RNA-stable isotope probing: From carbon flow within key microbiota to targeted transcriptomes

Current Opinion in Biotechnology

Volumn 41, Issue , 2016, Pages 83-89

  Lueders, Tillmann ^a   Dumont, Marc G ^b   Bradford, Lauren ^a   Manefield, Mike ^c  

^a INSTITUTE OF EPIDEMIOLOGY   (Germany)

^b UNIVERSITY OF SOUTHAMPTON   (United Kingdom)

^c UNIVERSITY OF NEW SOUTH WALES   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; ENVIRONMENTAL TECHNOLOGY; ISOTOPES; MICROORGANISMS; RNA;

CELLULAR REPLICATION; ENVIRONMENTAL BIOTECHNOLOGY; MICROBIAL COMMUNITIES; MICROBIAL FOOD WEB; MICROBIOTAS; NEXT-GENERATION SEQUENCING; STABLE-ISOTOPE PROBING; TRANSCRIPTOMES;

NUCLEIC ACIDS;

STABLE ISOTOPE; TRANSCRIPTOME; BACTERIAL RNA; CARBON; RNA PROBE;

CILIATE; DOWN REGULATION; ENVIRONMENTAL FACTOR; FRACTIONATION; HOST PATHOGEN INTERACTION; ISOTOPE LABELING; LIMIT OF DETECTION; METAGENOME; MICROBIAL COMMUNITY; MICROFLORA; NEXT GENERATION SEQUENCING; NONHUMAN; PRIORITY JOURNAL; REVIEW; RNA ANALYSIS; RNA EXTRACTION; CHEMISTRY; GENETIC PROCEDURES; GENETICS; METABOLISM; PROCEDURES; RNA PROBE;

CARBON ISOTOPES; ISOTOPE LABELING; MICROBIOTA; MOLECULAR PROBE TECHNIQUES; RNA PROBES; RNA, BACTERIAL; TRANSCRIPTOME;

EID: 84971483039     PISSN: 09581669     EISSN: 18790429     Source Type: Journal    
DOI: 10.1016/j.copbio.2016.05.001     Document Type: Review

References (51)

