Insights into the fundamental physiology of the uncultured Fe-oxidizing bacterium Leptothrix ochracea

Fleming EJ, Woyke T, Donatello AR, Kuypers MMM, Sczyrba A, Littmann S, Emerson D (2018)
Applied and Environmental Microbiology 84(9): e02239-17.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
Download
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
DOI
Autor*in
Fleming, E. J.; Woyke, T.; Donatello, A. R.; Kuypers, M. M. M.; Sczyrba, AlexanderUniBi ; Littmann, S.; Emerson, D.
Einrichtung
Technische Fakultät > Computational Metagenomics
Centrum für Biotechnologie > Arbeitsgruppe A. Sczyrba
Erscheinungsjahr
2018
Zeitschriftentitel
Applied and Environmental Microbiology
Band
84
Ausgabe
9
Art.-Nr.
e02239-17
ISSN
0099-2240
eISSN
1098-5336
Page URI
https://pub.uni-bielefeld.de/record/2918275

Zitieren

Fleming EJ, Woyke T, Donatello AR, et al. Insights into the fundamental physiology of the uncultured Fe-oxidizing bacterium Leptothrix ochracea. Applied and Environmental Microbiology. 2018;84(9): e02239-17.
Fleming, E. J., Woyke, T., Donatello, A. R., Kuypers, M. M. M., Sczyrba, A., Littmann, S., & Emerson, D. (2018). Insights into the fundamental physiology of the uncultured Fe-oxidizing bacterium Leptothrix ochracea. Applied and Environmental Microbiology, 84(9), e02239-17. doi:10.1128/aem.02239-17
Fleming, E. J., Woyke, T., Donatello, A. R., Kuypers, M. M. M., Sczyrba, Alexander, Littmann, S., and Emerson, D. 2018. “Insights into the fundamental physiology of the uncultured Fe-oxidizing bacterium Leptothrix ochracea”. Applied and Environmental Microbiology 84 (9): e02239-17.
Fleming, E. J., Woyke, T., Donatello, A. R., Kuypers, M. M. M., Sczyrba, A., Littmann, S., and Emerson, D. (2018). Insights into the fundamental physiology of the uncultured Fe-oxidizing bacterium Leptothrix ochracea. Applied and Environmental Microbiology 84:e02239-17.
Fleming, E.J., et al., 2018. Insights into the fundamental physiology of the uncultured Fe-oxidizing bacterium Leptothrix ochracea. Applied and Environmental Microbiology, 84(9): e02239-17.
E.J. Fleming, et al., “Insights into the fundamental physiology of the uncultured Fe-oxidizing bacterium Leptothrix ochracea”, Applied and Environmental Microbiology, vol. 84, 2018, : e02239-17.
Fleming, E.J., Woyke, T., Donatello, A.R., Kuypers, M.M.M., Sczyrba, A., Littmann, S., Emerson, D.: Insights into the fundamental physiology of the uncultured Fe-oxidizing bacterium Leptothrix ochracea. Applied and Environmental Microbiology. 84, : e02239-17 (2018).
Fleming, E. J., Woyke, T., Donatello, A. R., Kuypers, M. M. M., Sczyrba, Alexander, Littmann, S., and Emerson, D. “Insights into the fundamental physiology of the uncultured Fe-oxidizing bacterium Leptothrix ochracea”. Applied and Environmental Microbiology 84.9 (2018): e02239-17.

68 References

Daten bereitgestellt von Europe PubMed Central.

