DOCSLIB.ORG

Polyamine Distribution Profiles Among Some Members Within Delta-And Epsilon-Subclasses of Proteobacteria

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

Microbiol. Cult. Coll. June. 2004. p. 3 ― 8 Vol. 20, No. 1 Polyamine Distribution Profiles among Some Members within Delta-and Epsilon-Subclasses of Proteobacteria Koei Hamana1）＊, Tomoko Saito1）, Mami Okada1）, and Masaru Niitsu2） 1）Department of Laboratory Sciences, School of Health Sciences, Faculty of Medicine, Gunma University, 39- 15 Showa-machi 3-chome, Maebashi, Gunma 371-8514, Japan 2）Faculty of Pharmaceutical Sciences, Josai University, Keyakidai 1-chome-1, Sakado, Saitama 350-0295, Japan Cellular polyamines of 18 species（13 genera）belonging to the delta and epsilon subclasses of the class Proteobacteria were analyzed by HPLC and GC. In the delta subclass, the four marine myxobacteria（the order Myxococcales）, Enhygromyxa salina, Haliangium ochroceum, Haliangium tepidum and Plesiocystis pacifica contained spermidine. Fe（III）-reducing two Geobacter species and two Pelobacter species belonging to the order Desulfuromonadales con- tained spermidine. Bdellovibrio bacteriovorus was absent in cellular polyamines. Bacteriovorax starrii contained putrescine and spermidine. Bacteriovorax stolpii contained spermidine and homo- spermidine. Spermidine was the major polyamine in the sulfate-reducing delta proteobacteria belonging to the genera Desulfovibrio, Desulfacinum, Desulfobulbus, Desulfococcus and Desulfurella, and some species of them contained cadaverine. Within the epsilon subclass, three Sulfurospirillum species ubiquitously contained spermidine and one of the three contained sper- midine and cadaverine. Thiomicrospora denitrificans contained cadaverine and spermidine as the major polyamine. These data show that cellular polyamine profiles can be used as a chemotaxonomic marker within delta and epsilon subclasses. Key words: polyamine, spermidine, homospermidine, Proteobacteria The class Proteobacteria is a major taxon of the 18, 26）. Fe（Ⅲ）-reducing members belonging to the gen- domain Bacteria and is phylogenetically divided into the era Pelobacter, Geobacter, Desulfuromonas and alpha, beta, gamma, delta and epsilon subclasses. We Desulfuromusa, form a monophyletic group（the order have reported the cellular polyamine distribution profiles Desulfuromonadales（）2, 3, 4, 20）. Two Pelobacter species, within proteobacteria, as a chemotaxonomic marker（8- previously analyzed, contained spermidine as the major 15）. Within the delta subclass, homospermidine was polyamine（10）. Within the order Campylobacterales of found in some myxobacteria（the order Myxococcales） the epsilon subclass, various species belonging to the （10）comprising the two suborders, Sorangineae and four genera Helicobacter, Wolinella, Campylobacter and Cystobacterineae, and the four families, Myxococcaceae, Arcobacter（2, 6）scarcely contained any polyamines Cystobacteraceae, Polyangiaceae and Archangiaceae（2, but Sulfurospirillum deleyianum contained spermidine （10）. In the present study, polyamines of some new mem- ＊ Correspondence author bers of the delta and epsilon subclasses were analyzed. accepted: June 6, 2004 Newly validated 20 delta and epsilon proteobacteria ― 3 ― Polyamines of Delta and Epsilon Proteobacteria Hamana et al． Table 1. Polyamines of delta and epsilon subclasses of the class Proteobacteria Organism Medium ― Temp.（℃）Polyamine（µ mol/g wet cell） Dap Put Cad Spd HSpd Spm Agm Delta subclass Myxococcales Enhygromyxa salina JCM 11769T JCM 341 ― 30 －－－0.54 － 0.10 － Haliangium ochraceum JCM 11303T JCM 341 ― 30 －－－1.15 － 0.31 0.03 Haliangium tepidum JCM 11304T JCM 341 ― 37 －－－0.70 － 0.15 0.02 Plesiocystis pacifica JCM 11591T JCM 341 ― 30 － 0.10 － 0.65 － 0.02 － Desulfovibrionales Desulfovibrio africanus NCIMB 8401T NCIMB17 ― 37 0.01 0.12 0.02 0.95 － 0.02 0.03 Desulfovibrio desulfuricans IFO 13699 （a）－－－1.16 － 0.01 0.02 subsp. desulfuricans Desulfovibrio desulfuricans NCIMB 8307T NCIMB17 ― 30 － 0.24 1.98 0.40 －－－ subsp. desulfuricans Desulfovibrio desulfuricans NCIMB 9335T NCIMB104 ― 30 － 0.02 0.01 1.11 － 0.05 0.03 subsp. aestuarii Desulfovibrio salexigens NCIMB 8403T NCIMB104 ― 30 － 0.05 0.04 0.65 －－0.20 Desulfovibrio vulgaris NCIMB 9442T NCIMB17 ― 30 － 0.35 0.10 0.50 －－0.10 subsp. oxamicus Desulfovibrio vulgaris NCIMB 8303T NCIMB17 ― 30 － 0.02 0.01 1.50 － 0.10 0.03 subsp. vulgaris Syntrophobacterales Desulfacinum infernum NCIMB 13416T NCIMB109 ― 60 － 0.02 － 0.68 － 0.06 － Desulfobacterales Desulfobulbus propionicus NCIMB 12907T NCIMB17 ― 37 － 0.02 － 0.88 － 0.04 － Desulfococcus multivorans NCIMB 12965T NCIMB295 ― 30 － 0.02 － 0.70 － 0.04 － Desulfuromonadales Pelobacter acidigallici ATCC 49970T （a）－－－1.45 －－0.24 Pelobacter massiliensis ATCC 49973T （a）－－－1.20 －－0.20 Geobacter sulfurreducens ATCC 51573T ATCC1957 ― 30 －－－1.10 －－0.03 Geobacter hydrogenophilus ATCC 51590T ATCC1957 ― 30 －－－0.92 －－0.10 Desulfurellales Desulfurella