Advertisement

Principles of Enrichment, Isolation, Cultivation, and Preservation of Prokaryotes

Reference work entry

Abstract

Currently, a total of 9,409 prokaryotic species are recognized (as of January 2012, validly published names not including homotypic and heterotypic synonyms, comb. nov. and nomina nova; DSMZ 2012; Euzéby 2012). By comparison, the number of small subunit ribosomal RNA (SSU rRNA) gene sequences deposited in public databases keeps increasing exponentially (Pruesse et al. 2007; Yarza et al. 2008) and surmounted the species numbers already some 15 years ago (Fig. 7.1). Meanwhile, a total of 2,492,653 sequences are available of which 2,282,670 are prokaryotic whereas only 33,842 originate from cultured strains (SILVA 2012). In line with these cumulative data, culture-independent analyses of DNA reassociation kinetics and of 16S rRNA gene sequences in individual environmental samples also indicate that prokaryotic diversity is poorly represented by the species cultivated so far. Thus, estimates of bacterial species numbers in just one type of soil reached values of up to 53,000 (Sandaa et al. 1999; Roesch et al. 2007). Furthermore, molecular investigations of 16S rRNA gene sequences in natural bacterial assemblages typically yielded many more sequence types than those recovered by cultivation-based approaches (Fuhrman et al. 1992; Ward et al. 1992; Barns et al. 1994; DeLong et al. 1994; Hiorns et al. 1997; Kuske et al. 1997; Ludwig et al. 1997; Suzuki et al. 1997; Gich et al. 2001; Béjà et al. 2002; Roesch et al. 2007). In light of these findings, the earlier estimates of the fraction of already cultured bacterial species of 12–20% (Wayne et al. 1987; Bull et al. 1992) or even the commonly cited estimate of 1% appears to be far too optimistic. Based on recent estimates of total bacterial species numbers (107–109; Dykhuizen 1998; Curtis et al. 2002), the value more likely ranges between 0.1% and 0.001% and may be even lower (compare the higher estimates of bacterial species numbers in Sogin et al. 2006; Harwood and Buckley 2008).

Keywords

Prokaryotic Bacterial Species Number Retentostat Ultramicrobacteria Phototrophic Consortia 
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.
This is a preview of subscription content, log in to check access.

References

  1. Aagot N, Nybroe O, Nielsen P, Johnsen K (2001) An altered Pseudomonas diversity is recovered from soil by using nutrient-poor Pseudomonas-selective soil extract media. Appl Environ Microbiol 67:5233–5239PubMedGoogle Scholar
  2. Aaronson S (1970) Experimental microbial ecology. Academic, New YorkGoogle Scholar
  3. Abdul-Tehrani H, Hudson AJ, Chang YS, Timms AR, Hawkins C, Williams JM, Harrison PM, Guest JR, Andrews SC (1999) Ferritin mutants of Escherichia coli are iron deficient and growth impaired, and fur mutants are iron deficient. J Bacteriol 181:1415–1428PubMedGoogle Scholar
  4. Achberger AM, Brox TI, Skidmore ML, Christner BC (2011) Expression and partial characterization of an ice-binding protein from a bacterium isolated at a depth of 3,519 m in the Vostok ice core, Antarctica. Front Microbiol 2:255PubMedGoogle Scholar
  5. Ahn WS, Park SJ, Lee SY (2001) Production of poly (3-hydroxybutyrate) from whey by cell recycle fed-batch culture of recombinant Escherichia coli. Biotechnol Lett 23:235–240Google Scholar
  6. Aksoy S (1995) Wigglesworthia gen. nov. and Wigglesworthia glossinidia sp. nov., taxa consisting of the mycetocyte-associated, primary endosymbionts of Tsetse flies. Int J Syst Bacteriol 45:848–851PubMedGoogle Scholar
  7. Alden L, Demoling F, Baath E (2001) Rapid method of determining factors limiting bacterial growth in soil. Appl Environ Microbiol 67:1830–1838PubMedGoogle Scholar