AMD biofilms: using model communities to study microbial evolution and ecological complexity in nature.
Denef VJ, Mueller RS, Banfield JF., ISME J 4(5), 2010
PMID: 20164865
Bioaugmentation of soils by increasing microbial richness: missing links.
Dejonghe W, Boon N, Seghers D, Top EM, Verstraete W., Environ. Microbiol. 3(10), 2001
PMID: 11722545
A single-cell view on the ecophysiology of anaerobic phototrophic bacteria.
Musat N, Halm H, Winterholler B, Hoppe P, Peduzzi S, Hillion F, Horreard F, Amann R, Jorgensen BB, Kuypers MM., Proc. Natl. Acad. Sci. U.S.A. 105(46), 2008
PMID: 19004766
Where less may be more: how the rare biosphere pulls ecosystems strings.
Jousset A, Bienhold C, Chatzinotas A, Gallien L, Gobet A, Kurm V, Kusel K, Rillig MC, Rivett DW, Salles JF, van der Heijden MG, Youssef NH, Zhang X, Wei Z, Hol WH., ISME J 11(4), 2017
PMID: 28072420
Investigation of an Iron-Oxidizing Microbial Mat Community Located near Aarhus, Denmark: Field Studies.
Emerson D, Revsbech NP., Appl. Environ. Microbiol. 60(11), 1994
PMID: 16349433
Bacteria associated with iron seeps in a sulfur-rich, neutral pH, freshwater ecosystem.
Haaijer SC, Harhangi HR, Meijerink BB, Strous M, Pol A, Smolders AJ, Verwegen K, Jetten MS, Op den Camp HJ., ISME J 2(12), 2008
PMID: 18754044
Ecological succession among iron-oxidizing bacteria.
Fleming EJ, Cetinic I, Chan CS, Whitney King D, Emerson D., ISME J 8(4), 2013
PMID: 24225888
The Architecture of Iron Microbial Mats Reflects the Adaptation of Chemolithotrophic Iron Oxidation in Freshwater and Marine Environments.
Chan CS, McAllister SM, Leavitt AH, Glazer BT, Krepski ST, Emerson D., Front Microbiol 7(), 2016
PMID: 27313567
A comprehensive investigation of iron cycling in a freshwater seep including microscopy, cultivation and molecular community analysis
Bruun A-M, Finster K, Gunnlaugsson H, Nørnberg P, Friedrich MW., 2010
Insights into the global microbial community structure associated with iron oxyhydroxide minerals deposited in the aerobic biogeosphere
Fru EC, Piccinelli P, Fortin D., 2012
Removal of phosphorus from solution using biogenic iron oxides.
Rentz JA, Turner IP, Ullman JL., Water Res. 43(7), 2009
PMID: 19298996
Eisenbakterien als Anogoxydanten
Winogradsky S., 1922
The Sphaerotilus-Leptothrix group of bacteria.
van Veen WL, Mulder EG, Deinema MH., Microbiol. Rev. 42(2), 1978
PMID: 353479
Biology of iron- and manganese-depositing bacteria.
Ghiorse WC., Annu. Rev. Microbiol. 38(), 1984
PMID: 6388499
Characterization of a neutrophilic, chemolithoautotrophic Fe(II)-oxidizing β-proteobacterium from freshwater wetland sediments
Sobolev D, Roden EE., 2004
Iron-oxidizing bacteria: an environmental and genomic perspective.
Emerson D, Fleming EJ, McBeth JM., Annu. Rev. Microbiol. 64(), 2010
PMID: 20565252
What's new is old: resolving the identity of Leptothrix ochracea using single cell genomics, pyrosequencing and FISH.
Fleming EJ, Langdon AE, Martinez-Garcia M, Stepanauskas R, Poulton NJ, Masland ED, Emerson D., PLoS ONE 6(3), 2011
PMID: 21437234
The Genera Leptothrix and Sphaerotilus
Spring S., 2006
Tissue microbiology emerging.
Richter-Dahlfors A, Dumenil G., Curr. Opin. Microbiol. 15(1), 2011
PMID: 22209485
Tracking microbial interactions with NanoSIMS.
Musat N, Musat F, Weber PK, Pett-Ridge J., Curr. Opin. Biotechnol. 41(), 2016
PMID: 27419912
Enrichment and isolation of iron-oxidizing bacteria at neutral pH.
Emerson D, Floyd MM., Meth. Enzymol. 397(), 2005
PMID: 16260287
IMG 4 version of the integrated microbial genomes comparative analysis system.
Markowitz VM, Chen IM, Palaniappan K, Chu K, Szeto E, Pillay M, Ratner A, Huang J, Woyke T, Huntemann M, Anderson I, Billis K, Varghese N, Mavromatis K, Pati A, Ivanova NN, Kyrpides NC., Nucleic Acids Res. 42(Database issue), 2013
PMID: 24165883
New Insight into Microbial Iron Oxidation as Revealed by the Proteomic Profile of an Obligate Iron-Oxidizing Chemolithoautotroph.
Barco RA, Emerson D, Sylvan JB, Orcutt BN, Jacobson Meyers ME, Ramirez GA, Zhong JD, Edwards KJ., Appl. Environ. Microbiol. 81(17), 2015
