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Persisters, Biofilms, and the Problem of Cultivability

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Uncultivated Microorganisms

Part of the book series: Microbiology Monographs ((MICROMONO,volume 10))

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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.

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References

  • Allsopp, D, Colwell, RR, Hawksworth, DL (1995) Microbial diversity and ecosystem function: CAB InternationalWallingford UK:

    Google Scholar 

  • Balaban NQ, Merrin J, Chait R, Kowalik L, Leibler S (2004) Bacterial persistence as a phenotypic switch. Science 305:1622–1625

    Article  PubMed  CAS  Google Scholar 

  • Barer MR, Harwood, CR (1999) Bacterial viability and culturability. Adv Microb Physiol 41:93–137

    Article  PubMed  CAS  Google Scholar 

  • 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 91:1609–1613

    Article  PubMed  CAS  Google Scholar 

  • Bigger JW (1944) Treatment of staphylococcal infections with penicillin. Lancet ii:497–500

    Article  Google Scholar 

  • 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 173:5732–5739

    PubMed  CAS  Google Scholar 

  • 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 176:4081–4091

    PubMed  CAS  Google Scholar 

  • Bollmann A, Lewis K, Epstein SS (2007) Incubation of environmental samples in a diffusion chamber increases the diversity of recovered isolates. Appl Environ Microbiol 73:6386–6390

    Article  PubMed  CAS  Google Scholar 

  • Brooun A, Liu S, Lewis K (2000) A dose-response study of antibiotic resistance in Pseudomonas aeruginosa biofilms. Antimicrob Agents Chemother 44:640–646

    Article  PubMed  CAS  Google Scholar 

  • 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) 2:5–39

    Google Scholar 

  • Christensen SK, Gerdes K. (2003) RelE toxins from bacteria and Archaea cleave mRNAs on translating ribosomes, which are rescued by tmRNA. Mol Microbiol 48:1389–1400

    Article  PubMed  CAS  Google Scholar 

  • 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 332:809–819

    Article  PubMed  CAS  Google Scholar 

  • 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 66:1715–1719

    Article  PubMed  CAS  Google Scholar 

  • Colwell RR, Grimes, D.J. (2000) Nonculturable microorganisms in the environment. American Society for Microbiology, Washington, DC

    Google Scholar 

  • Connon SA, Giovannoni SJ (2002) High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates. Appl Environ Microbiol 68:3878–3885

    Article  PubMed  CAS  Google Scholar 

  • 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 

  • Costerton JW, Lewandowski Z, Caldwell DE, Korber DR, Lappin-Scott HM (1995) Microbial biofilms. Annu Rev Microbiol 49:711–745

    Article  PubMed  CAS  Google Scholar 

  • Curtis TP, Sloan WT, Scannell JW (2002) Estimating prokaryotic diversity and its limits. Proc Natl Acad Sci U S A 99:10494–10499

    Article  PubMed  CAS  Google Scholar 

  • 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 42:5523–5527

    Article  PubMed  Google Scholar 

  • DeLong EF (1992) Archaea in coastal marine environments. Proc Natl Acad Sci U S A 89:5685–5689

    Article  PubMed  CAS  Google Scholar 

  • Dojka MA, Harris JK, Pace NR (2000) Expanding the known diversity and environmental distribution of an uncultured phylogenetic division of bacteria. Appl Environ Microbiol 66:1617–1621

    Article  PubMed  CAS  Google Scholar 

  • Epstein SS (1997) Microbial food webs in marine sediments. II. seasonal changes in trophic interactions in a sandy tidal flat Community. Microb Ecol 34:199–209

    Article  PubMed  Google Scholar 

  • Falla TJ, Chopra I (1998) Joint tolerance to beta-lactam and fluoroquinolone antibiotics in Escherichia coli results from overexpression of hipA. Antimicrob Agents Chemother 42:3282–3284

    PubMed  CAS  Google Scholar 

  • Ferrari BC, Binnerup SJ, Gillings M (2005) Microcolony cultivation on a soil substrate membrane system selects for previously uncultured soil bacteria. Appl Environ Microbiol 71:8714–8720

    Article  PubMed  CAS  Google Scholar 

  • Fuhrman JA, McCallum K, Davis AA (1992) Novel major archaebacterial group from marine plankton. Nature 356:148–149

    Article  PubMed  CAS  Google Scholar 

  • Gans J, Wolinsky M, Dunbar J (2005) Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 309:1387–1390

