Advertisement

Persisters, Biofilms, and the Problem of Cultivability

  • Kim LewisEmail author
Chapter
  • 1.3k Downloads
Part of the Microbiology Monographs book series (MICROMONO, volume 10)

Abstract

The majority of bacterial species in the environment remain uncultured, and accumulating evidence suggests that this cannot be explained by inadequate nutrient supply. Good recovery of environmental bacteria can be obtained by cultivation in situ in diffusion chambers, and this produces “domesticated” variants that can subsequently grow on synthetic media on Petri dishes. In many cases, growth of otherwise unculturable bacteria is observed on rich media in the presence of a cultivable helper organism. In the marine sediment environment, a considerable part of these uncultivable bacteria are found to depend on siderophores produced by their neighbors. The absence of an ability to induce the synthesis of their own siderophores when iron levels drop is puzzling. It seems that these observations point to a signaling mechanism for uncultivability – most bacterial species evolved to grow only in a familiar environment. The default mode of most bacterial life is then dormancy, and growth factors are required for resuscitation. The adaptive advantage of such a strategy may stem from the fact that rapidly propagating bacteria are highly vulnerable to toxic factors such as unfamiliar antibiotics. By contrast, dormant cells are tolerant to antibiotics. This is exemplified by specialized dormant persister cells which are formed in all studied cultivable bacteria. In organisms such as E. coli or P. aeruginosa, persisters are formed stochastically and make up a small part of the population. It is possible that in the absence of a growth factor, unculturable species enter en mass into a persister state.

Keywords

Planktonic Cell Unculturable Bacterium Diffusion Chamber Dormant Cell Familiar Environment 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. Allsopp, D, Colwell, RR, Hawksworth, DL (1995) Microbial diversity and ecosystem function: CAB InternationalWallingford UK:Google Scholar
  2. Balaban NQ, Merrin J, Chait R, Kowalik L, Leibler S (2004) Bacterial persistence as a phenotypic switch. Science 305:1622–1625PubMedCrossRefGoogle Scholar
  3. Barer MR, Harwood, CR (1999) Bacterial viability and culturability. Adv Microb Physiol 41:93–137PubMedCrossRefGoogle Scholar
  4. Barns SM, Fundyga RE, Jeffries MW, Pace NR (1994) Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment. Proc Natl Acad Sci U S A 91:1609–1613PubMedCrossRefGoogle Scholar
  5. Bigger JW (1944) Treatment of staphylococcal infections with penicillin. Lancet ii:497–500CrossRefGoogle Scholar
  6. Black DS, Kelly AJ, Mardis MJ, Moyed HS (1991) Structure and organization of hip, an operon that affects lethality due to inhibition of peptidoglycan or DNA synthesis. J Bacteriol 173:5732–5739PubMedGoogle Scholar
  7. Black DS, Irwin B, Moyed HS (1994) Autoregulation of hip, an operon that affects lethality due to inhibition of peptidoglycan or DNA synthesis. J Bacteriol 176:4081–4091PubMedGoogle Scholar
  8. Bollmann A, Lewis K, Epstein SS (2007) Incubation of environmental samples in a diffusion chamber increases the diversity of recovered isolates. Appl Environ Microbiol 73:6386–6390PubMedCrossRefGoogle Scholar
  9. Brooun A, Liu S, Lewis K (2000) A dose-response study of antibiotic resistance in Pseudomonas aeruginosa biofilms. Antimicrob Agents Chemother 44:640–646PubMedCrossRefGoogle Scholar
