Recoding of the stop codon UGA to glycine by a BD1-5/SN-2 bacterium and niche partitioning between Alpha- and Gammaproteobacteria in a tidal sediment microbial community naturally selected in a laboratory chemostat.

Hanke A, Hamann E, Sharma R, Geelhoed JS, Hargesheimer T, Kraft B, Meyer V, Lenk S, Osmers H, Wu R, Makinwa K, et al. (2014)
Frontiers in microbiology 5(231).

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Sandy coastal sediments are global hotspots for microbial mineralization of organic matter and denitrification. These sediments are characterized by advective porewater flow, tidal cycling and an active and complex microbial community. Metagenomic sequencing of microbial communities sampled from such sediments showed that potential sulfur oxidizing Gammaproteobacteria and members of the enigmatic BD1-5/SN-2 candidate phylum were abundant in situ (>10% and ~2% respectively). By mimicking the dynamic oxic/anoxic environmental conditions of the sediment in a laboratory chemostat, a simplified microbial community was selected from the more complex inoculum. Metagenomics, proteomics and fluorescence in situ hybridization showed that this simplified community contained both a potential sulfur oxidizing Gammaproteobacteria (at 24 ± 2% abundance) and a member of the BD1-5/SN-2 candidate phylum (at 7 ± 6% abundance). Despite the abundant supply of organic substrates to the chemostat, proteomic analysis suggested that the selected gammaproteobacterium grew partially autotrophically and performed hydrogen/formate oxidation. The enrichment of a member of the BD1-5/SN-2 candidate phylum enabled, for the first time, direct microscopic observation by fluorescent in situ hybridization and the experimental validation of the previously predicted translation of the stop codon UGA into glycine.
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Frontiers in microbiology
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Hanke A, Hamann E, Sharma R, et al. Recoding of the stop codon UGA to glycine by a BD1-5/SN-2 bacterium and niche partitioning between Alpha- and Gammaproteobacteria in a tidal sediment microbial community naturally selected in a laboratory chemostat. Frontiers in microbiology. 2014;5(231).
Hanke, A., Hamann, E., Sharma, R., Geelhoed, J. S., Hargesheimer, T., Kraft, B., Meyer, V., et al. (2014). Recoding of the stop codon UGA to glycine by a BD1-5/SN-2 bacterium and niche partitioning between Alpha- and Gammaproteobacteria in a tidal sediment microbial community naturally selected in a laboratory chemostat. Frontiers in microbiology, 5(231). doi:10.3389/fmicb.2014.00231
Hanke, A., Hamann, E., Sharma, R., Geelhoed, J. S., Hargesheimer, T., Kraft, B., Meyer, V., Lenk, S., Osmers, H., Wu, R., et al. (2014). Recoding of the stop codon UGA to glycine by a BD1-5/SN-2 bacterium and niche partitioning between Alpha- and Gammaproteobacteria in a tidal sediment microbial community naturally selected in a laboratory chemostat. Frontiers in microbiology 5.
Hanke, A., et al., 2014. Recoding of the stop codon UGA to glycine by a BD1-5/SN-2 bacterium and niche partitioning between Alpha- and Gammaproteobacteria in a tidal sediment microbial community naturally selected in a laboratory chemostat. Frontiers in microbiology, 5(231).
A. Hanke, et al., “Recoding of the stop codon UGA to glycine by a BD1-5/SN-2 bacterium and niche partitioning between Alpha- and Gammaproteobacteria in a tidal sediment microbial community naturally selected in a laboratory chemostat.”, Frontiers in microbiology, vol. 5, 2014.
Hanke, A., Hamann, E., Sharma, R., Geelhoed, J.S., Hargesheimer, T., Kraft, B., Meyer, V., Lenk, S., Osmers, H., Wu, R., Makinwa, K., Hettich, R.L., Banfield, J.F., Tegetmeyer, H., Strous, M.: Recoding of the stop codon UGA to glycine by a BD1-5/SN-2 bacterium and niche partitioning between Alpha- and Gammaproteobacteria in a tidal sediment microbial community naturally selected in a laboratory chemostat. Frontiers in microbiology. 5, (2014).
Hanke, Anna, Hamann, Emmo, Sharma, Ritin, Geelhoed, Jeanine S, Hargesheimer, Theresa, Kraft, Beate, Meyer, Volker, Lenk, Sabine, Osmers, Harald, Wu, Rong, Makinwa, Kofi, Hettich, Robert L, Banfield, Jillian F, Tegetmeyer, Halina, and Strous, Marc. “Recoding of the stop codon UGA to glycine by a BD1-5/SN-2 bacterium and niche partitioning between Alpha- and Gammaproteobacteria in a tidal sediment microbial community naturally selected in a laboratory chemostat.”. Frontiers in microbiology 5.231 (2014).
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PMID: 30089740
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PMID: 30204767
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Vavourakis CD, Andrei AS, Mehrshad M, Ghai R, Sorokin DY, Muyzer G., Microbiome 6(1), 2018
PMID: 30231921
Impacts of chemical gradients on microbial community structure.
Chen J, Hanke A, Tegetmeyer HE, Kattelmann I, Sharma R, Hamann E, Hargesheimer T, Kraft B, Lenk S, Geelhoed JS, Hettich RL, Strous M., ISME J 11(4), 2017
PMID: 28094795
Transient exposure to oxygen or nitrate reveals ecophysiology of fermentative and sulfate-reducing benthic microbial populations.
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PMID: 28836729
Identification and Resolution of Microdiversity through Metagenomic Sequencing of Parallel Consortia.
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PMID: 26497460
Selective Pressure of Temperature on Competition and Cross-Feeding within Denitrifying and Fermentative Microbial Communities.
Hanke A, Berg J, Hargesheimer T, Tegetmeyer HE, Sharp CE, Strous M., Front Microbiol 6(), 2015
PMID: 26779132

