the world's highest plateau. A total of 36 bacterial phyla were detected. Proteobacteria (34.5% average relative abundance), Actinobacteria (17.3%) and Bacteroidetes (11%) had the highest relative abundances across all sites. Chloroflexi, Acidobacteria, Verrucomicrobia, Firmicutes, and Planctomycetes were also relatively abundant (1-10%). In addition, archaeal sequences belonging to Euryarchaea, Crenarchaea and Thaumarchaea were detected. Alphaproteobacteria sequences, especially of the order Rhodospirillales, were significantly more abundant in Maduo than Hongyuan and Dangxiong wetlands. Compared with Hongyuan soils, Dangxiong and Maduo had significantly higher relative abundances of Gammaproteobacteria sequences (mainly order Xanthomonadales). Hongyuan wetland had a relatively high abundance of methanogens (mainly genera Methanobacterium, Methanosarcina and Methanosaeta) and methanotrophs (mainly Methylocystis) compared with the other two wetlands. Principal coordinate analysis (PCoA) indicated that the microbial community structure differed between locations and microtopographies and canonical correspondence analysis indicated an association between microbial community structure and soil properties or geography. These insights into the microbial community structure and the main controlling factors in wetlands of the Qinghai

  12. Sediment Microbial Communities Influenced by Cool Hydrothermal Fluid Migration

    Directory of Open Access Journals (Sweden)

    Laura A. Zinke

    2018-06-01

    Full Text Available Cool hydrothermal systems (CHSs are prevalent across the seafloor and discharge fluid volumes that rival oceanic input from rivers, yet the microbial ecology of these systems are poorly constrained. The Dorado Outcrop on the ridge flank of the Cocos Plate in the northeastern tropical Pacific Ocean is the first confirmed CHS, discharging minimally altered <15°C fluid from the shallow lithosphere through diffuse venting and seepage. In this paper, we characterize the resident sediment microbial communities influenced by cool hydrothermal advection, which is evident from nitrate and oxygen concentrations. 16S rRNA gene sequencing revealed that Thaumarchaea, Proteobacteria, and Planctomycetes were the most abundant phyla in all sediments across the system regardless of influence from seepage. Members of the Thaumarchaeota (Marine Group I, Alphaproteobacteria (Rhodospirillales, Nitrospirae, Nitrospina, Acidobacteria, and Gemmatimonadetes were enriched in the sediments influenced by CHS advection. Of the various geochemical parameters investigated, nitrate concentrations correlated best with microbial community structure, indicating structuring based on seepage of nitrate-rich fluids. A comparison of microbial communities from hydrothermal sediments, seafloor basalts, and local seawater at Dorado Outcrop showed differences that highlight the distinct niche space in CHS. Sediment microbial communities from Dorado Outcrop differ from those at previously characterized, warmer CHS sediment, but are similar to deep-sea sediment habitats with surficial ferromanganese nodules, such as the Clarion Clipperton Zone. We conclude that cool hydrothermal venting at seafloor outcrops can alter the local sedimentary oxidation–reduction pathways, which in turn influences the microbial communities within the fluid discharge affected sediment.

  13. Communities of archaea and bacteria in a subsurface radioactive thermal spring in the Austrian Central Alps, and evidence of ammonia-oxidizing Crenarchaeota.

    Science.gov (United States)

    Weidler, Gerhard W; Dornmayr-Pfaffenhuemer, Marion; Gerbl, Friedrich W; Heinen, Wolfgang; Stan-Lotter, Helga

    2007-01-01

    Scanning electron microscopy revealed great morphological diversity in biofilms from several largely unexplored subterranean thermal Alpine springs, which contain radium 226 and radon 222. A culture-independent molecular analysis of microbial communities on rocks and in the water of one spring, the "Franz-Josef-Quelle" in Bad Gastein, Austria, was performed. Four hundred fifteen clones were analyzed. One hundred thirty-two sequences were affiliated with 14 bacterial operational taxonomic units (OTUs) and 283 with four archaeal OTUs. Rarefaction analysis indicated a high diversity of bacterial sequences, while archaeal sequences were less diverse. The majority of the cloned archaeal 16S rRNA gene sequences belonged to the soil-freshwater-subsurface (1.1b) crenarchaeotic group; other representatives belonged to the freshwater-wastewater-soil (1.3b) group, except one clone, which was related to a group of uncultivated Euryarchaeota. These findings support recent reports that Crenarchaeota are not restricted to high-temperature environments. Most of the bacterial sequences were related to the Proteobacteria (alpha, beta, gamma, and delta), Bacteroidetes, and Planctomycetes. One OTU was allied with Nitrospina sp. (delta-Proteobacteria) and three others grouped with Nitrospira. Statistical analyses suggested high diversity based on 16S rRNA gene analyses; the rarefaction plot of archaeal clones showed a plateau. Since Crenarchaeota have been implicated recently in the nitrogen cycle, the spring environment was probed for the presence of the ammonia monooxygenase subunit A (amoA) gene. Sequences were obtained which were related to crenarchaeotic amoA genes from marine and soil habitats. The data suggested that nitrification processes are occurring in the subterranean environment and that ammonia may possibly be an energy source for the resident communities.

  14. Habitat conditions drive phylogenetic structure of dominant bacterial phyla of microbialite communities from different locations in Mexico.

    Science.gov (United States)

    Centeno, Carla M; Mejía, Omar; Falcón, Luisa I

    2016-09-01

    Community structure and composition are dictated by evolutionary and ecological assembly processes which are manifested in signals of, species diversity, species abundance and species relatedness. Analysis of species coexisting relatedness, has received attention as a tool to identify the processes that influence the composition of a community within a particular habitat. In this study, we tested if microbialite genetic composition is dependent on random events versus biological/abiotical factors. This study was based on a large genetic data set of two hypervariable regions (V5 and V6) from previously generated barcoded 16S rRNA amplicons from nine microbialite communities distributed in Northeastern, Central and Southeastern Mexico collected in May and June of 2009. Genetic data of the most abundant phyla (Proteobacteria, Planctomycetes, Verrucomicrobia, Bacteroidetes, and Cyanobacteria) were investigated in order to state the phylogenetic structure of the complete communities as well as each phylum. For the complete dataset, Webb NTI index showed positive and significant values in the nine communities analysed, where values ranged from 31.5 in Pozas Azules I to 57.2 in Bacalar Pirate Channel; meanwhile, NRI index were positive and significant in six of the nine communities analysed with values ranging from 18.1 in Pozas Azules I to 45.1 in Río Mesquites. On the other hand, when comparing each individual phylum, NTI index were positive and significant in all groups, except in Cyanobacteria for which positive and significant values were only found in three localities; finally, NRI index was significant in only a few of the comparisons performed. The results suggest that habitat filtering is the main process that drives phylogenetic structure in bacterial communities associated to microbialites with the exception of Cyanobacteria where different lineages can contribute to microbialite formation and growth.

  15. High bacterial diversity in epilithic biofilms of oligotrophic mountain lakes.

    Science.gov (United States)

    Bartrons, Mireia; Catalan, Jordi; Casamayor, Emilio O

    2012-11-01

    Benthic microbial biofilms attached to rocks (epilithic) are major sites of carbon cycling and can dominate ecosystem primary production in oligotrophic lakes. We studied the bacterial community composition of littoral epilithic biofilms in five connected oligotrophic high mountain lakes located at different altitudes by genetic fingerprinting and clone libraries of the 16S rRNA gene. Different intra-lake samples were analyzed, and consistent changes in community structure (chlorophyll a and organic matter contents, and bacterial community composition) were observed along the altitudinal gradient, particularly related with the location of the lake above or below the treeline. Epilithic biofilm genetic fingerprints were both more diverse among lakes than within lakes and significantly different between montane (below the tree line) and alpine lakes (above the tree line). The genetic richness in the epilithic biofilm was much higher than in the plankton of the same lacustrine area studied in previous works, with significantly idiosyncratic phylogenetic composition (specifically distinct from lake plankton or mountain soils). Data suggest the coexistence of aerobic, anaerobic, phototrophic, and chemotrophic microorganisms in the biofilm, Bacteroidetes and Cyanobacteria being the most important bacterial taxa, followed by Alpha-, Beta-, Gamma-, and Deltaproteobacteria, Chlorobi, Planctomycetes, and Verrucomicrobia. The degree of novelty was especially high for epilithic Bacteroidetes, and up to 50 % of the sequences formed monophyletic clusters distantly related to any previously reported sequence. More than 35 % of the total sequences matched at <95 % identity to any previously reported 16S rRNA gene, indicating that alpine epilithic biofilms are unexplored habitats that contain a substantial degree of novelty within a short geographical distance. Further research is needed to determine whether these communities are involved in more biogeochemical pathways than

  16. Species specificity of bacteria associated to the brown seaweeds Lobophora (Dictyotales, Phaeophyceae and their potential for induction of rapid coral bleaching in Acropora muricata

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    Christophe William Vieira

    2016-03-01

    Full Text Available While reef degradation is occurring worldwide, it is not uncommon to see phase shifts from coral to macroalgal dominated reefs. Numerous studies have addressed the mechanisms by which macroalgae may outcompete corals and a few recent studies highlighted the putative role of bacteria at the interface between macroalgae and corals. Some studies suggest that macroalgae may act as vectors and/or foster proliferation of microorganisms pathogenic for corals. Using a combination of high throughput sequencing, bacterial culturing and in situ bioassays we question if the adversity of macroalgal-associated bacteria to corals is mediated by specific bacterial taxa. Using Illumina sequencing, we characterized and compared the bacterial community from two Lobophora (Dictyotales, Phaeophyceae species. The two species presented distinctive bacterial communities. Both species shared approximately half of their OTUs, mainly the most abundant bacteria. Species-specific OTUs belong to Planctomycetes, Proteobacteria and Bacteroidetes. In total, 16 culturable bacterial strain were isolated and identified from the Lobophora surface, consisting of 10 genera (from 9 families, 4 classes and 3 phyla, some of which are not known as, but are related to pathogens involved in coral diseases, and others naturally associated to corals. When patches of marine agar with 24 h cultures of each of these bacteria were placed in direct contact with the branches of the scleractinian coral Acropora muricata, they caused severe bleaching after 24 h exposure. Results suggest that regardless of taxonomic affinities, increase in density of any bacteria can be adverse to corals. Nevertheless, the microbial community associated to macroalgal surface may not represent a threat to corals, because the specific bacterial screening and control exerted by the alga preventing specific bacterial proliferation.

  17. Microbial community structure of relict niter-beds previously used for saltpeter production.

    Directory of Open Access Journals (Sweden)

    Takashi Narihiro

    Full Text Available From the 16th to the 18th centuries in Japan, saltpeter was produced using a biological niter-bed process and was formed under the floor of gassho-style houses in the historic villages of Shirakawa-go and Gokayama, which are classified as United Nations Educational, Scientific and Cultural Organization (UNESCO World Heritage Sites. The relict niter-beds are now conserved in the underfloor space of gassho-style houses, where they are isolated from destabilizing environmental factors and retain the ability to produce nitrate. However, little is known about the nitrifying microbes in such relict niter-bed ecosystems. In this study, the microbial community structures within nine relict niter-bed soils were investigated using 454 pyrotag analysis targeting the 16S rRNA gene and the bacterial and archaeal ammonia monooxygenase gene (amoA. The 16S rRNA gene pyrotag analysis showed that members of the phyla Proteobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Gemmatimonadetes, and Planctomycetes were major microbial constituents, and principal coordinate analysis showed that the NO3-, Cl-, K+, and Na+ contents were potential determinants of the structures of entire microbial communities in relict niter-bed soils. The bacterial and archaeal amoA libraries indicated that members of the Nitrosospira-type ammonia-oxidizing bacteria (AOB and "Ca. Nitrososphaera"-type ammonia-oxidizing archaea (AOA, respectively, predominated in relict niter-bed soils. In addition, soil pH and organic carbon content were important factors for the ecological niche of AOB and AOA in relict niter-bed soil ecosystems.

  18. Bacterial diversity in the bottom boundary layer of the inner continental shelf of Oregon, USA

    KAUST Repository

    Bertagnolli, AD

    2011-06-21

    There have been few studies of the bacterial community within the bottom boundary layer (BBL) the turbulent region of the water column above the benthos in shallow seas. Typically, the BBL has large amounts of particulate organic matter suspended by turbulence, and it is often the first region of the water column to become hypoxic when oxygen declines. Communities at the surface (5 m) and in the BBL (1 to 10 m above the sea floor) were compared by terminal restriction fragment length polymorphism (T-RFLP) analysis and sequencing of the 16S rRNA gene. Multivariate statistical methods (hierarchical clustering, non-metric multidimensional scaling, and analysis of similarity (ANOSIM)) indicated that the microbial community of the BBL is distinct from the surface community. ANOSIM supported the distinction between surface and BBLs (R values 0.427 and 0.463, based on analysis with restriction enzymes BsuR1 and Hin6I, respectively, p < 0.1%). Six terminal restriction fragments showed an increase in abundance with depth. Cloning, screening and sequencing identified these as a novel environmental clade (Eastern North Pacific Chromatiales (ENPC) clade), the ARTIC96BD-19 clade of Gammaproteobacteria, the 6N14 and Agg8 clades of the phylum Planctomycetes, the OM60/NOR5 clade of Gammaproteobacteria, and uncultivated members of the Roseobacter clade in the MB11C09 and ULA23 subgroups. To the best of our knowledge, this analysis is the first to focus on the unique composition of microbial communities of the BBL in shallow, inner-shelf regions off the coast of Oregon, USA, and the first to report that an uncharacterized clade of Chromatiales is indigenous in this habitat.

  19. Microbial community structures in high rate algae ponds for bioconversion of agricultural wastes from livestock industry for feed production.

    Science.gov (United States)

    Mark Ibekwe, A; Murinda, Shelton E; Murry, Marcia A; Schwartz, Gregory; Lundquist, Trygve

    2017-02-15

    Dynamics of seasonal microbial community compositions in algae cultivation ponds are complex. However, there is very limited knowledge on bacterial communities that may play significant roles with algae in the bioconversion of manure nutrients to animal feed. In this study, water samples were collected during winter, spring, summer, and fall from the dairy lagoon effluent (DLE), high rate algae ponds (HRAP) that were fed with diluted DLE, and municipal waste water treatment plant (WWTP) effluent which was included as a comparison system for the analysis of total bacteria, Cyanobacteria, and microalgae communities using MiSeq Illumina sequencing targeting the 16S V4 rDNA region. The main objective was to examine dynamics in microbial community composition in the HRAP used for the production of algal biomass. DNA was extracted from the different sample types using three commercially available DNA extraction kits; MoBio Power water extraction kit, Zymo fungi/bacterial extraction kit, and MP Biomedicals FastDNA SPIN Kit. Permutational analysis of variance (PERMANOVA) using distance matrices on each variable showed significant differences (P=0.001) in beta-diversity based on sample source. Environmental variables such as hydraulic retention time (HRT; P<0.031), total N (P<0.002), total inorganic N (P<0.002), total P (P<0.002), alkalinity (P<0.002), pH (P<0.022), total suspended solid (TSS; P<0.003), and volatile suspended solids (VSS; P<0.002) significantly affected microbial communities in DLE, HRAP, and WWTP. Of the operational taxonomic units (OTUs) identified to phyla level, the dominant classes of bacteria identified were: Cyanobacteria, Alpha-, Beta-, Gamma-, Epsilon-, and Delta-proteobacteria, Bacteroidetes, Firmicutes, and Planctomycetes. Our data suggest that microbial communities were significantly affected in HRAP by different environmental variables, and care must be taken in extraction procedures when evaluating specific groups of microbial communities for

  20. Biogeography of Deep-sea benthic bacteria at regional scale (LTER HAUSGARTEN, Fram Strait, Arctic.

    Directory of Open Access Journals (Sweden)

    Marianne Jacob

    Full Text Available Knowledge on spatial scales of the distribution of deep-sea life is still sparse, but highly relevant to the understanding of dispersal, habitat ranges and ecological processes. We examined regional spatial distribution patterns of the benthic bacterial community and covarying environmental parameters such as water depth, biomass and energy availability at the Arctic Long-Term Ecological Research (LTER site HAUSGARTEN (Eastern Fram Strait. Samples from 13 stations were retrieved from a bathymetric (1,284-3,535 m water depth, 54 km in length and a latitudinal transect (∼ 2,500 m water depth; 123 km in length. 454 massively parallel tag sequencing (MPTS and automated ribosomal intergenic spacer analysis (ARISA were combined to describe both abundant and rare types shaping the bacterial community. This spatial sampling scheme allowed detection of up to 99% of the estimated richness on phylum and class levels. At the resolution of operational taxonomic units (97% sequence identity; OTU3% only 36% of the Chao1 estimated richness was recovered, indicating a high diversity, mostly due to rare types (62% of all OTU3%. Accordingly, a high turnover of the bacterial community was also observed between any two sampling stations (average replacement of 79% of OTU3%, yet no direct correlation with spatial distance was observed within the region. Bacterial community composition and structure differed significantly with increasing water depth along the bathymetric transect. The relative sequence abundance of Verrucomicrobia and Planctomycetes decreased significantly with water depth, and that of Deferribacteres increased. Energy availability, estimated from phytodetrital pigment concentrations in the sediments, partly explained the variation in community structure. Overall, this study indicates a high proportion of unique bacterial types on relatively small spatial scales (tens of kilometers, and supports the sampling design of the LTER site HAUSGARTEN to

  1. A metagenomic approach to decipher the indigenous microbial communities of arsenic contaminated groundwater of Assam

    Directory of Open Access Journals (Sweden)

    Saurav Das

    2017-06-01

    Full Text Available Metagenomic approach was used to understand the structural and functional diversity present in arsenic contaminated groundwater of the Ganges Brahmaputra Delta aquifer system. A metagene dataset (coded as TTGW1 of 89,171 sequences (totaling 125,449,864 base pairs with an average length of 1406 bps was annotated. About 74,478 sequences containing 101,948 predicted protein coding regions passed the quality control. Taxonomical classification revealed abundance of bacteria that accounted for 98.3% of the microbial population of the metagenome. Eukaryota had an abundance of 1.1% followed by archea that showed 0.4% abundance. In phylum based classification, Proteobacteria was dominant (62.6% followed by Bacteroidetes (11.7%, Planctomycetes (7.7%, Verrucomicrobia (5.6%, Actinobacteria (3.7% and Firmicutes (1.9%. The Clusters of Orthologous Groups (COGs analysis indicated that the protein regulating the metabolic functions constituted a high percentage (18,199 reads; 39.3% of the whole metagenome followed by the proteins regulating the cellular processes (22.3%. About 0.07% sequences of the whole metagenome were related to genes coding for arsenic resistant mechanisms. Nearly 50% sequences of these coded for the arsenate reductase enzyme (EC. 1.20.4.1, the dominant enzyme of ars operon. Proteins associated with iron acquisition and metabolism were coded by 2% of the metagenome as revealed through SEED analysis. Our study reveals the microbial diversity and provides an insight into the functional aspect of the genes that might play crucial role in arsenic geocycle in contaminated ground water of Assam.

  2. Succession of Bacterial Community Structure and Diversity in Soil along a Chronosequence of Reclamation and Re-Vegetation on Coal Mine Spoils in China

    Science.gov (United States)

    Li, Yuanyuan; Wen, Hongyu; Chen, Longqian; Yin, Tingting

    2014-01-01

    The growing concern about the effectiveness of reclamation strategies has motivated the evaluation of soil properties following reclamation. Recovery of belowground microbial community is important for reclamation success, however, the response of soil bacterial communities to reclamation has not been well understood. In this study, PCR-based 454 pyrosequencing was applied to compare bacterial communities in undisturbed soils with those in reclaimed soils using chronosequences ranging in time following reclamation from 1 to 20 year. Bacteria from the Proteobacteria, Chloroflexi, Actinobacteria, Acidobacteria, Planctomycetes and Bacteroidetes were abundant in all soils, while the composition of predominant phyla differed greatly across all sites. Long-term reclamation strongly affected microbial community structure and diversity. Initial effects of reclamation resulted in significant declines in bacterial diversity indices in younger reclaimed sites (1, 8-year-old) compared to the undisturbed site. However, bacterial diversity indices tended to be higher in older reclaimed sites (15, 20-year-old) as recovery time increased, and were more similar to predisturbance levels nearly 20 years after reclamation. Bacterial communities are highly responsive to soil physicochemical properties (pH, soil organic matter, Total N and P), in terms of both their diversity and community composition. Our results suggest that the response of soil microorganisms to reclamation is likely governed by soil characteristics and, indirectly, by the effects of vegetation restoration. Mixture sowing of gramineae and leguminosae herbage largely promoted soil geochemical conditions and bacterial diversity that recovered to those of undisturbed soil, representing an adequate solution for soil remediation and sustainable utilization for agriculture. These results confirm the positive impacts of reclamation and vegetation restoration on soil microbial diversity and suggest that the most important

  3. Diffuse flow environments within basalt- and sediment-based hydrothermal vent ecosystems harbor specialized microbial communities.

    Science.gov (United States)

    Campbell, Barbara J; Polson, Shawn W; Zeigler Allen, Lisa; Williamson, Shannon J; Lee, Charles K; Wommack, K Eric; Cary, S Craig

    2013-01-01

    Hydrothermal vents differ both in surface input and subsurface geochemistry. The effects of these differences on their microbial communities are not clear. Here, we investigated both alpha and beta diversity of diffuse flow-associated microbial communities emanating from vents at a basalt-based hydrothermal system along the East Pacific Rise (EPR) and a sediment-based hydrothermal system, Guaymas Basin. Both Bacteria and Archaea were targeted using high throughput 16S rRNA gene pyrosequencing analyses. A unique aspect of this study was the use of a universal set of 16S rRNA gene primers to characterize total and diffuse flow-specific microbial communities from varied deep-sea hydrothermal environments. Both surrounding seawater and diffuse flow water samples contained large numbers of Marine Group I (MGI) Thaumarchaea and Gammaproteobacteria taxa previously observed in deep-sea systems. However, these taxa were geographically distinct and segregated according to type of spreading center. Diffuse flow microbial community profiles were highly differentiated. In particular, EPR dominant diffuse flow taxa were most closely associated with chemolithoautotrophs, and off axis water was dominated by heterotrophic-related taxa, whereas the opposite was true for Guaymas Basin. The diversity and richness of diffuse flow-specific microbial communities were strongly correlated to the relative abundance of Epsilonproteobacteria, proximity to macrofauna, and hydrothermal system type. Archaeal diversity was higher than or equivalent to bacterial diversity in about one third of the samples. Most diffuse flow-specific communities were dominated by OTUs associated with Epsilonproteobacteria, but many of the Guaymas Basin diffuse flow samples were dominated by either OTUs within the Planctomycetes or hyperthermophilic Archaea. This study emphasizes the unique microbial communities associated with geochemically and geographically distinct hydrothermal diffuse flow environments.

  4. The abundance of functional genes, cbbL, nifH, amoA and apsA, and bacterial community structure of intertidal soil from Arabian Sea.

    Science.gov (United States)

    Keshri, Jitendra; Yousuf, Basit; Mishra, Avinash; Jha, Bhavanath

    2015-06-01

    The Gulf of Cambay is a trumpet-shaped inlet of the Arabian Sea, located along the west coast of India and confronts a high tidal range with strong water currents. The region belongs to a semi-arid zone and saline alkaline intertidal soils are considered biologically extreme. The selected four soil types (S1-S4) were affected by salinity, alkalinity and sodicity. Soil salinity ranged from 20 to 126 dS/m, soil pH 8.6-10.0 with high sodium adsorption ratio (SAR) and exchangeable sodium percentage (ESP). Abundance of the key functional genes like cbbL, nifH, amoA and apsA involved in biogeochemical cycling were targeted using qPCR, which varied from (2.36 ± 0.03) × 10(4) to (2.87 ± 0.26) × 10(8), (1.18 ± 0.28) × 10(6) to (1.01 ± 0.26) × 10(9), (1.41 ± 0.21) × 10(6) to (1.29 ± 0.05) × 10(8) and (8.47 ± 0.23) × 10(4) to (1.73 ± 0.01) × 10(6) per gram dry weight, respectively. The microbial community structure revealed that soils S1 and S3 were dominated by phylum Firmicutes whereas S4 and S2 showed an abundance of Proteobacterial clones. These soils also represented Bacteroidetes, Chloroflexi, Actinobacteria, Planctomycetes and Acidobacteria clones. Molecular phylogeny showed a significant variation in the bacterial community distribution among the intertidal soil types. A high number of novel taxonomic units were observed which makes the intertidal zone a unique reservoir of unidentified bacterial taxa that may be explored further. Copyright © 2015 Elsevier GmbH. All rights reserved.

  5. Patterns of Bacterial and Archaeal Gene Expression through the Lower Amazon River

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    Brandon M. Satinsky

    2017-08-01

    Full Text Available Analysis of metatranscriptomic and metagenomic datasets from the lower reaches of the Amazon River between Óbidos and the river mouth revealed microbial transcript and gene pools dominated by Actinobacteria, Thaumarchaeota, Bacteroidetes, Acidobacteria, Betaproteobacteria, and Planctomycetes. Three mainstem stations spanning a 625 km reach had similar gene expression patterns (transcripts gene copy−1 across a diverse suite of element cycling genes, but two tributary-influenced stations at the mouth of the Tapajós River and near the Tocantins River at Belém had distinct transcriptome composition and expression ratios, particularly for genes encoding light-related energy capture (higher and iron acquisition and ammonia oxidation (lower. Environmental parameters that were useful predictors of gene expression ratios included concentrations of lignin phenols, suspended sediments, nitrate, phosphate, and particulate organic carbon and nitrogen. Similar to the gene expression data, these chemical properties reflected highly homogeneous mainstem stations punctuated by distinct tributary-influenced stations at Tapajós and Belém. Although heterotrophic processes were expected to dominate in the lower Amazon, transcripts from photosynthetic bacteria were abundant in tributary-influenced regions, and transcripts from Thaumarcheota taxa genetically capable of chemosynthetic ammonia oxidation accounted for up to 21% of the transcriptome at others. Based on regressions of transcript numbers against gene numbers, expression ratios of Thaumarchaeota populations were largely unchanged within the mainstem, suggesting a relatively minor role for gene regulation. These quantitative gene and transcript inventories detail a diverse array of energy acquisition strategies and metabolic capabilities for bacteria and archaea populations of the world's largest river system.

  6. Taxonomic and functional characteristics of microbial communities and their correlation with physicochemical properties of four geothermal springs in Odisha, India.