  8. Aldsworth TG, Sharman RL, Dodd CER (1999) Bacterial suicide through stress. Cell Mol Life Sci 56:378–383PubMedGoogle Scholar
  9. Alldredge AL, Youngbluth MJ (1985) The significance of macroscopic aggregates (marine snow) as sites for heterotrophic bacterial production in the mesopelagic zone of the subtropical Atlantic. Deep-Sea Res 32:1445–1456Google Scholar
  10. Amy PS, Morita RY (1983) Starvation-survival patterns of sixteen freshly isolated open-ocean bacteria. Appl Environ Microbiol 45:1109–1115PubMedGoogle Scholar
  11. Andrews JH (1984) Relevance of r-and K-theory to the ecology of plant pathogens. In: Klug MJ, Reddy CA (eds) Current perspectives in microbial ecology. ASM Press, Washington, DC, pp 1–7Google Scholar
  12. Andrews JH, Harris RF (1986) r-and K-selection and microbial ecology. In: Marshall KC (ed) Advanced microbiology and ecology, vol 9. Plenum, New York, pp 1–7Google Scholar
  13. Andrews SC, Robinson AK, Rodriguez-Quinones F (2003) Bacterial iron homeostasis. FEMS Microbiol Rev 27:215–237PubMedGoogle Scholar
  14. Angle JS, McGrath SP, Chaney RL (1991) New culture medium containing ionic concentrations of nutrients similar to concentrations found in the soil solution. Appl Environ Microbiol 57:3674–3676PubMedGoogle Scholar
  15. Arrhenius S (1889) Über die Reaktionsgeschwindigkeit bei der Inversion von Rohrzucker durch Säuren. Z Phys Chem 4:226–248Google Scholar
  16. Atlas RM, Bartha R (1993) Microbial ecology, 3rd edn. Benjamin/Cummings, Redwood CityGoogle Scholar
  17. Austin B (1988) Methods in aquatic bacteriology. Wiley, ChichesterGoogle Scholar
  18. Azam F (1998) Microbial control of oceanic carbon flux: The plot thickens. Science 280:694–696Google Scholar
  19. Bak F, Pfennig N (1991) Microbial sulfate reduction in littoral sediment of Lake Constance. FEMS Microbiol Ecol 85:31–42Google Scholar
  20. Balch WE, Wolfe RS (1976) New approach to the cultivation of methanogenic bacteria: 2-mercaptoethane sulfonic acid (HS-CoM)-dependent growth of Methanobacterium ruminantium in a pressurized atmosphere. Appl Environ Microbiol 32:781–791PubMedGoogle Scholar
  21. Bale SJ, Goodman K, Rochelle PA, Marchesi JR, Fry JC, Weightman AJ, Parkes RJ (1997) Desulfovibrio profundus sp. nov., a novel barophilic sulfate-reducing bacterium from deep sediment layers in the Japan Sea. Int J Syst Bacteriol 47:515–521PubMedGoogle Scholar
  22. Balestra GM, Misaghi IL (1997) Increasing the efficiency of the plate counting method for estimating bacterial diversity. J Microbiol Methods 30:111–117Google Scholar
  23. Barer MR, Harwood CR (1999) Bacterial viability and culturability. Adv Microb Physiol 41:93–137PubMedGoogle Scholar
  24. 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 USA 91:1609–1613PubMedGoogle Scholar
  25. Barns SM, Takala SL, Kuske CR (1999) Wide distribution and diversity of members of the bacterial kingdom Acidobacterium in the environment. Appl Environ Microbiol 65:1731–1737PubMedGoogle Scholar
  26. Baross JA, Morita RY (1978) Microbial life at low temperatures: ecological aspects. In: Kushner DJ (ed) Microbial life in extreme environments. Academic, London, pp 9–17Google Scholar
  27. Bartlett DH, Welch TJ (1995) ompH gene expression is regulated by multiple environmental cues in addition to high pressure in the deep-sea bacterium Photobacterium species strain SS9. J Bacteriol 177:1008–1016PubMedGoogle Scholar
  28. Bartlett D, Wright M, Yayanos AA, Silverman M (1989) Isolation of a gene regulated by hydrostatic pressure in a deep-sea bacterium. Nature 342:572–574PubMedGoogle Scholar
  29. Bartlett DH, Chi E, Wright ME (1993) Sequence of the ompH gene from the deep-sea bacterium Photobacterium SS9. Gene 131:125–128PubMedGoogle Scholar