1. Radajewski S., Ineson P., Parekh N.R., Murrell J.C. Stable-isotope probing as a tool in microbial ecology. Nature 2000, 403:646-649.
2. Manefield M., Whiteley A.S., Griffiths R.I., Bailey M.J. RNA stable isotope probing, a novel means of linking microbial community function to phylogeny. Appl Environ Microbiol 2002, 68:5367-5373.
3. Lueders T., Manefield M., Friedrich M.W. Enhanced sensitivity of DNA- and rRNA-based stable isotope probing by fractionation and quantitative analysis of isopycnic centrifugation gradients. Environ Microbiol 2004, 6:73-78.
4. Huang W.E., Ferguson A., Singer A.C., Lawson K., Thompson I.P., Kalin R.M., Larkin M.J., Bailey M.J., Whiteley A.S. Resolving genetic functions within microbial populations: in situ analyses using rRNA and mRNA stable isotope probing coupled with single-cell raman-fluorescence in situ hybridization. Appl Environ Microbiol 2009, 75:234-241.
5. Dumont M.G., Pommerenke B., Casper P., Conrad R. DNA-, rRNA- and mRNA-based stable isotope probing of aerobic methanotrophs in lake sediment. Environ Microbiol 2011, 13:1153-1167.
6. Dumont M.G., Pommerenke B., Casper P. Using stable isotope probing to obtain a targeted metatranscriptome of aerobic methanotrophs in lake sediment. Environ Microbiol Rep 2013, 5:757-764.
7. Franzosa E.A., Hsu T., Sirota-Madi A., Shafquat A., Abu-Ali G., Morgan X.C., Huttenhower C. Sequencing and beyond: integrating molecular 'omics' for microbial community profiling. Nat Rev Micro 2015, 13:360-372.
8. 2 fixation by archaea and bacteria in an agricultural soil. PNAS 2011, 108:4170-4175.
9. Pratscher J., Dumont M.G., Conrad R. Assimilation of acetate by the putative atmospheric methane oxidizers belonging to the USCα clade. Environ Microbiol 2011, 13:2692-2701.
10. von Bergen M., Jehmlich N., Taubert M., Vogt C., Bastida F., Herbst F.-A., Schmidt F., Richnow H.-H., Seifert J. Insights from quantitative metaproteomics and protein-stable isotope probing into microbial ecology. ISME J 2013, 7:1877-1885.
11. Haichar FeZ, Roncato M.-A., Achouak W. Stable isotope probing of bacterial community structure and gene expression in the rhizosphere of Arabidopsis thaliana. FEMS Microbiol Ecol 2012, 81:291-302.
12. Leng L., Chang J., Geng K., Lu Y., Ma K. Uncultivated Methylocystis species in paddy soil include facultative methanotrophs that utilize acetate. Microb Ecol 2015, 70:88-96.
13. Vogt C., Lueders T., Richnow H.H., Krüger M., von Bergen M., Seifert J. Stable isotope probing approaches to study anaerobic hydrocarbon degradation and degraders. J Mol Microbiol Biotechnol 2016, 26:195-210.
14. Aoyagi T., Hanada S., Itoh H., Sato Y., Ogata A., Friedrich M.W., Kikuchi Y., Hori T. Ultra-high-sensitivity stable-isotope probing of rRNA by high-throughput sequencing of isopycnic centrifugation gradients. Environ Microbiol Rep 2015, 7:282-287.
15. Zemb O., Lee M., Gutierrez-Zamora M.L., Hamelin J., Coupland K., Hazrin-Chong N.H., Taleb I., Manefield M. Improvement of RNA-SIP by pyrosequencing to identify putative 4-n-nonylphenol degraders in activated sludge. Water Res 2012, 46:601-610.
16. Hungate B.A., Mau R.L., Schwartz E., Caporaso J.G., Dijkstra P., van Gestel N., Koch B.J., Liu C.M., McHugh T.A., Marks J.C., Morrissey E.M., Price L.B. Quantitative microbial ecology through stable isotope probing. Appl Environ Microbiol 2015, 81:7570-7581.
17. Moreno A.M., Matz C., Kjelleberg S., Manefield M. Identification of ciliate grazers of autotrophic bacteria in ammonia-oxidizing activated sludge by RNA stable isotope probing. Appl Environ Microbiol 2010, 76:2203-2211.
18. Dolinšek J., Lagkouvardos I., Wanek W., Wagner M., Daims H. Interactions of nitrifying bacteria and heterotrophs: identification of a Micavibrio-like putative predator of Nitrospira spp. Appl Environ Microbiol 2013, 79:2027-2037.
19. Glaubitz S., Abraham W.R., Jost G., Labrenz M., Jurgens K. Pyruvate utilization by a chemolithoautotrophic epsilonproteobacterial key player of pelagic Baltic Sea redoxclines. FEMS Microbiol Ecol 2014, 87:770-779.
20. Anderson R., Wylezich C., Glaubitz S., Labrenz M., Jurgens K. Impact of protist grazing on a key bacterial group for biogeochemical cycling in Baltic Sea pelagic oxic/anoxic interfaces. Environ Microbiol 2013, 15:1580-1594.
21. Vandieken V., Pester M., Finke N., Hyun J.H., Friedrich M.W., Loy A., Thamdrup B. Three manganese oxide-rich marine sediments harbor similar communities of acetate-oxidizing manganese-reducing bacteria. ISME J 2012, 6:2078-2090.
22. Vandieken V., Thamdrup B. Identification of acetate-oxidizing bacteria in a coastal marine surface sediment by RNA-stable isotope probing in anoxic slurries and intact cores. FEMS Microbiol Ecol 2013, 84:373-386.
23. 2. PNAS 2010, 107:10938-10942.
24. 2 on rhizosphere carbon flow and microbial community dynamics. Glob Chang Biol 2013, 19:621-636.
25. Hernández M., Dumont M.G., Yuan Q., Conrad R. Different bacterial populations associated with the roots and rhizosphere of rice incorporate plant-derived carbon. Appl Environ Microbiol 2015, 81:2244-2253.
26. Dias A.C., Dini-Andreote F., Hannula S.E., Andreote F.D., Pereira E.S.M.C., Salles J.F., de Boer W., van Veen J., van Elsas J.D. Different selective effects on rhizosphere bacteria exerted by genetically modified versus conventional potato lines. PLoS One 2013, 8:e67948.