    Science.gov (United States)

    Badhai, Jhasketan; Ghosh, Tarini S; Das, Subrata K

    2015-01-01

    This study describes microbial diversity in four tropical hot springs representing moderately thermophilic environments (temperature range: 40-58°C; pH: 7.2-7.4) with discrete geochemistry. Metagenome sequence data showed a dominance of Bacteria over Archaea; the most abundant phyla were Chloroflexi and Proteobacteria, although other phyla were also present, such as Acetothermia, Nitrospirae, Acidobacteria, Firmicutes, Deinococcus-Thermus, Bacteroidetes, Thermotogae, Euryarchaeota, Verrucomicrobia, Ignavibacteriae, Cyanobacteria, Actinobacteria, Planctomycetes, Spirochaetes, Armatimonadetes, Crenarchaeota, and Aquificae. The distribution of major genera and their statistical correlation analyses with the physicochemical parameters predicted that the temperature, aqueous concentrations of ions (such as sodium, chloride, sulfate, and bicarbonate), total hardness, dissolved solids and conductivity were the main environmental variables influencing microbial community composition and diversity. Despite the observed high taxonomic diversity, there were only little variations in the overall functional profiles of the microbial communities in the four springs. Genes involved in the metabolism of carbohydrates and carbon fixation were the most abundant functional class of genes present in these hot springs. The distribution of genes involved in carbon fixation predicted the presence of all the six known autotrophic pathways in the metagenomes. A high prevalence of genes involved in membrane transport, signal transduction, stress response, bacterial chemotaxis, and flagellar assembly were observed along with genes involved in the pathways of xenobiotic degradation and metabolism. The analysis of the metagenomic sequences affiliated to the candidate phylum Acetothermia from spring TB-3 provided new insight into the metabolism and physiology of yet-unknown members of this lineage of bacteria.

  7. Composition and function of the microbial community related with the nitrogen cycling on the potato rhizosphere

    International Nuclear Information System (INIS)

    Florez Zapata, Nathalia; Garcia, Juan Carlos; Del Portillo, Patricia; Restrepo, Silvia; Uribe Velez, Daniel

    2013-01-01

    In the S. tuberosum group phureja crops, mineral fertilizer and organic amendments are applied to meet the plants nutritional demands, however the effect of such practices on the associated rizospheric microbial communities are still unknown. Nitrogen plays an important role in agricultural production, and a great diversity of microorganisms regulates its transformation in the soil, affecting its availability for the plant. The aim of this study was to assess the structure of microbial communities related with the N cycle of S. tuberosum group phureja rizospheric soil samples, with contrasting physical-chemical properties and fertilization strategy. Few significant differences between the community compositions at the phylum level were found, only Planctomycetes phylum was different between samples of different soil type and fertilization strategy. However, the analysis of nitrogen-associated functional groups made by ribotyping characterization, grouped soils in terms of such variables in a similar way to the physical-chemical properties. Major differences between soil samples were typified by higher percentages of the ribotypes from nitrite oxidation, nitrogen fixation and denitrification on organic amendment soils. Our results suggest that, the dominant rhizosphere microbial composition is very similar between soils, possibly as a result of population's selection mediated by the rhizosphere effect. However, agricultural management practices in addition to edaphic properties of sampled areas appear to affect some functional groups associated with the nitrogen cycling, due to differences found on soil's physicalchemical properties, like the concentration of ammonium that seems to have an effect regulating the distribution and activity of nitrogen related functional groups in the S. tuberosum rhizosphere.

  8. Linking Activity and Function to Ecosystem Dynamics in a Coastal Bacterioplankton Community

    Directory of Open Access Journals (Sweden)

    Scott Michael Gifford

    2014-04-01

    Full Text Available For bacterial communities containing hundreds to thousands of distinct populations, connecting functional processes and environmental dynamics at high taxonomic resolution has remained challenging. Here we use the expression of ribosomal proteins (%RP as a proxy for in situ activity of 200 taxa within 20 metatranscriptomic samples in a coastal ocean time series encompassing both seasonal variability and diel dynamics. %RP patterns grouped the taxa into seven activity clusters with distinct profiles in functional gene expression and correlations with environmental gradients. Clusters 1-3 had their highest potential activity in the winter and fall, and included some of the most active taxa, while Clusters 4-7 had their highest potential activity in the spring and summer. Cluster 1 taxa were characterized by gene expression for motility and complex carbohydrate degradation (dominated by Gammaproteobacteria and Bacteroidetes, and Cluster 2 taxa by transcription of genes for amino acid and aromatic compound metabolism and aerobic anoxygenic phototrophy (Roseobacter. Other activity clusters were enriched in transcripts for proteorhodopsin and methylotrophy (Cluster 4; SAR11 and methylotrophs, photosynthesis and attachment (Clusters 5 and 7; Synechococcus, picoeukaryotes, Verucomicrobia, and Planctomycetes, and sulfur oxidation (Cluster 7; Gammaproteobacteria. The seasonal patterns in activity were overlain, and sometimes obscured, by large differences in %RP over shorter day-night timescales. Seventy-eight taxa, many of them heterotrophs, had a higher %RP activity index during the day than night, indicating strong diel activity at this coastal site. Emerging from these taxonomically- and time-resolved estimates of in situ microbial activity are predictions of specific ecological groupings of microbial taxa in a dynamic coastal environment.

  9. Micro-organisms and divers exposure to radioactivity in spent fuel pools at nuclear power plants

    Energy Technology Data Exchange (ETDEWEB)

    Muniz de A, D. [Underwater Construction Corporation, Latin America, Fortaleza, Ceara (Brazil); Silva, R. [Universidade Federal do Rio de Janeiro, Instituto de Biofisica Carlos Chagas Filho, 21941-902 Rio de Janeiro (Brazil); Gomes N, C. A., E-mail: dmuniz@uccdive.com [Universidade Federal do Rio de Janeiro, Instituto de Biologia, Environmental Engineering Program, 21941-902 Rio de Janeiro (Brazil)

    2017-09-15

    Many nuclear power plants (NPPs) around the world are in the process of extending their lifespan from 40 to 60 years of operation. The NPP; Angra 1 (Brazil) has performed a thorough evaluation of its Life Extension Engineering project. In this context, the spent fuel pool (SFP) was one of the areas studied in order to demonstrate the plants integrity for a life extension. Micro-organisms growing on the liner of the fuel transfer channel (Ftc) and SFP can form a film of bacteria, which is highly resistant to radiation. This paper aims to compare the micro-organisms found in NPP Angra 1 with those reported to other NPPs and also relates their occurrence with the radiation levels at the sites. It also compares divers exposure to radioactivity during underwater activities in the SFP. Fourteen samples were collected on the surface of the liners of the Ftc, the SFP and the drains within the fuel building (FB) of Angra 1. For the identification of the micro-organisms, a metagenomics analysis was performed by random sequencing (Shotgun) and the use of Ion Torrent PGM Sequence r. Twelve micro-organisms phyla were identified; Acido-bacteria, Actino-bacteria, Bacteroidetes, Chlamydiae, Chlorobi, Chloroflexi, Cyano-bacteria, Deinococcus-Thermus, Firmicutes, Planctomycetes, Proteo-bacteria, and Verrucomicrobia as well as organisms not classified. In the SFP of Angra 1, the bacteria survived the exposure to a radiation of 0.416 Gy/h (high radiation). Deinococcus-thermus, bacteria identified in Angra 1, has resisted an exposure to 30,000 Gy/h in another plant. (Author)

  10. Microbial community composition of transiently wetted Antarctic Dry Valley soils.

    Science.gov (United States)

    Niederberger, Thomas D; Sohm, Jill A; Gunderson, Troy E; Parker, Alexander E; Tirindelli, Joëlle; Capone, Douglas G; Carpenter, Edward J; Cary, Stephen C

    2015-01-01

    During the summer months, wet (hyporheic) soils associated with ephemeral streams and lake edges in the Antarctic Dry Valleys (DVs) become hotspots of biological activity and are hypothesized to be an important source of carbon and nitrogen for arid DV soils. Recent research in the DV has focused on the geochemistry and microbial ecology of lakes and arid soils, with substantially less information being available on hyporheic soils. Here, we determined the unique properties of hyporheic microbial communities, resolved their relationship to environmental parameters and compared them to archetypal arid DV soils. Generally, pH increased and chlorophyll a concentrations decreased along transects from wet to arid soils (9.0 to ~7.0 for pH and ~0.8 to ~5 μg/cm(3) for chlorophyll a, respectively). Soil water content decreased to below ~3% in the arid soils. Community fingerprinting-based principle component analyses revealed that bacterial communities formed distinct clusters specific to arid and wet soils; however, eukaryotic communities that clustered together did not have similar soil moisture content nor did they group together based on sampling location. Collectively, rRNA pyrosequencing indicated a considerably higher abundance of Cyanobacteria in wet soils and a higher abundance of Acidobacterial, Actinobacterial, Deinococcus/Thermus, Bacteroidetes, Firmicutes, Gemmatimonadetes, Nitrospira, and Planctomycetes in arid soils. The two most significant differences at the genus level were Gillisia signatures present in arid soils and chloroplast signatures related to Streptophyta that were common in wet soils. Fungal dominance was observed in arid soils and Viridiplantae were more common in wet soils. This research represents an in-depth characterization of microbial communities inhabiting wet DV soils. Results indicate that the repeated wetting of hyporheic zones has a profound impact on the bacterial and eukaryotic communities inhabiting in these areas.

  11. Spatio-temporal interdependence of bacteria and phytoplankton during a Baltic Sea spring bloom

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    Carina eBunse

    2016-04-01

    Full Text Available In temperate systems, phytoplankton spring blooms deplete inorganic nutrients and are major sources of organic matter for the microbial loop. In response to phytoplankton exudates and environmental factors, heterotrophic microbial communities are highly dynamic and change their abundance and composition both on spatial and temporal scales. Yet, most of our understanding about these processes comes from laboratory model organism studies, mesocosm experiments or single temporal transects. Spatial-temporal studies examining interactions of phytoplankton blooms and bacterioplankton community composition and function, though being highly informative, are scarce. In this study, pelagic microbial community dynamics (bacteria and phytoplankton and environmental variables were monitored during a spring bloom across the Baltic Proper (two cruises between North Germany to Gulf of Finland. To test to what extent bacterioplankton community composition relates to the spring bloom, we used next generation amplicon sequencing of the 16S rRNA gene, phytoplankton diversity analysis based on microscopy counts and population genotyping of the dominating diatom Skeletonema marinoi. Several phytoplankton bloom related and environmental variables were identified to influence bacterial community composition. Members of Bacteroidetes and Alphaproteobacteria dominated the bacterial community composition but the bacterial groups showed no apparent correlation with direct bloom related variables. The less abundant bacterial phyla Actinobacteria, Planctomycetes, and Verrucomicrobia, on the other hand, were strongly associated with phytoplankton biomass, diatom:dinoflagellate ratio and colored dissolved organic matter (cDOM. Many bacterial operational taxonomic units (OTUs showed high niche specificities. For example, particular Bacteroidetes OTUs were associated with two distinct genetic clusters of S. marinoi. Our study revealed the complexity of interactions of bacterial

  12. Sterol Synthesis in Diverse Bacteria.

    Science.gov (United States)

    Wei, Jeremy H; Yin, Xinchi; Welander, Paula V

    2016-01-01

    Sterols are essential components of eukaryotic cells whose biosynthesis and function has been studied extensively. Sterols are also recognized as the diagenetic precursors of steranes preserved in sedimentary rocks where they can function as geological proxies for eukaryotic organisms and/or aerobic metabolisms and environments. However, production of these lipids is not restricted to the eukaryotic domain as a few bacterial species also synthesize sterols. Phylogenomic studies have identified genes encoding homologs of sterol biosynthesis proteins in the genomes of several additional species, indicating that sterol production may be more widespread in the bacterial domain than previously thought. Although the occurrence of sterol synthesis genes in a genome indicates the potential for sterol production, it provides neither conclusive evidence of sterol synthesis nor information about the composition and abundance of basic and modified sterols that are actually being produced. Here, we coupled bioinformatics with lipid analyses to investigate the scope of bacterial sterol production. We identified oxidosqualene cyclase (Osc), which catalyzes the initial cyclization of oxidosqualene to the basic sterol structure, in 34 bacterial genomes from five phyla (Bacteroidetes, Cyanobacteria, Planctomycetes, Proteobacteria, and Verrucomicrobia) and in 176 metagenomes. Our data indicate that bacterial sterol synthesis likely occurs in diverse organisms and environments and also provides evidence that there are as yet uncultured groups of bacterial sterol producers. Phylogenetic analysis of bacterial and eukaryotic Osc sequences confirmed a complex evolutionary history of sterol synthesis in this domain. Finally, we characterized the lipids produced by Osc-containing bacteria and found that we could generally predict the ability to synthesize sterols. However, predicting the final modified sterol based on our current knowledge of sterol synthesis was difficult. Some bacteria

  13. Micro-organisms and divers exposure to radioactivity in spent fuel pools at nuclear power plants

    International Nuclear Information System (INIS)

    Muniz de A, D.; Silva, R.; Gomes N, C. A.

    2017-09-01

    Many nuclear power plants (NPPs) around the world are in the process of extending their lifespan from 40 to 60 years of operation. The NPP; Angra 1 (Brazil) has performed a thorough evaluation of its Life Extension Engineering project. In this context, the spent fuel pool (SFP) was one of the areas studied in order to demonstrate the plants integrity for a life extension. Micro-organisms growing on the liner of the fuel transfer channel (Ftc) and SFP can form a film of bacteria, which is highly resistant to radiation. This paper aims to compare the micro-organisms found in NPP Angra 1 with those reported to other NPPs and also relates their occurrence with the radiation levels at the sites. It also compares divers exposure to radioactivity during underwater activities in the SFP. Fourteen samples were collected on the surface of the liners of the Ftc, the SFP and the drains within the fuel building (FB) of Angra 1. For the identification of the micro-organisms, a metagenomics analysis was performed by random sequencing (Shotgun) and the use of Ion Torrent PGM Sequence r. Twelve micro-organisms phyla were identified; Acido-bacteria, Actino-bacteria, Bacteroidetes, Chlamydiae, Chlorobi, Chloroflexi, Cyano-bacteria, Deinococcus-Thermus, Firmicutes, Planctomycetes, Proteo-bacteria, and Verrucomicrobia as well as organisms not classified. In the SFP of Angra 1, the bacteria survived the exposure to a radiation of 0.416 Gy/h (high radiation). Deinococcus-thermus, bacteria identified in Angra 1, has resisted an exposure to 30,000 Gy/h in another plant. (Author)

  14. Legacy effects of anaerobic soil disinfestation on soil bacterial community composition and production of pathogen-suppressing volatiles

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    Maaike evan Agtmaal

    2015-07-01

    Full Text Available There is increasing evidence that microbial volatiles (VOCs play an important role in natural suppression of soil-borne diseases, but little is known on the factors that influence production of suppressing VOCs. In the current study we examined whether a stress-induced change in soil microbial community composition would affect the production by soils of VOCs suppressing the plant-pathogenic oomycete Pythium. Using pyrosequencing of 16S ribosomal gene fragments we compared the composition of bacterial communities in sandy soils that had been exposed to anaerobic disinfestation (AD, a treatment used to kill harmful soil organisms, with the composition in untreated soils. Three months after the AD treatment had been finished, there was still a clear legacy effect of the former anaerobic stress on bacterial community composition with a strong increase in relative abundance of the phylum Bacteroidetes and a significant decrease of the phyla Acidobacteria, Planctomycetes, Nitrospirae, Chloroflexi and Chlorobi. This change in bacterial community composition coincided with loss of production of Pythium suppressing soil volatiles (VOCs and of suppression of Pythium impacts on Hyacinth root development. One year later, the composition of the bacterial community in the AD soils was reflecting that of the untreated soils. In addition, both production of Pythium-suppressing VOCs and suppression of Pythium in Hyacinth bioassays had returned to the levels of the untreated soil. GC/MS analysis identified several VOCs, among which compounds known to be antifungal, that were produced in the untreated soils but not in the AD soils. These compounds were again produced 15 months after the AD treatment. Our data indicate that soils exposed to a drastic stress can temporarily lose pathogen suppressive characteristics and that both loss and return of these suppressive characteristics coincides with shifts in the soil bacterial community composition. Our data are

  15. Inorganic Nitrogen Application Affects Both Taxonomical and Predicted Functional Structure of Wheat Rhizosphere Bacterial Communities

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    Vanessa N. Kavamura

    2018-05-01

    Full Text Available The effects of fertilizer regime on bulk soil microbial communities have been well studied, but this is not the case for the rhizosphere microbiome. The aim of this work was to assess the impact of fertilization regime on wheat rhizosphere microbiome assembly and 16S rRNA gene-predicted functions with soil from the long term Broadbalk experiment at Rothamsted Research. Soil from four N fertilization regimes (organic N, zero N, medium inorganic N and high inorganic N was sown with seeds of Triticum aestivum cv. Cadenza. 16S rRNA gene amplicon sequencing was performed with the Illumina platform on bulk soil and rhizosphere samples of 4-week-old and flowering plants (10 weeks. Phylogenetic and 16S rRNA gene-predicted functional analyses were performed. Fertilization regime affected the structure and composition of wheat rhizosphere bacterial communities. Acidobacteria and Planctomycetes were significantly depleted in treatments receiving inorganic N, whereas the addition of high levels of inorganic N enriched members of the phylum Bacteroidetes, especially after 10 weeks. Bacterial richness and diversity decreased with inorganic nitrogen inputs and was highest after organic treatment (FYM. In general, high levels of inorganic nitrogen fertilizers negatively affect bacterial richness and diversity, leading to a less stable bacterial community structure over time, whereas, more stable bacterial communities are provided by organic amendments. 16S rRNA gene-predicted functional structure was more affected by growth stage than by fertilizer treatment, although, some functions related to energy metabolism and metabolism of terpenoids and polyketides were enriched in samples not receiving any inorganic N, whereas inorganic N addition enriched predicted functions related to metabolism of other amino acids and carbohydrates. Understanding the impact of different fertilizers on the structure and dynamics of the rhizosphere microbiome is an important step

  16. Microbial diversity in sediment ecosystems (evaporites domes, microbial mats and crusts of hypersaline Laguna Tebenquiche, Salar de Atacama, Chile

    Directory of Open Access Journals (Sweden)

    Ana Beatriz Fernandez

    2016-08-01

    Full Text Available We combined nucleic acid-based molecular methods, biogeochemical measurements and physicochemical characteristics to investigate microbial sedimentary ecosystems of Laguna Tebenquiche, Atacama Desert, Chile. Molecular diversity and biogeochemistry of hypersaline microbial mats, rhizome-associated concretions and an endoevaporite were compared with: The V4 hypervariable region of the 16S rRNA gene was amplified by pyrosequencing to analyze the total microbial diversity (i.e., bacteria and archaea in bulk samples and, in addition, in detail on a millimeter scale in one microbial mat and in one evaporite. Archaea were more abundant than bacteria. Euryarchaeota was one of the most abundant phyla in all samples, and particularly dominant (97% of total diversity in the most lithified ecosystem, the evaporite. Most of the euryarchaeal OTUs could be assigned to the class Halobacteria or anaerobic and methanogenic archaea. Planctomycetes potentially also play a key role in mats and rhizome-associated concretions, notably the aerobic organoheterotroph members of the class Phycisphaerae. In addition to cyanobacteria, members of Chromatiales and possibly the candidate family Chlorotrichaceae contributed to photosynthetic carbon fixation. Other abundant uncultured taxa such as the candidate division MSBL1, the uncultured MBGB and the phylum Acetothermia potentially play an important metabolic role in these ecosystems. Lithifying microbial mats contained calcium carbonate precipitates, whereas endoevoporites consisted of gypsum and halite. Biogeochemical measurements revealed that based on depth profiles of O2 and sulfide, metabolic activities were much higher in the non-lithifying mat (peaking in the least lithified systems than in lithifying mats with the lowest activity in endoevaporites. This trend in decreasing microbial activity reflects the increase in salinity, which may play an important role in the biodiversity.

  17. Taxonomic and functional characteristics of microbial communities and their correlation with physicochemical properties of four geothermal springs in Odisha, India

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    Subrata K Das

    2015-10-01

    Full Text Available This study describes microbial diversity in four tropical hot springs representing moderately thermophilic environments (temperature range: 40-58 °C; pH: 7.2-7.4 with discrete geochemistry. Metagenome sequence data showed a dominance of Bacteria over Archaea; the most abundant phyla were Chloroflexi and Proteobacteria, although other phyla were also present, such as Acetothermia, Nitrospirae, Acidobacteria, Firmicutes, Deinococcus-Thermus, Bacteroidetes, Thermotogae, Euryarchaeota, Verrucomicrobia, Ignavibacteriae, Cyanobacteria, Actinobacteria, Planctomycetes, Spirochaetes, Armatimonadetes, Crenarchaeota, and Aquificae. The distribution of major genera and their statistical correlation analyses with the physicochemical parameters predicted that the temperature, aqueous concentrations of ions (such as sodium, chloride, sulfate, and bicarbonate, total hardness, dissolved solids and conductivity were the main environmental variables influencing microbial community composition and diversity. Despite the observed high taxonomic diversity, there were only little variations in the overall functional profiles of the microbial communities in the four springs. Genes involved in the metabolism of carbohydrates and carbon fixation were the most abundant functional class of genes present in these hot springs. The distribution of genes involved in carbon fixation predicted the presence of all the six known autotrophic pathways in the metagenomes. A high prevalence of genes involved in membrane transport, signal transduction, stress response, bacterial chemotaxis and flagellar assembly were observed along with genes involved in the pathways of xenobiotic degradation and metabolism. The analysis of the metagenomic sequences affiliated to the candidate phylum Acetothermia from spring TB-3 provided new insight into the metabolism and physiology of yet-unknown members of this lineage of bacteria.

  18. COMPOSITION AND FUNCTION OF THE MICROBIAL COMMUNITY RELATED WITH THE NITROGEN CYCLING ON THE POTATO RHIZOSPHERE

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    Nathalia Maria Vanesa Florez Zapata

    2013-09-01

    Full Text Available In the S. tuberosum group phureja crops, mineral fertilizer and organic amendments are applied to meet the plants’ nutritional demands, however the effect of such practices on the associated rizospheric microbial communities are still unknown. Nitrogen plays an important role in agricultural production, and a great diversity of microorganisms regulates its transformation in the soil, affecting its availability for the plant. The aim of this study was to assess the structure of microbal[trm1]  communities related with the N cycle of S. tuberosum group phureja  rizospheric soil samples, with contrasting physical-chemical properties and fertilization strategy.  Few significant differences between the community composition at the phylum level were found, only Planctomycetes phylum was different between samples of different soil type and fertilization strategy. However, the analysis of nitrogen-associated functional groups made by ribotyping characterization, grouped soils in terms of such variables in a similar way to the physical-chemical properties. Major differences between soil samples were typified by higher percentages of the ribotypes from nitrite oxidation, nitrogen fixation and denitrification on organic amendment soils. Our results suggest that, the dominant rhizosphere microbial composition is very similar between soils, possibly as a result of population’s selection mediated by the rhizosphere effect. However, agricultural management practices in addition to edaphic properties of sampled areas, appear to affect some functional groups associated with the nitrogen cycling, due to differences found on soil’s physical-chemical properties, like the concentration of ammonium that seems to have an effect regulating the distribution and activity of nitrogen related functional groups in the S. tuberosum rhizosphere.

  19. Structure, mineralogy and microbial diversity of geothermal spring microbialites associated with a deep oil drilling in Romania

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    Cristian eComan

    2015-03-01

    Full Text Available Modern mineral deposits play an important role in evolutionary studies by providing clues to the formation of ancient lithified microbial communities. Here we report the presence of microbialite-forming microbial mats in different microenvironments at 32ºC, 49ºC and 65ºC around the geothermal spring from an abandoned oil drill in Ciocaia, Romania. The mineralogy and the macro- and microstructure of the microbialites were investigated, together with their microbial diversity based on a 16S rRNA gene amplicon sequencing approach. The calcium carbonate is deposited mainly in the form of calcite. At 32ºC and 49ºC, the microbialites show a laminated structure with visible microbial mat-carbonate crystal interactions. At 65ºC, the mineral deposit is clotted, without obvious organic residues. Partial 16S rRNA gene amplicon sequencing showed that the relative abundance of the phylum Archaea was low at 32ºC (1%. The dominant bacterial groups at 32ºC were Cyanobacteria, Gammaproteobacteria, Firmicutes, Bacteroidetes, Chloroflexi, Thermi, Actinobacteria, Planctomycetes and Defferibacteres. At 49ºC, there was a striking dominance of the Gammaproteobacteria, followed by Firmicutes, Bacteroidetes, and Armantimonadetes. The 65ºC sample was dominated by Betaproteobacteria, Firmicutes, [OP1], Defferibacteres, Thermi, Thermotogae, [EM3] and Nitrospirae. Several groups from Proteobacteria and Firmicutes, together with Halobacteria and Melainabacteria were described for the first time in calcium carbonate deposits. Overall, the spring from Ciocaia emerges as a valuable site to probe microbes-minerals interrelationships along thermal and geochemical gradients.

  20. Characteristics of Bacterial Communities in Cyanobacteria-Blooming Aquaculture Wastewater Influenced by the Phytoremediation with Water Hyacinth

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    Qing Zhou

    2017-12-01

    Full Text Available Cyanobacterial blooms often occur in aquaculture wastewater in China. A floating plant, water hyacinth has been widely used to treat this wastewater. Little is known, however, about bacterial community characteristics and the risk of potential pathogens in cyanobacteria-blooming aquaculture wastewater remediated by water hyacinth. In wastewater treated with water hyacinth, we used culture enumeration and high-throughput sequencing to explore the characteristics of bacterial communities, the status of coliform bacteria, and pathogenic bacteria potentially conducive to human disease. Our results indicated that the relative abundance of Acidobacteria, Planctomycetes, Actinobacteria, Chlorobi, Cyanobacteria, Proteobacteria, and phylum OD1 in cyanobacteria-blooming aquaculture wastewater were significantly influenced by water hyacinth. After 30 days, the relative abundance of Proteobacteria and phylum OD1 in the water hyacinth treatments increased remarkably, while the relative abundance of the other 5 phyla in treatment was significantly reduced compared with the controls. In 21 major families, the relative abundance of Comamonadaceae, Oxalobacteraceae, Rhodocylclaceae, and an unnamed group from phylum OD1 increased significantly in the water hyacinth treatments compared with the controls. The number of total coliforms in wastewater treated by water hyacinth was significantly elevated and higher than controls during the first 6–18 days, with the maximum reaching 23,800 MPN/L. The level of potential pathogenic bacteria in wastewater treated by water hyacinth significantly reduced compared with the controls after 18 days, but it significantly increased from the initial level. It appears that water hyacinth by itself is not an effective treatment for reducing potential pathogens in aquaculture water.

  1. Environmental and Geographical Factors Structure Soil Microbial Diversity in New Caledonian Ultramafic Substrates: A Metagenomic Approach.