  30. Bartscht K, Cypionka H, Overmann J (1999) Evaluation of cell activity and of methods for the cultivation of bacteria from a natural lake community. FEMS Microbiol Ecol 28:249–259Google Scholar
  31. Basler BL, Losick R (2006) Bacterially speaking. Cell 125:237–246Google Scholar
  32. Bast E (2001) Mikrobiologische methoden, 2nd edn. Spektrum Akad, BerlinGoogle Scholar
  33. Bateson MM, Ward DM (1988) Photoexcretion and fate of glycolate in a hot spring cyanobacterial mat. Appl Environ Microbiol 54:1738–1743PubMedGoogle Scholar
  34. Battley EH (1995) An apparent anomaly in the calculation of ash-free dry weights for the determination of cellular yields. Appl Environ Microbiol 61:1655–1657PubMedGoogle Scholar
  35. Baxter RM, Gibbons NE (1962) Observations on the physiology of psychrophilism in a yeast. Can J Microbiol 8:511–517Google Scholar
  36. Beier S, Bertilsson S (2011) Uncoupling of chitinase activity and uptake of hydrolysis products in freshwater bacterioplankton. Limnol Oceanogr 56:1179–1188Google Scholar
  37. Béjà O, Aravind L, Koonin EV, Suzuki MT, Hadd A, Nguyen LP, Jovanovich SB, Gates CM, Feldman RA, Spudich JL, Spudich EN, DeLong EF (2000) Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science 289:1902–1906PubMedGoogle Scholar
  38. Béjà O, Suzuki MT, Heidelberg JF, Nelson WC, Preston CM, Hamadas T, Eisen JA, Fraser CM, DeLong EF (2002) Unsuspected diversity among marine aerobic anoxygenic phototrophs. Nature 415:630–633PubMedGoogle Scholar
  39. Benz M, Schink B, Brune A (1998) Humic acid reduction by Propionibacterium freudenreichii and other fermenting bacteria. Appl Environ Microbiol 64:4507–4512PubMedGoogle Scholar
  40. Bernard L, Schäfer H, Joux F, Courties C, Muyzer G, Lebaron P (2000) Genetic diversity of total, active and culturable marine bacteria in coastal seawater. Aquat Microb Ecol 23:1–11Google Scholar
  41. Bernhardt G, Lüdemann H-D, Jaenicke R, König H, Stetter KO (1984) Biomolecules are unstable under “black smoker” conditions. Naturwissenschaften 71:583–586Google Scholar
  42. Beudeker RF, Gottschal JC, Kuenen JG (1982) Reactivity versus flexibility in thiobacilli. Antonie Van Leeuwenhoek 48:39–51PubMedGoogle Scholar
  43. Beunink J, Rehm HJ (1988) Synchronous anaerobic and aerobic degradation of DDT by an immobilized mixed culture system. Appl Microbiol Biotechnol 29:72–80Google Scholar
  44. Bhakoo M, Herbert RA (1979) The effects of temperature on the fatty acid and phospholipid composition of four obligately psychrophilic Vibrio spp. Arch Microbiol 121:121–127Google Scholar
  45. Bi E, Lutkenhaus J (1993) Cell division inhibitors SulA and MinCD prevent formation of the FtsZ ring. J Bacteriol 175:1118–1125PubMedGoogle Scholar
  46. Bidle KD, Lee SH, Marchant DR, Falskowski PG (2007) Fossil genes and microbes in the oldest ice on Earth. Proc Natl Acad Sci USA 104:13455–13460PubMedGoogle Scholar
  47. Biebl H, Pfennig N (1978) Growth yields of green sulfur bacteria in mixed cultures with sulfur and sulfate reducing bacteria. Arch Microbiol 117:9–16Google Scholar
  48. Binnerup SJ, Jensen DF, Thordal-Christensen H, Sorgensen J (1993) Detection of viable, but non-culturable Pseudomonas fluorescens DF57 in soil using a microcolony epifluorescence technique. FEMS Microbiol Ecol 12:97–195Google Scholar
  49. Biville F, Laurent-Winter C, Danchin A (1996) In vivo positive effects of exogenous pyrophosphate on Escherichia coli cell growth and stationary phase survival. Res Microbiol 147:597–608PubMedGoogle Scholar
  50. Blochl E, Rachel R, Burggraf S, Hafenbradl D, Jannasch HW, Stetter KO (1997) Pyrolobus fumarii, gen. nov. and sp. nov., represents a novel group of archaea, extending the upper temperature limit for life to 113°C. Extremophiles 1:14–21PubMedGoogle Scholar