acetivorans ATCC 51451T ATCC1920 ― 55 －－－0.97 － 0.02 － Bdellovibrionales Bdellovibrio bacteriovorus NCIMB 9529T ATCC137 ― 30 －－－0.05 － 0.10 － 199 ― 30 －－－－－－－ Bdellovibrio bacteriovorus IFO 14261 （a）－2.10 －－－ －－ Incertae sedis Bacteriovorax starrii ATCC 15145T （a）－1.52 0.10 1.77 －－－ （Bdellovibrio starrii） Bacteriovorax stolpii ATCC 27052T （a）－－－0.70 0.90 0.07 － （Bdellovibrio stolpii） Epsilon subclass Campylobacterales Sulfurospirillum barnesii ATCC 700032T ATCC2034 ― 30 －－－1.10 － 0.01 － （“Geospirillum barnesii”） Sulfurospirillum arsenophilum ATCC 700056T ATCC2018 ― 30 0.02 － 0.85 0.10 － 0.03 － （“Geospirillum arsenophillus”） Sulfurospirillum deleyianum ATCC 51133T （a）－－－1.25 －－－ Incertae sedis Thiomicrospira denitrificans ATCC 33889 ATCC1255 ― 26 －－0.40 2.10 －－－ Note: Dap, 1, 3 ― diaminopropane; Put, putrescine; Cad, cadaverine; Spd, spermidine; HSpd, homospermidine; Spm, spermine; Agm, agmatine; NCIMB, The National Collections of Industrial, Food and Marine Bacteria, Aberdeen, Scotland, UK; ATCC, American Type Culture Collection, Manassas, Virginia, USA; IFO, Institute for Fermentation, Osaka, Japan; JCM, Japan Collection of Microorganisms, RIKEN, Saitama, Japan; T, Type strain; ―, not detectable （<0.005）. Quotation marks indicate that the scientific name has not been validly published. Former names are shown in parentheses.（a）was cited from Hamana and Takeuchi（10）. ― 4 ― Microbiol. Cult. Coll. June. 2004. p. 3 ― 8 Vol. 20, No. 1 were grown in the media designated by the culture col- um. A little amount of spermidine and spermine was lections（JCM Catalogue of Strains, 2002 and The incorporated into this organism from the ATCC 137 medi- Catalogue of Strains of NCIMB, 1994 and The Catalogue um containing these amines（Table 1）. The strain IFO of Strains of ATCC, 1996）and in the polyamine-free 199 14261 contained putrescine but not triamines（10）. The medium（Nissui Pharmaceutical Co., Tokyo, Japan）, at polyamine profile of Bdellovibrio bacteriovorus is unique the optimum growth temperature listed in Table 1. The within this subclass. The two Bacteriovorax species dif- cells in the stationary phase were harvested. The whole fer in their polyamine profiles, however, Bacteriovorax polyamine extract in 0.5 M perchloric acid was analyzed starrii contained putrescine and spermidine and by high-performance liquid chromatography（HPLC） Bacteriovorax stolpii contained spermidine and homo- （10）. Gas chromatography（GC）was performed after spermidine（10）. heptafluorobutyrization of the concentrated polyamine The sulfate reducers such as Desulfovibrio, sample（21）. Desulfobulbus, Desulfococcus, Desulfacinum, Desulfobacter, Cellular concentrations of 1, 3-diaminopropane, putre- Desulfobacterium, Desulfomicrobium, Desulfomonas, scine, cadaverine, agmatine, spermidine, homospermidine Desulfomonile, Desulfonema, Desulfosarcina, Desulforhopalus, and spermine are shown in Table 1. Spermine detected as Desulfohalobium, Desulfotulus, Desulforhobdus, a minor component was judged as a contaminant from Desulfuromonas, Syntrophus, and Syntrophobacter phy- the media containing spermine. logenetically spread within the delta subclass（5, 16, 19, 23）. Polyamine analysis of a strain of Desulfovibrio The delta subclass desulfuricans has been reported previously（10）. In the Our previous study showed that several myxobacteria present study, polyamines of Desulfobulbus propionicus, belonging to the genera Myxococcus, Cystobacter, Desulfococcus multivorans, Desulfacinum infernum, and Stigmatella, Melittangium, Polyangium and Archangium seven species of the genus Desulfovibrio, were analyzed. ubiquitously contained homospermidine as the major Cadaverine level differed among the three strains of polyamine（10）. The new marine myxobacteria, Desulfovibrio desulfuricans（Table 1）, correlating to Enhygromyxa salina, Haliangium ochroceum, their phylogenetic heterogeneity（5）. Spermidine was Haliangium tepidum and Plesiocystis pacifica phyloge- the major polyamine in all four Desulfovibrio species and netically located in Sorangineae of Myxococcales（7, 17- all three species belonging to the genera Desulfobulbus 19）contained spermidine as the major polyamine and （the order Desulfobacterales）, Desulfococcus（the order spermine as a minor polyamine, as shown in Table 1. Desulfobacterales）and Desulfacinum（Syntrophobacterales）, Although widespread occurrence of homospermidine which are located in other clusters divergent from the within terrestrial myxobacteria serves as a chemotaxo- Desulfovibrio clade（the order Desulfovibrionales）. nomic marker for Myxococcales, homospermidine was not Desulfurella acetivorans, a thermophilic, acetate-oxidizing found in the four marine slightly halophilic myxobacteria. and sulfur-reducing proteobacterium, contained spermi- The two Geobacter species,
Recommended publications
  • The 2014 Golden Gate National Parks Bioblitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event