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    Véronique Gourmelon

    Full Text Available Soil microorganisms play key roles in ecosystem functioning and are known to be influenced by biotic and abiotic factors, such as plant cover or edaphic parameters. New Caledonia, a biodiversity hotspot located in the southwest Pacific, is one-third covered by ultramafic substrates. These types of soils are notably characterised by low nutrient content and high heavy metal concentrations. Ultramafic outcrops harbour diverse vegetation types and remarkable plant diversity. In this study, we aimed to assess soil bacterial and fungal diversity in New Caledonian ultramafic substrates and to determine whether floristic composition, edaphic parameters and geographical factors affect this microbial diversity. Therefore, four plant formation types at two distinct sites were studied. These formations represent different stages in a potential chronosequence. Soil cores, according to a given sampling procedure, were collected to assess microbial diversity using a metagenomic approach, and to characterise the physico-chemical parameters. A botanical inventory was also performed. Our results indicated that microbial richness, composition and abundance were linked to the plant cover type and the dominant plant species. Furthermore, a large proportion of Ascomycota phylum (fungi, mostly in non-rainforest formations, and Planctomycetes phylum (bacteria in all formations were observed. Interestingly, such patterns could be indicators of past disturbances that occurred on different time scales. Furthermore, the bacteria and fungi were influenced by diverse edaphic parameters as well as by the interplay between these two soil communities. Another striking finding was the existence of a site effect. Differences in microbial communities between geographical locations may be explained by dispersal limitation in the context of the biogeographical island theory. In conclusion, each plant formation at each site possesses is own microbial community resulting from

  2. Soil pH Is the Primary Factor Correlating With Soil Microbiome in Karst Rocky Desertification Regions in the Wushan County, Chongqing, China

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    Daihua Qi

    2018-05-01

    Full Text Available Karst rocky desertification (KRD is a process of land degradation, which causes desert-like landscapes, deconstruction of endemic biomass, and declined soil quality. The relationship of KRD progression with above-ground communities (e.g. vegetation and animal is well-studied. Interaction of soil desertification with underground communities, such as soil microbiome, however, is vastly unknown. This study characterizes change in soil bacterial community in response to KRD progression. Soil bacterial communities were surveyed by deep sequencing of 16S amplicons. Eight soil properties, pH, soil organic matter (SOM, total and available nitrogen (TN and AN, total and available phosphorus (TP and AP, and total and available potassium (TK and AK, were measured to assess soil quality. We find that the overall soil quality decreases along with KRD progressive gradient. Soil bacterial community compositions are distinguishingly different in KRD stages. The richness and diversity in bacterial community do not significantly change with KRD progression although a slight increase in diversity was observed. A slight decrease in richness was seen in SKRD areas. Soil pH primarily correlates with bacterial community composition. We identified a core microbiome for KRD soils consisting of; Acidobacteria, Alpha-Proteobacteria, Planctomycetes, Beta-Proteobacteria, Actinobacteria, Firmicutes, Delta-Proteobacteria, Chloroflexi, Bacteroidetes, Nitrospirae, and Gemmatimonadetes in this study. Phylum Cyanobacteria is significantly abundant in non-degraded soils, suggesting that Cyanobacterial activities might be correlated to soil quality. Our results suggest that Proteobacteria are sensitive to changes in soil properties caused by the KRD progression. Alpha- and beta-Proteobacteria significantly predominated in SKRD compared to NKRD, suggesting that Proteobacteria, along with many others in the core microbiome (Acidobacteria, Actinobacteria, Firmicutes, and Nitrospirae

  3. Magnetotactic Bacteria from Extreme Environments

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    Christopher T. Lefèvre

    2013-03-01

    Full Text Available Magnetotactic bacteria (MTB represent a diverse collection of motile prokaryotes that biomineralize intracellular, membrane-bounded, tens-of-nanometer-sized crystals of a magnetic mineral called magnetosomes. Magnetosome minerals consist of either magnetite (Fe3O4 or greigite (Fe3S4 and cause cells to align along the Earth’s geomagnetic field lines as they swim, a trait called magnetotaxis. MTB are known to mainly inhabit the oxic–anoxic interface (OAI in water columns or sediments of aquatic habitats and it is currently thought that magnetosomes function as a means of making chemotaxis more efficient in locating and maintaining an optimal position for growth and survival at the OAI. Known cultured and uncultured MTB are phylogenetically associated with the Alpha-, Gamma- and Deltaproteobacteria classes of the phylum Proteobacteria, the Nitrospirae phylum and the candidate division OP3, part of the Planctomycetes-Verrucomicrobia-Chlamydiae (PVC bacterial superphylum. MTB are generally thought to be ubiquitous in aquatic environments as they are cosmopolitan in distribution and have been found in every continent although for years MTB were thought to be restricted to habitats with pH values near neutral and at ambient temperature. Recently, however, moderate thermophilic and alkaliphilic MTB have been described including: an uncultured, moderately thermophilic magnetotactic bacterium present in hot springs in northern Nevada with a probable upper growth limit of about 63 °C; and several strains of obligately alkaliphilic MTB isolated in pure culture from different aquatic habitats in California, including the hypersaline, extremely alkaline Mono Lake, with an optimal growth pH of >9.0.

  4. Temporal and Spatial Distribution of the Microbial Community of Winogradsky Columns.

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    David J Esteban

    Full Text Available Winogradsky columns are model microbial ecosystems prepared by adding pond sediment to a clear cylinder with additional supplements and incubated with light. Environmental gradients develop within the column creating diverse niches that allow enrichment of specific bacteria. The enrichment culture can be used to study soil and sediment microbial community structure and function. In this study we used a 16S rRNA gene survey to characterize the microbial community dynamics during Winogradsky column development to determine the rate and extent of change from the source sediment community. Over a period of 60 days, the microbial community changed from the founding pond sediment population: Cyanobacteria, Chloroflexi, Nitrospirae, and Planctomycetes increased in relative abundance over time, while most Proteobacteria decreased in relative abundance. A unique, light-dependent surface biofilm community formed by 60 days that was less diverse and dominated by a few highly abundant bacteria. 67-72% of the surface community was comprised of highly enriched taxa that were rare in the source pond sediment, including the Cyanobacteria Anabaena, a member of the Gemmatimonadetes phylum, and a member of the Chloroflexi class Anaerolinea. This indicates that rare taxa can become abundant under appropriate environmental conditions and supports the hypothesis that rare taxa serve as a microbial seed bank. We also present preliminary findings that suggest that bacteriophages may be active in the Winogradsky community. The dynamics of certain taxa, most notably the Cyanobacteria, showed a bloom-and-decline pattern, consistent with bacteriophage predation as predicted in the kill-the-winner hypothesis. Time-lapse photography also supported the possibility of bacteriophage activity, revealing a pattern of colony clearance similar to formation of viral plaques. The Winogradsky column, a technique developed early in the history of microbial ecology to enrich soil

  5. Prokaryotes in subsoil – evidence for spatial separation of oligotrophs and copiotrophs by co-occurrence networks

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    Michael eSchloter

    2015-11-01

    Full Text Available Soil microbial communities provide a wide range of soil functions including nutrient cycling, soil formation, and plant growth promotion. On the small scale, nutrient rich soil hotspots developed from soil animal or plant activity are important drivers for microbial communities and their activity pattern. Nevertheless, in subsoil, the spatial heterogeneity of microbes with diverging lifestyles has been barely considered so far. In this study, the phylogenetic composition of the bacterial and archaeal microbiome based on 16S rRNA gene pyrosequencing was investigated in the soil compartments bulk soil, drilosphere, and rhizosphere in topsoil and in the subsoil of an agricultural field. With co-occurrence network analysis, the spatial separation of typically oligotrophs and heterotrophs in subsoil and hotspots was assessed. Four co-occurring bacterial communities were identified and attributed to bulk topsoil, bulk subsoil, drilosphere, and rhizosphere. The bacterial phyla Proteobacteria and Bacteroidetes, which represent many copiotrophic bacteria, are affiliated to the hotspot communities – the rhizosphere and drilosphere – both in topsoil and subsoil. Acidobacteria, Actinobacteria, Gemmatimonadetes, Planctomycetes, and Verrucomicrobia with many oligotrophic bacteria, are the abundant groups of the bulk subsoil community. The bacterial core microbiome in this soil was estimated and only covers 7.6% of the bacterial sequencing reads but includes both oligotrophic and copiotrophic bacteria. Instead, the archaeal core microbiome includes 56% of the overall archaeal diversity and comprises only the ammonium oxidizing Nitrososphaera. Thus, the spatial variability of nutrient quality and quantity strongly shapes the bacterial community composition and their interaction in subsoil, whereas archaea are a stable backbone of the soil prokaryotes.

  6. Deterministic influences exceed dispersal effects on hydrologically-connected microbiomes: Deterministic assembly of hyporheic microbiomes

    Energy Technology Data Exchange (ETDEWEB)

    Graham, Emily B. [Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA USA; Crump, Alex R. [Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA USA; Resch, Charles T. [Geochemistry Department, Pacific Northwest National Laboratory, Richland WA USA; Fansler, Sarah [Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA USA; Arntzen, Evan [Environmental Compliance and Emergency Preparation, Pacific Northwest National Laboratory, Richland WA USA; Kennedy, David W. [Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA USA; Fredrickson, Jim K. [Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA USA; Stegen, James C. [Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA USA

    2017-03-28

    Subsurface zones of groundwater and surface water mixing (hyporheic zones) are regions of enhanced rates of biogeochemical cycling, yet ecological processes governing hyporheic microbiome composition and function through space and time remain unknown. We sampled attached and planktonic microbiomes in the Columbia River hyporheic zone across seasonal hydrologic change, and employed statistical null models to infer mechanisms generating temporal changes in microbiomes within three hydrologically-connected, physicochemically-distinct geographic zones (inland, nearshore, river). We reveal that microbiomes remain dissimilar through time across all zones and habitat types (attached vs. planktonic) and that deterministic assembly processes regulate microbiome composition in all data subsets. The consistent presence of heterotrophic taxa and members of the Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) superphylum nonetheless suggests common selective pressures for physiologies represented in these groups. Further, co-occurrence networks were used to provide insight into taxa most affected by deterministic assembly processes. We identified network clusters to represent groups of organisms that correlated with seasonal and physicochemical change. Extended network analyses identified keystone taxa within each cluster that we propose are central in microbiome composition and function. Finally, the abundance of one network cluster of nearshore organisms exhibited a seasonal shift from heterotrophic to autotrophic metabolisms and correlated with microbial metabolism, possibly indicating an ecological role for these organisms as foundational species in driving biogeochemical reactions within the hyporheic zone. Taken together, our research demonstrates a predominant role for deterministic assembly across highly-connected environments and provides insight into niche dynamics associated with seasonal changes in hyporheic microbiome composition and metabolism.

  7. Composition, diversity and function of intestinal microbiota in pacific white shrimp (Litopenaeus vannamei) at different culture stages.

    Science.gov (United States)

    Zeng, Shenzheng; Huang, Zhijian; Hou, Dongwei; Liu, Jian; Weng, Shaoping; He, Jianguo

    2017-01-01

    Intestinal microbiota is an integral component of the host and plays important roles in host health. The pacific white shrimp is one of the most profitable aquaculture species commercialized in the world market with the largest production in shrimp consumption. Many studies revealed that the intestinal microbiota shifted significantly during host development in other aquaculture animals. In the present study, 22 shrimp samples were collected every 15 days from larval stage (15 day post-hatching, dph) to adult stage (75 dph) to investigate the intestinal microbiota at different culture stages by targeting the V4 region of 16S rRNA gene, and the microbial function prediction was conducted by PICRUSt. The operational taxonomic unit (OTU) was assigned at 97% sequence identity. A total of 2,496 OTUs were obtained, ranging from 585 to 1,239 in each sample. Forty-three phyla were identified due to the classifiable sequence. The most abundant phyla were Proteobacteria, Cyanobacteria, Tenericutes, Fusobacteria, Firmicutes, Verrucomicrobia, Bacteroidetes, Planctomycetes, Actinobacteria and Chloroflexi. OTUs belonged to 289 genera and the most abundant genera were Candidatus_Xiphinematobacter , Propionigenium , Synechococcus , Shewanella and Cetobacterium . Fifty-nine OTUs were detected in all samples, which were considered as the major microbes in intestine of shrimp. The intestinal microbiota was enriched with functional potentials that were related to transporters, ABC transporters, DNA repair and recombination proteins, two component system, secretion system, bacterial motility proteins, purine metabolism and ribosome. All the results showed that the intestinal microbial composition, diversity and functions varied significantly at different culture stages, which indicated that shrimp intestinal microbiota depended on culture stages. These findings provided new evidence on intestinal microorganism microecology and greatly enhanced our understanding of stage

  8. Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone.

    Science.gov (United States)

    Ganesh, Sangita; Parris, Darren J; DeLong, Edward F; Stewart, Frank J

    2014-01-01

    Marine oxygen minimum zones (OMZs) support diverse microbial communities with roles in major elemental cycles. It is unclear how the taxonomic composition and metabolism of OMZ microorganisms vary between particle-associated and free-living size fractions. We used amplicon (16S rRNA gene) and shotgun metagenome sequencing to compare microbial communities from large (>1.6 μm) and small (0.2-1.6 μm) filter size fractions along a depth gradient in the OMZ off Chile. Despite steep vertical redox gradients, size fraction was a significantly stronger predictor of community composition compared to depth. Phylogenetic diversity showed contrasting patterns, decreasing towards the anoxic OMZ core in the small size fraction, but exhibiting maximal values at these depths within the larger size fraction. Fraction-specific distributions were evident for key OMZ taxa, including anammox planctomycetes, whose coding sequences were enriched up to threefold in the 0.2-1.6 μm community. Functional gene composition also differed between fractions, with the >1.6 μm community significantly enriched in genes mediating social interactions, including motility, adhesion, cell-to-cell transfer, antibiotic resistance and mobile element activity. Prokaryotic transposase genes were three to six fold more abundant in this fraction, comprising up to 2% of protein-coding sequences, suggesting that particle surfaces may act as hotbeds for transposition-based genome changes in marine microbes. Genes for nitric and nitrous oxide reduction were also more abundant (three to seven fold) in the larger size fraction, suggesting microniche partitioning of key denitrification steps. These results highlight an important role for surface attachment in shaping community metabolic potential and genome content in OMZ microorganisms.

  9. Bacterial diversity in the bottom boundary layer of the inner continental shelf of Oregon, USA

    KAUST Repository

    Bertagnolli, AD; Treusch, AH; Mason, OU; Stingl, Ulrich; Vergin, KL; Chan, F; Beszteri, B; Giovannoni, SJ

    2011-01-01

    There have been few studies of the bacterial community within the bottom boundary layer (BBL) the turbulent region of the water column above the benthos in shallow seas. Typically, the BBL has large amounts of particulate organic matter suspended by turbulence, and it is often the first region of the water column to become hypoxic when oxygen declines. Communities at the surface (5 m) and in the BBL (1 to 10 m above the sea floor) were compared by terminal restriction fragment length polymorphism (T-RFLP) analysis and sequencing of the 16S rRNA gene. Multivariate statistical methods (hierarchical clustering, non-metric multidimensional scaling, and analysis of similarity (ANOSIM)) indicated that the microbial community of the BBL is distinct from the surface community. ANOSIM supported the distinction between surface and BBLs (R values 0.427 and 0.463, based on analysis with restriction enzymes BsuR1 and Hin6I, respectively, p < 0.1%). Six terminal restriction fragments showed an increase in abundance with depth. Cloning, screening and sequencing identified these as a novel environmental clade (Eastern North Pacific Chromatiales (ENPC) clade), the ARTIC96BD-19 clade of Gammaproteobacteria, the 6N14 and Agg8 clades of the phylum Planctomycetes, the OM60/NOR5 clade of Gammaproteobacteria, and uncultivated members of the Roseobacter clade in the MB11C09 and ULA23 subgroups. To the best of our knowledge, this analysis is the first to focus on the unique composition of microbial communities of the BBL in shallow, inner-shelf regions off the coast of Oregon, USA, and the first to report that an uncharacterized clade of Chromatiales is indigenous in this habitat.

  10. Diversity of hydrolases from hydrothermal vent sediments of the Levante Bay, Vulcano Island (Aeolian archipelago) identified by activity-based metagenomics and biochemical characterization of new esterases and an arabinopyranosidase.

    Science.gov (United States)

    Placido, Antonio; Hai, Tran; Ferrer, Manuel; Chernikova, Tatyana N; Distaso, Marco; Armstrong, Dale; Yakunin, Alexander F; Toshchakov, Stepan V; Yakimov, Michail M; Kublanov, Ilya V; Golyshina, Olga V; Pesole, Graziano; Ceci, Luigi R; Golyshin, Peter N

    2015-12-01

    A metagenomic fosmid expression library established from environmental DNA (eDNA) from the shallow hot vent sediment sample collected from the Levante Bay, Vulcano Island (Aeolian archipelago) was established in Escherichia coli. Using activity-based screening assays, we have assessed 9600 fosmid clones corresponding to approximately 350 Mbp of the cloned eDNA, for the lipases/esterases/lactamases, haloalkane and haloacid dehalogenases, and glycoside hydrolases. Thirty-four positive fosmid clones were selected from the total of 120 positive hits and sequenced to yield ca. 1360 kbp of high-quality assemblies. Fosmid inserts were attributed to the members of ten bacterial phyla, including Proteobacteria, Bacteroidetes, Acidobateria, Firmicutes, Verrucomicrobia, Chloroflexi, Spirochaetes, Thermotogae, Armatimonadetes, and Planctomycetes. Of ca. 200 proteins with high biotechnological potential identified therein, we have characterized in detail three distinct α/β-hydrolases (LIPESV12_9, LIPESV12_24, LIPESV12_26) and one new α-arabinopyranosidase (GLV12_5). All LIPESV12 enzymes revealed distinct substrate specificities tested against 43 structurally diverse esters and 4 p-nitrophenol carboxyl esters. Of 16 different glycosides tested, the GLV12_5 hydrolysed only p-nitrophenol-α-(L)-arabinopyranose with a high specific activity of about 2.7 kU/mg protein. Most of the α/β-hydrolases were thermophilic and revealed a high tolerance to, and high activities in the presence of, numerous heavy metal ions. Among them, the LIPESV12_24 was the best temperature-adapted, retaining its activity after 40 min of incubation at 90 °C. Furthermore, enzymes were active in organic solvents (e.g., >30% methanol). Both LIPESV12_24 and LIPESV12_26 had the GXSXG pentapeptides and the catalytic triads Ser-Asp-His typical to the representatives of carboxylesterases of EC 3.1.1.1.

  11. Comparison of Fecal Microbiota of Mongolian and Thoroughbred Horses by High-throughput Sequencing of the V4 Region of the 16S rRNA Gene.

    Science.gov (United States)

    Zhao, Yiping; Li, Bei; Bai, Dongyi; Huang, Jinlong; Shiraigo, Wunierfu; Yang, Lihua; Zhao, Qinan; Ren, Xiujuan; Wu, Jing; Bao, Wuyundalai; Dugarjaviin, Manglai

    2016-09-01

    The hindgut of horses is an anaerobic fermentative chamber for a complex and dynamic microbial population, which plays a critical role in health and energy requirements. Research on the gut microbiota of Mongolian horses has not been reported until now as far as we know. Mongolian horse is a major local breed in China. We performed high-throughput sequencing of the 16S rRNA genes V4 hypervariable regions from gut fecal material to characterize the gut microbiota of Mongolian horses and compare them to the microbiota in Thoroughbred horses. Fourteen Mongolian and 19 Thoroughbred horses were used in the study. A total of 593,678 sequence reads were obtained from 33 samples analyzed, which were found to belong to 16 phyla and 75 genera. The bacterial community compositions were similar for the two breeds. Firmicutes (56% in Mongolian horses and 53% in Thoroughbred horses) and Bacteroidetes (33% and 32% respectively) were the most abundant and predominant phyla followed by Spirochaete, Verrucomicrobia, Proteobacteria, and Fibrobacteres. Of these 16 phyla, five (Synergistetes, Planctomycetes, Proteobacteria, TM7, and Chloroflexi) were significantly different (phorses vs 29% in Thoroughbred horses), followed by Ruminococcus, Roseburia, Pseudobutyrivibrio, and Anaeroplasma, which were detected in higher distribution proportion in Mongolian horses than in Thoroughbred horses. In contrast, Oscillibacter, Fibrobacter, Methanocorpusculum, and Succinivibrio levels were lower in Mongolian horses. Among 75 genera, 30 genera were significantly different (phorse gut microbiota. These findings provide novel information about the gut microbiota of Mongolian horses and a foundation for future investigations of gut bacterial factors that may influence the development and progression of gastrointestinal disease in horses.

  12. Dynamic succession of soil bacterial community during continuous cropping of peanut (Arachis hypogaea L..

    Directory of Open Access Journals (Sweden)

    Mingna Chen

    Full Text Available Plant health and soil fertility are affected by plant-microbial interactions in soils. Peanut is an important oil crop worldwide and shows considerable adaptability, but growth and yield are negatively affected by continuous cropping. In this study, 16S rRNA gene clone library analyses were used to study the succession of soil bacterial communities under continuous peanut cultivation. Six libraries were constructed for peanut over three continuous cropping cycles and during its seedling and pod-maturing growth stages. Cluster analyses indicated that soil bacterial assemblages obtained from the same peanut cropping cycle were similar, regardless of growth period. The diversity of bacterial sequences identified in each growth stage library of the three peanut cropping cycles was high and these sequences were affiliated with 21 bacterial groups. Eight phyla: Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Gemmatimonadetes, Planctomycetes, Proteobacteria and Verrucomicrobia were dominant. The related bacterial phylotypes dynamic changed during continuous cropping progress of peanut. This study demonstrated that the bacterial populations especially the beneficial populations were positively selected. The simplification of the beneficial microbial communities such as the phylotypes of Alteromonadales, Burkholderiales, Flavobacteriales, Pseudomonadales, Rhizobiales and Rhodospirillales could be important factors contributing to the decline in peanut yield under continuous cropping. The microbial phylotypes that did not successively changed with continuous cropping, such as populations related to Rhizobiales and Rhodospirillales, could potentially resist stress due to continuous cropping and deserve attention. In addition, some phylotypes, such as Acidobacteriales, Chromatiales and Gemmatimonadales, showed a contrary tendency, their abundance or diversity increased with continuous peanut cropping progress. Some bacterial phylotypes including

  13. Metagenome-based diversity analyses suggest a significant contribution of non-cyanobacterial lineages to carbonate precipitation in modern microbialites

    Directory of Open Access Journals (Sweden)

    Purificacion eLopez-Garcia

    2015-08-01

    Full Text Available Cyanobacteria are thought to play a key role in carbonate formation due to their metabolic activity, but other organisms carrying out oxygenic photosynthesis (photosynthetic eukaryotes or other metabolisms (e.g. anoxygenic photosynthesis, sulfate reduction, may also contribute to carbonate formation. To obtain more quantitative information than that provided by more classical PCR-dependent methods, we studied the microbial diversity of microbialites from the Alchichica crater lake (Mexico by mining for 16S/18S rRNA genes in metagenomes obtained by direct sequencing of environmental DNA. We studied samples collected at the Western (AL-W and Northern (AL-N shores of the lake and, at the latter site, along a depth gradient (1, 5, 10 and 15 m depth. The associated microbial communities were mainly composed of bacteria, most of which seemed heterotrophic, whereas archaea were negligible. Eukaryotes composed a relatively minor fraction dominated by photosynthetic lineages, diatoms in AL-W, influenced by Si-rich seepage waters, and green algae in AL-N samples. Members of the Gammaproteobacteria and Alphaproteobacteria classes of Proteobacteria, Cyanobacteria and Bacteroidetes were the most abundant bacterial taxa, followed by Planctomycetes, Deltaproteobacteria (Proteobacteria, Verrucomicrobia, Actinobacteria, Firmicutes and Chloroflexi. Community composition varied among sites and with depth. Although cyanobacteria were the most important bacterial group contributing to the carbonate precipitation potential, photosynthetic eukaryotes, anoxygenic photosynthesizers and sulfate reducers were also very abundant. Cyanobacteria affiliated to Pleurocapsales largely increased with depth. Scanning electron microscopy (SEM observations showed considerable areas of aragonite-encrusted Pleurocapsa-like cyanobacteria at microscale. Multivariate statistical analyses showed a strong positive correlation of Pleurocapsales and Chroococcales with aragonite formation at

  14. Multilayer Approach for Characterization of Bacterial Diversity in a Marginal Sea: From Surface to Seabed

    Science.gov (United States)

    Ivana, Babic; Maja, Mucko; Ivica, Vilibic; Hrvoje, Mihanovic; Reffaella, Casotti; Zrinka, Ljubesic; Ivona, Cetinic; Cecilia, Balestra; Ines, Petric; Suncica, Bosak; hide

    2018-01-01

    Bacteria are the most important microorganisms in the world oceans, accounting for up to 75% of the total biomass. They are responsible for fundamental biogeochemical processes and therefore often used as ecological indicators. In this study, bacteria were quantified by flow cytometry and their diversity assessed by High Throughput Sequencing (HTS) in the southern Adriatic Sea. The most abundant bacterial groups were also quantified by qPCR. The samples were collected from the surface to the seabed over a total of 16 different depths at four stations during the late winter BIOTA (BIO-Tracing Adriatic water masses) cruise conducted in March 2016. The investigated area showed unusual water mass properties and was characterized by a shallow mixed layer, which differed from the usual winter convection conditions, typical of middle-altitude ecosystems and important for the seasonal picoplankton dynamics of this area. Heterotrophic bacteria were separated into HNA (relative High Nucleic Acid content) and LNA (Low Nucleic Acid content) subpopulations with abundances up to 1.8×10(exp 5) and 8.8×10(exp 5) cells/mL, respectively. HNA dominated at offshore stations reaching their maximum at depths below the euphotic zone. The bacterial community was dominated by Alphaproteobacteria, accounting for greater than 40% of the total sequence reads and were mainly represented by the SAR11 clade (90.84%), followed by Marinimicrobia (18% of the total sequence reads), mainly represented by clade SAR406 (8.44%). Distinctive bacterial groups were found in the euphotic layer (Bacteroidetes and Actinobacteria) and aphotic layer samples (Deltaproteobacteria, Marinimicrobia, Chloroflexi, Acidobacteria and Planctomycetes). Results of the qPCR analyses further confirmed HTS results with highest abundances obtained for Alphaproteobacteria, followed by Gammaproteobacteria and Bacteroidetes. The adopted multiple approach, combining different molecular tools, critically supported by optics and

  15. Composition, diversity and function of intestinal microbiota in pacific white shrimp (Litopenaeus vannamei at different culture stages

    Directory of Open Access Journals (Sweden)

    Shenzheng Zeng

    2017-11-01

    Full Text Available Intestinal microbiota is an integral component of the host and plays important roles in host health. The pacific white shrimp is one of the most profitable aquaculture species commercialized in the world market with the largest production in shrimp consumption. Many studies revealed that the intestinal microbiota shifted significantly during host development in other aquaculture animals. In the present study, 22 shrimp samples were collected every 15 days from larval stage (15 day post-hatching, dph to adult stage (75 dph to investigate the intestinal microbiota at different culture stages by targeting the V4 region of 16S rRNA gene, and the microbial function prediction was conducted by PICRUSt. The operational taxonomic unit (OTU was assigned at 97% sequence identity. A total of 2,496 OTUs were obtained, ranging from 585 to 1,239 in each sample. Forty-three phyla were identified due to the classifiable sequence. The most abundant phyla were Proteobacteria, Cyanobacteria, Tenericutes, Fusobacteria, Firmicutes, Verrucomicrobia, Bacteroidetes, Planctomycetes, Actinobacteria and Chloroflexi. OTUs belonged to 289 genera and the most abundant genera were Candidatus_Xiphinematobacter, Propionigenium, Synechococcus, Shewanella and Cetobacterium. Fifty-nine OTUs were detected in all samples, which were considered as the major microbes in intestine of shrimp. The intestinal microbiota was enriched with functional potentials that were related to transporters, ABC transporters, DNA repair and recombination proteins, two component system, secretion system, bacterial motility proteins, purine metabolism and ribosome. All the results showed that the intestinal microbial composition, diversity and functions varied significantly at different culture stages, which indicated that shrimp intestinal microbiota depended on culture stages. These findings provided new evidence on intestinal microorganism microecology and greatly enhanced our understanding of stage

  16. Mechanisms of microbial destabilization of soil C shifts over decades of warming

    Science.gov (United States)

    DeAngelis, K.; Pold, G.; Chowdhury, P. R.; Schnabel, J.; Grandy, S.; Melillo, J. M.