  51. Bolen DW (2001) Protein stabilization by naturally occurring osmolytes. Methods Mol Biol 168:17–36PubMedGoogle Scholar
  52. Boone DR, Bryant MP (1980) Propionate degrading bacterium Syntrophobacter wolinii sp. nov., gen. nov. from methanogenic ecosystems. Appl Environ Microbiol 33:1162–1169Google Scholar
  53. Botsford JL, Harman JG (1992) Cyclic AMP in prokaryotes. Microbiol Rev 56:100–122PubMedGoogle Scholar
  54. Bovill RA, Mackey BM (1997) Resuscitation of “non-culturable” cells from aged cultures of Campylobacter jejuni. Microbiology 143:1575–1581PubMedGoogle Scholar
  55. Bowman JP, McCammon SA, Brown JL, Nichols PD, McMeekin TA (1997a) Psychroserpens burtonensis gen. nov., sp. nov., and Gelidibacter algens, gen. nov., sp. nov., psychrophilic bacteria isolated from Antarctic lacustrine and sea ice habitats. Int J Syst Evol Microbiol 47:670–677Google Scholar
  56. Bowman JP, McCammon SA, Nichols DS, Skerratt JH, Rea SM, Nichols PE, McMeekin TA (1997b) Shewanella gelidimarina sp. nov. and Shewanella frigidimarina sp. nov., novel Antarctic species with the ability to produce eicosapentaenoic acid (20:5w3) and grow anaerobically by dissimilatory Fe(III) reduction. Int J Syst Bacteriol 47:1040–1047PubMedGoogle Scholar
  57. Bowman JP, McCammon SA, Skerratt JH (1997c) Methylosphaera hansonii gen. nov., sp. nov., a psychrophilic, group I methanotroph from Antarctic marine-salinity, meromictic lakes. Microbiology 143:1451–1459PubMedGoogle Scholar
  58. Bowman JP, McCammon SA, Brown JL, McMeekin TA (1998a) Glaciecola punicea gen. nov., sp. nov., and Glaciecola pallidula gen. nov., sp. nov.: psychrophilic bacteria from Antarctic sea-ice habitats. Int J Syst Evol Microbiol 48:1213–1222Google Scholar
  59. Bowman JP, McCammon SA, Lewis T, Skerratt JH, Brown JL, Nichols DS, McMeekin TA (1998b) Psychroflexus torquis gen. nov., sp. nov., a psychrophilic species from Antarctic sea ice, and reclassification of Flavobacterium gondwanense (Dobson et al. 1993) as Psychroflexus gondwandense gen. nov., comb. nov. Microbiology 144:1601–1609PubMedGoogle Scholar
  60. Boyaval P (1989) Lactic acid bacteria and metal ions. Lait 69:87–113Google Scholar
  61. Bozal N, Montes MJ, Tudela E, Jimenez F, Guinea J (2002) Shewanella frigidimarina and Shewanella livingstonesis sp. nov. isolated from Antarctic coastal areas. Int J Syst Evol Microbiol 52:195–205PubMedGoogle Scholar
  62. Braun V (1997) Avoidance of iron toxicity through regulation of bacterial iron transport. Biol Chem 378:779–786PubMedGoogle Scholar
  63. Brefeld O (1881) Botanische Untersuchungen Über Schimmelpilze: Culturmethoden. Felix, LeipzigGoogle Scholar
  64. Brewer DG, Martin SE, Ordal ZJ (1977) Beneficial effects of catalase or pyruvate in a most-probable-number technique for the detection of Staphylococcus aureus. Appl Environ Microbiol 34:797–800PubMedGoogle Scholar
  65. Brock TD (1978) Thermophilic microorganisms and life at high temperatures. Springer, New YorkGoogle Scholar
  66. Brock TD (1987) Introduction: an overview of the thermophiles. In: Brock TD (ed) Thermophiles: general molecular and applied microbiology. Wiley, New York, pp 1–16Google Scholar
  67. Brock TD, O’Dea K (1977) Amorphous ferrous sulfide as a reducing agent for culture of anaerobes. Appl Environ Microbiol 33:254–256PubMedGoogle Scholar
  68. Broda E (1977) Two kinds of lithotrophs missing in nature. Z Allg Mikrobiol 17:491–493PubMedGoogle Scholar
  69. Broda DM, Saul DJ, Lawson PA, Bell RG, Musgrave DR (2000) Clostridium gasigenes sp. nov., a psychrophile causing spoilage of vacuum-packed meat. Int J Syst Evol Microbiol 50:107–118PubMedGoogle Scholar
  70. Bromke B, Hammel JM (1987) Gelatin as a complete endogenous source of calcium for Serratia marcescens protease activity. J Microbiol Methods 6:253–256Google Scholar