    Article  PubMed  CAS  Google Scholar 

  • Gerdes K, Christensen SK, Lobner-Olesen A (2005) Prokaryotic toxin–antitoxin stress response loci. Nat Rev Microbiol 3:371–382

    Article  PubMed  CAS  Google Scholar 

  • Giovannoni SJ, Britschgi TB, Moyer CL, Field KG (1990) Genetic diversity in Sargasso sea bacterioplankton. Nature 345:60–63

    Article  PubMed  CAS  Google Scholar 

  • 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: 1242–1245

    Article  PubMed  CAS  Google Scholar 

  • Giovannoni SJR (2000) Evolution, diversity and molecular ecology of marine prokaryotes. In: Kirchman D Microbial ecology of the oceans. Wiley-Liss, New York, 47–84

    Google Scholar 

  • 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, 209–227

    Google Scholar 

  • Hall-Stoodley L, Costerton JW, Stoodley P (2004) Bacterial biofilms: from the natural environment to infectious diseases. Nat Rev Microbiol 2:95–108

    Article  PubMed  CAS  Google Scholar 

  • Harrison JJ, Ceri H, Roper NJ, Badry EA, Sproule KM, Turner RJ (2005a) Persister cells mediate tolerance to metal oxyanions in Escherichia coli. Microbiology 151:3181–3195

    Article  CAS  Google Scholar 

  • 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 7:981–994

    Article  CAS  Google Scholar 

  • Hayes F (2003) Toxins-antitoxins: plasmid maintenance, programmed cell death, and cell cycle arrest. Science 301:1496–1499

    Article  PubMed  CAS  Google Scholar 

  • Hu Y, Coates AR (2005) Transposon mutagenesis identifies genes which control antimicrobial drug tolerance in stationary-phase Escherichia coli. FEMS Microbiol Lett 243:117–124

    Article  PubMed  CAS  Google Scholar 

  • Hugenholtz P, Goebel BM, Pace NR (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180: 4765–4774

    PubMed  CAS  Google Scholar 

  • 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 171:4329–4339

    PubMed  CAS  Google Scholar 

  • Kaeberlein T, Lewis K, Epstein SS (2002) Isolating “uncultivable” microorganisms in pure culture in a simulated natural environment. Science 296:1127–1129

    Article  PubMed  CAS  Google Scholar 

  • Keren I, Kaldalu N, Spoering A, Wang Y, Lewis K (2004a) Persister cells and tolerance to antimicrobials. FEMS Microbiol Lett 230:13–18

    Article  CAS  Google Scholar 

  • 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 186:8172–8180

    Article  CAS  Google Scholar 

  • 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 188:3826–3836

    Article  PubMed  CAS  Google Scholar 

  • 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 50:1199–1213

    Article  PubMed  CAS  Google Scholar 

  • Leid JG, Shirtliff ME, Costerton JW, Stoodley AP (2002) Human leukocytes adhere to, penetrate, and respond to Staphylococcus aureus biofilms. Infect Immun 70:6339–6345

    Article  PubMed  CAS  Google Scholar 

  • Lewis K (2001a) Riddle of biofilm resistance. Antimicrob Agents Chemother 45:999–1007

    Article  CAS  Google Scholar 

  • Lewis K (2001b) In search of natural substrates and inhibitors of MDR pumps. J Mol Microbiol Biotechnol 3:247–254

    CAS  Google Scholar 

  • Lewis K (2007) Persister cells, dormancy and infectious disease. Nat Rev Microbiol 5: 48–56

    Article  PubMed  CAS  Google Scholar 

  • Lewis K, Salyers A, Taber H, Wax R (2002) Bacterial resistance to antimicrobials: mechanisms, genetics, medical practice and public health. Marcel Dekker, New York

    Google Scholar 

  • Li XZ, Nikaido H, Poole K (1995) Role of mexA-mexB-oprM in antibiotic efflux in Pseudomonas aeruginosa. Antimicrob Agents Chemother 39:1948–1953

    PubMed  CAS  Google Scholar 

  • 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 174:5072–5078

    PubMed  CAS  Google Scholar 

  • 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 64:2691–2696

    PubMed  Google Scholar 

  • 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 294:203–212

    Article  PubMed  CAS  Google Scholar 

  • 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 155:768–775

    PubMed  CAS  Google Scholar 

  • 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 166:399–403

    PubMed  CAS  Google Scholar 

  • Munson MA, Banerjee A, Watson TF, Wade WG (2004) Molecular analysis of the microflora associated with dental caries. J Clin Microbiol 42:3023–3029