PMID: 26092463
Comparative Genomic Insights into Ecophysiology of Neutrophilic, Microaerophilic Iron Oxidizing Bacteria.
Kato S, Ohkuma M, Powell DH, Krepski ST, Oshima K, Hattori M, Shapiro N, Woyke T, Chan CS., Front Microbiol 6(), 2015
PMID: 26617599
Comparative genomics of freshwater Fe-oxidizing bacteria: implications for physiology, ecology, and systematics.
Emerson D, Field EK, Chertkov O, Davenport KW, Goodwin L, Munk C, Nolan M, Woyke T., Front Microbiol 4(), 2013
PMID: 24062729
Genomic insights into the uncultivated marine Zetaproteobacteria at Loihi Seamount.
Field EK, Sczyrba A, Lyman AE, Harris CC, Woyke T, Stepanauskas R, Emerson D., ISME J 9(4), 2015
PMID: 25303714
Metagenomic Analyses of the Autotrophic Fe(II)-Oxidizing, Nitrate-Reducing Enrichment Culture KS.
He S, Tominski C, Kappler A, Behrens S, Roden EE., Appl. Environ. Microbiol. 82(9), 2016
PMID: 26896135
Variation of carbon content among bacterial species under starvation condition
Troussellier M, Bouvy M, Courties C., 1997
Control of ferrous iron oxidation within circumneutral microbial iron mats by cellular activity and autocatalysis.
Rentz JA, Kraiya C, Luther GW 3rd, Emerson D., Environ. Sci. Technol. 41(17), 2007
PMID: 17937285
Evidence for rapid microscale bacterial redox cycling of iron in circumneutral environments.
Sobolev D, Roden EE., Antonie Van Leeuwenhoek 81(1-4), 2002
PMID: 12448754
Lithotrophic iron-oxidizing bacteria produce organic stalks to control mineral growth: implications for biosignature formation.
Chan CS, Fakra SC, Emerson D, Fleming EJ, Edwards KJ., ISME J 5(4), 2010
PMID: 21107443
Microbial polysaccharides template assembly of nanocrystal fibers.
Chan CS, De Stasio G, Welch SA, Girasole M, Frazer BH, Nesterova MV, Fakra S, Banfield JF., Science 303(5664), 2004
PMID: 15016997
A model for sheath formation coupled to motility in Leptothrix ochracea
Vesenka J, Havu J, Hruby K, Emerson D., 2018
Physiology and biochemistry of symbiotic and free-living chemoautotrophic sulfur bacteria
Nelson DC, Hagen K., 1995
Isolation and characterization of novel iron-oxidizing bacteria that grow at circumneutral pH.
Emerson D, Moyer C., Appl. Environ. Microbiol. 63(12), 1997
PMID: 9406396
Culture parameters regulating stalk formation and growth rate of Gallionella ferruginea
Hallbeck L, Pedersen K., 1990
Mariprofundus ferrooxydans PV-1 the first genome of a marine Fe(II) oxidizing Zetaproteobacterium.
Singer E, Emerson D, Webb EA, Barco RA, Kuenen JG, Nelson WC, Chan CS, Comolli LR, Ferriera S, Johnson J, Heidelberg JF, Edwards KJ., PLoS ONE 6(9), 2011
PMID: 21966516
Novel Pelagic Iron-Oxidizing Zetaproteobacteria from the Chesapeake Bay Oxic-Anoxic Transition Zone.
Chiu BK, Kato S, McAllister SM, Field EK, Chan CS., Front Microbiol 8(), 2017
PMID: 28769885
Low-oxygen and chemical kinetic constraints on the geochemical niche of neutrophilic iron(II) oxidizing microorganisms
Druschel GK, Emerson D, Sutka R, Suchecki P, Luther G., 2008
Morphology of biogenic iron oxides records microbial physiology and environmental conditions: toward interpreting iron microfossils.
Krepski ST, Emerson D, Hredzak-Showalter PL, Luther GW 3rd, Chan CS., Geobiology 11(5), 2013
PMID: 23790206
Operon mRNAs are organized into ORF-centric structures that predict translation efficiency
Burkhardt DH, Rouskin S, Zhang Y, Li G-W, Weissman JS, Gross CA., 2017
Effects of organic compounds on growth of chemostat cultures of Thiomicrospira pelophila, Thiobacillus thioparus and Thiobacillus neapolitanus.
Kuenen JG, Veldkamp H., Arch Mikrobiol 94(2), 1973
PMID: 4591719
Autotrophic metabolism of formate by Thiobacillus strain A2
Kelly DP, Wood AP, Gottschal JC., 1979
Competition in the chemostat between an obligately and a facultatively chemolithotrophic Thiobacillus
Smith AL, Kelly DP., 1979
Reactivity versus flexibility in thiobacilli.
Beudeker RF, Gottschal JC, Kuenen JG., Antonie Van Leeuwenhoek 48(1), 1982
PMID: 7092201