    The 2014 Golden Gate National Parks Bioblitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event

    National Park Service U.S. Department of the Interior Natural Resource Stewardship and Science The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 ON THIS PAGE Photograph of BioBlitz participants conducting data entry into iNaturalist. Photograph courtesy of the National Park Service. ON THE COVER Photograph of BioBlitz participants collecting aquatic species data in the Presidio of San Francisco. Photograph courtesy of National Park Service. The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 Elizabeth Edson1, Michelle O’Herron1, Alison Forrestel2, Daniel George3 1Golden Gate Parks Conservancy Building 201 Fort Mason San Francisco, CA 94129 2National Park Service. Golden Gate National Recreation Area Fort Cronkhite, Bldg. 1061 Sausalito, CA 94965 3National Park Service. San Francisco Bay Area Network Inventory & Monitoring Program Manager Fort Cronkhite, Bldg. 1063 Sausalito, CA 94965 March 2016 U.S. Department of the Interior National Park Service Natural Resource Stewardship and Science Fort Collins, Colorado The National Park Service, Natural Resource Stewardship and Science office in Fort Collins, Colorado, publishes a range of reports that address natural resource topics. These reports are of interest and applicability to a broad audience in the National Park Service and others in natural resource management, including scientists, conservation and environmental constituencies, and the public. The Natural Resource Report Series is used to disseminate comprehensive information and analysis about natural resources and related topics concerning lands managed by the National Park Service.
  • Table 1. Overview of Reactions Examined in This Study. ΔG Values Were Obtained from Thauer Et Al., 1977