  71. Brooke AG, Watling EM, Attwood MM, Tempest DW (1989) Environmental control of metabolic fluxes in thermotolerant methylotrophic Bacillus strains. Arch Microbiol 151:268–273Google Scholar
  72. Brown AD (1976) Microbial water stress. Bacteriol Rev 40:803–846PubMedGoogle Scholar
  73. Brown AD, Simpson JR (1972) Water relations of sugar-tolerant yeasts: the role of intracellular polyols. J Gen Microbiol 72:589–591PubMedGoogle Scholar
  74. Brown SA, Whiteley M (2007) A novel exclusion mechanism for carbon resource partitioning in Aggregatibacter actinomycetemcomitans. J Bacteriol 189:6407–6414PubMedGoogle Scholar
  75. Bruhn JB, Nielsen KF, Hjelm M, Hansen M, Brescani J, Schulz S, Gram L (2005) Ecology, inhibitory activity, and morphogenesis of a marine antagonistic bacterium belonging to the Roseobacter clade. Appl Environ Microbiol 71:7263–7270PubMedGoogle Scholar
  76. Bruns A, Cypionka H, Overmann J (2002) Cyclic AMP and acyl homoserine lactones increase the cultivation efficiency of heterotrophic bacteria from the central Baltic Sea. Appl Environ Microbiol 68:3978–3987PubMedGoogle Scholar
  77. Bruns A, Hoffelner H, Overmann J (2003a) A novel approach for high throughput assays and the isolation of planktonic bacteria. FEMS Microbiol Ecol 45:161–171PubMedGoogle Scholar
  78. Bruns A, Nübel U, Cypionka H, Overmann J (2003b) Effect of signal compounds and incubation conditions on the culturability of freshwater bacterioplankton. Appl Environ Microbiol 69:1980–1989PubMedGoogle Scholar
  79. Bryant MP (1976) The microbiology of anaerobic degradation and methanogenesis with special reference to sewage. In: Schlegel HW, Barnea J (eds) Microbial energy conversion. Erick Goltze KG, Göttingen, pp 107–1167Google Scholar
  80. Bryson V, Szybalski W (1952) Microbial selection. Science 116:45–51Google Scholar
  81. Bull AT, Slater JH (1982) Microbial interactions and community structure. In: Bull AT, Slater JH (eds) Microbial interactions and communities, vol 1. Academic, London, pp 13–44Google Scholar
  82. Bull AT, Goodfellow M, Slater JH (1992) Biodiversity as a source of innovation in biotechnology. Annu Rev Microbiol 46:219–252PubMedGoogle Scholar
  83. Bulthuis BA, Koningstein GM, Stouthamer AH, van Verseveld HW (1989) A comparison between aerobic growth of Bacillus licheniformis in continuous culture and partial-recycling fermenter, with contributions to the discussion on maintenance energy demand. Arch Microbiol 152:499–507Google Scholar
  84. Bungay HR, Bungay ML (1968) Microbial interactions in continuous culture. Adv Appl Microbiol 10:269–290PubMedGoogle Scholar
  85. Bunt JG (1961) Nitrogen-fixing blue-green algae in Australian rice soils. Nature 192:479–480Google Scholar
  86. Burchard RP (1980) Gliding motility of bacteria. Bioscience 30:157–162Google Scholar
  87. Burkhardt F (1992) Mikrobiologische diagnostik georg. Thieme, New YorkGoogle Scholar
  88. Burnham JC, Conti SF (1984) Genus Bdellovibrio. In: Krieg NR (ed) Bergey’s manual of systematic bacteriology, vol 1. Williams and Wilkins, Baltimore, pp 118–124Google Scholar
  89. Bussmann I, Philipp B, Schink B (2001) Factors influencing the cultivability of lake water bacteria. J Microbiol Methods 47:41–50PubMedGoogle Scholar
  90. Button DK, Schut F, Quang P, Martin R, Robertson BR (1993) Viability and isolation of marine bacteria by dilution culture: theory, procedures, and initial results. Appl Environ Microbiol 59:881–891PubMedGoogle Scholar
  91. Button DK, Robertson BR, Lepp PW, Schmidt TM (1998) A small, dilute-cytoplasm, high-affinity, novel bacterium isolated by extinction culture and having kinetic constants compatible with growth at ambient concentrations of dissolved nutrients in seawater. Appl Environ Microbiol 64:4467–4476PubMedGoogle Scholar