  10. Butkevich VS (1932) Zür Methodik der bakterioloschen Meeresuntersuchungen und einige Angaben über die Verteilung der Bakterien im Wasser und in den Büden des Barents Meeres. Trans. Oceanogr. Inst. Moscow 2: 5–39 (in Russian with German summary) 2:5–39Google Scholar
  11. Christensen SK, Gerdes K. (2003) RelE toxins from bacteria and Archaea cleave mRNAs on translating ribosomes, which are rescued by tmRNA. Mol Microbiol 48:1389–1400PubMedCrossRefGoogle Scholar
  12. Christensen SK, Pedersen K, Hansen FG, Gerdes K (2003) Toxin–antitoxin loci as stress-response-elements: ChpAK/MazF and ChpBK cleave translated RNAs and are counteracted by tmRNA. J Mol Biol 332:809–819PubMedCrossRefGoogle Scholar
  13. Cifuentes A, Anton J, Benlloch S, Donnelly A, Herbert RA, Rodriguez-Valera F (2000) Prokaryotic diversity in Zostera noltii-colonized marine sediments. Appl Environ Microbiol 66:1715–1719PubMedCrossRefGoogle Scholar
  14. Colwell RR, Grimes, D.J. (2000) Nonculturable microorganisms in the environment. American Society for Microbiology, Washington, DCGoogle Scholar
  15. Connon SA, Giovannoni SJ (2002) High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates. Appl Environ Microbiol 68:3878–3885PubMedCrossRefGoogle Scholar
  16. Correia F, Donofrio A, Rejtar T, Lingyun L, Karger B, Makarova K, Koonin E, Lewis K (2006) Escherichia coli high-persistence hipa protein contains a kinase domain required for its function (submitted).Google Scholar
  17. Costerton JW, Lewandowski Z, Caldwell DE, Korber DR, Lappin-Scott HM (1995) Microbial biofilms. Annu Rev Microbiol 49:711–745PubMedCrossRefGoogle Scholar
  18. Curtis TP, Sloan WT, Scannell JW (2002) Estimating prokaryotic diversity and its limits. Proc Natl Acad Sci U S A 99:10494–10499PubMedCrossRefGoogle Scholar
  19. de Lillo A, Booth V, Kyriacou L, Weightman AJ, Wade WG (2004) Culture-independent identification of periodontitis-associated Porphyromonas and Tannerella populations by targeted molecular analysis. J Clin Microbiol 42:5523–5527PubMedCrossRefGoogle Scholar
  20. DeLong EF (1992) Archaea in coastal marine environments. Proc Natl Acad Sci U S A 89:5685–5689PubMedCrossRefGoogle Scholar
  21. Dojka MA, Harris JK, Pace NR (2000) Expanding the known diversity and environmental distribution of an uncultured phylogenetic division of bacteria. Appl Environ Microbiol 66:1617–1621PubMedCrossRefGoogle Scholar
  22. Epstein SS (1997) Microbial food webs in marine sediments. II. seasonal changes in trophic interactions in a sandy tidal flat Community. Microb Ecol 34:199–209PubMedCrossRefGoogle Scholar
  23. Falla TJ, Chopra I (1998) Joint tolerance to beta-lactam and fluoroquinolone antibiotics in Escherichia coli results from overexpression of hipA. Antimicrob Agents Chemother 42:3282–3284PubMedGoogle Scholar
  24. Ferrari BC, Binnerup SJ, Gillings M (2005) Microcolony cultivation on a soil substrate membrane system selects for previously uncultured soil bacteria. Appl Environ Microbiol 71:8714–8720PubMedCrossRefGoogle Scholar
  25. Fuhrman JA, McCallum K, Davis AA (1992) Novel major archaebacterial group from marine plankton. Nature 356:148–149PubMedCrossRefGoogle Scholar
  26. Gans J, Wolinsky M, Dunbar J (2005) Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 309:1387–1390PubMedCrossRefGoogle Scholar