    Table 1. Overview of Reactions Examined in This Study. ΔG Values Were Obtained from Thauer Et Al., 1977

    Supplemental Information: Table 1. Overview of reactions examined in this study. ΔG values were obtained from Thauer et al., 1977. No. Equation ∆G°' (kJ/reaction)* Acetogenic reactions – – – + 1 Propionate + 3 H2O → Acetate + HCO3 + 3 H2 + H +76.1 Sulfate-reducing reactions – 2– – – – + 2 Propionate + 0.75 SO4 → Acetate + 0.75 HS + HCO3 + 0.25 H –37.8 2– + – 3 4 H2 + SO4 + H → HS + 4 H2O –151.9 – 2– – – 4 Acetate + SO4 → 2 HCO3 + HS –47.6 Methanogenic reactions – – + 5 4 H2 + HCO3 + H → CH4 + 3 H2O –135.6 – – 6 Acetate + H2O → CH4 + HCO3 –31.0 Syntrophic propionate conversion – – – + 1+5 Propionate + 0.75 H2O → Acetate + 0.75 CH4 + 0.25 HCO3 + 0.25 H –25.6 Complete propionate conversion by SRB – 2– – – + 2+4 Propionate + 1.75 SO4 → 1.75 HS + 3 HCO3 + 0.25 H –85.4 Complete propionate conversion by syntrophs and methanogens 1+5+6 Propionate– + 1.75 H O → 1.75 CH + 1.25 HCO – + 0.25 H+ –56.6 2 4 3 1 Table S2. Overview of all enrichment slurries fed with propionate and the total amounts of the reactants consumed and products formed during the enrichment period. The enrichment slurries consisted of sediment from either the sulfate zone (SZ), sulfate-methane transition zone (SMTZ) or methane zone (MZ) and were incubated at 25°C or 10°C, with 3 mM, 20 mM or without (-) sulfate amendments along the study. The slurries P1/P2, P3/P4, P5/P6, P7/P8 from each sediment zone are biological replicates. Slurries with * are presented in the propionate conversion graphs and used for molecular analysis.
  • Supplementary Information

    Supplementary Information

    doi: 10.1038/nature06269 SUPPLEMENTARY INFORMATION METAGENOMIC AND FUNCTIONAL ANALYSIS OF HINDGUT MICROBIOTA OF A WOOD FEEDING HIGHER TERMITE TABLE OF CONTENTS MATERIALS AND METHODS 2 • Glycoside hydrolase catalytic domains and carbohydrate binding modules used in searches that are not represented by Pfam HMMs 5 SUPPLEMENTARY TABLES • Table S1. Non-parametric diversity estimators 8 • Table S2. Estimates of gross community structure based on sequence composition binning, and conserved single copy gene phylogenies 8 • Table S3. Summary of numbers glycosyl hydrolases (GHs) and carbon-binding modules (CBMs) discovered in the P3 luminal microbiota 9 • Table S4. Summary of glycosyl hydrolases, their binning information, and activity screening results 13 • Table S5. Comparison of abundance of glycosyl hydrolases in different single organism genomes and metagenome datasets 17 • Table S6. Comparison of abundance of glycosyl hydrolases in different single organism genomes (continued) 20 • Table S7. Phylogenetic characterization of the termite gut metagenome sequence dataset, based on compositional phylogenetic analysis 23 • Table S8. Counts of genes classified to COGs corresponding to different hydrogenase families 24 • Table S9. Fe-only hydrogenases (COG4624, large subunit, C-terminal domain) identified in the P3 luminal microbiota. 25 • Table S10. Gene clusters overrepresented in termite P3 luminal microbiota versus soil, ocean and human gut metagenome datasets. 29 • Table S11. Operational taxonomic unit (OTU) representatives of 16S rRNA sequences obtained from the P3 luminal fluid of Nasutitermes spp. 30 SUPPLEMENTARY FIGURES • Fig. S1. Phylogenetic identification of termite host species 38 • Fig. S2. Accumulation curves of 16S rRNA genes obtained from the P3 luminal microbiota 39 • Fig. S3. Phylogenetic diversity of P3 luminal microbiota within the phylum Spirocheates 40 • Fig.
  • Novel Bacterial Diversity in an Anchialine Blue Hole On