27. Kovatcheva-Datchary P., Egert M., Maathuis A., Stojanovi M.R., Graaf AAd, Smidt H., Vos WMd, Venema K. Linking phylogenetic identities of bacteria to starch fermentation in an in vitro model of the large intestine by RNA-based stable isotope probing. Environ Microbiol 2009, 11:914-926.
28. Godwin S., Kang A., Gulino L.-M., Manefield M., Gutierrez-Zamora M.-L., Kienzle M., Ouwerkerk D., Dawson K., Klieve A.V. Investigation of the microbial metabolism of carbon dioxide and hydrogen in the kangaroo foregut by stable isotope probing. ISME J 2014, 8:1855-1865.
29. Tannock G.W., Lawley B., Munro K., Sims I.M., Lee J., Butts C.A., Roy N. RNA-stable isotope probing shows utilization of carbon from inulin by specific bacterial populations in the rat large bowel. Appl Environ Microbiol 2014, 80:2240-2247.
30. Jechalke S., Franchini A.G., Bastida F., Bombach P., Rosell M., Seifert J., von Bergen M., Vogt C., Richnow H.H. Analysis of structure, function, and activity of a benzene-degrading microbial community. FEMS Microbiol Ecol 2013, 85:14-26.
31. Kleindienst S., Herbst F.-A., Stagars M., von Netzer F., von Bergen M., Seifert J., Peplies J., Amann R., Musat F., Lueders T., Knittel K. Diverse sulfate-reducing bacteria of the Desulfosarcina/Desulfococcus clade are the key alkane degraders at marine seeps. ISME J 2014, 8:2029-2044.
32. Fowler S.J., Gutierrez-Zamora M.-L., Manefield M., Gieg L.M. Identification of toluene degraders in a methanogenic enrichment culture. FEMS Microbiol Ecol 2014, 89:625-636.
33. Nielsen J.L., Nguyen H., Meyer R.L., Nielsen P.H. Identification of glucose-fermenting bacteria in a full-scale enhanced biological phosphorus removal plant by stable isotope probing. Microbiology 2012, 158:1818-1825.
34. Ito T., Yoshiguchi K., Ariesyady H.D., Okabe S. Identification of a novel acetate-utilizing bacterium belonging to Synergistes group 4 in anaerobic digester sludge. ISME J 2011, 5:1844-1856.
35. Ito T., Yoshiguchi K., Ariesyady H.D., Okabe S. Identification and quantification of key microbial trophic groups of methanogenic glucose degradation in an anaerobic digester sludge. Bioresour Technol 2012, 123:599-607.
36. Angel R., Conrad R. Elucidating the microbial resuscitation cascade in biological soil crusts following a simulated rain event. Environ Microbiol 2013, 15:2799-2815.
37. 18O. Microbiol Open 2015, 4:208-219.
38. Urich T., Lanzén A., Qi J., Huson D.H., Schleper C., Schuster S.C. Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome. PLoS ONE 2008, 3:e2527.
39. Munro S.A., Lund S.P., Pine P.S., Binder H., Clevert D.-A., Conesa A., Dopazo J., Fasold M., Hochreiter S., Hong H., et al. Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures. Nat Commun 2014, 5.
40. Moran M.A., Satinsky B., Gifford S.M., Luo H., Rivers A., Chan L.K., Meng J., Durham B.P., Shen C., Varaljay V.A., Smith C.B., Yager P.L., Hopkinson B.M. Sizing up metatranscriptomics. ISME J 2013, 7:237-243.
41. 18O-water to investigate microbial growth and death in environmental samples. Curr Opin Biotechnol 2016, 41:14-18.
42. Pepe-Ranney C., Koechli C., Potrafka R., Andam C., Eggleston E., Garcia-Pichel F., Buckley D.H. Non-cyanobacterial diazotrophs mediate dinitrogen fixation in biological soil crusts during early crust formation. ISME J 2015, 10.1038/ismej.2015.1106.
43. Whiteley A.S., Manefield M., Lueders T. Unlocking the 'microbial black box' using RNA-based stable isotope probing technologies. Curr Opin Biotechnol 2006, 17:67-71.
44. Buckley D.H., Huangyutitham V., Hsu S.-F., Nelson T.A. Stable isotope probing with 15N achieved by disentangling the effects of genome G+C content and isotope enrichment on DNA density. Appl Environ Microbiol 2007, 73:3189-3190.
45. Cadisch G., Espana M., Causey R., Richter M., Shaw E., Morgan J.A., Rahn C., Bending G.D. Technical considerations for the use of 15N-DNA stable-isotope probing for functional microbial activity in soils. Rapid Commun Mass Spectrom 2005, 19:1424-1430.
46. Mayali X., Weber P.K., Brodie E.L., Mabery S., Hoeprich P.D., Pett-Ridge J. High-throughput isotopic analysis of RNA microarrays to quantify microbial resource use. ISME J 2012, 6:1210-1220.
47. Mayali X., Stewart B., Mabery S., Weber P.K. Temporal succession in carbon incorporation from macromolecules by particle-attached bacteria in marine microcosms. Environ Microbiol Rep 2016, 10.1111/1758-2229.12352.
48. Mayali X., Weber P.K., Pett-Ridge J. Taxon-specific C/N relative use efficiency for amino acids in an estuarine community. FEMS Microbiol Ecol 2013, 83:402-412.
49. 13C-enriched nucleic acids via ultrahigh-performance liquid chromatography-tandem mass spectrometry for applications in stable isotope probing. Appl Environ Microbiol 2014, 80:7206-7210.
50. Gutierrez-Zamora M.-L., Zemb O., Manefield M. Direct rRNA fingerprinting, a novel method to profile low diversity microbial communities. Microbial Ecol 2011, 62:177-187.
51. Fortunato C.S., Huber J.A. Coupled RNA-SIP and metatranscriptomics of active chemolithoautotrophic communities at a deep-sea hydrothermal vent. ISME J 2016, 10.1038/ismej.2015.1258.