60 References

Daten bereitgestellt von Europe PubMed Central.

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes.
Albertsen M, Hugenholtz P, Skarshewski A, Nielsen KL, Tyson GW, Nielsen PH., Nat. Biotechnol. 31(6), 2013
PMID: 23707974
Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations.
Amann RI, Binder BJ, Olson RJ, Chisholm SW, Devereux R, Stahl DA., Appl. Environ. Microbiol. 56(6), 1990
PMID: 2200342
r- and K-selection and microbial ecology
Andrews J., Harris R.., 1986
Enigmatic, ultrasmall, uncultivated Archaea.
Baker BJ, Comolli LR, Dick GJ, Hauser LJ, Hyatt D, Dill BD, Land ML, Verberkmoes NC, Hettich RL, Banfield JF., Proc. Natl. Acad. Sci. U.S.A. 107(19), 2010
PMID: 20421484
Cultivation and quantitative proteomic analyses of acidophilic microbial communities.
Belnap CP, Pan C, VerBerkmoes NC, Power ME, Samatova NF, Carver RL, Hettich RL, Banfield JF., ISME J 4(4), 2009
PMID: 20033068
The future is now: single-cell genomics of bacteria and archaea.
Blainey PC., FEMS Microbiol. Rev. 37(3), 2013
PMID: 23298390
BLAST+: architecture and applications.
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL., BMC Bioinformatics 10(), 2009
PMID: 20003500
UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota.
Campbell JH, O'Donoghue P, Campbell AG, Schwientek P, Sczyrba A, Woyke T, Soll D, Podar M., Proc. Natl. Acad. Sci. U.S.A. 110(14), 2013
PMID: 23509275
A cryptic sulfur cycle in oxygen-minimum-zone waters off the Chilean coast.
Canfield DE, Stewart FJ, Thamdrup B, De Brabandere L, Dalsgaard T, Delong EF, Revsbech NP, Ulloa O., Science 330(6009), 2010
PMID: 21071631
Ocean-atmosphere trace gas exchange.
Carpenter LJ, Archer SD, Beale R., Chem Soc Rev 41(19), 2012
PMID: 22821066
Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment.
Castelle CJ, Hug LA, Wrighton KC, Thomas BC, Williams KH, Wu D, Tringe SG, Singer SW, Eisen JA, Banfield JF., Nat Commun 4(), 2013
PMID: 23979677
Structure and evolution of chlorate reduction composite transposons.
Clark IC, Melnyk RA, Engelbrektson A, Coates JD., MBio 4(4), 2013
PMID: 23919996
Microbial perchlorate reduction: rocket-fueled metabolism.
Coates JD, Achenbach LA., Nat. Rev. Microbiol. 2(7), 2004
PMID: 15197392
FACIL: Fast and Accurate Genetic Code Inference and Logo.
Dutilh BE, Jurgelenaite R, Szklarczyk R, van Hijum SA, Harhangi HR, Schmid M, de Wild B, Francoijs KJ, Stunnenberg HG, Strous M, Jetten MS, Op den Camp HJ, Huynen MA., Bioinformatics 27(14), 2011
PMID: 21653513
Accelerated Profile HMM Searches.
Eddy SR., PLoS Comput. Biol. 7(10), 2011
PMID: 22039361
Isolation of novel pelagic bacteria from the German bight and their seasonal contributions to surface picoplankton.
Eilers H, Pernthaler J, Peplies J, Glockner FO, Gerdts G, Amann R., Appl. Environ. Microbiol. 67(11), 2001
PMID: 11679337

