Applications of flow cytometry in environmental microbiology and biotechnology

Extremophiles

Volumn 13, Issue 3, 2009, Pages 389-401

  Bergquist, Peter L ^a,b   Hardiman, Elizabeth M ^a   Ferrari, Belinda C ^c   Winsley, Tristrom ^c  

^a MACQUARIE UNIVERSITY   (Australia)

^b UNIVERSITY OF AUCKLAND   (New Zealand)

^c UNIVERSITY OF NEW SOUTH WALES   (Australia)

Author keywords

Directed evolution; Fluorescence activated cell sorting; In vitro compartmentalisation; Non culturable bacteria; Protein optimisation; Random (neutral) drift; Random mutagenesis; Single cell analysis

Indexed keywords

BIOTECHNOLOGY; FLOW CYTOMETRY; MUTAGENESIS; REVIEW;

BIOTECHNOLOGY; FLOW CYTOMETRY; MUTAGENESIS;

BACTERIA (MICROORGANISMS);

EID: 67349280639     PISSN: 14310651     EISSN: 14334909     Source Type: Journal    
DOI: 10.1007/s00792-009-0236-4     Document Type: Review

References (79)

1. A Aharoni G Amitai K Bernath S Magdassi DS Tawfik 2005 High-throughput screening of enzyme libraries: thiolactonases evolved by fluorescence-activated sorting of single cells in emulsion compartments Chem Biol 12 1281 1289 (Pubitemid 41779468)
2. A Aharoni AD Griffiths DS Tawfik 2005 High-throughput screens and selections of enzyme-encoding genes Curr Opin Chem Biol 9 210 216 (Pubitemid 40462492)
3. A Aharoni K Thieme CPC Chiu S Buchini LL Lairson H Chen NCJ Strynadka WW Wakarchuk SG Withers 2006 High-throughput screening methodology for the directed evolution of glycosyltransferases Nat Methods 3 609 614 (Pubitemid 44123427)
4. A Alagappan NA Tujula M Power CM Ferguson PL Bergquist BC Ferrari 2008 Development of fluorescent in situ hybridisation for Cryptosporidium detection reveals zoonotic and anthroponotic transmission of sporadic cryptosporidiosis in Sydney J Microbiol Meth 75 535 539
5. RI Amann L Krumholz DA Stahl 1990 Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology J Bacteriol 172 762 770 (Pubitemid 20070387)
6. RI Amann W Ludwig KH Schleife 1995 Phylogenetic identification and in situ detection of individual microbial cells without cultivation Microbiol Rev 59 143 169
7. G Amitai RD Gupta DS Tawfik 2007 Latent evolutionary potentials under the neutral mutational drift of an enzyme HFSP J 1 67 78
8. MJ Bahl LH Hansen TR Licht SJ Sorensen 2004 In vivo detection and quantification of tetracycline by use of a whole-cell biosensor in the rat intestine Antimicrob Agents Chemother 48 1112 1117 (Pubitemid 38405462)
9. AM Baty CC Eastburn Z Diwu S Techkarnjanaruk AE Goodman GG Geesey 2000 Differentiation of chitinase-active and non-chitinase-active subpopulations of a marine bacterium during chitin degradation Appl Environ Microbiol 66 3566 3573 (Pubitemid 30627451)
10. PJL Bell D Deere J Shen B Chapman PH Bissenger PA Attfield DA Veal 1998 A flow cytometric method for rapid selection of novel industrial yeast hybrids Appl Environ Microbiol 64 1669 1672 (Pubitemid 28234767)
11. Bergquist PL, Gibbs MD (2006) Degenerate oligonucleotide gene shuffling (DOGS). In: Mueller K, Arndt K (eds) Protein engineering protocols, methods in molecular biology series, vol 352, pp 191-204
12. PL Bergquist RA Reeves MD Gibbs 2005 Degenerate oligonucleotide gene shuffling (DOGS) and random drift mutagenesis (RNDM): two complementary techniques for enzyme evolution Biomol Eng 22 63 72 (Pubitemid 40602595)
13. K Bernath M Hai E Mastrobattista A Griffiths S Magdassi DS Tawfik 2003 In vitro compartmentalization by double emulsions: sorting and gene enrichment by fluorescence activated cell sorting Anal Biochem 325 151 157 (Pubitemid 38050278)
14. S Bershtein DS Tawfik 2008 Advances in the laboratory evolution of enzymes Curr Opin Chem Biol 12 151 158
15. S Bershtein K Goldin DS Dawfik 2008 Intense neutral drifts yield robust and evolvable consensus proteins J Mol Biol 379 1029 1044