    2017-12-01

    Microbes are major actors in regulating the earth's biogeochemical cycles, with temperature-sensitive microbial tradeoffs improving ecosystem biogeochemical models. Meanwhile, the Earth's climate is changing, with decades of warming undercutting the ability of soil to store carbon. Our work explores trends of 26 years of experimental warming in temperate deciduous forest soils, which is associated with cycles of soil carbon degradation punctuated by periods of changes in soil microbial dynamics. Using a combination of biogeochemistry and molecular analytical methods, we explore the hypotheses that substrate availability, community structure, altered temperature sensitivity of microbial turnover-growth efficiency tradeoff, and microbial evolution are responsible for observations of accelerated degradation of soil carbon over time. Amplicon sequencing of microbial communities suggests a small role of changing microbial community composition over decades of warming, but a sustained suppression of fungal biomass is accompanied by increased biomass of Actinobacteria, Actinobacteria, Alphaproteobacteria, Verrucomicrobia and Planctomycetes. Substrate availability plays an important role in microbial dynamics, with depleted labile carbon in the first decade and depleted lignin in the second decade. Increased lignin-degrading enzyme activity supports the suggestion that lignin-like organic matter is an important substrate in chronically warmed soils. Metatranscriptomics data support the suggestion that increased turnover is associated with long-term warming, with metagenomic signals of increased carbohydrate-degrading enzymes in the organic horizon but decreased in the mineral soils. Finally, traits analysis of over 200 cultivated isolates of bacterial species from heated and control soils suggests an expanded ability for degradation of cellulose and hemicellulose but not chitin, supporting the hypothesis that long-term warming is exerting evolutionary pressure on microbial

  17. Paleolimnological reconstruction of environmental variability during the Late Pleistocene and Holocene in the south-east Baltic region

    Science.gov (United States)

    Kublitskiy, Iurii; Subetto, Dmitriy; Druzhinina, Olga; Kulkova, Marianna; Arslanov, Khikmatula

    2016-04-01

    Kamyshovoe Lake : history of vegetation during late Pleistocene and early Holocene (Kaliningrad District, Russia). Baltica, 28 (2). (in press). Kublitskiy, I., Subetto, D., Kulkova, M., Druzhinina, O., Arslanov, Kh., 2015. Analysis of the climatic changes at the Late Pleistocene and the Holocene based on palaeolimnological studies of the Kamyshovoe Lake (Kaliningrad Region). Proceeding of the IX Russian conference on Quaternary Research (Irkutsk, 15-20 September 2015) [In Russian].

  18. The Origin of the Chinese Central Tianshan Block in the Southern Central Asian Orogenic Belt: Evidence from Detrital Zircon Study

    Science.gov (United States)

    Huang, Z.; Long, X.; Yuan, C.

    2016-12-01

    The Chinese Central Tianshan Block (CTB) is one of the oldest continental fragments in the southern Central Asian Orogenic Belt (CAOB). Although it is vital for understanding the evolution of the CAOB, its origin has been poorly studied. The CTB was previously suggested to have been originated from the North China, the South China, the Tarim cratons or the East European Craton (Baltica). A total of 165 concordant U-Pb and Hf isotopic analyses of detrital zircon are obtained from three meta-sediments in the CTB, including one meta-sandstone from Xingxingxia formation and one meta-sandstone as well as one quartzite from Kawabulake formation. Detrital zircon grains from the Xingxingxia and Kawabulake formations are dominated by respective youngest age populations at 1002 Ma and 930-960 Ma, providing constraints on the maximum depositional ages for these two formations. Zircon grains from the meta-sediments have very similar age distributions, with two dominant peaks at 0.93-1.0 Ga and 1.0-1.6 Ga and a minor peak at 2.3-2.7 Ga. They have similar Hf isotopic signatures, suggesting that the meta-sediments in the CTB share similar sedimentary provenance. The early Neoproterozoic detrital zircon grains are mainly local-derived, whereas the Paleo-Mesoproterozoic grains are both autochthonous and allochthonous. The occurrence of these Mesoproterozoic and Neoproterozoic zircon grains are coincident with the Nuna breakup and the Rodinia assembly. This suggests that the CTB might experience the tectonic switching of the Nuna to the Rodinia. The distinct Meso-Neoproterozoic age patterns and Hf isotopic compositions of these detrital grains from the CTB and the surrounding blocks indicate that the CTB was not located close to the North China, the South China or the Tarim cratons in Precambrian. Our new data suggest that the CTB was most likely once a part of the East European Craton before the Neoproterozoic. This study was supported by National Basic Research Program of China

  19. Redox Sensing within the Genus Shewanella

    Directory of Open Access Journals (Sweden)

    Howard W. Harris

    2018-01-01

    Full Text Available A novel bacterial behavior called congregation was recently described in Shewanella oneidensis MR-1 as the accumulation of cells around insoluble electron acceptors (IEA. It is the result of a series of “run-and-reversal” events enabled by modulation of swimming speed and direction. The model proposed that the swimming cells constantly sense their surroundings with specialized outer membrane cytochromes capable of extracellular electron transport (EET. Up to this point, neither the congregation nor attachment behavior have been studied in any other strains. In this study, the wild type of S. oneidensis MR-1 and several deletion mutants as well as eight other Shewanella strains (Shewanella putrefaciens CN32, S. sp. ANA-3, S. sp. W3-18-1, Shewanella amazonensis SB2B, Shewanella loihica PV-4, Shewanella denitrificans OS217, Shewanella baltica OS155, and Shewanella frigidimarina NCIMB400 were screened for the ability to congregate. To monitor congregation and attachment, specialized cell-tracking techniques, as well as a novel cell accumulation after photo-bleaching (CAAP confocal microscopy technique were utilized in this study. We found a strong correlation between the ability of strain MR-1 to accumulate on mineral surface and the presence of key EET genes such as mtrBC/omcA (SO_1778, SO_1776, and SO_1779 and gene coding for methyl-accepting protein (MCPs with Ca+ channel chemotaxis receptor (Cache domain (SO_2240. These EET and taxis genes were previously identified as essential for characteristic run and reversal swimming around IEA surfaces. CN32, ANA-3, and PV-4 congregated around both Fe(OH3 and MnO2. Two other Shewanella spp. showed preferences for one oxide over the other: preferences that correlated with the metal content of the environments from which the strains were isolated: e.g., W3-18-1, which was isolated from an iron-rich habitat congregated and attached preferentially to Fe(OH3, while SB2B, which was isolated from a MnO2-rich

  20. Two new marine Gastrotricha from the Indian Ocean coast of South Africa.

    Science.gov (United States)

    Todaro, M Antonio; Perissinotto, Renzo; Bownes, Sarah J

    2015-01-12

    The study is part of a larger research programme aimed at shedding light on the gastrotrich communities of the subtropical east coast province of KwaZulu-Natal, South Africa. In previous papers, faunistic and preliminary taxonomic data on marine and freshwater gastrotrichs found in the iSimangaliso Wetland Park, were reported. Here two new interesting marine macrodasyidan species in the families Dactylopodolidae and Thaumastodermatidae are described based on observations carried out on living specimens and using differential interference contrast microscopy. The two novel species are named in honor of two great South African icons recently deceased: Nadine Gordimer and Nelson Mandela. Dactylopodola nadine sp. n. is the third species in the genus to bear red eye-spots; it can easily be distinguished from the closely-related red-eyed D. baltica and D. roscovita by its smaller size (Total length = 230 μm vs 275 μm vs 450 μm, respectively) and the lower number of adhesive tubes of the anterior, lateral and posterior series (on each side: 3, 4 and 4 vs 5, 6 and 8 vs 2, 9 and 12-15). Pseudostomella mandela sp. n. is a fairly large species (up to 481 μm in length), with a cuticular covering made up of tetrancres and relatively long caudal pedicles (up to 44 μm in length ). The most evident autoapomorphic trait of the new species is the presence of 7 pairs of 'cirrata' tubes, two emerging in a lateral position along the pharyngeal region and five from the dorsolateral sides of the trunk. Additional relevant taxonomic characters include: 4 tubes of the anterior series, 11 tubes of the ventrolateral series and 3 tubes of the posterior series per side, 5 papillae on the dorsal margin and 6 papillae on the ventral margin of the oral palps. The high number of putative new species discovered among the South African gastrotrich fauna during our relatively short survey, highlights the relevance of this region with regard to the diversity of this group and stresses once again

  1. Caledonian and late Caledonian Europe: a working hypothesis involving two contrasted compressional/extensional scenarios

    Directory of Open Access Journals (Sweden)

    Oyarzun, R.

    1990-08-01

    Full Text Available The tectonomagmatic and metamorphic structuration of the European Caledonian realm suggests that two mutually perpendicular compressional/extensional scenarios developed during the Ordovician-Devonian time-span. As a result of the mid Ordovician Grampian compressional scheme (Caledonian s.s., a major extensional province developed further east from the Caledonian foldbelt in continental Europe. This scenario ended by early/mid Devonian, with the complete locking of North America, Baltica and Gondwana into a Pangaea supercontinent, thus triggering a contrasted tectonic environment which might be termed La estructuración tectonomagmática y metamórfica del dominio caledónico europeo sugiere que dos escenarios, compresional y extensional, mutuamente perpendiculares, se desarrollaron durante el Ordovícico-Devónico. Como resultado del esquema compresional del Ordovícico medio (Grampian, caledónico s.s., en el O de Europa continental se desarrolló una provincia extensional localizada al E de la faja de plegamiento caledónica. Esta situación finalizó hacia el Devónico inferior/medio, cuando la convergencia de América del Norte, Báltica y Gondwana dió origen al supercontinente Pangea. Esta colisión generó un ambiente tectónico caracterizado por: 1. plegamiento y plutonismo en Europa continental occidental, y 2. extensión y volcanismo en la parte N de la faja de plegamiento caledónica (Escocia, SO de Noruega y E de Groenlandia. Este evento puede ser tentativamente denominado «Tardicaledónico». En términos globales, la evolución del dominio caledónico puede ser explicada en términos de «tectónica de inversión» (s.l., esto es, períodos de adelgazamiento cortical (extensionales seguidos por períodos de engrosamiento cortical (compresionales y viceversa

  2. Analysing the geothermal state of the ICDP COSC-1 well bore, Central Sweden

    Science.gov (United States)

    Löwe, R.; Pascal, C.; Renner, J.

    2017-12-01

    In 2014 the first well of the ICDP project "Collisional Orogeny in the Scandinavian Caledonides (COSC)" was drilled to 2495.8 m (MD) near Åre in Central Sweden. The well penetrates the Seve Nappe complex, a result of subduction/exhumation processes during the collision of Baltica and Laurentia 400 Ma. To gain detailed understanding of the geothermal state of fossil mountain belts and cratonic areas, it is necessary to study present-day heat transfer in the Earth's crust in appropriate deep wells. Heat transfer in the crust is governed by heat conduction and hydrothermal convection. The primary aims of our study are to determine which heat transfer mechanisms dominate in the study area around COSC-1 and how much heat flows to the surface. Permeability was determined for selected samples for various confining pressures using an oscillatory pore pressure method. The determined values range from 5.8 10-19 to 1.3 10-22 m2 and an empirical permeability-pressure trend was derived. Our results imply that convection plays a negligible role for heat transfer in the study area. A modified "Ångström" device was used to determine thermal diffusivity (α) from transient (oscillatory) temperature signals. It was tested on selected COSC-1 cores in an inter-laboratory round robin involving five international research organisations. Determination of specific heat capacity, density, and α for the 105 core samples, allowed us to calculate thermal conductivity (λ). In addition, we conducted measurements to assess the anisotropy of λ and α and their temperature dependencies. For the first 2000 m λ amounts to 2.8±0.4 W/(m.K) on average and increases to 4.1±1 W/(m.K) in the lowermost section of the well. Average heat generation, as derived from spectral gamma ray logs, is as low as 0.8 µW/m3. Three temperature logs were measured about one week, one month, and one year after drilling, with the latest log measured close to thermal equilibrium below 1500 m depth. Based on the logs

  3. Barents Sea Crustal and Upper Mantle Structure from Deep Seismic and Potential Field Data

    Science.gov (United States)

    Aarseth, I.; Mjelde, R.; Breivik, A. J.; Minakov, A.; Huismans, R. S.; Faleide, J. I.

    2016-12-01

    The Barents Sea basement comprises at least two different domains; the Caledonian in the west and the Timanian in the east. Contrasting interpretations have been published recently, as the transition between these two domains is not well constrained. Interpretations of new high-quality magnetic data covering most of the SW Barents Sea challenged previous studies of the Late Paleozoic basin configurations in the western and central Barents Sea. Two major directions of Caledonian structures have been proposed by different authors: N-S and SW-NE. Two regional ocean bottom seismic (OBS) profiles, crossing these two major directions, were acquired in 2014.The primary goal in this project is to locate the main Caledonian suture in the western Barents Sea, as well as the possible Barentsia-Baltica suture postulated further eastwards. High velocity anomalies associated with Caledonian eclogites are particularly interesting as they may be related to Caledonian suture zones. The collapse of the Caledonian mountain range predominantly along these suture zones is expected to be closely linked to the deposition of Devonian erosional products, and subsequent rifting is likely to be influenced by inheritance of Caledonian trends. P-wave travel-time modelling is done by use of a combined ray-tracing and inversion scheme, and gravity modelling has been used to support the seismic model. The results indicate high P-wave velocities (mostly over 4 km/s) close to the seafloor as well as high velocity (around 6 km/s) zones at shallow depths which are interpreted as volcanic sills. The crustal transect reveals areas of complex geology and velocity inversions. Strong reflections from within the crystalline crust indicate a heterogeneous basement terrain. Gravity modelling agrees with this, as several blocks with variable densities had to be introduced in order to reproduce the observed gravity anomalies. Refractions from the top of the crystalline basement together with reflections from

  4. Barents Sea Paleozoic basement and basin configurations: Crustal structure from deep seismic and potential field data

    Science.gov (United States)

    Aarseth, Iselin; Mjelde, Rolf; Breivik, Asbjørn Johan; Huismans, Ritske; Faleide, Jan Inge

    2016-04-01

    The Barents Sea is underlain by at least two different basement domains; the Caledonian in the west and the Timanian in the east. The transition between these two domains is not well constrained and contrasting interpretations have been published recently. Interpretations of new high-quality magnetic data covering most of the SW Barents Sea has challenged the Late Paleozoic basin configurations in the western and central Barents Sea as outlined in previous studies. Two regional ocean bottom seismic (OBS) profiles were acquired in 2014. This new dataset crosses the two major directions of Caledonian deformation proposed by different authors: N-S direction and SW-NE direction. Of particular importance are the high velocity anomalies related to Caledonian eclogites, revealing the location of Caledonian suture zones in the northern Barents Sea. One of the main objectives with this project is to locate the main Caledonian suture in the western Barents Sea, as well as the possible Barentsia-Baltica suture postulated further eastwards. The collapse of the Caledonian mountain range predominantly along these suture zones is expected to be tightly linked to the deposition of large thicknesses of Devonian erosional products, and later rifting is expected to be influenced by inheritance of Caledonian trends. The P-wave travel-time modelling is done by use of a combined ray-tracing and inversion scheme, and gravity- and magnetic modelling will be used to augment the seismic model. The preliminary results indicate high P-wave velocities (mostly over 4 km/s) close to the seafloor as well as high velocity (around 6 km/s) zones at shallow depths which are interpreted as volcanic sills. The crustal transects reveal areas of complex geology and velocity inversions. A low seismic impedance contrast between the sedimentary section and top crystalline basement makes identification of this interface uncertain. Depth to Moho mostly lies around 30 km, except in an area of rapid change in

  5. Historical and Epistemological Reflections on the Culture of Machines around the Renaissance: How Science and Technique Work?

    Directory of Open Access Journals (Sweden)

    Raffaele Pisano

    2014-10-01

    Full Text Available This paper is divided into two parts, this being the first one. The second is entitled ‘Historical and Epistemological Reflections on the Culture of Machines around Renaissance: Machines, Machineries and Perpetual Motion’ and will be published in Acta Baltica Historiae et Philosophiae Scientiarum in 2015. Based on our recent studies, we provide here a historical and epistemological feature on the role played by machines and machineries. Ours is an epistemological thesis based on a series of historical examples to show that the relations between theoretical science and the construction of machines cannot be taken for granted, a priori. Our analysis is mainly based on the culture of machines around 15th and 17th centuries, namely the epoch of Late Renaissance and Early Modern Age. For this is the period of scientific revolution and this age offers abundant interesting material for researches into the relations of theoretical science/construction of machines as well. However, to prove our epistemological thesis, we will also exploit examples of machines built in other historical periods. Particularly, a discussion concerning the relationship between science theory and the development of science art crafts produced by non-recognized scientists in a certain historical time is presented. The main questions are: when and why did the tension between science (physics, mathematics and geometry give rise to a new scientific approach to applied discipline such as studies on machines and machineries? What kind of science was used (if at all for projecting machines and machineries? Was science at the time a necessary precondition to build a machine? In the first part we will focus on the difference between Aristotelian-Euclidean and Archimedean approaches and we will outline the heritage of these two different approaches in late medieval and Renaissance science. In the second part, we will apply our reconstructions to some historical and epistemological

  6. Towards an integrated magmatic, structural and metamorphic model for the 1.1-0.9 Ga Sveconorwegian orogeny

    Science.gov (United States)

    Slagstad, Trond; Roberts, Nick M. W.; Røhr, Torkil S.; Marker, Mogens K.

    2013-04-01

    Orogeny involves magmatic, metamorphic, deformational and erosional processes that are caused by or lead to crustal thickening and the development of high topography. In general, these processes operate along the margins of continental plates, either as a result of subduction of oceanic crust (accretionary) or collision between two or more continental plates (collisional). Many of these processes are common to accretionary and collisional orogeny, and do not uniquely discriminate between the two. With only a fragmented geological record, unravelling the style of orogenesis in ancient orogens may, therefore, be far from straightforward. Adding to the complexity, modern continental margins, e.g., the southern Asian margin, display significant variation in orogenic style along strike, rendering along-strike comparisons and correlations unreliable. The late Mesoproterozoic Sveconorwegian province in SW Baltica is traditionally interpreted as the eastward continuation of the Grenville province in Canada, resulting from collision with Amazonia and forming a central part in the assembly of the Rodinia supercontinent. We recently proposed that the Sveconorwegian segment of this orogen formed as a result of accretionary processes rather than collision. This hypothesis was based mainly on considerations of the Sveconorwegian magmatic evolution. Here, we show how the metamorphic/structural record supports (or at least may be integrated in) our model as well. The key elements in our accretionary model are: 1) formation of the Sirdal Magmatic Belt (SMB) between 1070 and 1020 Ma, most likely representing a continental arc batholith. Coeval deformation and high-grade metamorphism farther east in the orogen could represent deformation in the retroarc. 2) cessation of SMB magmatism at 1020 Ma followed by UHT conditions at 1010-1005 Ma, with temperatures in excess of 1000°C at 7.5 kbar. Subduction of a spreading ridge at ca. 1020 Ma would result in an end to arc magmatism and

  7. The complete mitochondrial genome of the common sea slater, Ligia oceanica (Crustacea, Isopoda bears a novel gene order and unusual control region features

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    Podsiadlowski Lars

    2006-09-01

    Full Text Available Abstract Background Sequence data and other characters from mitochondrial genomes (gene translocations, secondary structure of RNA molecules are useful in phylogenetic studies among metazoan animals from population to phylum level. Moreover, the comparison of complete mitochondrial sequences gives valuable information about the evolution of small genomes, e.g. about different mechanisms of gene translocation, gene duplication and gene loss, or concerning nucleotide frequency biases. The Peracarida (gammarids, isopods, etc. comprise about 21,000 species of crustaceans, living in many environments from deep sea floor to arid terrestrial habitats. Ligia oceanica is a terrestrial isopod living at rocky seashores of the european North Sea and Atlantic coastlines. Results The study reveals the first complete mitochondrial DNA sequence from a peracarid crustacean. The mitochondrial genome of Ligia oceanica is a circular double-stranded DNA molecule, with a size of 15,289 bp. It shows several changes in mitochondrial gene order compared to other crustacean species. An overview about mitochondrial gene order of all crustacean taxa yet sequenced is also presented. The largest non-coding part (the putative mitochondrial control region of the mitochondrial genome of Ligia oceanica is unexpectedly not AT-rich compared to the remainder of the genome. It bears two repeat regions (4× 10 bp and 3× 64 bp, and a GC-rich hairpin-like secondary structure. Some of the transfer RNAs show secondary structures which derive from the usual cloverleaf pattern. While some tRNA genes are putative targets for RNA editing, trnR could not be localized at all. Conclusion Gene order is not conserved among Peracarida, not even among isopods. The two isopod species Ligia oceanica and Idotea baltica show a similarly derived gene order, compared to the arthropod ground pattern and to the amphipod Parhyale hawaiiensis, suggesting that most of the translocation events were already

  8. Contemporaneous assembly of Western Gondwana and final Rodinia break-up: Implications for the supercontinent cycle

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    Sebastián Oriolo

    2017-11-01

    Full Text Available Geological, geochronological and isotopic data are integrated in order to present a revised model for the Neoproterozoic evolution of Western Gondwana. Although the classical geodynamic scenario assumed for the period 800–700 Ma is related to Rodinia break-up and the consequent opening of major oceanic basins, a significantly different tectonic evolution can be inferred for most Western Gondwana cratons. These cratons occupied a marginal position in the southern hemisphere with respect to Rodinia and recorded subduction with back-arc extension, island arc development and limited formation of oceanic crust in internal oceans. This period was thus characterized by increased crustal growth in Western Gondwana, resulting from addition of juvenile continental crust along convergent margins. In contrast, crustal reworking and metacratonization were dominant during the subsequent assembly of Gondwana. The Río de la Plata, Congo-São Francisco, West African and Amazonian cratons collided at ca. 630–600 Ma along the West Gondwana Orogen. These events overlap in time with the onset of the opening of the Iapetus Ocean at ca. 610–600 Ma, which gave rise to the separation of Baltica, Laurentia and Amazonia and resulted from the final Rodinia break-up. The East African/Antarctic Orogen recorded the subsequent amalgamation of Western and Eastern Gondwana after ca. 580 Ma, contemporaneously with the beginning of subduction in the Terra Australis Orogen along the southern Gondwana margin. However, the Kalahari Craton was lately incorporated during the Late Ediacaran–Early Cambrian. The proposed Gondwana evolution rules out the existence of Pannotia, as the final Gondwana amalgamation postdates latest connections between Laurentia and Amazonia. Additionally, a combination of introversion and extroversion is proposed for the assembly of Gondwana. The contemporaneous record of final Rodinia break-up and Gondwana assembly has major implications for the

  9. Late Carboniferous remagnetisation of Palaeozoic rocks in the NE Rhenish Massif, Germany

    Science.gov (United States)

    Zwing, A.; Bachtadse, V.; Soffel, H. C.

    During stepwise thermal and alternating field demagnetisation experiments on Devonian and Lower Carboniferous carbonate and clastic rocks from the north-eastern part of the Rhenish Massif, Germany, three components of magnetisation (A, B, C) are identified. Component A is a recent viscous overprint that parallels the local present day geomagnetic field. Component B is mainly observed from 260 up to 550 °C during thermal demagnetisation and is carried by magnetite. In two localities, where red siltstones and red carbonate rocks were sampled, component B is stable up to 670 °C, indicating the presence of hematite. Three clusters of in situ B directions can be identified, which are controlled by the tectonic position of the sampling areas. These are from NW to SE: the Remscheid anticline (RA), the Lüdenscheid syncline (LS) and the Attendorn and Wittgenstein synclines (AS/WS). Standard and inclination-only fold tests, using parametric resampling, yield optimal statistical parameters at increasing amounts of untilting ranging from 0% in the South up to 57% in the North of the NE Rhenish Massif. Despite the variations in optimal untilting, the resulting site mean directions of component B do not differ significantly in inclination. These results are interpreted to reflect the acquisition of magnetisation during progressive northward migration of the deformation front in Late Carboniferous times. The resulting palaeolatitudes (RA: 1°S +2°-3°; LS: 2°S +3°-2°; AS/WS: 1°S +3°-4°) are in good agreement with the predicted position of the sampling area in the Late Carboniferous, as derived from a published Apparent Polar Wander Path for Baltica and Laurentia. The unblocking temperature spectra and the synfolding nature of B yield strong evidence that chemical processes, possibly driven by fluid migration during orogenesis, caused this remagnetisation. A third component C was observed in zones of tight folding with steeply dipping to overturned bedding planes and is

  10. Pan African Collisional Tectonics Along the Moroccan West African Craton Continued to Ediacaran-Cambrian Boundary

    Science.gov (United States)

    Hefferan, K. P.; Samson, S. D.; Rice, K.; Soulaimani, A.