    Novel Bacterial Diversity in an Anchialine Blue Hole On

    NOVEL BACTERIAL DIVERSITY IN AN ANCHIALINE BLUE HOLE ON ABACO ISLAND, BAHAMAS A Thesis by BRETT CHRISTOPHER GONZALEZ Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE December 2010 Major Subject: Wildlife and Fisheries Sciences NOVEL BACTERIAL DIVERSITY IN AN ANCHIALINE BLUE HOLE ON ABACO ISLAND, BAHAMAS A Thesis by BRETT CHRISTOPHER GONZALEZ Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE Approved by: Chair of Committee, Thomas Iliffe Committee Members, Robin Brinkmeyer Daniel Thornton Head of Department, Thomas Lacher, Jr. December 2010 Major Subject: Wildlife and Fisheries Sciences iii ABSTRACT Novel Bacterial Diversity in an Anchialine Blue Hole on Abaco Island, Bahamas. (December 2010) Brett Christopher Gonzalez, B.S., Texas A&M University at Galveston Chair of Advisory Committee: Dr. Thomas Iliffe Anchialine blue holes found in the interior of the Bahama Islands have distinct fresh and salt water layers, with vertical mixing, and dysoxic to anoxic conditions below the halocline. Scientific cave diving exploration and microbiological investigations of Cherokee Road Extension Blue Hole on Abaco Island have provided detailed information about the water chemistry of the vertically stratified water column. Hydrologic parameters measured suggest that circulation of seawater is occurring deep within the platform. Dense microbial assemblages which occurred as mats on the cave walls below the halocline were investigated through construction of 16S rRNA clone libraries, finding representatives across several bacterial lineages including Chlorobium and OP8.
  • Geomicrobiological Processes in Extreme Environments: a Review

    Geomicrobiological Processes in Extreme Environments: a Review

    202 Articles by Hailiang Dong1, 2 and Bingsong Yu1,3 Geomicrobiological processes in extreme environments: A review 1 Geomicrobiology Laboratory, China University of Geosciences, Beijing, 100083, China. 2 Department of Geology, Miami University, Oxford, OH, 45056, USA. Email: [email protected] 3 School of Earth Sciences, China University of Geosciences, Beijing, 100083, China. The last decade has seen an extraordinary growth of and Mancinelli, 2001). These unique conditions have selected Geomicrobiology. Microorganisms have been studied in unique microorganisms and novel metabolic functions. Readers are directed to recent review papers (Kieft and Phelps, 1997; Pedersen, numerous extreme environments on Earth, ranging from 1997; Krumholz, 2000; Pedersen, 2000; Rothschild and crystalline rocks from the deep subsurface, ancient Mancinelli, 2001; Amend and Teske, 2005; Fredrickson and Balk- sedimentary rocks and hypersaline lakes, to dry deserts will, 2006). A recent study suggests the importance of pressure in the origination of life and biomolecules (Sharma et al., 2002). In and deep-ocean hydrothermal vent systems. In light of this short review and in light of some most recent developments, this recent progress, we review several currently active we focus on two specific aspects: novel metabolic functions and research frontiers: deep continental subsurface micro- energy sources. biology, microbial ecology in saline lakes, microbial Some metabolic functions of continental subsurface formation of dolomite, geomicrobiology in dry deserts, microorganisms fossil DNA and its use in recovery of paleoenviron- Because of the unique geochemical, hydrological, and geological mental conditions, and geomicrobiology of oceans. conditions of the deep subsurface, microorganisms from these envi- Throughout this article we emphasize geomicrobiological ronments are different from surface organisms in their metabolic processes in these extreme environments.
  • Microbial Fe(III) Oxide Reduction Potential in Chocolate Pots Hot Spring, Yellowstone National Park N

    Microbial Fe(III) Oxide Reduction Potential in Chocolate Pots Hot Spring, Yellowstone National Park N