  27. Gerdes K, Christensen SK, Lobner-Olesen A (2005) Prokaryotic toxin–antitoxin stress response loci. Nat Rev Microbiol 3:371–382PubMedCrossRefGoogle Scholar
  28. Giovannoni SJ, Britschgi TB, Moyer CL, Field KG (1990) Genetic diversity in Sargasso sea bacterioplankton. Nature 345:60–63PubMedCrossRefGoogle Scholar
  29. Giovannoni SJ, Tripp HJ, Givan S, Podar M, Vergin KL, Baptista D, Bibbs L, Eads J, Richardson TH, Noordewier M, Rappe MS, Short JM, Carrington JC, Mathur EJ (2005) Genome streamlining in a cosmopolitan oceanic bacterium. Science 309: 1242–1245PubMedCrossRefGoogle Scholar
  30. Giovannoni SJR (2000) Evolution, diversity and molecular ecology of marine prokaryotes. In: Kirchman D Microbial ecology of the oceans. Wiley-Liss, New York, 47–84Google Scholar
  31. Grimes DJ, Mills AL, Nealson KH (2000) The importance of viable but nonculturable bacteria in biogeochemistry. In: Colwell RR and Grimes DJ Nonculturable microorganisms in the environment. ASM, Washington DC, 209–227Google Scholar
  32. Hall-Stoodley L, Costerton JW, Stoodley P (2004) Bacterial biofilms: from the natural environment to infectious diseases. Nat Rev Microbiol 2:95–108PubMedCrossRefGoogle Scholar
  33. Harrison JJ, Ceri H, Roper NJ, Badry EA, Sproule KM, Turner RJ (2005a) Persister cells mediate tolerance to metal oxyanions in Escherichia coli. Microbiology 151:3181–3195CrossRefGoogle Scholar
  34. Harrison JJ, Turner RJ, Ceri H (2005b) Persister cells, the biofilm matrix and tolerance to metal cations in biofilm and planktonic Pseudomonas aeruginosa. Environ Microbiol 7:981–994CrossRefGoogle Scholar
  35. Hayes F (2003) Toxins-antitoxins: plasmid maintenance, programmed cell death, and cell cycle arrest. Science 301:1496–1499PubMedCrossRefGoogle Scholar
  36. Hu Y, Coates AR (2005) Transposon mutagenesis identifies genes which control antimicrobial drug tolerance in stationary-phase Escherichia coli. FEMS Microbiol Lett 243:117–124PubMedCrossRefGoogle Scholar
  37. Hugenholtz P, Goebel BM, Pace NR (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180: 4765–4774PubMedGoogle Scholar
  38. Jesaitis AJ, Franklin MJ, Berglund D, Sasaki M, Lord CI, Bleazard JB, Duffy JE, Beyenal H, Lewandowski Z (2003) Compromised host defense on Pseudomonas aeruginosa biofilms: characterization of neutrophil and biofilm interactions. J Immunol 171:4329–4339PubMedGoogle Scholar
  39. Kaeberlein T, Lewis K, Epstein SS (2002) Isolating “uncultivable” microorganisms in pure culture in a simulated natural environment. Science 296:1127–1129PubMedCrossRefGoogle Scholar
  40. Keren I, Kaldalu N, Spoering A, Wang Y, Lewis K (2004a) Persister cells and tolerance to antimicrobials. FEMS Microbiol Lett 230:13–18CrossRefGoogle Scholar
  41. Keren I, Shah D, Spoering A, Kaldalu N, Lewis K (2004b) Specialized persister cells and the mechanism of multidrug tolerance in Escherichia coli. J Bacteriol 186:8172–8180CrossRefGoogle Scholar
  42. Korch SB, Hill TM (2006) Ectopic overexpression of wild-type and mutant hipA genes in Escherichia coli: effects on macromolecular synthesis and persister formation. J Bacteriol 188:3826–3836PubMedCrossRefGoogle Scholar
  43. Korch SB, Henderson TA, Hill TM (2003) Characterization of the hipA7 allele of Escherichia coli and evidence that high persistence is governed by (p)ppGpp synthesis. Mol Microbiol 50:1199–1213PubMedCrossRefGoogle Scholar
  44. Leid JG, Shirtliff ME, Costerton JW, Stoodley AP (2002) Human leukocytes adhere to, penetrate, and respond to Staphylococcus aureus biofilms. Infect Immun 70:6339–6345PubMedCrossRefGoogle Scholar