    2016-12-01

    -Middle Cambrian time. This time frame is not limited to the Anti-Atlas but coincides with a global pattern. Similar to the West African Craton, convergent margin activity in Northern Gondwana (southern Europe), the Trans-Saharan Belt, Laurentia, Baltica and Siberia likely was not completed until the end of the Neoproterozoic.

  11. U-Pb baddeleyite ages and geochemistry of dolerite dykes in the Bas Drâa Inlier of the Anti-Atlas of Morocco: Newly identified 1380 Ma event in the West African Craton

    Science.gov (United States)

    El Bahat, Abdelhakim; Ikenne, Moha; Söderlund, Ulf; Cousens, Brian; Youbi, Nasrrddine; Ernst, Richard; Soulaimani, Abderrahmane; El Janati, M'hamed; Hafid, Ahmid

    2013-08-01

    In the Bas-Drâa Inlier (Anti-Atlas, Morocco), the Paleoproterozoic basement which is cut by the Ediacaran Taourgha granite is also crosscut by numerous dykes of a variety of trends, mostly of uncertain age. Two doleritic dykes are dated by the ID-TIMS U-Pb method on baddeleyite and yield emplacement ages of 1381 ± 8 Ma (MSWD = 0.84) and 1384 ± 6 Ma (MSWD = 1.4) determined for a N135°E and a N40°E trending dyke, respectively. These dates represent the first geochronological evidence of a Mesoproterozoic magmatic event in the Anti-Atlas. This magmatic event falls in the previously considered ca 1.7-1.0 Ga (Mesoproterozoic) gap in geological activity in the Anti-Atlas. The poorly dated Taghdout and Taarotihate sequences could represent remnants of the ca. 1380 Ma magmatism and rift-related sedimentation. The Mesoproterozoic sedimentary succession of the Atar Group in the Taoudeni basin (Mauritania) could also represent a good candidate for rift-related sedimentation but it postdates the 1380 Ma magmatic event by 270 Ma. The dated 1380 Ma dykes are transitional to mildly alkaline basalts, not unlike some Hawaiian lavas. However, these dykes have a distinct negative Nb anomaly (a common features in many Large Igneous Provinces, LIPs), and this requires interaction with the lithosphere. This interaction may have occurred at the level of the lithospheric mantle or the crust. These newly dated 1380 Ma dykes may converge to the north, speculatively suggesting a magmatic center (associated with a 1380 Ma mantle plume?) along the northern margin, and possibly linked to rifting and possible breakup on that margin, and also to a regional uplift that largely removed the evidence of a 1380 Ma cover sequence. Contemporaneous 1380-1390 Ma magmatism is reported elsewhere on other crustal blocks, and that in northeastern Laurentia (northern Greenland), northern Siberia (Anabar shield), and Baltica (southern Urals) can be reconstructed with that of the Bas Drâa Inlier (Anti

  12. Paleomagnetism and magnetic fabric of the Triassic rocks from Spitsbergen

    Science.gov (United States)

    Dudzisz, K.; Szaniawski, R.; Michalski, K.; Manby, G.

    2017-12-01

    Understanding the origin and directions of the natural remanent magnetization and the tectonic deformation pattern reflected in magnetic fabric is of importance for investigation of the West Spitsbergen Fold and Thrust Belt (WSFTB) and its foreland. Previous research carried out on Triassic rocks from the study area concluded that these rocks record a composite magnetization of both, normal and reverse polarity, consisting of a primary Triassic remanence that is overlapped by a secondary post-folding component. Standard paleomagnetic procedures were conducted in order to determine the remanence components and a low-field AMS was applied to assess the degree and pattern of deformation. The AMS results from the WSFTB reveal a magnetic foliation that parallels the bedding planes and a dominantly NNW-SSE oriented magnetic lineation that is sub-parallel to the regional fold axial trend. These results imply a low to moderate degree of deformation and a maximum strain orientation parallel to that of the fold belt. These data are consistent with an orthogonal convergence model for the WSFTB formation. In turn, the magnetic fabric on the undeformed foreland displays a distinct NNE-SSW orientation that we attribute to the paleocurrent direction. Rock-magnetic analyses reveal that the dominant ferrimagnetic carriers are magnetite and titanomagnetite. The Triassic rocks are characterised by complicated NRM patterns often with overlapping unblocking temperature spectra of particular components. The dominant magnetisation is characterised, however, by a steep inclination of 70-80º. The derived paleomagnetic direction from the WSFTB falls on the Jurassic - recent sector of the apparent polar wander path (APWP) of Baltica after tectonic unfolding. These data imply that at least some of the identified secondary components could have originated before the Eurekan folding event (K/Pg), for example, in Early Cretaceous time which corresponds to the period of rifting events on Barents

  13. Stable isotopes in Lithuanian bioarcheological material

    Science.gov (United States)

    Skipityte, Raminta; Jankauskas, Rimantas; Remeikis, Vidmantas

    2015-04-01

    Investigation of bioarcheological material of ancient human populations allows us to understand the subsistence behavior associated with various adaptations to the environment. Feeding habits are essential to the survival and growth of ancient populations. Stable isotope analysis is accepted tool in paleodiet (Schutkowski et al, 1999) and paleoenvironmental (Zernitskaya et al, 2014) studies. However, stable isotopes can be useful not only in investigating human feeding habits but also in describing social and cultural structure of the past populations (Le Huray and Schutkowski, 2005). Only few stable isotope investigations have been performed before in Lithuanian region suggesting a quite uniform diet between males and females and protein intake from freshwater fish and animal protein. Previously, stable isotope analysis has only been used to study a Stone Age population however, more recently studies have been conducted on Iron Age and Late medieval samples (Jacobs et al, 2009). Anyway, there was a need for more precise examination. Stable isotope analysis were performed on human bone collagen and apatite samples in this study. Data represented various ages (from 5-7th cent. to 18th cent.). Stable carbon and nitrogen isotope analysis on medieval populations indicated that individuals in studied sites in Lithuania were almost exclusively consuming C3 plants, C3 fed terrestrial animals, and some freshwater resources. Current investigation demonstrated social differences between elites and country people and is promising in paleodietary and daily life reconstruction. Acknowledgement I thank prof. dr. G. Grupe, Director of the Anthropological and Palaeoanatomical State Collection in Munich for providing the opportunity to work in her laboratory. The part of this work was funded by DAAD. Antanaitis-Jacobs, Indre, et al. "Diet in early Lithuanian prehistory and the new stable isotope evidence." Archaeologia Baltica 12 (2009): 12-30. Le Huray, Jonathan D., and Holger

  14. Two possibilities for New Siberian Islands terrane tectonic history during the Early Paleozoic based on paleomagnetic data

    Science.gov (United States)

    Metelkin, Dmitry V.; Chernova, Anna I.; Vernikovsky, Valery A.; Matushkin, Nikolay Yu.

    2017-04-01

    The New Siberian Islands (NSI), located in the East Siberian Sea in the junction region of various structural elements, are a key target for deciphering the tectonic evolution of the Eastern Arctic. In recent years, we went on several expeditions and gathered an extensive geological material for this territory. Among other things, we could prove that the basement of the De Long and Anjou archipelagos structures is Precambrian and the overlying Paleozoic sections formed within the same terrane. The form of the boundaries of the NSI terrane are actively debated and are probably continued from the Lyakhovsky islands in the south-west to the southern parts of the submerged Mendeleev Ridge, for which there is increasing evidence of continental crust. Today there are several models that interpret the Paleozoic-Mesozoic tectonic history and structural affiliation of the NSI terrane. Some propose that the Paleozoic sedimentary section formed in a passive margin setting of the Siberian paleocontinent. Others compare its history with marginal basins of the Baltica and Laurentia continents or consider the NSI terrane as an element of the Chukotka-Alaska microplate. These models are mainly based on results of paleobiogeographical and lithological-facies analyses, including explanations of probable sources for detrital zircons. Our paleomagnetic research on sedimentary, volcanogenic-sedimentary and igneous rocks of the Anjou (Kotelny and Bel'kovsky islands) and De Long (Bennett, Jeannette and Henrietta islands) archipelagos let us calculate an apparent polar wander path for the early Paleozoic interval of geological history, which allows us to conclude that the NSI terrane could not have been a part of the continental plates listed above, but rather had active tectonic boundaries with them. Our paleomagnetic data indicate that the NSI terrane drifted slowly and steadily in the tropical and subtropical regions no higher than 40 degrees. However, the main uncertainty for the

  15. New paleomagnetic results on ˜ ˜2367 Ma Dharwar giant dyke swarm, Dharwar craton, southern India: implications for Paleoproterozoic continental reconstruction

    Science.gov (United States)

    Babu, N. Ramesh; Venkateshwarlu, M.; Shankar, Ravi; Nagaraju, E.; Parashuramulu, V.

    2018-02-01

    dykes of Kola-Karelia craton (Baltica Shield).

  16. Aquatic indicator organisms as a tool to monitor discharges from nuclear power plants

    Energy Technology Data Exchange (ETDEWEB)

    Outola, Iisa; Vartti, Vesa-Pekka; Klemola, Seppo [STUK - Radiation and Nuclear Safety Authority, P.O. Box 14, 00881 Helsinki (Finland)

    2014-07-01

    There are four operating nuclear power plant units in Finland at two separate locations. The units started operation during 1977-1980. The surveillance of radioactive substances in the vicinities of the nuclear power plant is carried out under the permanent monitoring programs. Some 1000 samples are taken annually from the surroundings of the power plants to confirm that the discharges from the power plants are within permissible release limits and to monitor the dispersion of discharges in the environment. Aquatic indicator organisms (macro-algae, periphyton, mussels, crustacean, submerged aquatic plants) are included in the monitoring program. The indicator organisms are valuable monitoring objects both in normal and emergency situations because they accumulate effectively and often very rapidly radioactive substances from the medium. Six different species (Periphyton, Fucus vesiculosus, Myriophyllum spicatum, Potamogeton pectinatus, Saduria entomon, Macoma Baltica/Mytilus edulis) are collected regularly. Number of sampling location for each species varies from 1 to 7. Some species are collected continuously, some 1-2 times in a year. In this study we have evaluated the monitoring results for the aquatic indicator organisms for the period of 2005-2010 concerning concentration of discharge nuclides. Our aim was to answer the following questions using the monitoring data from aquatic organisms: 1) Which radionuclides are released to the marine environment and how often do we detect them? 2) How far from the nuclear power plants discharge radionuclides are detected? 3) How concentration of discharge radionuclides has changed with time in aquatic organisms? The number of discharge nuclides detected in the aquatic indicator samples was 11. Most of them were only detected in few samples, but {sup 58}Co, {sup 60}Co, {sup 54}Mn and {sup 110m}Ag were detected more frequently. Most of the observations above detection limits were made within the 5 km distance from the

  17. Ion microprobe (SHRIMP) dating of detrital zircon grains from quartzites of the Eckergneiss Complex, Harz Mountains (Germany): implications for the provenance and the geological history

    Science.gov (United States)

    Geisler, Thorsten; Vinx, Roland; Martin-Gombojav, Nergui; Pidgeon, Robert T.

    2005-07-01

    The Eckergneiss Complex (EGC) is a geologically unique medium- to high-grade metamorphic unit within the Rhenohercynian domain of the Mid-European Variscides. A previously, poorly defined conventional lower U Pb intercept age of about 560 Ma from detrital zircons of metasedimentary rocks has led to speculations about an East Avalonian affinity of the EGC. In order to unravel the provenance and to constrain the age of the sediment protolith, we carried out sensitive high-resolution ion microprobe U Pb analyses on detrital zircons from five different EGC quartzite occurrences. The obtained age spectrum indicates a SW Baltica provenance of the detritus. Sveconorwegian ages between 0.9 1.2 Ga are particularly well represented by analyses from metamorphic recrystallization/alteration zones penetrating into igneous zircon. Cadomian (Pan-African) ages, which might reflect a metamorphic event, could not be substantiated. Instead, zircons of igneous origin yielded concordant Lower Devonian and Silurian ages of 410±10, 419±10, and 436±6 Ma (1σ), implying that sedimentation of the EG protolith must have taken place after 410±10 Ma. The lower age limit of the EGC metamorphism is constrained by 295 Ma intrusion ages of the adjacent, nonmetamorphosed Harzburg Gabbronorite and Brocken Granite. Sedimentation and metamorphism must thus have taken place between about 410 Ma and 295 Ma. Given that this time span coincides with most of the sedimentation within the virtually nonmetamorphosed (lowest grade) Rhenohercynian in the Harz Mountains, including the direct vicinity of the EGC, along with the high-grade metamorphism, the EGC can hardly be seen as uplifted local basement. A possible candidate for the root region is an easterly, concealed marginal segment of the Rhenohercynian domain of the Variscides, which is tectonically overridden and suppressed by the Mid-German Crystalline Rise during continent collision. However, based on the concept of strike-slip movement of Variscan

  18. On protolith-, metamorphic overprint, microstructure and rheology of mineral assemblages in orogenic peridotites of the central Scandinavian Caledonides

    Science.gov (United States)

    Gilio, Mattia; Clos, Frediano; Van Roermund, Herman L. M.

    2013-04-01

    The Scandinavian Caledonides (SC) are a deeply eroded Alpine-type orogenic belt formed by closure of the Iapetus ocean and collision between Baltica and Laurentia (500-380 Ma). The SC consists of a stack of Nappe Complexes (from bottom to top called Lower, Middle, Upper and Uppermost Allochthons) thrusted to the east over the Baltic Shield (Brueckner and Van Roermund, 2004; Gee et al., 2008). Fossil lithospheric mantle fragments, called orogenic peridotites, have been found within the (upper part of) middle, upper and uppermost Allochthons, as well as in the reworked basement gneisses (a.o Western Gneiss Complex (WGC)) along the Norwegian west coast. They occur as isolated lenses that contain diverse mineral parageneses and/or bulk rock compositions. Crustal incorporation of orogenic peridotite is classically interpreted to be the result of plate collisional processes related to orogeny (Brueckner and Medaris, 2000). The WGC and parts of the upper part of the Middle Allochthon (a.o. Seve Nappe Complex (SNC) in N Jämtland/S Västerbotten, central Sweden), are well known for the occurrence of high (HP) and ultrahigh pressure (UHP) metamorphic terranes (of Caledonian age). The (U)HPM evidence clearly demonstrates the deep metamorphic origin of these rocks interpreted to be caused by continental subduction and/or collision. Other metamorphic rocks (of Caledonian age) exposed in allochthonous nappes are solely characterised by greenschist-, amphibolite- and/or MP granulite "facies" mineral assemblages that can be interpreted, in the absence of retrogression, to have formed in less deeply subducted (and/or metamorphic) environments. This duality in metamorphic "facies" allows for a discrimination (at least theoretically) between "deep" versus "shallow" rooted nappes (in central parts of the Scandinavian Caledonides). Conform this reasoning, this duality should also be present within the Caledonian mineral assemblages (= metamorphic overprint) of orogenic peridotites (in

  19. Aproximación a las comunidades de carófitos que existieron en la Albufera de Valencia a partir del estudio de las oósporas del sedimento

    Directory of Open Access Journals (Sweden)

    Soulié-Märsche, Ingeborg

    2009-12-01

    Full Text Available Charophyte oospores and their features (size, shape, colour, outer wall ornamentation, etc. are able to persist in seed banks of aquatic ecosystems. Thus, these characteristics can be used for taxonomic species identification, thereby providing knowledge about the specific composition of the charophyte community in a habitat that currently lacks, or has greatly altered, submerged vegetation. Several years ago, l’Albufera de València lost the charophyte meadows that covered the lake bottom in the past, which had never been studied in detail. Several sediment cores were extracted from the lagoon at three sites and the oospores and gyrogonites were isolated and characterized. The oospore/gyrogonite densities in the sediment layers were estimated. Ten different taxa have been identified: six belonging to genus Chara [Ch. vulgaris, Ch. Hispida var. major, Ch. fragilis (Ch. globularis, Ch. Hispida var. baltica, Ch. aspera, Ch. tomentosa]; one Nitella species (N. hyalina, two Tolypella species (T. glomerata and T. hispanica and one Lamprothamnium species (L. papulosum. The latter, which indicates the period when water salinity was high in the lagoon, was found in the deepest sediment layers. An increase in the oospore abundance and diversity was observed in line with sediment depth. This indicates, on the one hand, that the lagoon went through different ecological stages (with important changes in salinity, mainly and, on the other hand, the eutrophication process that the lagoon has been undergoing for at least the last 45 years, has progressively affected the abundance and diversity of the charophyte community.

    Las oósporas de carófitos y sus características (tamaño, forma, color, ornamentación de la pared, etc. pueden persistir en los bancos de semillas del sedimento de ecosistemas acuáticos, y pueden ser utilizadas para identificar los diferentes táxones y obtener de este modo una

  20. Fertilization Shapes Bacterial Community Structure by Alteration of Soil pH

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    Yuting Zhang

    2017-07-01

    Full Text Available Application of chemical fertilizer or manure can affect soil microorganisms directly by supplying nutrients and indirectly by altering soil pH. However, it remains uncertain which effect mostly shapes microbial community structure. We determined soil bacterial diversity and community structure by 454 pyrosequencing the V1-V3 regions of 16S rRNA genes after 7-years (2007–2014 of applying chemical nitrogen, phosphorus and potassium (NPK fertilizers, composted manure or their combination to acidic (pH 5.8, near-neutral (pH 6.8 or alkaline (pH 8.4 Eutric Regosol soil in a maize-vegetable rotation in southwest China. In alkaline soil, nutrient sources did not affect bacterial Operational Taxonomic Unit (OTU richness or Shannon diversity index, despite higher available N, P, K, and soil organic carbon in fertilized than in unfertilized soil. In contrast, bacterial OTU richness and Shannon diversity index were significantly lower in acidic and near-neutral soils under NPK than under manure or their combination, which corresponded with changes in soil pH. Permutational multivariate analysis of variance showed that bacterial community structure was significantly affected across these three soils, but the PCoA ordination patterns indicated the effect was less distinct among nutrient sources in alkaline than in acidic and near-neural soils. Distance-based redundancy analysis showed that bacterial community structures were significantly altered by soil pH in acidic and near-neutral soils, but not by any soil chemical properties in alkaline soil. The relative abundance (% of most bacterial phyla was higher in near-neutral than in acidic or alkaline soils. The most dominant phyla were Proteobacteria (24.6%, Actinobacteria (19.7%, Chloroflexi (15.3% and Acidobacteria (12.6%; the medium dominant phyla were Bacterioidetes (5.3%, Planctomycetes (4.8%, Gemmatimonadetes (4.5%, Firmicutes (3.4%, Cyanobacteria (2.1%, Nitrospirae (1.8%, and candidate division TM7 (1

  1. Fertilization Shapes Bacterial Community Structure by Alteration of Soil pH.

    Science.gov (United States)

    Zhang, Yuting; Shen, Hong; He, Xinhua; Thomas, Ben W; Lupwayi, Newton Z; Hao, Xiying; Thomas, Matthew C; Shi, Xiaojun

    2017-01-01

    Application of chemical fertilizer or manure can affect soil microorganisms directly by supplying nutrients and indirectly by altering soil pH. However, it remains uncertain which effect mostly shapes microbial community structure. We determined soil bacterial diversity and community structure by 454 pyrosequencing the V1-V3 regions of 16S rRNA genes after 7-years (2007-2014) of applying chemical nitrogen, phosphorus and potassium (NPK) fertilizers, composted manure or their combination to acidic (pH 5.8), near-neutral (pH 6.8) or alkaline (pH 8.4) Eutric Regosol soil in a maize-vegetable rotation in southwest China. In alkaline soil, nutrient sources did not affect bacterial Operational Taxonomic Unit (OTU) richness or Shannon diversity index, despite higher available N, P, K, and soil organic carbon in fertilized than in unfertilized soil. In contrast, bacterial OTU richness and Shannon diversity index were significantly lower in acidic and near-neutral soils under NPK than under manure or their combination, which corresponded with changes in soil pH. Permutational multivariate analysis of variance showed that bacterial community structure was significantly affected across these three soils, but the PCoA ordination patterns indicated the effect was less distinct among nutrient sources in alkaline than in acidic and near-neural soils. Distance-based redundancy analysis showed that bacterial community structures were significantly altered by soil pH in acidic and near-neutral soils, but not by any soil chemical properties in alkaline soil. The relative abundance (%) of most bacterial phyla was higher in near-neutral than in acidic or alkaline soils. The most dominant phyla were Proteobacteria (24.6%), Actinobacteria (19.7%), Chloroflexi (15.3%) and Acidobacteria (12.6%); the medium dominant phyla were Bacterioidetes (5.3%), Planctomycetes (4.8%), Gemmatimonadetes (4.5%), Firmicutes (3.4%), Cyanobacteria (2.1%), Nitrospirae (1.8%), and candidate division TM7 (1

  2. Vertical microbial community variability of carbonate-based cones may provide insight into ancient conical stromatolite formation

    Science.gov (United States)

    Bradley, James; Daille, Leslie; Trivedi, Christopher; Bojanowski, Caitlin; Nunn, Heather; Stamps, Blake; Johnson, Hope; Stevenson, Bradley; Berelson, Will; Corsetti, Frank; Spear, John

    2016-04-01

    Stromatolite morphogenesis is poorly understood, and the process by which microbial mats become mineralized is a primary question in microbialite formation. Ancient conical stromatolites are primarily carbonate-based whereas the few modern analogues in hot springs are either non-mineralized or mineralized by silica. A team from the 2015 International GeoBiology Course investigated carbonate-rich microbial cones from near Little Hot Creek (LHC), Long Valley Caldera, California, to investigate how conical stromatolites might form in a hot spring carbonate system. The cones rise up from a layered microbial mat on the east side of a 45° C pool with very low flow that is super-saturated with respect to CaCO3. Cone structures are 8-30 mm in height, are rigid and do not deform when removed from the pool. Morphological characterization through environmental scanning electronic microscopy revealed that the cone structure is maintained by a matrix of intertwining microbial filaments around carbonate grains. This matrix gives rise to cone-filaments that are arranged vertically or horizontally, and provides further stability to the cone. Preliminary 16S rRNA gene analysis indicated variability of community composition between different vertical levels of the cone. The cone tip had comparatively greater abundance of filamentous cyanobacteria including Leptolingbya, Phormidium and Isosphaera and fewer heterotrophs (e.g. Chloroflexi) compared to the cone bottom. This supports the hypothesis that cone formation may depend on the differential abundance of the microbial community and their potential functional roles. Metagenomic analyses of the cones revealed potential genes related to chemotaxis and motility. Specifically, a genomic bin identified as a member of the genus Isosphaera contained an hmp chemotaxis operon implicated in gliding motility in the cyanobacterium Nostoc punctiforme. Isosphaera is a Planctomycete shown to have phototactic capabilities, and may play a role in

  3. Enriquecimento de microrganismos metanotróficos a partir de lodo de reator UASB tratando esgotos domésticos

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    Luciene Alves Batista Siniscalchi

    2016-03-01

    Full Text Available RESUMO Nesse estudo, microrganismos metanotróficos foram enriquecidos a partir de lodo proveniente de um reator UASB tratando esgotos domésticos em reator em batelada sequencial (RBS com meio autotrófico contendo nitrito e nitrato. As eficiências médias de remoção de nitrito e nitrato foram de 68% e 53%, respectivamente, provavelmente devido à atividade heterotrófica desnitrificante. A detecção de arquéias dos grupos ANME-I e ANME-II foram realizadas por PCR durante todo período de cultivo. A estrutura da comunidade microbiana presente no inóculo e enriquecida no RBS após 100 dias de operação foi estudada por pirosequenciamento. Os resultados das análises demonstraram que a comunidade enriquecida no reator foi diferente à inoculada. Os filos dominantes no inóculo foram Synergistestes , Firmicutes e Euryarchaeota , ao passo que na biomassa enriquecida Planctomycetes, Verrucomicrobia, Chloroflexi e Proteobacteria predominaram. As condições de cultivo do RBS reduziram a abundância de Methanobacterium (8% para 1% e selecionaram bactérias metanotróficas como Methylocaldum , Methylocistis e Methylosinus . As sequências de Methylocaldum sp. apresentaram abundância relativa de 2.5%. A presença e elevada predominância do filo Verrucomicrobia na biomassa enriquecida do RBS sugere que outras espécies de metanotróficas, ainda pouco conhecidas, relacionadas a este filo podem estar presentes no reator. O potencial de oxidação anaeróbia do metano foi determinado para ambas amostras e revelaram que a atividade metanotrófica da biomassa foi aproximadamente três vezes maior que a do inóculo. Em suma, estes resultados sugerem que o inóculo usado e as condições de cultivo aplicadas foram adequados para o enriquecimento de metanotróficas.

  4. Evaluation of the ecotoxicological impact of the organochlorine chlordecone on soil microbial community structure, abundance, and function.

    Science.gov (United States)

    Merlin, Chloé; Devers, Marion; Béguet, Jérémie; Boggio, Baptiste; Rouard, Nadine; Martin-Laurent, Fabrice

    2016-03-01

    The insecticide chlordecone applied for decades in banana plantations currently contaminates 20,000 ha of arable land in the French West Indies. Although the impact of various pesticides on soil microorganisms has been studied, chlordecone toxicity to the soil microbial community has never been assessed. We investigated in two different soils (sandy loam and silty loam) exposed to different concentrations of CLD (D0, control; D1 and D10, 1 and 10 times the agronomical dose) over different periods of time (3, 7, and 32 days): (i) the fate of chlordecone by measuring (14)C-chlordecone mass balance and (ii) the impact of chlordecone on microbial community structure, abundance, and function, using standardized methods (-A-RISA, taxon-specific quantitative PCR (qPCR), and (14)C-compounds mineralizing activity). Mineralization of (14)C-chlordecone was inferior below 1 % of initial (14)C-activity. Less than 2 % of (14)C-activity was retrieved from the water-soluble fraction, while most of it remained in the organic-solvent-extractable fraction (75 % of initial (14)C-activity). Only 23 % of the remaining (14)C-activity was measured in nonextractable fraction. The fate of chlordecone significantly differed between the two soils. The soluble and nonextractable fractions were significantly higher in sandy loam soil than in silty loam soil. All the measured microbiological parameters allowed discriminating statistically the two soils and showed a variation over time. The genetic structure of the bacterial community remained insensitive to chlordecone exposure in silty loam soil. In response to chlordecone exposure, the abundance of Gram-negative bacterial groups (β-, γ-Proteobacteria, Planctomycetes, and Bacteroidetes) was significantly modified only in sandy loam soil. The mineralization of (14)C-sodium acetate and (14)C-2,4-D was insensitive to chlordecone exposure in silty loam soil. However, mineralization of (14)C-sodium acetate was significantly reduced in soil

  5. The Response of a 16S Ribosomal RNA Gene Fragment Amplified Community to Lead, Zinc, and Copper Pollution in a Shanghai Field Trial

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    Shumeng Kou

    2018-03-01

    Full Text Available Industrial and agricultural activities have caused extensive metal contamination of land throughout China and across the globe. The pervasive nature of metal pollution can be harmful to human health and can potentially cause substantial negative impact to the biosphere. To investigate the impact of anthropogenic metal pollution found in high concentrations in industrial, agricultural, and urban environments, 16S ribosomal RNA gene amplicon sequencing was used to track change in the amplified microbial community after metal contamination in a large-scale field experiment in Shanghai. A total of 1,566 operational taxonomic units (OTUs identified from 448,108 sequences gathered from 20 plots treated as controls or with lead, zinc, copper, or all three metals. Constrained Analysis of Principal Coordinates ordination did not separate control and lead treatment but could separate control/lead, zinc, copper, and three metal treatment. DESeq2 was applied to identify 93 significantly differentially abundant OTUs varying in 211 pairwise instances between the treatments. Differentially abundant OTUs representing genera or species belonging to the phyla Chloroflexi, Cyanobacteria, Firmicutes, Latescibacteria, and Planctomycetes were almost universally reduced in abundance due to zinc, copper, or three metal treatment; with three metal treatment abolishing the detection of some OTUs, such as Leptolyngbya, Desmonostoc muscorum, and Microcoleus steenstrupii. The greatest increases due to metal treatment were observed in Bacteroidetes, Actinobacteria, Chlamydiae, Nitrospirae, and Proteobacteria (α, β, δ, and γ; the most (relative abundant being uncharacterized species within the genera Methylobacillus, Solirubrobacter, and Ohtaekwangia. Three metal treatment alone resulted in identification of 22 OTUs (genera or species which were not detected in control soil, notably including Yonghaparkia alkaliphila, Pedobacter steynii, Pseudolabrys taiwanensis

  6. Continuously Monocropped Jerusalem Artichoke Changed Soil Bacterial Community Composition and Ammonia-Oxidizing and Denitrifying Bacteria Abundances.