    Geobiology (2016), 14, 255–275 DOI: 10.1111/gbi.12173 Microbial Fe(III) oxide reduction potential in Chocolate Pots hot spring, Yellowstone National Park N. W. FORTNEY,1 S. HE,1 B. J. CONVERSE,1 B. L. BEARD,1 C. M. JOHNSON,1 E. S. BOYD2 ANDE.E.RODEN1 1Department of Geoscience, NASA Astrobiology Institute, University of Wisconsin-Madison, Madison, WI, USA 2Department of Microbiology and Immunology, NASA Astrobiology Institute, Montana State University, Bozeman, MT, USA ABSTRACT Chocolate Pots hot springs (CP) is a unique, circumneutral pH, iron-rich, geothermal feature in Yellowstone National Park. Prior research at CP has focused on photosynthetically driven Fe(II) oxidation as a model for mineralization of microbial mats and deposition of Archean banded iron formations. However, geochemical and stable Fe isotopic data have suggested that dissimilatory microbial iron reduction (DIR) may be active within CP deposits. In this study, the potential for microbial reduction of native CP Fe(III) oxides was inves- tigated, using a combination of cultivation dependent and independent approaches, to assess the potential involvement of DIR in Fe redox cycling and associated stable Fe isotope fractionation in the CP hot springs. Endogenous microbial communities were able to reduce native CP Fe(III) oxides, as documented by most probable number enumerations and enrichment culture studies. Enrichment cultures demonstrated sus- tained DIR driven by oxidation of acetate, lactate, and H2. Inhibitor studies and molecular analyses indicate that sulfate reduction did not contribute to observed rates of DIR in the enrichment cultures through abi- otic reaction pathways. Enrichment cultures produced isotopically light Fe(II) during DIR relative to the bulk solid-phase Fe(III) oxides.
  • Supplementary Information for Microbial Electrochemical Systems Outperform Fixed-Bed Biofilters for Cleaning-Up Urban Wastewater

    Supplementary Information for Microbial Electrochemical Systems Outperform Fixed-Bed Biofilters for Cleaning-Up Urban Wastewater

    Electronic Supplementary Material (ESI) for Environmental Science: Water Research & Technology. This journal is © The Royal Society of Chemistry 2016 Supplementary information for Microbial Electrochemical Systems outperform fixed-bed biofilters for cleaning-up urban wastewater AUTHORS: Arantxa Aguirre-Sierraa, Tristano Bacchetti De Gregorisb, Antonio Berná, Juan José Salasc, Carlos Aragónc, Abraham Esteve-Núñezab* Fig.1S Total nitrogen (A), ammonia (B) and nitrate (C) influent and effluent average values of the coke and the gravel biofilters. Error bars represent 95% confidence interval. Fig. 2S Influent and effluent COD (A) and BOD5 (B) average values of the hybrid biofilter and the hybrid polarized biofilter. Error bars represent 95% confidence interval. Fig. 3S Redox potential measured in the coke and the gravel biofilters Fig. 4S Rarefaction curves calculated for each sample based on the OTU computations. Fig. 5S Correspondence analysis biplot of classes’ distribution from pyrosequencing analysis. Fig. 6S. Relative abundance of classes of the category ‘other’ at class level. Table 1S Influent pre-treated wastewater and effluents characteristics. Averages ± SD HRT (d) 4.0 3.4 1.7 0.8 0.5 Influent COD (mg L-1) 246 ± 114 330 ± 107 457 ± 92 318 ± 143 393 ± 101 -1 BOD5 (mg L ) 136 ± 86 235 ± 36 268 ± 81 176 ± 127 213 ± 112 TN (mg L-1) 45.0 ± 17.4 60.6 ± 7.5 57.7 ± 3.9 43.7 ± 16.5 54.8 ± 10.1 -1 NH4-N (mg L ) 32.7 ± 18.7 51.6 ± 6.5 49.0 ± 2.3 36.6 ± 15.9 47.0 ± 8.8 -1 NO3-N (mg L ) 2.3 ± 3.6 1.0 ± 1.6 0.8 ± 0.6 1.5 ± 2.0 0.9 ± 0.6 TP (mg
  • Constraint-Based Modeling Analysis of the Metabolism of Two Pelobacter Species Jun Sun1*, Shelley a Haveman2,3, Olivia Bui1, Tom R Fahland1,4, Derek R Lovley2

    Constraint-Based Modeling Analysis of the Metabolism of Two Pelobacter Species Jun Sun1*, Shelley a Haveman2,3, Olivia Bui1, Tom R Fahland1,4, Derek R Lovley2