16. C Bessler J Schmitt KH Maurer RD Schmid 2003 Directed evolution of a bacterial α-amylase: toward enhanced pH performance and higher specific activity Protein Sci 12 2141 2149 (Pubitemid 37163349)
17. TJ Beveridge 1999 Structures of gram-negative cell walls and their derived membrane vesicles J Bacteriol 181 4725 4733 (Pubitemid 29383496)
18. JD Bloom ST Labthavikul CR Otey FH Arnold 2006 Protein stability promotes evolvability Proc Natl Acad Sci USA 103 5869 5874
19. JD Bloom PA Romero Z Lu FH Arnold 2007 Neutral genetic drift can alter promiscuous protein functions, potentially aiding functional evolution Biol Direct 17 2 (Pubitemid 47079755)
20. C Breton J Mucha C Jeanneau 2001 Structural and functional features of glycosyltransferases Biochimie 83 713 718 (Pubitemid 32821235)
21. M Burmolle LH Hansen SJ Sorensen 2005 Use of a whole-cell biosensor and flow cytometry to detect AHL production by an indigenous soil community during decomposition of litter Microb Ecol 50 221 229 (Pubitemid 41712621)
22. S Chopra A Rananathan 2003 Protein evolution by "codon shuffling": a novel method for generating highly variant mutant libraries by assembly of hexamer DNA duplexes Chem Biol 10 917 926 (Pubitemid 37316909)
23. J Clausell-Tormos D Lieber J-C Baret A El-Harrak OJ Miller L Frenz J Blouwolff KJ Humphry S Köster H Duan C Holtze DA Weitz AD Griffiths CA Merten 2008 Droplet-based microfluidic platforms for the encapsulation and screening of mammalian cells and multicellular organisms Chem Biol 15 427 437
24. K Czechowska DR Johnson JR van der Meer 2008 Use of flow cytometric methods for single-cell analysis in environmental microbiology Curr Opin Microbiol 11 205 212
25. HM Davey 2002 Flow cytometric techniques for the detection of microorganisms Methods Cell Sci 24 91 97 (Pubitemid 36826792)
26. HM Davey DB Kell 1996 Flow cytometry and cell sorting of heterogeneous microbial populations: the importance of single-cell analyses Microbiol Rev 60 641 696 (Pubitemid 26415671)
27. K Davis Y Lin B Abrams SD Jayasena 1998 Staining of cell surface human CD4 with 2'-F-pyrimidine-containing RNA aptamers for flow cytometry Nucl Acids Res 26 3915 3924 (Pubitemid 28401340)
28. M Dignum H Hoogveld HCP Matthijs HJ Laanbroek R Pel 2004 Detecting the phosphate status of phytoplankton by enzyme-labelled fluorescence and flow cytometry EMS Microbiol Ecol 48 29 38 (Pubitemid 38393773)
29. N Doi S Kumadaki Y Oishi N Matsumura H Yanagawa 2004 In vitro selection of restriction endonucleases by in vitro compartmentalization Nucl Acids Res 32 e95
30. BC Ferrari PL Bergquist 2007 Quantum Dots as alternatives to organic fluorophores for Cryptosporidium detection using conventional flow cytometry and specific monoclonal antibodies: lessons learned Cytometry A 71 265 271 (Pubitemid 46581288)
31. Ferrari BC, Winsley T (2009) Fluorescence-activated cell sorting combined with a soil substrate membrane system allows for novel filamentous bacteria from the CFB group to be targeted for cultivation in the laboratory Environ Microbiol (in press)
32. BC Ferrari G Oregaard SJ Sorensen 2004 Recovery of GFP-labeled bacteria for culturing and molecular analysis after cell sorting using a benchtop flow cytometer Microb Ecol 48 239 245 (Pubitemid 40383326)
33. BC Ferrari T Winsley M Gillings S Binnerup 2008 Cultivating previously uncultured soil bacteria using a soil substrate membrane system Nat Protoc 3 1261 1269
34. R Festin B Bjorklund YH Totterman 1987 Detection of triple antibody-binding lymphocytes in standard single laser flow cytometry with colloidal gold, fluorescein and phycoerythrin as labels J Immunol Methods 101 23 28 (Pubitemid 17097893)
35. BM Fuchs MV Zubkov K Sahm PH Burkill R Amann 2000 Changes in community composition during dilution cultures of marine bacterioplankton as assessed by flow cytometric and molecular biological techniques Environ Microbiol 2 191 201 (Pubitemid 33136714)