  92. Byrer DE, Rainey FA, Wiegel J (2000) Novel strains of Moorella thermoacetica form unusually heat-resistant spores. Arch Microbiol 174:334–339PubMedGoogle Scholar
  93. Calcott PH (1981) The construction and operation of continuous cultures. In: Calcott PH (ed) Continuous cultures of cells, vol 1. CRC Press, Boca Raton, pp 13–26Google Scholar
  94. Calcott PH, Calvert TJ (1981) Characterization of 3′:5′cyclic AMP phosphodiesterase in Klebsiella aerogenes and its role in substrate accelerated death. J Gen Microbiol 122:313–321PubMedGoogle Scholar
  95. Calcott PH, Postgate JR (1972) On substrate-accelerated death in Klebsiella aerogenes. J Gen Microbiol 70:115–122PubMedGoogle Scholar
  96. Calcott PH, Montague W, Postgate JR (1972) The levels of cyclic AMP during substrate accelerated death. J Gen Microbiol 73:197–200PubMedGoogle Scholar
  97. Cangelosi GA, Brabant WH (1997) Depletion of pre-16S rRNA in starved Escherichia coli cells. J Bacteriol 179:4457–4463PubMedGoogle Scholar
  98. Carlsson J, Granberg GPD, Nyberg GK, Edlund M-BK (1979) Bactericidal effect of cysteine exposed to atmospheric oxygen. Appl Environ Microbiol 37:383–390PubMedGoogle Scholar
  99. Carpenter EJ, Lin S, Capone DG (2000) Bacterial activity in South Pole snow. Appl Environ Microbiol 66:4514–4517PubMedGoogle Scholar
  100. Castenholz RW (1973) Movements. In: Carr NG, Whitton BA (eds) The biology of blue-green algae. Blackwell, London, pp 320–339Google Scholar
  101. Cavicchioli R (2006) Cold-adapted archaea. Nat Rev Microbiol 4:331–343PubMedGoogle Scholar
  102. Cayley S, Record MT, Lewis BA (1989) Accumulation of 3-[N-morpholino] propanesulfonate by osmotically stressed Escherichia coli K-12. J Bacteriol 171:3597–3602PubMedGoogle Scholar
  103. Cayley S, Lewis BA, Record MT (1992) Origins of osmoprotective properties of betaine and proline in Escherichia coli K-12. J Bacteriol 174:1586–1595PubMedGoogle Scholar
  104. Chan M, Himes RH, Akagi JM (1971) Fatty acid composition of thermophilic, mesophilic, and psychrophilic clostridia. J Bacteriol 106:876–881PubMedGoogle Scholar
  105. Chao H, Davies PL, Carpenter JF (1996) Effects of antifreeze proteins in red blood cell survival during cryopreservation. J Exp Biol 199:2071–2076PubMedGoogle Scholar
  106. Chen X, Schauder S, Potier N, Van Dorsselaer A, Pelczer I, Bassler BL, Hughson FM (2002) Structural identification of a bacterial quorum-sensing signal containing boron. Nature 415:545–549PubMedGoogle Scholar
  107. Chen H, Jogler M, Rohde M, Klenk H-P, Busse H-J, Tindall B, Spröer C, Overmann J (2012) Reclassification and amended description of Caulobacter leidyi as Sphingomonas leidyi comb. nov., and emendation of the genus Sphingomonas. Int J Syst Evol Microbiol (in press)Google Scholar
  108. Chesbro W (1988) The domains of slow bacterial growth. Can J Microbiol 34:427–435PubMedGoogle Scholar
  109. Chesbro WR, Evans T, Eifert R (1979) Very slow growth of Escherichia coli. J Bacteriol 139:625–638PubMedGoogle Scholar
  110. Chi E, Bartlett DH (1995) An rpoE-like locus controls outer membrane protein synthesis and growth at cold temperatures and high pressures in the deep-sea bacterium Photobacterium sp. strain SS9. Mol Microbiol 17:713–726PubMedGoogle Scholar
  111. Chisholm SW, Frankel SL, Goericke R, Olson RJ, Palenik B, Waterbury JB, West-Johnsrud L, Zettler ER (1992) Prochiorococcus marinus nov. gen. nov. sp.: an oxyphototrophic marine prokaryote containing divinyl chlorophyll a and b. Arch Microbiol 157:297–300Google Scholar
  112. Cho JC, Giovannoni SJ (2004) Cultivation and growth characteristics of a diverse group of oligotrophic marine Gammaproteobacteria. Appl Environ Microbiol 70:432–440PubMedGoogle Scholar