    Sun et al. BMC Systems Biology 2010, 4:174 http://www.biomedcentral.com/1752-0509/4/174 RESEARCH ARTICLE Open Access Constraint-based modeling analysis of the metabolism of two Pelobacter species Jun Sun1*, Shelley A Haveman2,3, Olivia Bui1, Tom R Fahland1,4, Derek R Lovley2 Abstract Background: Pelobacter species are commonly found in a number of subsurface environments, and are unique members of the Geobacteraceae family. They are phylogenetically intertwined with both Geobacter and Desulfuromonas species. Pelobacter species likely play important roles in the fermentative degradation of unusual organic matters and syntrophic metabolism in the natural environments, and are of interest for applications in bioremediation and microbial fuel cells. Results: In order to better understand the physiology of Pelobacter species, genome-scale metabolic models for Pelobacter carbinolicus and Pelobacter propionicus were developed. Model development was greatly aided by the availability of models of the closely related Geobacter sulfurreducens and G. metallireducens. The reconstructed P. carbinolicus model contains 741 genes and 708 reactions, whereas the reconstructed P. propionicus model contains 661 genes and 650 reactions. A total of 470 reactions are shared among the two Pelobacter models and the two Geobacter models. The different reactions between the Pelobacter and Geobacter models reflect some unique metabolic capabilities such as fermentative growth for both Pelobacter species. The reconstructed Pelobacter models were validated by simulating published growth conditions including fermentations, hydrogen production in syntrophic co-culture conditions, hydrogen utilization, and Fe(III) reduction. Simulation results matched well with experimental data and indicated the accuracy of the models. Conclusions: We have developed genome-scale metabolic models of P.
  • The Gut Microbiome of the Sea Urchin, Lytechinus Variegatus, from Its Natural Habitat Demonstrates Selective Attributes of Micro

    The Gut Microbiome of the Sea Urchin, Lytechinus Variegatus, from Its Natural Habitat Demonstrates Selective Attributes of Micro

    FEMS Microbiology Ecology, 92, 2016, fiw146 doi: 10.1093/femsec/fiw146 Advance Access Publication Date: 1 July 2016 Research Article RESEARCH ARTICLE The gut microbiome of the sea urchin, Lytechinus variegatus, from its natural habitat demonstrates selective attributes of microbial taxa and predictive metabolic profiles Joseph A. Hakim1,†, Hyunmin Koo1,†, Ranjit Kumar2, Elliot J. Lefkowitz2,3, Casey D. Morrow4, Mickie L. Powell1, Stephen A. Watts1,∗ and Asim K. Bej1,∗ 1Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, Birmingham, AL 35294, USA, 2Center for Clinical and Translational Sciences, University of Alabama at Birmingham, Birmingham, AL 35294, USA, 3Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA and 4Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, 1918 University Blvd., Birmingham, AL 35294, USA ∗Corresponding authors: Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, CH464, Birmingham, AL 35294-1170, USA. Tel: +1-(205)-934-8308; Fax: +1-(205)-975-6097; E-mail: [email protected]; [email protected] †These authors contributed equally to this work. One sentence summary: This study describes the distribution of microbiota, and their predicted functional attributes, in the gut ecosystem of sea urchin, Lytechinus variegatus, from its natural habitat of Gulf of Mexico. Editor: Julian Marchesi ABSTRACT In this paper, we describe the microbial composition and their predictive metabolic profile in the sea urchin Lytechinus variegatus gut ecosystem along with samples from its habitat by using NextGen amplicon sequencing and downstream bioinformatics analyses. The microbial communities of the gut tissue revealed a near-exclusive abundance of Campylobacteraceae, whereas the pharynx tissue consisted of Tenericutes, followed by Gamma-, Alpha- and Epsilonproteobacteria at approximately equal capacities.
  • Evolution and Design Governing Signal Precision and Amplification

    Evolution and Design Governing Signal Precision and Amplification

    Evolution and Design Governing Signal Precision and Amplification in a Bacterial Chemosensory Pathway Mathilde Guzzo, Rym Agrebi, Leon Espinosa, Gregory Baronian, Virginie Molle, Emilia M. F. Mauriello, Céline Brochier-Armanet, Tam Mignot To cite this version: Mathilde Guzzo, Rym Agrebi, Leon Espinosa, Gregory Baronian, Virginie Molle, et al.. Evolution and Design Governing Signal Precision and Amplification in a Bacterial Chemosensory Pathway. PLoS Genetics, Public Library of Science, 2015, 11 (8), pp.e1005460. 10.1371/journal.pgen.1005460. hal- 01452074 HAL Id: hal-01452074 https://hal.archives-ouvertes.fr/hal-01452074 Submitted on 27 Sep 2018 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License RESEARCH ARTICLE Evolution and Design Governing Signal Precision and Amplification in a Bacterial Chemosensory Pathway Mathilde Guzzo1☯, Rym Agrebi1☯¤, Leon Espinosa1, Grégory Baronian2, Virginie Molle2, Emilia M. F. Mauriello1, Céline Brochier-Armanet3, Tâm Mignot1* 1 Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, CNRS Aix-Marseille University UMR 7283, Marseille, France, 2 Laboratoire de Dynamique des Interactions Membranaires Normales et Pathologiques, CNRS Universités de Montpellier II et I, UMR 5235, case 107, Montpellier, France, 3 Université de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France ☯ These authors contributed equally to this work.
  • Metagenomes of Native and Electrode-Enriched Microbial Communities from the Soudan Iron Mine Jonathan P