    Article  PubMed  CAS  Google Scholar 

  • 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 43:345–353

    PubMed  CAS  Google Scholar 

  • Pedersen K, Christensen SK, Gerdes K (2002) Rapid induction and reversal of a bacteriostatic condition by controlled expression of toxins and antitoxins. Mol Microbiol 45:501–510

    Article  PubMed  CAS  Google Scholar 

  • Rappe MS, Connon SA, Vergin KL, Giovannoni SJ (2002) Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418:630–633

    Article  PubMed  CAS  Google Scholar 

  • Rappe MS, Giovannoni SJ (2003) The uncultured microbial majority. Annu Rev Microbiol 57:369–394

    Article  PubMed  CAS  Google Scholar 

  • Ravenschlag K, Sahm K, Pernthaler J, Amann R (1999) High bacterial diversity in permanently cold marine sediments. Appl Environ Microbiol 65:3982–3989

    PubMed  CAS  Google Scholar 

  • 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 183:2041–2045

    Article  PubMed  CAS  Google Scholar 

  • Scherrer R, Moyed HS (1988) Conditional impairment of cell division and altered lethality in hipA mutants of Escherichia coli K-12. J Bacteriol 170:3321–3326

    PubMed  CAS  Google Scholar 

  • Schmelzle T, Hall MN (2000) TOR, a central controller of cell growth. Cell 103:253–262

    Article  PubMed  CAS  Google Scholar 

  • Setlow P (2003) Spore germination. Curr Opin Microbiol 6:550–556

    Article  PubMed  CAS  Google Scholar 

  • Shah DV, Zhang Z, Kurg K, Kaldalu N, Khodursky A, Lewis K (2006) Persisters: A distinct physiological state of E. coli. BMC Microbiol 6:53

    Article  PubMed  Google Scholar 

  • 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 407:762–764

    Article  PubMed  CAS  Google Scholar 

  • Spoering AL, Lewis K (2001) Biofilms and planktonic cells of Pseudomonas aeruginosa have similar resistance to killing by antimicrobials. J Bacteriol 183:6746–6751

    Article  PubMed  CAS  Google Scholar 

  • Spoering AL, Vulic M, Lewis K (2006) GlpD and PlsB participate in persister cell formation in Escherichia coli. J Bacteriol 188:5136–5144

    Article  PubMed  CAS  Google Scholar 

  • 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, 57–75

    Google Scholar 

  • Staley JT, Konopka A (1985) Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Annu Rev Microbiol 39:321–346

    Article  PubMed  CAS  Google Scholar 

  • 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, MA

    Google Scholar 

  • Tiedje JM (1994) Microbial diversity: of value to whom? ASM News 60:524–525

    Google Scholar 

  • Torsvik V, Goksoyr J, Daae FL (1990) High diversity in DNA of soil bacteria. Appl Environ Microbiol 56:782–787

    PubMed  CAS  Google Scholar 

  • 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 188:3494–3497

    Article  PubMed  CAS  Google Scholar 

  • 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 6:269–275

    Article  PubMed  CAS  Google Scholar 

  • Walker GC (1996) The SOS response of Escherichia coli Escherichia coli and Samonella cellular and molecular biology. ASM, Washington DC, 1400–1416

    Google Scholar 

  • Ward DM, Weller R, Bateson MM (1990) 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 345:63–65

    Article  PubMed  CAS  Google Scholar 

  • 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 49:1483–1494

    Article  PubMed  CAS  Google Scholar 

  • 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 132:983–989

    PubMed  CAS  Google Scholar 

  • 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 99:15681–15686

    Article  PubMed  CAS  Google Scholar 

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  1. Antimicrobial Discovery Center and The Department of Biology, Northeastern University, 360 Huntington Ave, Boston, MA, USA

    Kim Lewis

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Correspondence to Kim Lewis .

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  1. Dept. Biology, Northeastern University, Boston, 02115, U.S.A.

    Slava S. Epstein

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Lewis, K. (2009). Persisters, Biofilms, and the Problem of Cultivability. In: Epstein, S. (eds) Uncultivated Microorganisms. Microbiology Monographs, vol 10. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-85465-4_7

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