    Science.gov (United States)

    Zhou, Xingang; Wang, Zhilin; Jia, Huiting; Li, Li; Wu, Fengzhi

    2018-01-01

    Soil microbial communities have profound effects on the growth, nutrition and health of plants in agroecosystems. Understanding soil microbial dynamics in cropping systems can assist in determining how agricultural practices influence soil processes mediated by microorganisms. In this study, soil bacterial communities were monitored in a continuously monocropped Jerusalem artichoke (JA) system, in which JA was successively monocropped for 3 years in a wheat field. Soil bacterial community compositions were estimated by amplicon sequencing of the 16S rRNA gene. Abundances of ammonia-oxidizing and denitrifying bacteria were estimated by quantitative PCR analysis of the amoA , nirS , and nirK genes. Results showed that 1-2 years of monocropping of JA did not significantly impact the microbial alpha diversity, and the third cropping of JA decreased the microbial alpha diversity ( P < 0.05). Principal coordinates analysis and permutational multivariate analysis of variance analyses revealed that continuous monocropping of JA changed soil bacterial community structure and function profile ( P < 0.001). At the phylum level, the wheat field was characterized with higher relative abundances of Latescibacteria , Planctomycetes , and Cyanobacteria , the first cropping of JA with Actinobacteria , the second cropping of JA with Acidobacteria , Armatimonadetes , Gemmatimonadetes , and Proteobacteria . At the genus level, the first cropping of JA was enriched with bacterial species with pathogen-antagonistic and/or plant growth promoting potentials, while members of genera that included potential denitrifiers increased in the second and third cropping of JA. The first cropping of JA had higher relative abundances of KO terms related to lignocellulose degradation and phosphorus cycling, the second cropping of JA had higher relative abundances of KO terms nitrous-oxide reductase and nitric-oxide reductase, and the third cropping of JA had higher relative abundances of KO terms

  7. Metagenome-assembled genomes of deep-branching magnetotactic bacteria in the Nitrospirae phylum

    Science.gov (United States)

    Zhang, W.; He, M.; Gu, L.; Tang, X.; Pan, Y.; Lin, W.

    2017-12-01

    Magnetotactic bacteria (MTB) are aquatic microorganisms that synthesize intracellular magnetic nanoparticles composed of magnetite and/or greigite. MTB have thus far been identified in the phyla of Proteobacteria, Nitrospirae, Omnitrophica, Latescibacteria and Planctomycetes (Lin et al., 2017b). Among these organisms, MTB belonging to the Nitrospirae phylum are of great interest because of the formation of hundreds of magnetite magnetosomes in a single cell and of the great potential for iron, sulfur, nitrogen, and carbon cycling in natural environments. However, due to the lack of genomic information, our current knowledge on magnetotactic Nitrospirae remains very limited. In the present study, we have identified and characterized two novel populations of uncultivated MTB from freshwater lakes in Shaanxi province, China. 16S rRNA gene-based analyses revealed that they belonged to two different clusters in the Nitrospirae. The draft population genomes of these two Nitrospirae MTB were successfully recovered through genome-resolved metagenomics, both of which containing nearly complete magnetosome gene clusters (MGCs) responsible for magnetosome biomineralization and organization. In consistent with our previous study (Lin et al., 2017a), we found that the gene content and gene organization of the MGCs in the Nitrospirae MTB were highly conserved, indicating that Nitrospirae gene clusters represent one of the ancestral types of MGCs. The population genome sequences suggest that magnetotactic Nitrospirae are capable of CO2 fixtion through Wood-Ljungdahl pathway. They may also reduce sulfate and nitrate/nitrite through sulfate reduction pathway and denitrification pathway, respectively. Our genomic analyses revealed the potential metabolic capability of the Nitrospirae MTB and shed light on their ecology, evolution and biomineralization mechanism. References: Lin W, Paterson GA, Zhu Q, Wang Y, Kopylova E, Li Y, Knight R, Bazylinski DA, Zhu R, Kirschvink JL, Pan Y

  8. Archaeal and Bacterial Variation Across Geochemical Gradients in an Arsenic-Rich, Shallow Submarine Vent, Papua New Guinea

    Science.gov (United States)

    Meyer-Dombard, D. R.; Osburn, M. R.; Amend, J. P.

    2005-12-01

    Near the Feni Islands of Papua New Guinea, reduced hydrothermal fluids mix with seawater, establishing redox disequilibria that may serve as energy sources for chemotrophic Archaea and Bacteria. Of particular interest are elevated arsenite concentrations (1000 μg/L) in the vent water and arsenate-rich ferrihydrite deposits (up to 7 wt.%) that envelope the sediment and coral. In sediment pore waters out to > 200m from the vents, a steeply decreasing arsenic gradient is observed. To establish a baseline of microbial community composition at the vent fluid-seawater interface, bulk DNA was extracted from ferrihydrite coatings, then amplified (16S rRNA, targeting both Archaea and Bacteria), cloned, and sequenced. Red and green biofilms associated with the coatings revealed archaeal communities exclusively composed of deeply-branching, uncultured Crenarchaea. The bacterial members of the community differed in the two biofilms; the red biofilm is primarily composed of gamma Proteobacteria, Chloroflexis, and Planctomycetes, but 60% of clones from the green biofilm community affiliates with the alpha Proteobacteria and candidate group OP11. The remaining portion of the bacterial community in the red coating is made of Thermotogales, Aquificales, Thermales phylotypes and uncultured Bacteria, while OP10, Chloroflexis and Plantomycetales complete the community in the green coatings. No clones associating with thermophilic bacterial groups were found in the green coatings. To provide a comparison to the vent source communities, a sediment core was taken 2.5m from the vent and two depths (10 and 40cm) were analyzed by similar molecular analysis. In both core horizons, the archaeal community is composed of > 75% uncultured Crenarchaea, similar to phylotypes found in deep-sea and terrestrial hydrothermal locations, with the remainder of the communities from known crenarchaeal phylotypes. The bacterial communities are primarily Chloroflexis and gamma Proteobacteria-like phylotypes

  9. Biodiversity of the microbial mat of the Garga hot spring.

    Science.gov (United States)

    Rozanov, Alexey Sergeevich; Bryanskaya, Alla Victorovna; Ivanisenko, Timofey Vladimirovich; Malup, Tatyana Konstantinovna; Peltek, Sergey Evgenievich

    2017-12-28

    Microbial mats are a good model system for ecological and evolutionary analysis of microbial communities. There are more than 20 alkaline hot springs on the banks of the Barguzin river inflows. Water temperature reaches 75 °C and pH is usually 8.0-9.0. The formation of microbial mats is observed in all hot springs. Microbial communities of hot springs of the Baikal rift zone are poorly studied. Garga is the biggest hot spring in this area. In this study, we investigated bacterial and archaeal diversity of the Garga hot spring (Baikal rift zone, Russia) using 16S rRNA metagenomic sequencing. We studied two types of microbial communities: (i) small white biofilms on rocks in the points with the highest temperature (75 °C) and (ii) continuous thick phototrophic microbial mats observed at temperatures below 70 °C. Archaea (mainly Crenarchaeota; 19.8% of the total sequences) were detected only in the small biofilms. The high abundance of Archaea in the sample from hot springs of the Baikal rift zone supplemented our knowledge of the distribution of Archaea. Most archaeal sequences had low similarity to known Archaea. In the microbial mats, primary products were formed by cyanobacteria of the genus Leptolyngbya. Heterotrophic microorganisms were mostly represented by Actinobacteria and Proteobacteria in all studied samples of the microbial mats. Planctomycetes, Chloroflexi, and Chlorobi were abundant in the middle layer of the microbial mats, while heterotrophic microorganisms represented mostly by Firmicutes (Clostridia, strict anaerobes) dominated in the bottom part. Besides prokaryotes, we detect some species of Algae with help of detection their chloroplasts 16 s rRNA. High abundance of Archaea in samples from hot springs of the Baikal rift zone supplemented our knowledge of the distribution of Archaea. Most archaeal sequences had low similarity to known Archaea. Metagenomic analysis of microbial communities of the microbial mat of Garga hot spring showed that

  10. Elucidation of rice rhizosphere metagenome in relation to methane and nitrogen metabolism under elevated carbon dioxide and temperature using whole genome metagenomic approach.

    Science.gov (United States)

    Bhattacharyya, P; Roy, K S; Das, M; Ray, S; Balachandar, D; Karthikeyan, S; Nayak, A K; Mohapatra, T

    2016-01-15

    Carbon (C) and nitrogen (N) mineralization is one of the key processes of biogeochemical cycling in terrestrial ecosystem in general and rice ecology in particular. Rice rhizosphere is a rich niche of microbial diversity influenced by change in atmospheric temperature and concentration of carbon dioxide (CO2). Structural changes in microbial communities in rhizosphere influence the nutrient cycling. In the present study, the bacterial diversity and population dynamics were studied under ambient CO2 (a-CO2) and elevated CO2+temperature (e-CO2T) in lowland rice rhizosphere using whole genome metagenomic approach. The whole genome metagenomic sequence data of lowland rice exhibited the dominance of bacterial communities including Proteobacteria, Firmicutes, Acidobacteria, Actinobacteria and Planctomycetes. Interestingly, four genera related to methane production namely, Methanobacterium, Methanosphaera, Methanothermus and Methanothermococcus were absent in a-CO2 but noticed under e-CO2T. The acetoclastic pathway was found as the predominant pathway for methanogenesis, whereas, the serine pathway was found as the principal metabolic pathway for CH4 oxidation in lowland rice. The abundances of reads of enzymes in the acetoclastic methanogenesis pathway and serine pathways of methanotrophy were much higher in e-CO2T (328 and 182, respectively) as compared with a-CO2 (118 and 98, respectively). Rice rhizosphere showed higher structural diversities and functional activities in relation to N metabolism involving nitrogen fixation, assimilatory and dissimilatory nitrate reduction and denitrification under e-CO2T than that of a-CO2. Among the three pathways of N metabolism, dissimilarity pathways were predominant in lowland rice rhizosphere and more so under e-CO2T. Consequently, under e-CO2T, CH4 emission, microbial biomass nitrogen (MBN) and dehydrogenase activities were 45%, 20% and 35% higher than a-CO2, respectively. Holistically, a high bacterial diversity and

  11. Successful hydraulic strategies to start up OLAND sequencing batch reactors at lab scale.

    Science.gov (United States)

    Schaubroeck, Thomas; Bagchi, Samik; De Clippeleir, Haydée; Carballa, Marta; Verstraete, Willy; Vlaeminck, Siegfried E

    2012-05-01

    Oxygen-limited autotrophic nitrification/denitrification (OLAND) is a one-stage combination of partial nitritation and anammox, which can have a challenging process start-up. In this study, start-up strategies were tested for sequencing batch reactors (SBR), varying hydraulic parameters, i.e. volumetric exchange ratio (VER) and feeding regime, and salinity. Two sequential tests with two parallel SBR were performed, and stable removal rates > 0.4 g N l(-1) day(-1) with minimal nitrite and nitrate accumulation were considered a successful start-up. SBR A and B were operated at 50% VER with 3 g NaCl l(-1) in the influent, and the influent was fed over 8% and 82% of the cycle time respectively. SBR B started up in 24 days, but SBR A achieved no start-up in 39 days. SBR C and D were fed over 65% of the cycle time at 25% VER, and salt was added only to the influent of SBR D (5 g NaCl l(-1)). Start-up of both SBR C and D was successful in 9 and 32 days respectively. Reactor D developed a higher proportion of small aggregates (0.10-0.25 mm), with a high nitritation to anammox rate ratio, likely the cause of the observed nitrite accumulation. The latter was overcome by temporarily including an anoxic period at the end of the reaction phase. All systems achieved granulation and similar biomass-specific nitrogen removal rates (141-220 mg N g(-1) VSS day(-1)). FISH revealed a close juxtapositioning of aerobic and anoxic ammonium-oxidizing bacteria (AerAOB and AnAOB), also in small aggregates. DGGE showed that AerAOB communities had a lower evenness than Planctomycetes communities. A higher richness of the latter seemed to be correlated with better reactor performance. Overall, the fast start-up of SBR B, C and D suggests that stable hydraulic conditions are beneficial for OLAND while increased salinity at the tested levels is not needed for good reactor performance. © 2012 The Authors. Microbial Biotechnology © 2012 Society for Applied Microbiology and Blackwell Publishing

  12. The Response of a 16S Ribosomal RNA Gene Fragment Amplified Community to Lead, Zinc, and Copper Pollution in a Shanghai Field Trial.

    Science.gov (United States)

    Kou, Shumeng; Vincent, Gilles; Gonzalez, Emmanuel; Pitre, Frederic E; Labrecque, Michel; Brereton, Nicholas J B

    2018-01-01

    Industrial and agricultural activities have caused extensive metal contamination of land throughout China and across the globe. The pervasive nature of metal pollution can be harmful to human health and can potentially cause substantial negative impact to the biosphere. To investigate the impact of anthropogenic metal pollution found in high concentrations in industrial, agricultural, and urban environments, 16S ribosomal RNA gene amplicon sequencing was used to track change in the amplified microbial community after metal contamination in a large-scale field experiment in Shanghai. A total of 1,566 operational taxonomic units (OTUs) identified from 448,108 sequences gathered from 20 plots treated as controls or with lead, zinc, copper, or all three metals. Constrained Analysis of Principal Coordinates ordination did not separate control and lead treatment but could separate control/lead, zinc, copper, and three metal treatment. DESeq2 was applied to identify 93 significantly differentially abundant OTUs varying in 211 pairwise instances between the treatments. Differentially abundant OTUs representing genera or species belonging to the phyla Chloroflexi, Cyanobacteria, Firmicutes, Latescibacteria, and Planctomycetes were almost universally reduced in abundance due to zinc, copper, or three metal treatment; with three metal treatment abolishing the detection of some OTUs, such as Leptolyngbya , Desmonostoc muscorum , and Microcoleus steenstrupii . The greatest increases due to metal treatment were observed in Bacteroidetes, Actinobacteria, Chlamydiae, Nitrospirae, and Proteobacteria (α, β, δ, and γ); the most (relative) abundant being uncharacterized species within the genera Methylobacillus , Solirubrobacter , and Ohtaekwangia . Three metal treatment alone resulted in identification of 22 OTUs (genera or species) which were not detected in control soil, notably including Yonghaparkia alkaliphila , Pedobacter steynii , Pseudolabrys taiwanensis , Methylophilus

  13. Tundrisphaera lichenicola gen. nov., sp. nov., a psychrotolerant representative of the family Isosphaeraceae from lichen-dominated tundra soils.

    Science.gov (United States)

    Kulichevskaya, Irina S; Ivanova, Anastasia A; Detkova, Ekaterina N; Rijpstra, W Irene C; Sinninghe Damsté, Jaap S; Dedysh, Svetlana N

    2017-09-01

    Two strains of aerobic, budding, pink-pigmented bacteria, P12T and P515, were isolated from a lichen-dominated peatland and a forested tundra soil of north-western Siberia, respectively. Cells of these isolates were represented by non-motile spheres that occurred singly or were arranged in short chains and aggregates. While growing on solid media, cells of strains P12T and P515 attached to the surface by means of holdfast-like appendages. These isolates were mildly acidophilic (optimum growth at pH 5.5-6.0), psychrotolerant bacteria, which displayed tolerance of low temperatures (4-15 °C), grew optimally at 15-22 °C and did not grow at temperatures above 28 °C. The preferred growth substrates were sugars and some heteropolysaccharides. The major fatty acids were C18 : 1ω9c, C16 : 0 and C14 : 0. Trimethylornithine lipid was the major polar lipid. The only quinone was MK-6, and the G+C content of the DNA was 61.2-62.2 mol%. Strains P12T and P515 possessed identical 16S rRNA gene sequences, which affiliated them with the family Isosphaeraceae, order Planctomycetales, and these displayed the highest similarity (93-94 %) to 16S rRNA gene sequences from members of the genus Singulisphaera. However, the signature fatty acid of species of the genus Singulisphaera, i.e. C18 : 2ω6c,12c, was absent in cells of strains P12T and P515. They also differed from members of the genus Singulisphaera by substrate utilization pattern and a number of physiological characteristics. Based on these data, the novel isolates should be considered as representing a novel genus and species of planctomycetes, for which the name Tundrisphaera lichenicola gen. nov., sp. nov, is proposed. The type strain is P12T (=LMG 29571T=VKM B-3044T).

  14. Evaluating primers for profiling anaerobic ammonia oxidizing bacteria within freshwater environments.

    Directory of Open Access Journals (Sweden)

    Puntipar Sonthiphand

    Full Text Available Anaerobic ammonia oxidizing (anammox bacteria play an important role in transforming ammonium to nitrogen gas and contribute to fixed nitrogen losses in freshwater environments. Understanding the diversity and abundance of anammox bacteria requires reliable molecular tools, and these are not yet well established for these important Planctomycetes. To help validate PCR primers for the detection of anammox bacteria within freshwater ecosystems, we analyzed representative positive controls and selected samples from Grand River and groundwater sites, both from Ontario, Canada. The objectives of this study were to identify a suitable anammox denaturing gradient gel electrophoresis (DGGE fingerprint method by using GC-clamp modifications to existing primers, and to verify the specificity of anammox-specific primers used for DGGE, cloning and qPCR methods. Six primer combinations were tested from four published primer sets (i.e. A438f/A684r, Amx368f/Amx820r, An7f/An1388r, and Pla46/1392r for both direct and nested PCR amplifications. All PCR products were run subsequently on DGGE gels to compare the resulting patterns. Two anammox-specific primer combinations were also used to generate clone libraries and quantify anammox bacterial 16S rRNA genes with qPCR. The primer set A438f/A684r was highly specific to anammox bacteria, provided reliable DGGE fingerprints and generated a high proportion of anammox-related clones. A second primer set (Amx368f/Amx820r was anammox specific, based on clone library analysis, but PCR products from different candidate species of anammox bacteria resolved poorly using DGGE analysis. Both DGGE and cloning results revealed that Ca. Brocadia and an uncharacterized anammox bacterial cluster represented the majority of anammox bacteria found in Grand River sediment and groundwater samples, respectively. Together, our results demonstrate that although Amx368f/Amx820r was useful for anammox-specific qPCR and clone library

  15. Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia

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    Stott Matthew B

    2008-07-01

    Full Text Available Abstract Background The phylum Verrucomicrobia is a widespread but poorly characterized bacterial clade. Although cultivation-independent approaches detect representatives of this phylum in a wide range of environments, including soils, seawater, hot springs and human gastrointestinal tract, only few have been isolated in pure culture. We have recently reported cultivation and initial characterization of an extremely acidophilic methanotrophic member of the Verrucomicrobia, strain V4, isolated from the Hell's Gate geothermal area in New Zealand. Similar organisms were independently isolated from geothermal systems in Italy and Russia. Results We report the complete genome sequence of strain V4, the first one from a representative of the Verrucomicrobia. Isolate V4, initially named "Methylokorus infernorum" (and recently renamed Methylacidiphilum infernorum is an autotrophic bacterium with a streamlined genome of ~2.3 Mbp that encodes simple signal transduction pathways and has a limited potential for regulation of gene expression. Central metabolism of M. infernorum was reconstructed almost completely and revealed highly interconnected pathways of autotrophic central metabolism and modifications of C1-utilization pathways compared to other known methylotrophs. The M. infernorum genome does not encode tubulin, which was previously discovered in bacteria of the genus Prosthecobacter, or close homologs of any other signature eukaryotic proteins. Phylogenetic analysis of ribosomal proteins and RNA polymerase subunits unequivocally supports grouping Planctomycetes, Verrucomicrobia and Chlamydiae into a single clade, the PVC superphylum, despite dramatically different gene content in members of these three groups. Comparative-genomic analysis suggests that evolution of the M. infernorum lineage involved extensive horizontal gene exchange with a variety of bacteria. The genome of M. infernorum shows apparent adaptations for existence under extremely

  16. Multi-Analytical Approach Reveals Potential Microbial Indicators in Soil for Sugarcane Model Systems.

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    Acacio Aparecido Navarrete

    Full Text Available This study focused on the effects of organic and inorganic amendments and straw retention on the microbial biomass (MB and taxonomic groups of bacteria in sugarcane-cultivated soils in a greenhouse mesocosm experiment monitored for gas emissions and chemical factors. The experiment consisted of combinations of synthetic nitrogen (N, vinasse (V; a liquid waste from ethanol production, and sugarcane-straw blankets. Increases in CO2-C and N2O-N emissions were identified shortly after the addition of both N and V to the soils, thus increasing MB nitrogen (MB-N and decreasing MB carbon (MB-C in the N+V-amended soils and altering soil chemical factors that were correlated with the MB. Across 57 soil metagenomic datasets, Actinobacteria (31.5%, Planctomycetes (12.3%, Deltaproteobacteria (12.3%, Alphaproteobacteria (12.0% and Betaproteobacteria (11.1% were the most dominant bacterial groups during the experiment. Differences in relative abundance of metagenomic sequences were mainly revealed for Acidobacteria, Actinobacteria, Gammaproteobacteria and Verrucomicrobia with regard to N+V fertilization and straw retention. Differential abundances in bacterial groups were confirmed using 16S rRNA gene-targeted phylum-specific primers for real-time PCR analysis in all soil samples, whose results were in accordance with sequence data, except for Gammaproteobacteria. Actinobacteria were more responsive to straw retention with Rubrobacterales, Bifidobacteriales and Actinomycetales related to the chemical factors of N+V-amended soils. Acidobacteria subgroup 7 and Opitutae, a verrucomicrobial class, were related to the chemical factors of soils without straw retention as a surface blanket. Taken together, the results showed that MB-C and MB-N responded to changes in soil chemical factors and CO2-C and N2O-N emissions, especially for N+V-amended soils. The results also indicated that several taxonomic groups of bacteria, such as Acidobacteria, Actinobacteria and

  17. Continuously Monocropped Jerusalem Artichoke Changed Soil Bacterial Community Composition and Ammonia-Oxidizing and Denitrifying Bacteria Abundances

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    Xingang Zhou

    2018-04-01

    Full Text Available Soil microbial communities have profound effects on the growth, nutrition and health of plants in agroecosystems. Understanding soil microbial dynamics in cropping systems can assist in determining how agricultural practices influence soil processes mediated by microorganisms. In this study, soil bacterial communities were monitored in a continuously monocropped Jerusalem artichoke (JA system, in which JA was successively monocropped for 3 years in a wheat field. Soil bacterial community compositions were estimated by amplicon sequencing of the 16S rRNA gene. Abundances of ammonia-oxidizing and denitrifying bacteria were estimated by quantitative PCR analysis of the amoA, nirS, and nirK genes. Results showed that 1–2 years of monocropping of JA did not significantly impact the microbial alpha diversity, and the third cropping of JA decreased the microbial alpha diversity (P < 0.05. Principal coordinates analysis and permutational multivariate analysis of variance analyses revealed that continuous monocropping of JA changed soil bacterial community structure and function profile (P < 0.001. At the phylum level, the wheat field was characterized with higher relative abundances of Latescibacteria, Planctomycetes, and Cyanobacteria, the first cropping of JA with Actinobacteria, the second cropping of JA with Acidobacteria, Armatimonadetes, Gemmatimonadetes, and Proteobacteria. At the genus level, the first cropping of JA was enriched with bacterial species with pathogen-antagonistic and/or plant growth promoting potentials, while members of genera that included potential denitrifiers increased in the second and third cropping of JA. The first cropping of JA had higher relative abundances of KO terms related to lignocellulose degradation and phosphorus cycling, the second cropping of JA had higher relative abundances of KO terms nitrous-oxide reductase and nitric-oxide reductase, and the third cropping of JA had higher relative abundances of KO

  18. Metagenomic investigation of the microbial diversity in a chrysotile asbestos mine pit pond, Lowell, Vermont, USA

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    Heather E. Driscoll

    2016-12-01

    Full Text Available Here we report on a metagenomics investigation of the microbial diversity in a serpentine-hosted aquatic habitat created by chrysotile asbestos mining activity at the Vermont Asbestos Group (VAG Mine in northern Vermont, USA. The now-abandoned VAG Mine on Belvidere Mountain in the towns of Eden and Lowell includes three open-pit quarries, a flooded pit, mill buildings, roads, and >26 million metric tons of eroding mine waste that contribute alkaline mine drainage to the surrounding watershed. Metagenomes and water chemistry originated from aquatic samples taken at three depths (0.5 m, 3.5 m, and 25 m along the water column at three distinct, offshore sites within the mine's flooded pit (near 44°46′00.7673″, −72°31′36.2699″; UTM NAD 83 Zone 18 T 0695720 E, 4960030 N. Whole metagenome shotgun Illumina paired-end sequences were quality trimmed and analyzed based on a translated nucleotide search of NCBI-NR protein database and lowest common ancestor taxonomic assignments. Our results show strata within the pit pond water column can be distinguished by taxonomic composition and distribution, pH, temperature, conductivity, light intensity, and concentrations of dissolved oxygen. At the phylum level, metagenomes from 0.5 m and 3.5 m contained a similar distribution of taxa and were dominated by Actinobacteria (46% and 53% of reads, respectively, Proteobacteria (45% and 38%, respectively, and Bacteroidetes (7% in both. The metagenomes from 25 m showed a greater diversity of phyla and a different distribution of reads than the two upper strata: Proteobacteria (60%, Actinobacteria (18%, Planctomycetes, (10%, Bacteroidetes (5% and Cyanobacteria (2.5%, Armatimonadetes (<1%, Verrucomicrobia (<1%, Firmicutes (<1%, and Nitrospirae (<1%. Raw metagenome sequence data from each sample reside in NCBI's Short Read Archive (SRA ID: SRP056095 and are accessible through NCBI BioProject PRJNA277916.