    Metagenomes of Native and Electrode-Enriched Microbial Communities from the Soudan Iron Mine Jonathan P

    Metagenomes of native and electrode-enriched microbial communities from the Soudan Iron Mine Jonathan P. Badalamenti and Daniel R. Bond Department of Microbiology and BioTechnology Institute, University of Minnesota - Twin Cities, Saint Paul, Minnesota, USA Twitter: @JonBadalamenti @wanderingbond Summary Approach - compare metagenomes from native and electrode-enriched deep subsurface microbial communities 30 Despite apparent carbon limitation, anoxic deep subsurface brines at the Soudan ) enriched 2 Underground Iron Mine harbor active microbial communities . To characterize these 20 A/cm µ assemblages, we performed shotgun metagenomics of native and enriched samples. enrich ( harvest cells collect inoculate +0.24 V extract 10 Follwing enrichment on poised electrodes and long read sequencing, we recovered Soudan brine electrode 20° C from DNA biodreactors current electrodes from the metagenome the closed, circular genome of a novel Desulfuromonas sp. 0 0 10 20 30 40 filtrate PacBio RS II Illumina HiSeq with remarkable genomic features that were not fully resolved by short read assem- extract time (d) long reads short reads TFF DNA unenriched bly alone. This organism was essentially absent in unenriched Soudan communities, 0.1 µm retentate assembled metagenomes reconstruct long read return de novo complete genome(s) assembly indicating that electrodes are highly selective for putative metal reducers. Native HGAP assembly community metagenomes suggest that carbon cycling is driven by methyl-C me- IDBA_UD 1 hybrid tabolism, in particular methylotrophic methanogenesis. Our results highlight the 3 µm prefilter assembly N4 binning promising potential for long reads in metagenomic surveys of low-diversity environ- borehole N4 binning read trimming and filtering brine de novo ments.
  • Phylogenetic and Functional Characterization of Symbiotic Bacteria in Gutless Marine Worms (Annelida, Oligochaeta)

    Phylogenetic and Functional Characterization of Symbiotic Bacteria in Gutless Marine Worms (Annelida, Oligochaeta)

    Phylogenetic and functional characterization of symbiotic bacteria in gutless marine worms (Annelida, Oligochaeta) Dissertation zur Erlangung des Grades eines Doktors der Naturwissenschaften -Dr. rer. nat.- dem Fachbereich Biologie/Chemie der Universität Bremen vorgelegt von Anna Blazejak Oktober 2005 Die vorliegende Arbeit wurde in der Zeit vom März 2002 bis Oktober 2005 am Max-Planck-Institut für Marine Mikrobiologie in Bremen angefertigt. 1. Gutachter: Prof. Dr. Rudolf Amann 2. Gutachter: Prof. Dr. Ulrich Fischer Tag des Promotionskolloquiums: 22. November 2005 Contents Summary ………………………………………………………………………………….… 1 Zusammenfassung ………………………………………………………………………… 2 Part I: Combined Presentation of Results A Introduction .…………………………………………………………………… 4 1 Definition and characteristics of symbiosis ...……………………………………. 4 2 Chemoautotrophic symbioses ..…………………………………………………… 6 2.1 Habitats of chemoautotrophic symbioses .………………………………… 8 2.2 Diversity of hosts harboring chemoautotrophic bacteria ………………… 10 2.2.1 Phylogenetic diversity of chemoautotrophic symbionts …………… 11 3 Symbiotic associations in gutless oligochaetes ………………………………… 13 3.1 Biogeography and phylogeny of the hosts …..……………………………. 13 3.2 The environment …..…………………………………………………………. 14 3.3 Structure of the symbiosis ………..…………………………………………. 16 3.4 Transmission of the symbionts ………..……………………………………. 18 3.5 Molecular characterization of the symbionts …..………………………….. 19 3.6 Function of the symbionts in gutless oligochaetes ..…..…………………. 20 4 Goals of this thesis …….…………………………………………………………..