Growth of Thiobacillus A2 under alternating growth conditions in the chemostat
Gottschal JC, Nanninga HJ, Kuenen JG., 1981
Anaerobic and aerobic metabolism of diverse aromatic compounds by the photosynthetic bacterium Rhodopseudomonas palustris.
Harwood CS, Gibson J., Appl. Environ. Microbiol. 54(3), 1988
PMID: 3377491
Carbon dioxide fixation as a central redox cofactor recycling mechanism in bacteria.
McKinlay JB, Harwood CS., Proc. Natl. Acad. Sci. U.S.A. 107(26), 2010
PMID: 20558750
Sources of iron (Fe) and factors regulating the development of flocculate from Fe-oxidizing bacteria in regenerative streamwater conveyance structures
Williams MR, Wessel BM, Filoso S., 2016
Review of the inorganic geochemistry of peats and peatland waters
Shotyk W., 1988
Velvet: algorithms for de novo short read assembly using de Bruijn graphs.
Zerbino DR, Birney E., Genome Res. 18(5), 2008
PMID: 18349386
High-quality draft assemblies of mammalian genomes from massively parallel sequence data.
Gnerre S, Maccallum I, Przybylski D, Ribeiro FJ, Burton JN, Walker BJ, Sharpe T, Hall G, Shea TP, Sykes S, Berlin AM, Aird D, Costello M, Daza R, Williams L, Nicol R, Gnirke A, Nusbaum C, Lander ES, Jaffe DB., Proc. Natl. Acad. Sci. U.S.A. 108(4), 2010
PMID: 21187386
Prodigal: prokaryotic gene recognition and translation initiation site identification.
Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ., BMC Bioinformatics 11(), 2010
PMID: 20211023
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.
Lowe TM, Eddy SR., Nucleic Acids Res. 25(5), 1997
PMID: 9023104
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB.
Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glockner FO., Nucleic Acids Res. 35(21), 2007
PMID: 17947321
Comparative genomics of the Archaea (Euryarchaeota): evolution of conserved protein families, the stable core, and the variable shell.
Makarova KS, Aravind L, Galperin MY, Grishin NV, Tatusov RL, Wolf YI, Koonin EV., Genome Res. 9(7), 1999
PMID: 10413400
Assembling the marine metagenome, one cell at a time.
Woyke T, Xie G, Copeland A, Gonzalez JM, Han C, Kiss H, Saw JH, Senin P, Yang C, Chatterji S, Cheng JF, Eisen JA, Sieracki ME, Stepanauskas R., PLoS ONE 4(4), 2009
PMID: 19390573
Genome sequencing of a single cell of the widely distributed marine subsurface Dehalococcoidia, phylum Chloroflexi.
Wasmund K, Schreiber L, Lloyd KG, Petersen DG, Schramm A, Stepanauskas R, Jorgensen BB, Adrian L., ISME J 8(2), 2013
PMID: 23966099
BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons.
Alikhan NF, Petty NK, Ben Zakour NL, Beatson SA., BMC Genomics 12(), 2011
PMID: 21824423
Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega.
Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Soding J, Thompson JD, Higgins DG., Mol. Syst. Biol. 7(), 2011
PMID: 21988835
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies.
Stamatakis A., Bioinformatics 30(9), 2014
PMID: 24451623
Bacterial iron oxidation in circumneutral freshwater habitats: findings from the field and the laboratory
Emerson D, Weiss J., 2004
Bacterial disproportionation of elemental sulfur coupled to chemical reduction of iron or manganese.
Thamdrup B, Finster K, Hansen JW, Bak F., Appl. Environ. Microbiol. 59(1), 1993
PMID: 16348835
Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria.
Pernthaler A, Pernthaler J, Amann R., Appl. Environ. Microbiol. 68(6), 2002
PMID: 12039771
Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology.
Amann RI, Krumholz L, Stahl DA., J. Bacteriol. 172(2), 1990
PMID: 1688842
Look@NanoSIMS--a tool for the analysis of nanoSIMS data in environmental microbiology.
Polerecky L, Adam B, Milucka J, Musat N, Vagner T, Kuypers MM., Environ. Microbiol. 14(4), 2012
PMID: 22221878
Ferrozine—a new spectrophotometric reagent for iron
Stookey LL., 1970
Rapid, small-volume, flow injection analysis for SCO2, and NH4+ in marine and freshwaters
Hall POJ, Aller RC., 1992
Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®
Quellen

PMID: 29453262
PubMed | Europe PMC

Suchen in

Google Scholar