Flood B.., 2010
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
Single-cell genomics.
Kalisky T, Quake SR., Nat. Methods 8(4), 2011
PMID: 21451520
Methods to study consortia and mixed cultures
Kartal B., Strous M.., 2008
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.
Katoh K, Misawa K, Kuma K, Miyata T., Nucleic Acids Res. 30(14), 2002
PMID: 12136088
Seasonal variation in denitrification rates and nitrous oxide fluxes in intertidal sediments of the western Wadden Sea
Kieskamp W., Epping W., Helder W.., 1991
The ecology of Cytophaga-Flavobacteria in aquatic environments.
Kirchman DL., FEMS Microbiol. Ecol. 39(2), 2002
PMID: 19709188
Metaproteomics of a gutless marine worm and its symbiotic microbial community reveal unusual pathways for carbon and energy use.
Kleiner M, Wentrup C, Lott C, Teeling H, Wetzel S, Young J, Chang YJ, Shah M, VerBerkmoes NC, Zarzycki J, Fuchs G, Markert S, Hempel K, Voigt B, Becher D, Liebeke M, Lalk M, Albrecht D, Hecker M, Schweder T, Dubilier N., Proc. Natl. Acad. Sci. U.S.A. 109(19), 2012
PMID: 22517752
Fast gapped-read alignment with Bowtie 2.
Langmead B, Salzberg SL., Nat. Methods 9(4), 2012
PMID: 22388286
ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences.
Laslett D, Canback B., Nucleic Acids Res. 32(1), 2004
PMID: 14704338
Detoxification of sulphidic African shelf waters by blooming chemolithotrophs.
Lavik G, Stuhrmann T, Bruchert V, Van der Plas A, Mohrholz V, Lam P, Mussmann M, Fuchs BM, Amann R, Lass U, Kuypers MM., Nature 457(7229), 2008
PMID: 19078958
Novel groups of Gammaproteobacteria catalyse sulfur oxidation and carbon fixation in a coastal, intertidal sediment.
Lenk S, Arnds J, Zerjatke K, Musat N, Amann R, Mussmann M., Environ. Microbiol. 13(3), 2010
PMID: 21134098
Microbial Community Composition of Wadden Sea Sediments as Revealed by Fluorescence In Situ Hybridization.
Llobet-Brossa E, Rossello-Mora R, Amann R., Appl. Environ. Microbiol. 64(7), 1998
PMID: 9647850
Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria.
Lo I, Denef VJ, Verberkmoes NC, Shah MB, Goltsman D, DiBartolo G, Tyson GW, Allen EE, Ram RJ, Detter JC, Richardson P, Thelen MP, Hettich RL, Banfield JF., Nature 446(7135), 2007
PMID: 17344860
Protein measurement with the Folin phenol reagent.
LOWRY OH, ROSEBROUGH NJ, FARR AL, RANDALL RJ., J. Biol. Chem. 193(1), 1951
PMID: 14907713
IDPicker 2.0: Improved protein assembly with high discrimination peptide identification filtering.
Ma ZQ, Dasari S, Chambers MC, Litton MD, Sobecki SM, Zimmerman LJ, Halvey PJ, Schilling B, Drake PM, Gibson BW, Tabb DL., J. Proteome Res. 8(8), 2009
PMID: 19522537
Phylogenetic oligodeoxynucleotide probes for the major subclasses of proteobacteria-problems and solutions
Manz W., Amann R., Ludwig W., Wagner M., Schleifer K.., 1992
EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data.
Miller CS, Baker BJ, Thomas BC, Singer SW, Banfield JF., Genome Biol. 12(5), 2011
PMID: 21595876