  113. Christensen BB, Haagensen JAJ, Heydorn A, Molin S (2002) Metabolic commensalism and competition in a two-species microbial consortium. Appl Environ Microbiol 68:2495–2502PubMedGoogle Scholar
  114. Christner BC (2010) Bioprospecting for microbial products that affect ice crystal formation and growth. Appl Microbiol Biotechnol 85:481–489PubMedGoogle Scholar
  115. Clark C, Schmidt EL (1966) Effect of mixed culture on Nitrosomonas europaea simulated by uptake and utilization of pyruvate. J Bacteriol 91:367–373PubMedGoogle Scholar
  116. Cleland N, Enfors SO (1983) Control of glucose fed batch cultivations of E. coli by means of an oxygen stabilized enzyme electrode. Eur J Appl Microbiol Biotechnol 18:141–147Google Scholar
  117. Coates JD, Ellis DJ, Blunt-Harris EL, Gaw CV, Roden E, Lovley DR (1998) Recovery of humic-reducing bacteria from a diversity of environments. Appl Environ Microbiol 64:1504–1509PubMedGoogle Scholar
  118. Coates JD, Cole KA, Chakraborty R, O’Connor SM, Achenbach LA (2002) Diversity and ubiquity of bacteria capable of utilizing humic substances as electron donors for anaerobic respiration. Appl Environ Microbiol 68:2445–2453PubMedGoogle Scholar
  119. Cohen Y, de Jonge I, Kuenen JG (1979) Excretion of glycolate by Thiobacillus neapolitanus grown in continuous culture. Arch Microbiol 122:189–194Google Scholar
  120. Cohn F (1872) Über bacterien, die kleinsten lebenden. Wesen Carl Habel, BerlinGoogle Scholar
  121. Connon SA, Giovannoni SJ (2002) High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates. Appl Environ Microbiol 68:3878–3885PubMedGoogle Scholar
  122. Coolen MJL, Cypionka H, Smock A, Sass H, Overmann J (2002) Ongoing modification of Mediterranean Pleistocene sapropels mediated by prokaryotes. Science 296:2407–2410PubMedGoogle Scholar
  123. Cottrell MT, Kirchman DL (2000) Natural assemblages of marine proteobacteria and members of the Cytophaga-Flavobacteria cluster consuming low-and high-molecular-weight dissolved organic matter. Appl Environ Microbiol 66:1692–1697PubMedGoogle Scholar
  124. Coveney MF (1982) Bacterial uptake of photosynthetic carbon from freshwater phytoplankton. Oikos 38:8–20Google Scholar
  125. Crevel RWR, Fedyk JK, Spurgeon MJ (2002) Antifreeze proteins: characteristics, occurrence and human exposure. Food Chem Toxicol 40:899–903PubMedGoogle Scholar
  126. Crocker FH, Guerin WF, Boyd SA (1995) Bioavailability of naphthalene sorbed to cationic surfactant-modified smectite clay. Environ Sci Technol 29:2953–2958PubMedGoogle Scholar
  127. Csonka LN (1989) Physiological and genetic responses of bacteria to osmotic stress. Microbiol Rev 53:121–147PubMedGoogle Scholar
  128. Csonka LN, Epstein W (1996) Osmoregulation. In: Neidhardt FC (ed) Escherichia coli and Salmonella, 2nd edn. ASM Press, Washington, DC, pp 1210–1223Google Scholar
  129. Csonka LN, Hanson A (1991) Prokaryotic osmoregulation: genetics and physiology. Annu Rev Microbiol 45:569–606PubMedGoogle Scholar
  130. Currie DJ, Kalff J (1984) Can bacteria outcompete phytoplankton for phosphorus? A chemostat test. Microb Ecol 10:205–216Google Scholar
  131. Curtis TP, Sloan WT, Scannell JW (2002) Estimating prokaryotic diversity and its limits. Proc Natl Acad Sci USA 99:10494–10499PubMedGoogle Scholar
  132. Cypionka H (1986) Sulfide-controlled continuous culture of sulfate-reducing bacteria. J Microbiol Methods 5:1–9Google Scholar
  133. Cypionka H (1999) Grundlagen der mikrobiologie. Springer, New YorkGoogle Scholar
  134. Cypionka H, Widdel F, Pfennig N (1985) Survival of sulfate-reducing bacteria after oxygen stress, and growth in sulfate-free oxygen-sulfide gradients. FEMS Microbiol Ecol 31:39–45Google Scholar