36. FJ Ghadessy P Holliger 2004 A novel emulsion mixture for in vitro compartmentalization of transcription and translation in the rabbit reticulocyte system" Protein Eng Des Sel 17 201 204 (Pubitemid 38781192)
37. FJ Ghadessy JL Ong P Holliger 2001 Directed evolution of polymerase function by compartmentalized self-replication Proc Natl Acad Sci USA 98 4552 4557 (Pubitemid 32295014)
38. MD Gibbs KMH Nevalainen PL Bergquist 2001 Degenerate oligonucleotide gene shuffling (DOGS): a method for enhancing the frequency of recombination with family shuffling Gene 271 13 20 (Pubitemid 32539141)
39. BD Green M Keller 2006 Capturing the uncultivated majority Curr Opin Biotechnol 17 236 240 (Pubitemid 43850262)
40. AD Griffiths DS Tawfik 2003 Directed evolution of an extremely fast phosphotriesterase by in vitro compartmentalization EMBO J 22 24 35 (Pubitemid 36091266)
41. AD Griffiths DS Tawfik 2006 Miniaturising the laboratory in emulsion droplets Trends Biotech 24 395 402 (Pubitemid 44223819)
42. RD Gupta DS Tawfik 2008 Directed enzyme evolution via small and effective neutral drift libraries Nat Methods 5 939 942
43. LH Hansen B Ferrari AH Sorensen D Veal SJ Sorensen 2001 Detection of oxytetracycline production by Streptomyces rimosus in soil microcosms by combining whole-cell biosensors and flow cytometry Appl Environ Microbiol 67 239 244 (Pubitemid 32044424)
44. D Hoefel PT Monis WL Grooby S Andrews CP Saint 2005 Culture-independent techniques for rapid detection of bacteria associated with loss of chloramine residual in a drinking water system Appl Environ Microbiol 71 6479 6488 (Pubitemid 43194127)
45. P Hugenholtz GW Tyson 2008 Microbiology: metagenomics Nature 455 481 483
46. v Ibáñez-Peral PL Bergquist M Walter M Gibbs EM Goldys B Ferrari 2008 Potential use of quantum dots in flow cytometry Int J Mol Sci 9 2622 2638
47. T Ishoey T Wayk R Stepanauskas M Novotny RS Lasken 2008 Genomic sequencing of single microbial cells from environmental samples Curr Opinion Microbiol 11 198 204
48. C Jäckel P Kast D Hilvert 2008 Protein design by directed evolution Ann Rev Biophys 37 153 173
49. MG Kalyuzhnaya ME Lidstrom L Chistoserdova 2008 Real-time detection of actively metabolizing microbes by redox sensing as applied to methylotroph populations in Lake Washington ISME J 2 696 706
50. M Keller K Zengler 2004 Tapping into microbial diversity Nat Rev Microbiol 2 141 150 (Pubitemid 39490067)
51. Kelly BT, Baret J-C, Taly V, Griffiths AD (2007) Miniaturizing chemistry and biology in microdroplets. Chem Commun 1773-1778
52. MF Kramer G Vesey NL Look BR Herbert JM Simpson-Stroot DV Lim 2007 Development of a Cryptosporidium oocyst assay using an automated fiber optic-based biosensor J Biol Eng 1 3
53. JR Leadbetter 2003 Cultivation of recalcitrant microbes: cells are alive, well and revealing their secrets in the 21st century laboratory Curr Opin Microbiol 6 274 281 (Pubitemid 36841671)
54. KA Martemyanov VA Shirokov OV Kurnasov AT Gudkov AS Spirin 2001 Cell-free production of biologically active polypeptides: application to the synthesis of antibacterial peptide Cecropin Protein Expr Purif 21 456 461 (Pubitemid 34179419)
55. E Mastrobattista V Taly E Chanudet P Treacy BT Kelly AD Griffiths 2005 High-throughput screening of enzyme libraries: in vitro evolution of a beta-galactosidase by fluorescence-activated sorting of double emulsions Chem Biol 12 1291 1300 (Pubitemid 41779469)
56. T Matsuuraa T Yomo 2006 In vitro evolution of proteins J Biosci Bioeng 101 449 456 (Pubitemid 44355025)
57. D Mattanovich N Borth 2006 Applications of cell sorting in biotechnology Microb Cell Fact 5 12
58. OJ Miller K Bernath JJ Agresti G Amitai BT Kelly E Mastrobattista V Taly S Magdassi DS Tawfik AD Griffiths 2006 Directed evolution by in vitro compartmentalization Nat Methods 3 561 570 (Pubitemid 43941775)
