Impacts of chemical gradients on microbial community structure

Chen J, Hanke A, Tegetmeyer H, Kattelmann I, Sharma R, Hamann E, Hargesheimer T, Kraft B, Lenk S, Geelhoed JS, Hettich RL, et al. (2017)
The ISME Journal 11(4): 920-931.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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Autor*in
Chen, Jianwei; Hanke, Anna; Tegetmeyer, HalinaUniBi ; Kattelmann, InesUniBi; Sharma, Ritin; Hamann, Emmo; Hargesheimer, Theresa; Kraft, Beate; Lenk, Sabine; Geelhoed, Jeanine S; Hettich, Robert L; Strous, Marc
Alle
Abstract / Bemerkung
Succession of redox processes is sometimes assumed to define a basic microbial community structure for ecosystems with oxygen gradients. In this paradigm, aerobic respiration, denitrification, fermentation and sulfate reduction proceed in a thermodynamically determined order, known as the 'redox tower'. Here, we investigated whether redox sorting of microbial processes explains microbial community structure at low-oxygen concentrations. We subjected a diverse microbial community sampled from a coastal marine sediment to 100 days of tidal cycling in a laboratory chemostat. Oxygen gradients (both in space and time) led to the assembly of a microbial community dominated by populations that each performed aerobic and anaerobic metabolism in parallel. This was shown by metagenomics, transcriptomics, proteomics and stable isotope incubations. Effective oxygen consumption combined with the formation of microaggregates sustained the activity of oxygen-sensitive anaerobic enzymes, leading to braiding of unsorted redox processes, within and between populations. Analyses of available metagenomic data sets indicated that the same ecological strategies might also be successful in some natural ecosystems.
Erscheinungsjahr
2017
Zeitschriftentitel
The ISME Journal
Band
11
Ausgabe
4
Seite(n)
920 - 931
ISSN
1751-7362, 1751-7370
Page URI
https://pub.uni-bielefeld.de/record/2908403

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Chen J, Hanke A, Tegetmeyer H, et al. Impacts of chemical gradients on microbial community structure. The ISME Journal. 2017;11(4):920-931.
Chen, J., Hanke, A., Tegetmeyer, H., Kattelmann, I., Sharma, R., Hamann, E., Hargesheimer, T., et al. (2017). Impacts of chemical gradients on microbial community structure. The ISME Journal, 11(4), 920-931. doi:10.1038/ismej.2016.175
Chen, J., Hanke, A., Tegetmeyer, H., Kattelmann, I., Sharma, R., Hamann, E., Hargesheimer, T., Kraft, B., Lenk, S., Geelhoed, J. S., et al. (2017). Impacts of chemical gradients on microbial community structure. The ISME Journal 11, 920-931.
Chen, J., et al., 2017. Impacts of chemical gradients on microbial community structure. The ISME Journal, 11(4), p 920-931.
J. Chen, et al., “Impacts of chemical gradients on microbial community structure”, The ISME Journal, vol. 11, 2017, pp. 920-931.
Chen, J., Hanke, A., Tegetmeyer, H., Kattelmann, I., Sharma, R., Hamann, E., Hargesheimer, T., Kraft, B., Lenk, S., Geelhoed, J.S., Hettich, R.L., Strous, M.: Impacts of chemical gradients on microbial community structure. The ISME Journal. 11, 920-931 (2017).
Chen, Jianwei, Hanke, Anna, Tegetmeyer, Halina, Kattelmann, Ines, Sharma, Ritin, Hamann, Emmo, Hargesheimer, Theresa, Kraft, Beate, Lenk, Sabine, Geelhoed, Jeanine S, Hettich, Robert L, and Strous, Marc. “Impacts of chemical gradients on microbial community structure”. The ISME Journal 11.4 (2017): 920-931.