  19. Quantitative Metaproteomics Highlight the Metabolic Contributions of Uncultured Phylotypes in a Thermophilic Anaerobic Digester.

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    Hagen, Live H; Frank, Jeremy A; Zamanzadeh, Mirzaman; Eijsink, Vincent G H; Pope, Phillip B; Horn, Svein J; Arntzen, Magnus Ø

    2017-01-15

    In this study, we used multiple meta-omic approaches to characterize the microbial community and the active metabolic pathways of a stable industrial biogas reactor with food waste as the dominant feedstock, operating at thermophilic temperatures (60°C) and elevated levels of free ammonia (367 mg/liter NH 3 -N). The microbial community was strongly dominated (76% of all 16S rRNA amplicon sequences) by populations closely related to the proteolytic bacterium Coprothermobacter proteolyticus. Multiple Coprothermobacter-affiliated strains were detected, introducing an additional level of complexity seldom explored in biogas studies. Genome reconstructions provided metabolic insight into the microbes that performed biomass deconstruction and fermentation, including the deeply branching phyla Dictyoglomi and Planctomycetes and the candidate phylum "Atribacteria" These biomass degraders were complemented by a synergistic network of microorganisms that convert key fermentation intermediates (fatty acids) via syntrophic interactions with hydrogenotrophic methanogens to ultimately produce methane. Interpretation of the proteomics data also suggested activity of a Methanosaeta phylotype acclimatized to high ammonia levels. In particular, we report multiple novel phylotypes proposed as syntrophic acetate oxidizers, which also exert expression of enzymes needed for both the Wood-Ljungdahl pathway and β-oxidation of fatty acids to acetyl coenzyme A. Such an arrangement differs from known syntrophic oxidizing bacteria and presents an interesting hypothesis for future studies. Collectively, these findings provide increased insight into active metabolic roles of uncultured phylotypes and presents new synergistic relationships, both of which may contribute to the stability of the biogas reactor. Biogas production through anaerobic digestion of organic waste provides an attractive source of renewable energy and a sustainable waste management strategy. A comprehensive understanding

  20. Multi-Analytical Approach Reveals Potential Microbial Indicators in Soil for Sugarcane Model Systems

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    Navarrete, Acacio Aparecido; Diniz, Tatiana Rosa; Braga, Lucas Palma Perez; Silva, Genivaldo Gueiros Zacarias; Franchini, Julio Cezar; Rossetto, Raffaella; Edwards, Robert Alan; Tsai, Siu Mui

    2015-01-01

    This study focused on the effects of organic and inorganic amendments and straw retention on the microbial biomass (MB) and taxonomic groups of bacteria in sugarcane-cultivated soils in a greenhouse mesocosm experiment monitored for gas emissions and chemical factors. The experiment consisted of combinations of synthetic nitrogen (N), vinasse (V; a liquid waste from ethanol production), and sugarcane-straw blankets. Increases in CO2-C and N2O-N emissions were identified shortly after the addition of both N and V to the soils, thus increasing MB nitrogen (MB-N) and decreasing MB carbon (MB-C) in the N+V-amended soils and altering soil chemical factors that were correlated with the MB. Across 57 soil metagenomic datasets, Actinobacteria (31.5%), Planctomycetes (12.3%), Deltaproteobacteria (12.3%), Alphaproteobacteria (12.0%) and Betaproteobacteria (11.1%) were the most dominant bacterial groups during the experiment. Differences in relative abundance of metagenomic sequences were mainly revealed for Acidobacteria, Actinobacteria, Gammaproteobacteria and Verrucomicrobia with regard to N+V fertilization and straw retention. Differential abundances in bacterial groups were confirmed using 16S rRNA gene-targeted phylum-specific primers for real-time PCR analysis in all soil samples, whose results were in accordance with sequence data, except for Gammaproteobacteria. Actinobacteria were more responsive to straw retention with Rubrobacterales, Bifidobacteriales and Actinomycetales related to the chemical factors of N+V-amended soils. Acidobacteria subgroup 7 and Opitutae, a verrucomicrobial class, were related to the chemical factors of soils without straw retention as a surface blanket. Taken together, the results showed that MB-C and MB-N responded to changes in soil chemical factors and CO2-C and N2O-N emissions, especially for N+V-amended soils. The results also indicated that several taxonomic groups of bacteria, such as Acidobacteria, Actinobacteria and

  1. Contrasting spatial patterns and ecological attributes of soil bacterial and archaeal taxa across a landscape.

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    Constancias, Florentin; Saby, Nicolas P A; Terrat, Sébastien; Dequiedt, Samuel; Horrigue, Wallid; Nowak, Virginie; Guillemin, Jean-Philippe; Biju-Duval, Luc; Chemidlin Prévost-Bouré, Nicolas; Ranjard, Lionel

    2015-06-01

    Even though recent studies have clarified the influence and hierarchy of environmental filters on bacterial community structure, those constraining bacterial populations variations remain unclear. In consequence, our ability to understand to ecological attributes of soil bacteria and to predict microbial community response to environmental stress is therefore limited. Here, we characterized the bacterial community composition and the various bacterial taxonomic groups constituting the community across an agricultural landscape of 12 km(2) , by using a 215 × 215 m systematic grid representing 278 sites to precisely decipher their spatial distribution and drivers at this scale. The bacterial and Archaeal community composition was characterized by applying 16S rRNA gene pyrosequencing directly to soil DNA from samples. Geostatistics tools were used to reveal the heterogeneous distribution of bacterial composition at this scale. Soil physical parameters and land management explained a significant amount of variation, suggesting that environmental selection is the major process shaping bacterial composition. All taxa systematically displayed also a heterogeneous and particular distribution patterns. Different relative influences of soil characteristics, land use and space were observed, depending on the taxa, implying that selection and spatial processes might be differentially but not exclusively involved for each bacterial phylum. Soil pH was a major factor determining the distribution of most of the bacterial taxa and especially the most important factor explaining the spatial patterns of α-Proteobacteria and Planctomycetes. Soil texture, organic carbon content and quality were more specific to a few number of taxa (e.g., β-Proteobacteria and Chlorobi). Land management also influenced the distribution of bacterial taxa across the landscape and revealed different type of response to cropping intensity (positive, negative, neutral or hump-backed relationships

  2. Long-term field application of sewage sludge increases the abundance of antibiotic resistance genes in soil.

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    Chen, Qinglin; An, Xinli; Li, Hu; Su, Jianqiang; Ma, Yibing; Zhu, Yong-Guan

    2016-01-01

    Sewage sludge and manure are common soil amendments in crop production; however, their impact on the abundance and diversity of the antibiotic resistome in soil remains elusive. In this study, by using high-throughput sequencing and high-throughput quantitative PCR, the patterns of bacterial community and antibiotic resistance genes (ARGs) in a long-term field experiment were investigated to gain insights into these impacts. A total of 130 unique ARGs and 5 mobile genetic elements (MGEs) were detected and the long-term application of sewage sludge and chicken manure significantly increased the abundance and diversity of ARGs in the soil. Genes conferring resistance to beta-lactams, tetracyclines, and multiple drugs were dominant in the samples. Sewage sludge or chicken manure applications caused significant enrichment of 108 unique ARGs and MGEs with a maximum enrichment of up to 3845 folds for mexF. The enrichment of MGEs suggested that the application of sewage sludge or manure may accelerate the dissemination of ARGs in soil through horizontal gene transfer (HGT). Based on the co-occurrence pattern of ARGs subtypes revealed by network analysis, aacC, oprD and mphA-02, were proposed to be potential indicators for quantitative estimation of the co-occurring ARGs subtypes abundance by power functions. The application of sewage sludge and manure resulted in significant increase of bacterial diversity in soil, Proteobacteria, Acidobacteria, Actinobacteria and Chloroflexi were the dominant phyla (>10% in each sample). Five bacterial phyla (Chloroflexi, Planctomycetes, Firmicutes, Gemmatimonadetes and Bacteroidetes) were found to be significantly correlated with the ARGs in soil. Mantel test and variation partitioning analysis (VPA) suggested that bacterial community shifts, rather than MGEs, is the major driver shaping the antibiotic resistome. Additionally, the co-occurrence pattern between ARGs and microbial taxa revealed by network analysis indicated that four

  3. Tissue-associated bacterial alterations in rectal carcinoma patients revealed by 16S rRNA community profiling

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    Andrew Maltez Thomas

    2016-12-01

    Full Text Available Sporadic and inflammatory forms of colorectal cancer (CRC account for more than 80% of cases. Recent publications have shown mechanistic evidence for the involvement of gut bacteria in the development of both CRC-forms. Whereas colon and rectal cancer have been routinely studied together as CRC, increasing evidence show these to be distinct diseases. Also, the common use of fecal samples to study microbial communities may reflect disease state but possibly not the tumor microenvironment. We performed this study to evaluate differences in bacterial communities found in tissue samples of 18 rectal-cancer subjects when compared to 18 non-cancer controls. Samples were collected during exploratory colonoscopy (non-cancer group or during surgery for tumor excision (rectal-cancer group. High throughput 16S rRNA amplicon sequencing of the V4-V5 region was conducted on the Ion PGM platform, reads were filtered using Qiime and clustered using UPARSE. We observed significant increases in species richness and diversity in rectal cancer samples, evidenced by the total number of OTUs and the Shannon and Simpson indexes. Enterotyping analysis divided our cohort into two groups, with the majority of rectal cancer samples clustering into one enterotype, characterized by a greater abundance of Bacteroides and Dorea. At the phylum level, rectal-cancer samples had increased abundance of candidate phylum OD1 (also known as Parcubacteria whilst non-cancer samples had increased abundance of Planctomycetes. At the genera level, rectal-cancer samples had higher abundances of Bacteroides, Phascolarctobacterium, Parabacteroides, Desulfovibrio and Odoribacter whereas non-cancer samples had higher abundances of Pseudomonas, Escherichia, Acinetobacter, Lactobacillus and Bacillus. Two Bacteroides fragilis OTUs were more abundant among rectal-cancer patients seen through 16S rRNA amplicon sequencing, whose presence was confirmed by immunohistochemistry and enrichment verified

  4. Salt Marsh Bacterial Communities before and after the Deepwater Horizon Oil Spill.

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    Engel, Annette Summers; Liu, Chang; Paterson, Audrey T; Anderson, Laurie C; Turner, R Eugene; Overton, Edward B

    2017-10-15

    Coastal salt marshes along the northern Gulf of Mexico shoreline received varied types and amounts of weathered oil residues after the 2010 Deepwater Horizon oil spill. At the time, predicting how marsh bacterial communities would respond and/or recover to oiling and other environmental stressors was difficult because baseline information on community composition and dynamics was generally unavailable. Here, we evaluated marsh vegetation, physicochemistry, flooding frequency, hydrocarbon chemistry, and subtidal sediment bacterial communities from 16S rRNA gene surveys at 11 sites in southern Louisiana before the oil spill and resampled the same marshes three to four times over 38 months after the spill. Calculated hydrocarbon biomarker indices indicated that oil replaced native natural organic matter (NOM) originating from Spartina alterniflora and marine phytoplankton in the marshes between May 2010 and September 2010. At all the studied marshes, the major class- and order-level shifts among the phyla Proteobacteria , Firmicutes , Bacteroidetes , and Actinobacteria occurred within these first 4 months, but another community shift occurred at the time of peak oiling in 2011. Two years later, hydrocarbon levels decreased and bacterial communities became more diverse, being dominated by Alphaproteobacteria ( Rhizobiales ), Chloroflexi ( Dehalococcoidia ), and Planctomycetes Compositional changes through time could be explained by NOM source differences, perhaps due to vegetation changes, as well as marsh flooding and salinity excursions linked to freshwater diversions. These findings indicate that persistent hydrocarbon exposure alone did not explain long-term community shifts. IMPORTANCE Significant deterioration of coastal salt marshes in Louisiana has been linked to natural and anthropogenic stressors that can adversely affect how ecosystems function. Although microorganisms carry out and regulate most biogeochemical reactions, the diversity of bacterial

  5. Response of Methanogenic Microbial Communities to Desiccation Stress in Flooded and Rain-Fed Paddy Soil from Thailand

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    Andreas Reim

    2017-05-01

    mostly detected on the level of operational taxonomic units (OTUs; 97% sequence similarity. The treatments resulted in change of the relative abundance of several archaeal OTUs. Some OTUs of Methanobacterium, Methanosaeta, Methanosarcina, Methanocella and Methanomassiliicoccus increased, while some of Methanolinea and Methanosaeta decreased. Bacterial OTUs within Firmicutes, Cyanobacteria, Planctomycetes and Deltaproteobacteria increased, while OTUs within other proteobacterial classes decreased.

  6. Changes in the Bacterial Community Structure of Remediated Anthracene-Contaminated Soils

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    Delgado-Balbuena, Laura; Bello-López, Juan M.; Navarro-Noya, Yendi E.; Rodríguez-Valentín, Analine; Luna-Guido, Marco L.; Dendooven, Luc

    2016-01-01

    Mixing soil or adding earthworms (Eisenia fetida (Savigny, 1826)) accelerated the removal of anthracene, a polycyclic aromatic hydrocarbon, from a pasture and an arable soil, while a non-ionic surfactant (Surfynol® 485) inhibited the removal of the contaminant compared to the untreated soil. It was unclear if the treatments affected the soil bacterial community and consequently the removal of anthracene. Therefore, the bacterial community structure was monitored by means of 454 pyrosequencing of the 16S rRNA gene in the pasture and arable soil mixed weekly, amended with Surfynol® 485, E. fetida or organic material that served as food for the earthworms for 56 days. In both soils, the removal of anthracene was in the order: mixing soil weekly (100%) > earthworms applied (92%) > organic material applied (77%) > untreated soil (57%) > surfactant applied (34%) after 56 days. There was no clear link between removal of anthracene from soil and changes in the bacterial community structure. On the one hand, application of earthworms removed most of the contaminant from the arable soil and had a strong effect on the bacterial community structure, i.e. a decrease in the relative abundance of the Acidobacteria, Chloroflexi and Gemmatimonadetes, and an increase in that of the Proteobacteria compared to the unamended soil. Mixing the soil weekly removed all anthracene from the arable soil, but had little or no effect on the bacterial community structure. On the other hand, application of the surfactant inhibited the removal of anthracene from the arable soil compared to the untreated soil, but had a strong effect on the bacterial community structure, i.e. a decrease in the relative abundance of Cytophagia (Bacteroidetes), Chloroflexi, Gemmatimonadetes and Planctomycetes and an increase in that of the Flavobacteria (Bacteroidetes) and Proteobacteria. Additionally, the removal of anthracene was similar in the different treatments of both the arable and pasture soil, but the

  7. Changes in the Bacterial Community Structure of Remediated Anthracene-Contaminated Soils.

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    Laura Delgado-Balbuena

    Full Text Available Mixing soil or adding earthworms (Eisenia fetida (Savigny, 1826 accelerated the removal of anthracene, a polycyclic aromatic hydrocarbon, from a pasture and an arable soil, while a non-ionic surfactant (Surfynol® 485 inhibited the removal of the contaminant compared to the untreated soil. It was unclear if the treatments affected the soil bacterial community and consequently the removal of anthracene. Therefore, the bacterial community structure was monitored by means of 454 pyrosequencing of the 16S rRNA gene in the pasture and arable soil mixed weekly, amended with Surfynol® 485, E. fetida or organic material that served as food for the earthworms for 56 days. In both soils, the removal of anthracene was in the order: mixing soil weekly (100% > earthworms applied (92% > organic material applied (77% > untreated soil (57% > surfactant applied (34% after 56 days. There was no clear link between removal of anthracene from soil and changes in the bacterial community structure. On the one hand, application of earthworms removed most of the contaminant from the arable soil and had a strong effect on the bacterial community structure, i.e. a decrease in the relative abundance of the Acidobacteria, Chloroflexi and Gemmatimonadetes, and an increase in that of the Proteobacteria compared to the unamended soil. Mixing the soil weekly removed all anthracene from the arable soil, but had little or no effect on the bacterial community structure. On the other hand, application of the surfactant inhibited the removal of anthracene from the arable soil compared to the untreated soil, but had a strong effect on the bacterial community structure, i.e. a decrease in the relative abundance of Cytophagia (Bacteroidetes, Chloroflexi, Gemmatimonadetes and Planctomycetes and an increase in that of the Flavobacteria (Bacteroidetes and Proteobacteria. Additionally, the removal of anthracene was similar in the different treatments of both the arable and pasture soil

  8. Genetic Markers Are Associated with the Ruminal Microbiome and Metabolome in Grain and Sugar Challenged Dairy Heifers

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    Helen M. Golder

    2018-02-01

    Full Text Available Dairy heifers were subjected to a non-life-threatening challenge designed to induce ruminal acidosis by feeding grain and sugar. Large among animal variation in clinical signs of acidosis, rumen metabolite concentrations, and the rumen microbiome occurred. This exploratory study investigates sources of the variation by examining associations between the genome, metabolome, and microbiome, albeit with a limited population. The broader objective is to provide a rationale for a larger field study to identify markers for susceptibility to ruminal acidosis. Initially, heifers (n = 40 allocated to five feed additive groups were fed 20-days pre-challenge with a total mixed ration and additives. Fructose (0.1% of bodyweight/day was added for the last 10 days pre-challenge. On day 21 heifers were challenged with 1.0% of bodyweight dry matter wheat + 0.2% of bodyweight fructose + additives. Rumen samples were collected via stomach tube weekly (day 0, 7, and 14 and at five times over 3.6 h after challenge and analyzed for pH and volatile fatty acid, ammonia, D-, and L-lactate concentrations. Relative abundance of bacteria and archaea were determined using Illumina MiSeq. Genotyping was undertaken using a 150K Illumina SNPchip. Genome-wide association was performed for metabolite and microbiome measures (n = 33. Few genome associations occurred with rumen pH, concentration of acetate, propionate, total volatile fatty acids, or ammonia, or the relative abundance of the Firmicutes, Bacteroidetes, and Spirochaetes phyla. Metabolites and microbial phyla that had markers associated and quantitative trait loci (QTL were: acetate to propionate ratio (A:P, D-, L-, and total lactate, butyrate, acidosis eigenvalue, Actinobacteria, Chloroflexi, Euryarchaeota, Fibrobacteres, Planctomycetes, Proteobacteria, and Tenericutes. A putative genomic region overlapped for Actinobacteria, Euryarchaeota, and Fibrobacteres and covered the region that codes for matrix extracellular

  9. Cultivation-Based and Molecular Assessment of Bacterial Diversity in the Rhizosheath of Wheat under Different Crop Rotations.

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    Muhammad Tahir

    Full Text Available A field study was conducted to compare the formationand bacterial communities of rhizosheaths of wheat grown under wheat-cotton and wheat-rice rotation and to study the effects of bacterial inoculation on plant growth. Inoculation of Azospirillum sp. WS-1 and Bacillus sp. T-34 to wheat plants increased root length, root and shoot dry weight and dry weight of rhizosheathsoil when compared to non-inoculated control plants, and under both crop rotations. Comparing both crop rotations, root length, root and shoot dry weight and dry weight of soil attached with roots were higher under wheat-cotton rotation. Organic acids (citric acid, malic acid, acetic acid and oxalic acid were detected in rhizosheaths from both rotations, with malic acid being most abundant with 24.8±2 and 21.3±1.5 μg g(-1 dry soil in wheat-cotton and wheat-rice rotation, respectively. Two sugars (sucrose, glucose were detected in wheat rhizosheath under both rotations, with highest concentrations of sucrose (4.08±0.5 μg g(-1 and 7.36±1.0 μg g(-1 and glucose (3.12±0.5 μg g(-1 and 3.01± μg g(-1 being detected in rhizosheaths of non-inoculated control plants under both rotations. Diversity of rhizosheath-associated bacteria was evaluated by cultivation, as well as by 454-pyrosequencing of PCR-tagged 16S rRNA gene amplicons. A total of 14 and 12 bacterial isolates predominantly belonging to the genera Arthrobacter, Azospirillum, Bacillus, Enterobacter and Pseudomonaswere obtained from the rhizosheath of wheat grown under wheat-cotton and wheat-rice rotation, respectively. Analysis of pyrosequencing data revealed Proteobacteria, Bacteriodetes and Verrucomicrobia as the most abundant phyla in wheat-rice rotation, whereas Actinobacteria, Firmicutes, Chloroflexi, Acidobacteria, Planctomycetes and Cyanobacteria were predominant in wheat-cotton rotation. From a total of 46,971 sequences, 10.9% showed ≥97% similarity with 16S rRNA genes of 32 genera previously shown to include

  10. Preservation and Significance of Extracellular DNA in Ferruginous Sediments from Lake Towuti, Indonesia

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    Aurèle Vuillemin

    2017-07-01

    Full Text Available Extracellular DNA is ubiquitous in soil and sediment and constitutes a dominant fraction of environmental DNA in aquatic systems. In theory, extracellular DNA is composed of genomic elements persisting at different degrees of preservation produced by processes occurring on land, in the water column and sediment. Extracellular DNA can be taken up as a nutrient source, excreted or degraded by microorganisms, or adsorbed onto mineral matrices, thus potentially preserving information from past environments. To test whether extracellular DNA records lacustrine conditions, we sequentially extracted extracellular and intracellular DNA from anoxic sediments of ferruginous Lake Towuti, Indonesia. We applied 16S rRNA gene Illumina sequencing on both fractions to discriminate exogenous from endogenous sources of extracellular DNA in the sediment. Environmental sequences exclusively found as extracellular DNA in the sediment originated from multiple sources. For instance, Actinobacteria, Verrucomicrobia, and Acidobacteria derived from soils in the catchment. Limited primary productivity in the water column resulted in few sequences of Cyanobacteria in the oxic photic zone, whereas stratification of the water body mainly led to secondary production by aerobic and anaerobic heterotrophs. Chloroflexi and Planctomycetes, the main degraders of sinking organic matter and planktonic sequences at the water-sediment interface, were preferentially preserved during the initial phase of burial. To trace endogenous sources of extracellular DNA, we used relative abundances of taxa in the intracellular DNA to define which microbial populations grow, decline or persist at low density with sediment depth. Cell lysis became an important additional source of extracellular DNA, gradually covering previous genetic assemblages as other microbial genera became more abundant with depth. The use of extracellular DNA as nutrient by active microorganisms led to selective removal of

  11. Lunatimonas lonarensis gen. nov., sp. nov., a haloalkaline bacterium of the family Cyclobacteriaceae with nitrate reducing activity.

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    Srinivas, T N R; Aditya, S; Bhumika, V; Kumar, P Anil

    2014-02-01

    Novel pinkish-orange pigmented, Gram-negative staining, half-moon shaped, non-motile, strictly aerobic strains designated AK24(T) and AK26 were isolated from water and sediment samples of Lonar Lake, Buldhana district, Maharahstra, India. Both strains were positive for oxidase, catalase and β-galactosidase activities. The predominant fatty acids were iso-C15:0 (41.5%), anteiso-C15:0 (9.7%), iso-C17:0 3OH (9.6%), iso-C17:1 ω9c (10.2%) and C16:1 ω7c/C16:1 ω6c/iso-C15:0 2OH (summed feature 3) (14.4%). The strains contained MK-7 as the major respiratory quinone, and phosphatidylethanolamine and five unidentified lipids as the polar lipids. Blast analysis of the 16S rRNA gene sequence of strain AK24(T) showed that it was closely related to Aquiflexum balticum, with a pair-wise sequence similarity of 91.6%, as well as to Fontibacter ferrireducens, Belliella baltica and Indibacter alkaliphilus (91.3, 91.2 and 91.2% pair-wise sequence similarity, respectively), but it only had between 88.6 and 91.0% pair-wise sequence similarity to the rest of the family members. The MALDI-TOF assay reported no significant similarities for AK24(T) and AK26, since they potentially represented a new species. A MALDI MSP dendrogram showed close similarity between the two strains, but they maintained a distance from their phylogenetic neighbors. The genome of AK24(T) showed the presence of heavy metal tolerance genes, including the genes providing resistance to arsenic, cadmium, cobalt and zinc. A cluster of heat shock resistance genes was also found in the genome. Two lantibiotic producing genes, LanR and LasB, were also found in the genome of AK24(T). Strains AK24(T) and AK26 were very closely related to each other with 99.5% pair-wise sequence similarity. Phylogenetic analysis indicated that the strains were members of the family Cyclobacteriaceae and they clustered with the genus Mariniradius, as well as with the genera Aquiflexum, Cecembia, Fontibacter, Indibacter, and Shivajiella

  12. Global plate boundary evolution and kinematics since the late Paleozoic

    Science.gov (United States)

    Matthews, Kara J.; Maloney, Kayla T.; Zahirovic, Sabin; Williams, Simon E.; Seton, Maria; Müller, R. Dietmar

    2016-11-01

    Many aspects of deep-time Earth System models, including mantle convection, paleoclimatology, paleobiogeography and the deep Earth carbon cycle, require high-resolution plate motion models that include the evolution of the mosaic of plate boundaries through time. We present the first continuous late Paleozoic to present-day global plate model with evolving plate boundaries, building on and extending two previously published models for the late Paleozoic (410-250 Ma) and Mesozoic-Cenozoic (230-0 Ma). We ensure continuity during the 250-230 Ma transition period between the two models, update the absolute reference frame of the Mesozoic-Cenozoic model and add a new Paleozoic reconstruction for the Baltica-derived Alexander Terrane, now accreted to western North America. This 410-0 Ma open access model provides a framework for deep-time whole Earth modelling and acts as a base for future extensions and refinement. We analyse the model in terms of the number of plates, predicted plate size distribution, plate and continental root mean square (RMS) speeds, plate velocities and trench migration through time. Overall model trends share many similarities to those for recent times, which we use as a first order benchmark against which to compare the model and identify targets for future model refinement. Except for during the period 260-160 Ma, the number of plates (16-46) and ratio of "large" plates (≥ 107.5 km2) to smaller plates ( 2.7-6.6) are fairly similar to present-day values (46 and 6.6, respectively), with lower values occurring during late Paleozoic assembly and growth of Pangea. This temporal pattern may also reflect difficulties in reconstructing small, now subducted oceanic plates further back in time, as well as whether a supercontinent is assembling or breaking up. During the 260-160 Ma timeframe the model reaches a minima in the number of plates, in contrast to what we would expect during initial Pangea breakup and thus highlighting the need for refinement

  13. Seafloor mapping at Olkiluoto western coast of Finland

    International Nuclear Information System (INIS)

    Ilmarinen, K.; Leinikki, J.; Oulasvirta, P.