  45. Lewis K (2001a) Riddle of biofilm resistance. Antimicrob Agents Chemother 45:999–1007CrossRefGoogle Scholar
  46. Lewis K (2001b) In search of natural substrates and inhibitors of MDR pumps. J Mol Microbiol Biotechnol 3:247–254Google Scholar
  47. Lewis K (2007) Persister cells, dormancy and infectious disease. Nat Rev Microbiol 5: 48–56PubMedCrossRefGoogle Scholar
  48. Lewis K, Salyers A, Taber H, Wax R (2002) Bacterial resistance to antimicrobials: mechanisms, genetics, medical practice and public health. Marcel Dekker, New YorkGoogle Scholar
  49. Li XZ, Nikaido H, Poole K (1995) Role of mexA-mexB-oprM in antibiotic efflux in Pseudomonas aeruginosa. Antimicrob Agents Chemother 39:1948–1953PubMedGoogle Scholar
  50. Liesack W, Stackebrandt E (1992) Occurrence of novel groups of the domain Bacteria as revealed by analysis of genetic material isolated from an Australian terrestrial environment. J Bacteriol 174:5072–5078PubMedGoogle Scholar
  51. Llobet-Brossa E, Rossello-Mora R, Amann R (1998) Microbial community composition of wadden sea sediments as revealed by fluorescence in situ hybridization. Appl Environ Microbiol 64:2691–2696PubMedGoogle Scholar
  52. Mack D, Becker P, Chatterjee I, Dobinsky S, Knobloch JK, Peters G, Rohde H, Herrmann M (2004) Mechanisms of biofilm formation in Staphylococcus epidermidis and Staphylococcus aureus: functional molecules, regulatory circuits, and adaptive responses. Int J Med Microbiol 294:203–212PubMedCrossRefGoogle Scholar
  53. Moyed HS, Bertrand KP (1983) hipA, a newly recognized gene of Escherichia coli K-12 that affects frequency of persistence after inhibition of murein synthesis. J Bacteriol 155:768–775PubMedGoogle Scholar
  54. Moyed HS, Broderick SH (1986) Molecular cloning and expression of hipA, a gene of Escherichia coli K- 12 that affects frequency of persistence after inhibition of murein synthesis. J Bacteriol 166:399–403PubMedGoogle Scholar
  55. Munson MA, Banerjee A, Watson TF, Wade WG (2004) Molecular analysis of the microflora associated with dental caries. J Clin Microbiol 42:3023–3029PubMedCrossRefGoogle Scholar
  56. Park HK, Shim SS, Kim SY, Park JH, Park SE, Kim HJ, Kang BC, Kim CM (2005) Molecular analysis of colonized bacteria in a human newborn infant gut. J Microbiol 43:345–353PubMedGoogle Scholar
  57. Pedersen K, Christensen SK, Gerdes K (2002) Rapid induction and reversal of a bacteriostatic condition by controlled expression of toxins and antitoxins. Mol Microbiol 45:501–510PubMedCrossRefGoogle Scholar
  58. Rappe MS, Connon SA, Vergin KL, Giovannoni SJ (2002) Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418:630–633PubMedCrossRefGoogle Scholar
  59. Rappe MS, Giovannoni SJ (2003) The uncultured microbial majority. Annu Rev Microbiol 57:369–394PubMedCrossRefGoogle Scholar
  60. Ravenschlag K, Sahm K, Pernthaler J, Amann R (1999) High bacterial diversity in permanently cold marine sediments. Appl Environ Microbiol 65:3982–3989PubMedGoogle Scholar
  61. Sat B, Hazan R, Fisher T, Khaner H, Glaser G, Engelberg-Kulka H (2001) Programmed cell death in Escherichia coli: some antibiotics can trigger mazEF lethality. J Bacteriol 183:2041–2045PubMedCrossRefGoogle Scholar
  62. Scherrer R, Moyed HS (1988) Conditional impairment of cell division and altered lethality in hipA mutants of Escherichia coli K-12. J Bacteriol 170:3321–3326PubMedGoogle Scholar