59. R Miyauchi K Oki Y Aoi S Tsuneda 2007 Diversity of nitrite reductase genes in "Candidatus Accumulibacter phosphatis"-dominated cultures enriched by flow-cytometric sorting Appl Environ Microbiol 73 5331 5337 (Pubitemid 47326666)
60. S Musovic G Oregaard N Kroer SJ Sorensen 2006 Cultivation-independent examination of horizontal transfer and host range of an IncP-1 plasmid among gram-positive and gram-negative bacteria indigenous to the barley rhizosphere Appl Environ Microbiol 72 6687 6692 (Pubitemid 44582910)
61. J-D Pédelacq S Cabantous T Tran TC Terwilliger GS Waldo 2006 Engineering and characterization of a superfolder green fluoroescent protein Nat Biotechnol 24 79 88 (Pubitemid 43083170)
62. C Roodveldt A Aharoni DS Tawfik 2005 Directed evolution of proteins for heterologous expression and stability Curr Opin Struct Biol 15 50 56 (Pubitemid 40249509)
63. A Rothe RN Surjadi BE Power 2006 Novel proteins in emulsions using in vitro compartmentalization Trends Biotechnol 24 587 592
64. Shapiro HM (2003) Practical Flow Cytometry. Wiley, Hoboken
65. SJ Sorensen AH Sorensen LH Hansen G Oregaard D Veal 2003 Direct detection and quantification of horizontal gene transfer by using flow cytometry and gfp as a reporter gene Curr Microbiol 47 129 133 (Pubitemid 37021421)
66. V Taly BT Kelly AD Griffiths 2007 Droplets as microreactors for high-throughput biology ChemBiochem 8 263 272 (Pubitemid 47194505)
67. DS Tawfik AD Griffiths 1998 Man-made cell-like compartments for molecular evolution Nat Biotechnol 16 652 656 (Pubitemid 28334323)
68. NJ Turner 2003 Directed evolution of enzymes for applied biocatalysis Trends Biotech 21 474 478 (Pubitemid 37324198)
69. T Uchiyama T Abe T Ikemura K Watanabe 2005 Substrate-induced gene-expression screening of environmental metagenome libraries for isolation of catabolic genes Nat Biotechnol 23 88 93 (Pubitemid 41724630)
70. DA Veal D Deere B Ferrari J Piper PV Attfield 2000 Fluorescent staining and flow cytometry for monitoring microbial cells J Immunol Methods 243 191 210
71. G Vesey JS Slade M Byrne K Shepherd PJ Dennis CR Fricker 1993 Routine monitoring of Cryptosporidium oocysts in water using flow cytometry J Appl Bacteriol 75 87 90 (Pubitemid 23203170)
72. G Vesey P Hutton A Champion N Ashbolt KL Williams A Warton DA Veal 1994 Application of flow cytometric methods for the routine detection of Cryptosporidium and Giardia in water Cytometry 16 1 6 (Pubitemid 2068861)
73. Vesey G, Narai J, Ashbolt N, Williams K, Veal D (1994b) Detection of specific microorganisms in environmental samples using flow cytometry. In: Darzynkiewicz Z, Robinson JP, Crissman HA (eds) Methods in cell biology, flow cytometry, 2nd edn. Academic Press, New York
74. G Wallner I Steinmetz D Bitter-Suermann R Amann 1996 Combination of rRNA-targeted probes and immuno-probes for the identification of bacteria by flow cytometry Syst Appl Microbiol 19 569 576 (Pubitemid 27029322)
75. G Wallner B Fuchs S Spring W Beisker R Amann 1997 Flow sorting of microorganisms for molecular analysis Appl Environ Microbiol 63 4223 4231 (Pubitemid 27485743)
76. CR Woese 1987 Bacterial evolution Microbiol Rev 51 221 271 (Pubitemid 17082512)
77. K Zengler G Toledo M Rappe J Elkins EJ Mathur JM Short M Keller 2002 Cultivating the uncultured Proc Natl Acad Sci USA 99 15681 15686 (Pubitemid 35403991)
78. K Zengler M Walcher G Clark I Haller G Toledo T Holland EJ Mathur G Woodnutt JM Short M Keller 2005 High-throughput cultivation of microorganisms using microcapsules Methods Enzymol 397 124 130 (Pubitemid 41562896)
79. M Zhou RH Upson Z Diwu RP Haugland 1996 A fluorogenic substrate for β-glucuronidase: applications in fluorometric, polyacrylamide gel and histochemical assays J Biochem Biophys Methods 33 197 205 (Pubitemid 27037999)