    2009-02-01

    explained by the more variable bottom and the more exposed location compared to the corresponding transects 2 and 3, 4 and 5a. The somewhat sheltered transect 5 and the exposed transects 1 and 2 had the highest biomasses of individuals. The biomass was high because of the bivalvia Macoma baltica which is very common in 2-5 meters depth on the sand, silt and mud bottoms. At the transects 1, 2 and 5 were found Oligochaeta which are more common in clear water. These transects had slightly less turbid water than the other transects. The biomass of Polychaeta Marenzelleria (arctia) was high at the transects 3 and 4. This species can tolerate low oxygen levels. Transect 5a is extremely shallow and located in a flad - an enclosed bay in a land uplift region that still receives sea water regularly. High biomass of chironomids (Chironomidae) were found at the transect 5a and especially the species Chironomus f. l. plumosus, which was only found at this transect, indicates high eutrofication. Depth mapping by echo sounding was carried out at a transect interval of 50 meters in the sea area that was estimated to be less than 2 meters deep. The mapping area also included a few kilometers of the lower parts of the rivers Eurajoki and Lapinjoki. The mapping material was handed to the Geological Survey of Finland for creating a depth model. It was not a surprise to the survey team that much of the measured area was deeper than 2 meters, as the depth information printed on nautical charts aims primarily at maritime safety. (orig.)

  14. Seafloor mapping at Olkiluoto western coast of Finland

    Energy Technology Data Exchange (ETDEWEB)

    Ilmarinen, K.; Leinikki, J.; Oulasvirta, P. (Alleco Oy, Helsinki (Finland))

    2009-02-15

    the more variable bottom and the more exposed location compared to the corresponding transects 2 and 3, 4 and 5a. The somewhat sheltered transect 5 and the exposed transects 1 and 2 had the highest biomasses of individuals. The biomass was high because of the bivalvia Macoma baltica which is very common in 2-5 meters depth on the sand, silt and mud bottoms. At the transects 1, 2 and 5 were found Oligochaeta which are more common in clear water. These transects had slightly less turbid water than the other transects. The biomass of Polychaeta Marenzelleria (arctia) was high at the transects 3 and 4. This species can tolerate low oxygen levels. Transect 5a is extremely shallow and located in a flad - an enclosed bay in a land uplift region that still receives sea water regularly. High biomass of chironomids (Chironomidae) were found at the transect 5a and especially the species Chironomus f. l. plumosus, which was only found at this transect, indicates high eutrofication. Depth mapping by echo sounding was carried out at a transect interval of 50 meters in the sea area that was estimated to be less than 2 meters deep. The mapping area also included a few kilometers of the lower parts of the rivers Eurajoki and Lapinjoki. The mapping material was handed to the Geological Survey of Finland for creating a depth model. It was not a surprise to the survey team that much of the measured area was deeper than 2 meters, as the depth information printed on nautical charts aims primarily at maritime safety. (orig.)

  15. Tectonic context of the penetrative fracture system origin in the Early Paleozoic shale complex (Baltic Basin, Poland/Sweden).

    Science.gov (United States)

    Jarosiński, Marek; Gluszynski, Andrzej; Bobek, Kinga; Dyrka, Ireneusz

    2017-04-01

    Characterization of natural fracture and fault pattern play significant role for reservoir stimulation design and evaluation of its results. Having structural observations limited to immediate borehole surrounding it is a common need to build up a fracture model of reservoir in a range of stimulation reservoir volume or even beyond. To do this we need both a 3D seismic model and a consistent concept of the regional tectonic evolution. We present the result of integrated tectonic study in several deep boreholes target the Lower Paleozoic shale complex of Baltic Basin (BB), combined with analysis of 3D seismic survey and outcrop screening in Scania (Swedish part of the BB). During deposition of shale complex in the Ordovician and Silurian the research area was located 200-300 km away from the continental margin of Baltica involved in the Caledonian collision with the Eastern Avalonia. This distance allowed the shale complex to avoid significant tectonic deformation. Regional seismic cross section reveals the general pattern of the BB infill characteristic for the foreland basin underwent post-collisional isostatic rebound. Due to stress changes in collisional context the shale complex was cross-cut by steep, mostly inverse faults trending NW-SE and NE-SW. The fault zones oriented NW-SE are associated with an array of en echelon faults characteristic for strike-slip displacement. In our interpretation, these faults of Silurian (Wenlock) age create pattern of the regional pop-up structure, which is simultaneously involved in the plate flexure extension. Seismic attributes (e.g. curvature or ant tracking) highlight lineaments which mostly mimic the faults orientation. However, attributes show also some artefacts that come from regular array of seismic sources and receivers, which mimic the orthogonal joint system. Structural observations on borehole core lead us to conclusion that regular, orthogonal fracture system developed after maximum burial of the complex

  16. 3D inversion based on multi-grid approach of magnetotelluric data from Northern Scandinavia

    Science.gov (United States)

    Cherevatova, M.; Smirnov, M.; Korja, T. J.; Egbert, G. D.

    2012-12-01

    solver is implemented within the framework of the modular system for EM inversion (ModEM by G. Egbert, A. Kelbert, N. Meqbel), using the ModEM 3D finite difference staggered grid forward solver (second order PDE in the electric field, with divergence correction) as a starting point for our development. The first 3D inversion model for the crust and upper mantle shows the highly conducting bodies in the crust which can be interpreted as alum shales. The eastern and central parts are presented by resistive Precambrian rocks of the Svecofennian and Archaean domains. The upper mantle is resistive and relates to the Baltica basement. We also compare 3D inversion model with the results of 2D inversion along several profiles. We are able to explain some of the features in the data (out of quadrant phase) with 3D model, thus providing more reliable results compared to routine 2D approach.

  17. Reconstructing Rodinia by Fitting Neoproterozoic Continental Margins

    Science.gov (United States)

    Stewart, John H.

    2009-01-01

    extensional in origin, supports recognition of the Neoproterozoic fragmentation pattern of Rodinia and outlines the major continental masses that, prior to the breakup, formed the supercontinent. Using this pattern, Rodinia can be assembled by fitting the pieces together. Evidence for Neoproterozoic margins is fragmentary. The most apparent margins are marked by miogeoclinal deposits (passive-margin deposits). The margins can also be outlined by the distribution of continental-margin magmatic-arc rocks, by juvenile ocean-floor rocks, or by the presence of continent-ward extending aulacogens. Most of the continental margins described here are Neoproterozoic, and some had an older history suggesting that they were major, long-lived lithospheric flaws. In particular, the western margin of North America appears to have existed for at least 1,470 Ma and to have been reactivated many times in the Neoproterozoic and Phanerozoic. The inheritance of trends from the Mesoproterozoic by the Neoproterozoic is particularly evident along the eastern United States, where a similarity of Mesoproterozoic (Grenville) and Neoproterozoic trends, as well as Paleozoic or Mesozoic trends, is evident. The model of Rodinia presented here is based on both geologic and paleomagnetic information. Geologic evidence is based on the distribution and shape of Neoproterozoic continents and on assembling these continents so as to match the shape, history, and scale of adjoining margins. The proposed model places the Laurasian continents?Baltica, Greenland, and Laurentia?west of the South American continents (Amazonia, Rio de La Plata, and Sa? Francisco). This assembly is indicated by conjugate pairs of Grenville-age rocks on the east side of Laurentia and on the west side of South America. In the model, predominantly late Neoproterozoic magmatic-arc rocks follow the trend of the Grenville rocks. The boundary between South America and Africa is interpreted as the site of a Wilson cycle

  18. Secular trends in the geologic record and the supercontinent cycle

    Science.gov (United States)

    Bradley, Dwight C.

    2011-01-01

    to form Rodinia. Rodinia broke up in stages from ca. 1000 to ca. 520 Ma. Before Rodinia had completely come apart, some of its pieces had already been reassembled in a new configuration, Gondwana, which was completed by 530 Ma. Gondwana later collided with Laurentia, Baltica, and Siberia to form Pangea by about 300 Ma. Breakup of Pangea began at about 180 Ma (Early Jurassic) and continues today. In the suggested scenario, no supercontinent cycle in Earth history corresponded to the ideal, in which all the continents were gathered together, then broke apart, then reassembled in a new configuration. Nuna and Gondwana ended their tenures not by breakup but by collision and name change; Rodinia's assembly overlapped in time with its disassembly; and Pangea spalled Tethyan microcontinents throughout much of its tenure. Many other secular trends show a weak or uneven imprint of the supercontinent cycle, no imprint at all. Instead, these secular trends together reveal aspects of the shifting background against which the supercontinents came and went, making each cycle unique. Global heat production declined; plate tectonics sped up through the Proterozoic and slowed down through the Phanerozoic; the atmosphere and oceans became oxidized; life emerged as a major geochemical agent; some rock types went extinct or nearly so (BIF, massif-type anorthosite, komatiite); and other rock types came into existence or became common (blueschists, bioclastic limestone, coal).

  19. Between carbonatite and lamproite—Diamondiferous Torngat ultramafic lamprophyres formed by carbonate-fluxed melting of cratonic MARID-type metasomes

    Science.gov (United States)

    Tappe, Sebastian; Foley, Stephen F.; Kjarsgaard, Bruce A.; Romer, Rolf L.; Heaman, Larry M.; Stracke, Andreas; Jenner, George A.

    2008-07-01

    New U-Pb perovskite ages reveal that diamondiferous ultramafic lamprophyre magmas erupted through the Archean crust of northern Labrador and Quebec (eastern Canada) between ca. 610 and 565 Ma, a period of strong rifting activity throughout contiguous Laurentia and Baltica. The observed Torngat carbonate-rich aillikite/carbonatite and carbonate-poor mela-aillikite dyke varieties show a large spread in Sr-Nd-Hf-Pb isotope ratios with pronounced correlations between isotope systems. An isotopically depleted component is identified solely within aillikites ( 87Sr/ 86Sr i = 0.70323-0.70377; ɛNd i = +1.2-+1.8; ɛHf i = +1.4-+3.5; 206Pb/ 204Pb i = 18.2-18.5), whereas some aillikites and all mela-aillikites range to more enriched isotope signatures ( 87Sr/ 86Sr i = 0.70388-0.70523; ɛNd i = -0.5 to -3.9; ɛHf i = -0.6 to -6.0; 206Pb/ 204Pb i = 17.8-18.2). These contrasting isotopic characteristics of aillikites/carbonatites and mela-aillikites, along with subtle differences in their modal carbonate, SiO 2, Al 2O 3, Na 2O, Cs-Rb, and Zr-Hf contents, are consistent with two distinctive metasomatic assemblages of different age in the mantle magma source region. Integration of petrologic, geochemical, and isotopic information leads us to propose that the isotopically enriched component originated from a reduced phlogopite-richterite-Ti-oxide dominated source assemblage that is reminiscent of MARID suite xenoliths. In contrast, the isotopically depleted component was derived from a more oxidized phlogopite-carbonate dominated source assemblage. We argue that low-degree CO 2-rich potassic silicate melts from the convective upper mantle were preferentially channelled into an older, pre-existing MARID-type vein network at the base of the North Atlantic craton lithosphere, where they froze to form new phlogopite-carbonate dominated veins. Continued stretching and thinning of the cratonic lithosphere during the Late Neoproterozoic remobilized the carbonate-rich vein material and

  20. Evidences of Silurian dextral transpression in the Scandinavian Caledonides

    Science.gov (United States)

    Torgersen, Espen; Viola, Giulio

    2017-04-01

    The Scandinavian Caledonides are classically interpreted as a fold and thrust belt resulting from the collision between Laurentia and Baltica during the Silurian, which involved the up-to-400 km ESE-wards translation of nappes onto the Baltoscandian platform. It has been suggested that the Caledonian fold and thrust belt formed through several distinct orogenic episodes, from early shortening in the Late Ordovician to orogenic collapse in the Devonian. The classic Caledonian, orogen-perpendicular ESE-ward nappe transport is constrained by abundant and consistently oriented stretching lineations across the entire orogen and unambiguous kinematic indicators. However, there is also a large number of NW-SE-trending and roughly orogen-parallel lineations, particularly in the upper ophiolite- and eclogite-bearing nappes, which are more challenging to interpret with the traditional orogeny evolution model. The analysis of the areal extent, spatial distribution and geometrical relationships of the Caledonian nappes in southern and central Norway, however, offers new insights and allows for new constraints on the bulk kinematic framework of the shortening history of the belt. Here we present new, first-order geological observations that demonstrate a two-fold compressional history and associated strain partitioning during Caledonian convergence. More specifically, we propose that Late Ordovician NNW-SSE shortening caused early compression, followed by WNW-ESE Early Silurian shortening, which resulted in strain partitioning along the planar fabrics and discontinuities from the earlier event. In detail, orogen-parallel dextral wrench tectonics caused significant lateral displacement along at least three, orogen-scale NE-SW striking corridors, wherein the nappes appear to be consistently displaced in a dextral fashion. We propose that the Møre-Trøndelag Fault Complex, which accommodated significant sinistral displacements during the later Devonian orogenic collapse

  1. Characterization of Microbial Communities Associated With Deep-Sea Hydrothermal Vent Animals of the East Pacific Rise and the Galápagos Rift

    Science.gov (United States)

    Ward, N.; Page, S.; Heidelberg, J.; Eisen, J. A.; Fraser, C. M.

    2002-12-01

    epsilon proteobacteria, low GC Gram positive bacteria (firmicutes), spirochetes, CFB (Cytophaga-Flavobacterium-Bacteroides) group, green nonsulfur bacteria, acidobacteria, verrucomicrobia, and planctomycetes. The presence of the latter three taxonomic groups is of special interest, as they represent phylogenetically distinct groups within the Bacteria for which specific ecological functions have not yet been identified, but which have been found to be widely distributed and often numerically significant in diverse terrestrial and aquatic habitats. Although further sequencing is required to demonstrate the presence of a Riftia-associated microbial population distinct from that of the surrounding seawater, results available from three Riftia individuals from the East Pacific Rise suggest this to be the case. Analysis of microbial communities associated with the gill tissue of the mussel Bathymodiolus thermophilus shows a population dominated by gamma-Proteobacterial chemoautotrophic symbionts, although lower frequency novel phylotypes have been detected. Representatives of specific taxonomic groups have been selected for sequencing of the complete 16S rRNA gene, and the sequences used to reconstruct phylogenetic trees to more accurately determine the evolutionary relationships between the novel sequences, and available sequences for both cultured and non-cultured bacteria.

  2. Bioprospecting Sediments from Red Sea Coastal Lagoons for Microorganisms and Their Antimicrobial Potential

    KAUST Repository

    Al-Amoudi, Soha

    2016-12-08

    showed a higher percentage of enzymes associated with antibiotic synthesis, PKS and NRPS. When considering sediment type, mangrove mud samples showed a higher percentage of enzymes associated with antibiotic synthesis than microbial mat samples. Taken together, RHL was shown to be the better location with an increased probability of successful antibiotic bioprospecting, while the best sediment type in RHL for this purpose is microbial mat. Moreover, the phylum Actinobacteria tends to be the common target for research when it comes to antibiotic bioprospecting. However this culture-independent metagenomic study suggests the tremendous potential of Proteobacteria, Bacteroidetes, Cyanobacteria and Firmicutes for this purpose. Taking into account that the metagenomic screen suggests other phyla beyond Actinobacteria for antibiotic bioprospecting, the culture-dependent experiments were not designed to target actinobacteria alone. A total of 251 bacterial strains were isolated from the three collected sediments. Phylogenetic characterization of 251 bacterial isolates, based on 16S rRNA gene sequencing, supported their assignment to five different phyla: Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, and Planctomycetes. Fifteen putative novel species were identified based on a 16S rRNA gene sequence similarity of ≤ 98 % to other strain sequences in the NCBI database. We demonstrate that 52 of the 251 isolates exhibit the potential to produce an antimicrobial effect. Additionally, at least one type of biosynthetic gene sequence, responsible for the synthesis of secondary metabolites, was recovered from 25 of the 52 isolates. Moreover, 10 of the isolates had a growth inhibition effect towards all target strains. In conclusion, this study demonstrated the significant microbial diversity associated with Red Sea harbor/lagoon systems and their potential to produce antimicrobial compounds and novel secondary metabolites. To the best of our knowledge, this is the first

  3. Sequence-based identification of inositol monophosphatase-like histidinol-phosphate phosphatases (HisN) in Corynebacterium glutamicum, Actinobacteria, and beyond.

    Science.gov (United States)

    Kulis-Horn, Robert Kasimir; Rückert, Christian; Kalinowski, Jörn; Persicke, Marcus

    2017-07-18

    paralog groups from each other and other IMPases. The kinetic data obtained for HisN from C. glutamicum, as an example for an IMPase-like HolPases, shows remarkable differences in enzyme properties as compared to HAD- or PHP-type HolPases. The six sequence motifs and the HMMs presented in this study can be used to reliably differentiate between IMPase-like HolPases and IMPase-like proteins with no such activity, with the potential to enhance current and future genome annotations. A phylogenetic analysis reveals that IMPase-like HolPases are not only present in Actinobacteria and plant but can be found in further bacterial phyla, including, among others, Proteobacteria, Chlorobi and Planctomycetes.

  4. Siberia, the wandering northern terrane, and its changing geography through the Palaeozoic

    Science.gov (United States)

    Cocks, L. Robin M.; Torsvik, Trond H.

    2007-05-01

    -Siberia, the North China Terrane, the Manchurides terranes (including the Khingan-Bureya Massif area), the Gurvanshayan Terrane, the Ala Shan Terrane, the Qaidam-Qilian Terrane, the Tarim Terrane, the Junggar Terrane, the Tien Shan terranes and the various Kazakh terranes, did not become part of the Siberian Terrane assemblage until they accreted to it in the Upper Palaeozoic or later during the formation of Pangea. The Farewell Terrane of Alaska includes typical Lower and Middle Palaeozoic Siberian endemic faunas, but its Palaeozoic position is unknown. Cambrian to Early Silurian palaeomagnetic poles from the southern and northern parts of the Siberian Craton differ, but can be matched with an Euler pole of 60°N, 120°E and a rotation angle of 13°. We link this observation with Devonian rifting in the Viljuy Basin near the centre of the craton and also postulate that this rifting rejuvenated an older Precambrian rift zone, since 1-1.1 Ga poles from southern and northern Siberia differ as much as 23° around the same Euler pole. A revised Palaeozoic apparent polar wander (APW) path is presented for the Siberian Craton in which pre-Devonian poles are corrected for Viljuy Basin rifting. There is also much Late Devonian tectonic activity in the Altai-Sayan area, which may be linked. The APW path implies that Siberia was located at low southerly latitudes at the dawn of the Palaeozoic and slowly drifted northward (different APW path alternatives that result in two very different convergence scenarios between Siberia and Baltica/Kazakh terranes. There are a newly-constructed succession of palaeogeographic maps of Siberia and its nearby areas at various times from the Cambrian to the Permian as, firstly, the peri-Siberian terranes and, secondly, the remainder of the Central Asian terranes accreted to it. Prior to the Early Ordovician, Siberia was in the southern hemisphere, but after that it drifted northwards and for most of the Phanerozoic it has been one of the few larger

  5. Reworked Middle Jurassic sandstones as a marker for Upper Cretaceous basin inversion in Central Europe—a case study for the U-Pb detrital zircon record of the Upper Cretaceous Schmilka section and their implication for the sedimentary cover of the Lausitz Block (Saxony, Germany)

    Science.gov (United States)

    Hofmann, Mandy; Voigt, Thomas; Bittner, Lucas; Gärtner, Andreas; Zieger, Johannes; Linnemann, Ulf

    2018-04-01

    Elbtal Group (Schmilka section), the zircon age patterns change significantly towards the Lower Coniacian (topmost sample of the analysed section), where a major input of Meso- and Paleoproterozoic grains was obtained. Comparable ages are generally scarce in the working area. To have a reference for the detrital zircon age spectra of Triassic and Jurassic sediments of the area, two Upper Triassic und two Middle Jurassic clastic sediments of Germany were analysed. Surprisingly, the two Middle Jurassic (Dogger) sandstones from Bavaria and Lower Saxony showed similar detrital zircon age compositions as the Coniacian sediments on top of the Schmilka section (Elbe valley, Elbtal Group). In contrast, the two Upper Triassic sediments could be excluded as possible source rocks for the Upper Cretaceous sandstones of the Elbe valley (Schmilka section, Elbtal Group). The Meso- and Paleoproterozoic zircon age populations in the uppermost sandstone sample of the Schmilka section are assumed to originate from recycled Jurassic (Dogger) sandstones, resting on the Lausitz Block. These Middle Jurassic deposits were strongly influenced by a sedimentary input from the Scandinavian region (southern Baltica and North Sea Dome). The Turonian sandstones of the Schmilka section (samples below the topmost Coniacian sample) are interpreted to represent re-deposited Lower Cretaceous sediments resting on the Lausitz Block. A proposed synsedimentary uplift of about 5 km during the Upper Cretaceous along the Lausitz Fold (Lange et al., Zeitschrift der Deutschen Gesellschaft für Geowissenschaften 159(1):123-132, 2008) would have caused erosion of the pre-existing sedimentary cover of the Lausitz Block followed by inverse accumulation of the detritus into the Cretaceous Basin (Elbe valley, Elbtal Group). The Permian and Triassic cover units of the Lausitz Block were not exposed during the Upper Cretaceous, but are assumed to have contributed to younger (post-Coniacian) sediments of the Elbtal Group

  6. New calibration of Ji - Di clinopyroxene barometer for Eclogites, pyroxenites and peridotites and eclogite - pyroxenite mantle geotherms.

    Science.gov (United States)

    Ashchepkov, Igor; Vishnyakova, Elena

    2010-05-01

    .275*(1-0.17*Na/Al+0.0115*Fe/Na)*Kd^3/4*ToK/(1+Fe)* (1+5*Fe*(ToK-600)/50)-35*ln(1273/ToK)*(Al+Ti+2.5Na+1.5Fe3+)+(0.9-xx(2,8))*10+xx(2,9)/xx(2,3)* ToK /300-4*(Fe*33.2-4) -(Al-5.5)*( ToK -1300)/70-( ToK -1200)*0.015 with the second correction P=P*0.65+10+Mg*Al*( ToK -1400)/500 Where KD = Na*Mg/xAlCr*/Ca; XAlCr= Al*((T0-800)/800)**0.25+Cr-K+(4*Ti-0.0125)/(T0-600)*400+(Fe-0.21)*(T0-600)/14000 This equations reproduces the experimental pressures for 300 experimental runs with the R=0.84 and for the best set of the experimental data (Walter, 1999; Taylor ea 1998; Brey Kohler, 1990; 2009) with the E=0.95 (s=7) within the 100 kbar interval. They allow to work with the wide range of the pyroxenite compositions giving the practically coinciding PT parameters with the pressures determined for ilmenites and chromites as well as the (Brey, Kohler, 1900) pressure estimates. The PT parameters reconstructed for the mantle lithosphere beneath > 120 pipes from Yakutia , Baltica, Africa , North America and other world wide kimberlites have shown very good coincidence with the estimates from the other methods of monomineral (Nimis, Taylor, 2000; McGregor, 1974; Ashchepkov ea. 2009 ) and Gar-Opx barometers (Brey, Kohler, 1900; Nickel, Green, 1975). For the garnet and spinel xenoliths of the alkali basalts representing fertile or regenerated peridotites with high Al content of the clinopyroxenes the modified equation allows to determine the pressures together for megacrysts, pyroxeniets and peridotites using the following equation P=0.035*Kd*ToK)/(1+3.5*Fe)- 50*ln(1273/(ToK-100)*(Al+5*Na-Ti+2*Cr) -(Na-0.050)*(ToK-1200)*(Ca-0.85)/7000+5 Where KD = Na*Mg/xAlCr*/Ca; xAlCr= (Al+Si-2)*((ToK-700)/900)^0.35+Cr+Fe3-K +(4*Ti-0.0125)/(ToK-600)*700 +(Fe-0.21)*(ToK-400)/17000 This equations also very good reproduce the experimental runs in the pressure interval from 10 to 80 kbar but better to 50 kbars (R=0.92) (S=5) for 170 experimental runs (Putirka ea, 1996; Fallon ea, 1999; Taylor ea, 1998; Drapper Green

  7. The Lower Cambrian of Scandinavia: Depositional environment, sequence stratigraphy and palaeogeography

    Science.gov (United States)

    Nielsen, Arne Thorshøj; Schovsbo, Niels Hemmingsen

    2011-08-01

    impact related. Sequences are defined as transgressive-regressive depositional cycles bounded by maximum regressive surfaces and their correlative conformities. Sea-level rises are identified by fining-upward lithologies, cratonwards shifts in facies and depocentres, formation of widespread thin lime- and ironstones as well as precipitation of phosphorite and glaucony; the latter formed at remarkably shallow depth in comparison with the modern world. Sea-level falls are identified by coarsening-upwards lithologies, basinwards shifts in facies and gaps in the sedimentary record relating to non-deposition/erosion during falling stage and lowstand. Due to the pronounced clastic starvation neither lowstand nor highstand system tracts are developed subsequent to the earliest transgressive phases and eustasy was the primary control on depth changes. The Lower Cambrian comprises two supersequences (2nd order sequences), separated by regional subaerial unconformities reflecting the Rispebjerg Lowstand (new name) and the Hawke Bay Event. The Rispebjerg Lowstand was likely glacio-eustatic. Supersequence 1 (Rovnian-Lontovan-Dominopolian-'Ljubomlian') comprises about nine 3rd order sequences but the exact number of sequences in the Lontovan is unsettled. Supersequence 2 (Vergalian-Rausvian-lower Kibartian) comprises five sequences. Two or more subsequences (new term = 4th order sequences) are recognized in all sequences but long-distance correlation is usually difficult. The sequence stratigraphical resolution of the Lower Cambrian is more than twice as high as the acritarch biozonation. Baltica became intensively peneplained during the Neoproterozoic and was by and large completely flat at the dawn of the Cambrian. The profound Early Cambrian sea-level rise, comprising a series of individual 3rd order drowning events, was associated with step-wise transgression of Baltoscandia and concomitantly the sedimentary supply declined. The sequence stratigraphical analysis indicates onset