  63. Schmelzle T, Hall MN (2000) TOR, a central controller of cell growth. Cell 103:253–262PubMedCrossRefGoogle Scholar
  64. Setlow P (2003) Spore germination. Curr Opin Microbiol 6:550–556PubMedCrossRefGoogle Scholar
  65. Shah DV, Zhang Z, Kurg K, Kaldalu N, Khodursky A, Lewis K (2006) Persisters: A distinct physiological state of E. coli. BMC Microbiol 6:53PubMedCrossRefGoogle Scholar
  66. Singh PK, Schaefer AL, Parsek MR, Moninger TO, Welsh MJ, Greenberg EP (2000) Quorum-sensing signals indicate that cystic fibrosis lungs are infected with bacterial biofilms. Nature 407:762–764PubMedCrossRefGoogle Scholar
  67. Spoering AL, Lewis K (2001) Biofilms and planktonic cells of Pseudomonas aeruginosa have similar resistance to killing by antimicrobials. J Bacteriol 183:6746–6751PubMedCrossRefGoogle Scholar
  68. Spoering AL, Vulic M, Lewis K (2006) GlpD and PlsB participate in persister cell formation in Escherichia coli. J Bacteriol 188:5136–5144PubMedCrossRefGoogle Scholar
  69. Stackebrandt E, Embley TM (2000) Diversity of uncultured microorganisms in the environment. In: Colwell RR and Grimes DJNonculturable microorganisms in the environment. ASM, Washington DC, 57–75Google Scholar
  70. Staley JT, Konopka A (1985) Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Annu Rev Microbiol 39:321–346PubMedCrossRefGoogle Scholar
  71. Stewart E, D’Onofrio A, Witt K, Epstein S, Lewis K (2008) Identification of natural growth factors allows increased recovery of environmental bacterial isolates. Abstract N-042/0709. In ASM General Meeting ASM, Boston, MAGoogle Scholar
  72. Tiedje JM (1994) Microbial diversity: of value to whom? ASM News 60:524–525Google Scholar
  73. Torsvik V, Goksoyr J, Daae FL (1990) High diversity in DNA of soil bacteria. Appl Environ Microbiol 56:782–787PubMedGoogle Scholar
  74. Vazquez-Laslop N, Lee H, Neyfakh AA (2006) Increased persistence in Escherichia coli caused by controlled expression of toxins or other unrelated proteins. J Bacteriol 188:3494–3497PubMedCrossRefGoogle Scholar
  75. Vuong C, Voyich JM, Fischer ER, Braughton KR, Whitney AR, DeLeo FR, Otto M (2004) Polysaccharide intercellular adhesin (PIA) protects Staphylococcus epidermidis against major components of the human innate immune system. Cell Microbiol 6:269–275PubMedCrossRefGoogle Scholar
  76. Walker GC (1996) The SOS response of Escherichia coli Escherichia coli and Samonella cellular and molecular biology. ASM, Washington DC, 1400–1416Google Scholar
  77. Ward DM, Weller R, Bateson MM (1990) 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 345:63–65PubMedCrossRefGoogle Scholar
  78. Wiuff C, Zappala RM, Regoes RR, Garner KN, Baquero F, Levin BR (2005) Phenotypic tolerance: antibiotic enrichment of noninherited resistance in bacterial populations. Antimicrob Agents Chemother 49:1483–1494PubMedCrossRefGoogle Scholar
  79. Yoshida H, Maki Y, Kato H, Fujisawa H, Izutsu K, Wada C, Wada A (2002) The ribosome modulation factor (RMF) binding site on the 100S ribosome of Escherichia coli. J Biochem 132:983–989PubMedGoogle Scholar
  80. Zengler K, Toledo G, Rappe M, Elkins J, Mathur EJ, Short JM, Keller M (2002) Cultivating the uncultured. Proc Natl Acad Sci U S A 99:15681–15686PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  1. 1.Antimicrobial Discovery Center and The Department of BiologyNortheastern UniversityBostonMA

Personalised recommendations