15 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Thickness determines microbial community structure and function in nitrifying biofilms via deterministic assembly.
Suarez C, Piculell M, Modin O, Langenheder S, Persson F, Hermansson M., Sci Rep 9(1), 2019
PMID: 30911066
The Effect of Dissimilatory Manganese Reduction on Lactate Fermentation and Microbial Community Assembly.
Novotnik B, Zorz J, Bryant S, Strous M., Front Microbiol 10(), 2019
PMID: 31156573
The DNRA-Denitrification Dichotomy Differentiates Nitrogen Transformation Pathways in Mountain Lake Benthic Habitats.
Palacin-Lizarbe C, Camarero L, Hallin S, Jones CM, Cáliz J, Casamayor EO, Catalan J., Front Microbiol 10(), 2019
PMID: 31214153
Inhibitory Effects of Sulfate and Nitrate Reduction on Reductive Dechlorination of PCP in a Flooded Paddy Soil.
Xu Y, Xue L, Ye Q, Franks AE, Zhu M, Feng X, Xu J, He Y., Front Microbiol 9(), 2018
PMID: 29643842
Electron acceptors for anaerobic oxidation of methane drive microbial community structure and diversity in mud volcanoes.
Ren G, Ma A, Zhang Y, Deng Y, Zheng G, Zhuang X, Zhuang G, Fortin D., Environ Microbiol 20(7), 2018
PMID: 29624877
Antibiotic-induced changes in the microbiota disrupt redox dynamics in the gut.
Reese AT, Cho EH, Klitzman B, Nichols SP, Wisniewski NA, Villa MM, Durand HK, Jiang S, Midani FS, Nimmagadda SN, O'Connell TM, Wright JP, Deshusses MA, David LA., Elife 7(), 2018
PMID: 29916366
Comparative microbial communities in tidal flats sediment on Incheon, South Korea.
Choi HJ, Jeong TY, Yoon H, Oh BY, Han YS, Hur MJ, Kang S, Kim JG., J Gen Appl Microbiol 64(5), 2018
PMID: 30033973
The distribution of active iron-cycling bacteria in marine and freshwater sediments is decoupled from geochemical gradients.
Otte JM, Harter J, Laufer K, Blackwell N, Straub D, Kappler A, Kleindienst S., Environ Microbiol 20(7), 2018
PMID: 29708639
Temperature Driven Changes in Benthic Bacterial Diversity Influences Biogeochemical Cycling in Coastal Sediments.
Hicks N, Liu X, Gregory R, Kenny J, Lucaci A, Lenzi L, Paterson DM, Duncan KR., Front Microbiol 9(), 2018
PMID: 30190707
Systems biology approaches towards predictive microbial ecology.
Otwell AE, López García de Lomana A, Gibbons SM, Orellana MV, Baliga NS., Environ Microbiol 20(12), 2018
PMID: 30106224
Metabolic Roles of Uncultivated Bacterioplankton Lineages in the Northern Gulf of Mexico "Dead Zone".
Thrash JC, Seitz KW, Baker BJ, Temperton B, Gillies LE, Rabalais NN, Henrissat B, Mason OU., MBio 8(5), 2017
PMID: 28900024
Transient exposure to oxygen or nitrate reveals ecophysiology of fermentative and sulfate-reducing benthic microbial populations.
Saad S, Bhatnagar S, Tegetmeyer HE, Geelhoed JS, Strous M, Ruff SE., Environ Microbiol 19(12), 2017
PMID: 28836729

56 References

Daten bereitgestellt von Europe PubMed Central.


AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0
Trimmomatic: a flexible trimmer for Illumina sequence data.
Bolger AM, Lohse M, Usadel B., Bioinformatics 30(15), 2014
PMID: 24695404

AUTHOR UNKNOWN, 0
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
Aerobic denitrification of Pseudomonas aeruginosa monitored by online NAD(P)H fluorescence.
Chen F, Xia Q, Ju LK., Appl. Environ. Microbiol. 69(11), 2003
PMID: 14602632
The Warburg and Crabtree effects: On the origin of cancer cell energy metabolism and of yeast glucose repression.
Diaz-Ruiz R, Rigoulet M, Devin A., Biochim. Biophys. Acta 1807(6), 2010
PMID: 20804724
Search and clustering orders of magnitude faster than BLAST.
Edgar RC., Bioinformatics 26(19), 2010
PMID: 20709691
Reconstruction of ribosomal RNA genes from metagenomic data.
Fan L, McElroy K, Thomas T., PLoS ONE 7(6), 2012
PMID: 22761935

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0
Aerobic denitrification in permeable Wadden Sea sediments.
Gao H, Schreiber F, Collins G, Jensen MM, Svitlica O, Kostka JE, Lavik G, de Beer D, Zhou HY, Kuypers MM., ISME J 4(3), 2009
PMID: 20010631
Size-fraction partitioning of community gene transcription and nitrogen metabolism in a marine oxygen minimum zone.
Ganesh S, Bristow LA, Larsen M, Sarode N, Thamdrup B, Stewart FJ., ISME J 9(12), 2015
PMID: 25848875
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, Hettich RL, Banfield JF, Tegetmeyer HE, Strous M., Front Microbiol 5(), 2014
PMID: 24904545
Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes.
Hawley AK, Brewer HM, Norbeck AD, Pasa-Tolic L, Hallam SJ., Proc. Natl. Acad. Sci. U.S.A. 111(31), 2014
PMID: 25053816
A black box mathematical model to calculate auto- and heterotrophic biomass yields based on Gibbs energy dissipation.
Hoijnen JJ, van Loosdrecht MC, Tijhuis L., Biotechnol. Bioeng. 40(10), 1992
PMID: 18601065

AUTHOR UNKNOWN, 0
Cytochrome bd terminal oxidase.
Junemann S., Biochim. Biophys. Acta 1321(2), 1997
PMID: 9332500
Method for the determination of inorganic polysulfide distribution in aquatic systems.
Kamyshny A Jr, Ekeltchik I, Gun J, Lev O., Anal. Chem. 78(8), 2006
PMID: 16615773
Simultaneous nitrification and denitrification by diverse Diaphorobacter sp.
Khardenavis AA, Kapley A, Purohit HJ., Appl. Microbiol. Biotechnol. 77(2), 2007
PMID: 17876578
Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies.
Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, Glockner FO., Nucleic Acids Res. 41(1), 2012
PMID: 22933715
Nitrogen cycling. The environmental controls that govern the end product of bacterial nitrate respiration.
Kraft B, Tegetmeyer HE, Sharma R, Klotz MG, Ferdelman TG, Hettich RL, Geelhoed JS, Strous M., Science 345(6197), 2014
PMID: 25104387