Neef A.., 1997
FastTree 2--approximately maximum-likelihood trees for large alignments.
Price MN, Dehal PS, Arkin AP., PLoS ONE 5(3), 2010
PMID: 20224823
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools.
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glockner FO., Nucleic Acids Res. 41(Database issue), 2012
PMID: 23193283

AUTHOR UNKNOWN, 2011
Insights into the phylogeny and coding potential of microbial dark matter.
Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng JF, Darling A, Malfatti S, Swan BK, Gies EA, Dodsworth JA, Hedlund BP, Tsiamis G, Sievert SM, Liu WT, Eisen JA, Hallam SJ, Kyrpides NC, Stepanauskas R, Rubin EM, Hugenholtz P, Woyke T., Nature 499(7459), 2013
PMID: 23851394
The binning of metagenomic contigs for microbial physiology of mixed cultures.
Strous M, Kraft B, Bisdorf R, Tegetmeyer HE., Front Microbiol 3(), 2012
PMID: 23227024
Identification of microorganisms using the ribosomal RNA approach and fluorescence in situ hybridization
Thiele S., Fuchs B., Amann R.., 2011
Genome sequences of Pelagibaca bermudensis HTCC2601T and Maritimibacter alkaliphilus HTCC2654T, the type strains of two marine Roseobacter genera.
Thrash JC, Cho JC, Ferriera S, Johnson J, Vergin KL, Giovannoni SJ., J. Bacteriol. 192(20), 2010
PMID: 20729358
Community structure and metabolism through reconstruction of microbial genomes from the environment.
Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF., Nature 428(6978), 2004
PMID: 14961025
Metagenome of a versatile chemolithoautotroph from expanding oceanic dead zones.
Walsh DA, Zaikova E, Howes CG, Song YC, Wright JJ, Tringe SG, Tortell PD, Hallam SJ., Science 326(5952), 2009
PMID: 19900896
Universal sample preparation method for proteome analysis.
Wisniewski JR, Zougman A, Nagaraj N, Mann M., Nat. Methods 6(5), 2009
PMID: 19377485
Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla.
Wrighton KC, Thomas BC, Sharon I, Miller CS, Castelle CJ, VerBerkmoes NC, Wilkins MJ, Hettich RL, Lipton MS, Williams KH, Long PE, Banfield JF., Science 337(6102), 2012
PMID: 23019650
A 21b ±40mV range read-out IC for bridge transducers
Wu R., Huijsing J., Makinwa K.., 2012
Anoxic incubation of sediment in gas-tight plastic bags: a method for biogeochemical process studies
Würgler J., Thamdrup B., Jørgensen B.., 2000
UGA is read as tryptophan in Mycoplasma capricolum.
Yamao F, Muto A, Kawauchi Y, Iwami M, Iwagami S, Azumi Y, Osawa S., Proc. Natl. Acad. Sci. U.S.A. 82(8), 1985
PMID: 3887399
DNA recovery from soils of diverse composition.
Zhou J, Bruns MA, Tiedje JM., Appl. Environ. Microbiol. 62(2), 1996
PMID: 8593035

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