AUTHOR UNKNOWN, 0
Rules of engagement: interspecies interactions that regulate microbial communities.
Little AE, Robinson CJ, Peterson SB, Raffa KF, Handelsman J., Annu. Rev. Microbiol. 62(), 2008
PMID: 18544040
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
Protein measurement with the Folin phenol reagent.
LOWRY OH, ROSEBROUGH NJ, FARR AL, RANDALL RJ., J. Biol. Chem. 193(1), 1951
PMID: 14907713
Microbial ecology of the dark ocean above, at, and below the seafloor.
Orcutt BN, Sylvan JB, Knab NJ, Edwards KJ., Microbiol. Mol. Biol. Rev. 75(2), 2011
PMID: 21646433
Whither or wither geomicrobiology in the era of 'community metagenomics'.
Oremland RS, Capone DG, Stolz JF, Fuhrman J., Nat. Rev. Microbiol. 3(7), 2005
PMID: 15953928

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0
Aerobic denitrification in various heterotrophic nitrifiers.
Robertson LA, Cornelisse R, De Vos P, Hadioetomo R, Kuenen JG., Antonie Van Leeuwenhoek 56(4), 1989
PMID: 2619286
Energy-based models for environmental biotechnology.
Rodriguez J, Lema JM, Kleerebezem R., Trends Biotechnol. 26(7), 2008
PMID: 18513813
Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities.
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF., Appl. Environ. Microbiol. 75(23), 2009
PMID: 19801464
Big bacteria.
Schulz HN, Jorgensen BB., Annu. Rev. Microbiol. 55(), 2001
PMID: 11544351
Phenotypic heterogeneity driven by nutrient limitation promotes growth in fluctuating environments.
Schreiber F, Littmann S, Lavik G, Escrig S, Meibom A, Kuypers MM, Ackermann M., Nat Microbiol 1(6), 2016
PMID: 27572840
Prokka: rapid prokaryotic genome annotation.
Seemann T., Bioinformatics 30(14), 2014
PMID: 24642063
Microbial metatranscriptomics in a permanent marine oxygen minimum zone.
Stewart FJ, Ulloa O, DeLong EF., Environ. Microbiol. 14(1), 2011
PMID: 21210935
Aerobic growth at nanomolar oxygen concentrations.
Stolper DA, Revsbech NP, Canfield DE., Proc. Natl. Acad. Sci. U.S.A. 107(44), 2010
PMID: 20974919
Growth yields in bacterial denitrification and nitrate ammonification.
Strohm TO, Griffin B, Zumft WG, Schink B., Appl. Environ. Microbiol. 73(5), 2007
PMID: 17209072
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
Heterotrophic nitrification and aerobic denitrification at low nutrient conditions by a newly isolated bacterium, Acinetobacter sp. SYF26.
Su JF, Zhang K, Huang TL, Wen G, Guo L, Yang SF., Microbiology (Reading, Engl.) 161(Pt 4), 2015
PMID: 25667009
Aerobic denitrifying bacteria that produce low levels of nitrous oxide.
Takaya N, Catalan-Sakairi MA, Sakaguchi Y, Kato I, Zhou Z, Shoun H., Appl. Environ. Microbiol. 69(6), 2003
PMID: 12788710
Glycerol fermentation by (open) mixed cultures: a chemostat study.
Temudo MF, Poldermans R, Kleerebezem R, van Loosdrecht MC., Biotechnol. Bioeng. 100(6), 2008
PMID: 18553403
Resurrecting ancestral alcohol dehydrogenases from yeast.
Thomson JM, Gaucher EA, Burgan MF, De Kee DW, Li T, Aris JP, Benner SA., Nat. Genet. 37(6), 2005
PMID: 15864308

AUTHOR UNKNOWN, 0
On the origin of cancer cells.
WARBURG O., Science 123(3191), 1956
PMID: 13298683
Neutral assembly of bacterial communities.
Woodcock S, van der Gast CJ, Bell T, Lunn M, Curtis TP, Head IM, Sloan WT., FEMS Microbiol. Ecol. 62(2), 2007
PMID: 17937674
Mimicking the oxygen minimum zones: stimulating interaction of aerobic archaeal and anaerobic bacterial ammonia oxidizers in a laboratory-scale model system.
Yan J, Haaijer SC, Op den Camp HJ, van Niftrik L, Stahl DA, Konneke M, Rush D, Sinninghe Damste JS, Hu YY, Jetten MS., Environ. Microbiol. 14(12), 2012
PMID: 23057688
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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