  135. Czeczuga B (1968) An attempt to determine the primary production of the green sulphur bacteria, Chlorobium limicola Nads, (Chlorobacteriaceae). Hydrobiologia 31:317–333Google Scholar
  136. Dalluge JJ, Hamamoto T, Horikoshi K, Morita RY, Stetter KO, McCloskey JA (1997) Posttranscriptional modification of tRNA in psychrophilic bacteria. J Bacteriol 179:1918–1923PubMedGoogle Scholar
  137. Damoglou AP, Dawes EA (1968) Studies on the lipid content and phosphate requirement for glucose-and acetate-grown Escherichia coli. Biochem J 110:775–781PubMedGoogle Scholar
  138. Dang HY, Lovell CR (2000) Bacterial primary colonization and early succession on surfaces in marine waters as determined by amplified rRNA gene restriction analysis and sequence analysis of 16S rRNA genes. Appl Environ Microbiol 66:467–475PubMedGoogle Scholar
  139. Dawson MW, Maddox IS, Boag IF, Brooks JD (1988) Application of fed-batch culture to citric acid production by Aspergillus niger: the effects of dilution rate and dissolved oxygen tension. Biotechnol Bioeng 32:220–226PubMedGoogle Scholar
  140. De Bary A (1879) Die Erscheinung der Symbiose Naturforschung Versammlung CasselGoogle Scholar
  141. de Freitas MJ, Fredrickson AG (1978) Inhibition as a factor in the maintenance of the diversity of microbial ecosystems. J Gen Microbiol 106:307–320Google Scholar
  142. de la Broise D, Durand A (1989) Osmotic, biomass, and oxygen effects on the growth rate of Fusarium oxysporum using a dissolved oxygen controlled turbidstat. Biotechnol Bioeng 33:699–705PubMedGoogle Scholar
  143. De Wit R, van Gemerden H (1988) Interactions between phototrophic bacteria in sediment ecosystems. Hydrobiol Bull 22:135–145Google Scholar
  144. Dedysh SN (2011) Cultivating uncultured bacteria from northern wetlands: knowledge gained and remaining gaps. Front Microbiol 2:184PubMedGoogle Scholar
  145. DeLong EF, Yayamos AA (1986) Biochemical function and ecological significance of novel bacterial lipids in deep-sea prokaryotes. Appl Environ Microbiol 51:730–737PubMedGoogle Scholar
  146. DeLong EF, Ying Wu K, Prézelin BB, Jovine RVM (1994) High abundance of Archaea in Antarctic marine picoplankton. Nature 371:695–697PubMedGoogle Scholar
  147. DeLong EF, Franks DG, Yayanos AA (1997) Evolutionary relationships of cultivated psychrophilic and barophilic deep-sea bacteria. Appl Environ Microbiol 63:2105–2108PubMedGoogle Scholar
  148. Deming JW (1986) Ecological strategies of barophilic bacteria in the deep ocean. Microbiol Sci 3:205–207PubMedGoogle Scholar
  149. Deming JW, Colwell RR (1985) Observations of barophilic microbial activity in samples of sediments and intercepted particulates from the Demerara abyssal plain. Appl Environ Microbiol 50:1002–1006PubMedGoogle Scholar
  150. Deming JW, Somers LW, Straube WL, Swartz DG, MacDonell MT (1988) Isolation of an obligately barophilic bacterium and description of a new genus, Colwellia gen. nov. Syst Appl Microbiol 10:152–160Google Scholar
  151. Dinara S, Sengoku K, Tamate K et al (2001) Effects of supplementation with free radical scavengers on the survival and fertilization rates of mouse cryopreserved oocytes. Human Reprod 16:1976–1981Google Scholar
  152. Dobell C (1932) Anthony van Leeuwenhoek and his “little animals”. Harcourt Brace, New YorkGoogle Scholar
  153. Dolfing J, Tiedje JM (1986) Hydrogen cycling in a three-tiered food web growing on the methanogenic conversion of 3-chlorobenzoate. FEMS Microbiol Ecol 38:293–298Google Scholar
  154. Dong K, Liu H, Zhang J, Zhou Y, Xin Y (2011) Flavobacterium xueshanense sp. nov. and Flavobacterium urumqiense sp. nov., two psychrophilic bacteria isolated from the China No. 1 glacier. Int J Syst Evol Microbiol 62:1151–1157Google Scholar
  155. Douglas AE (1998) Nutritional interactions in insect-microbial symbioses: aphids and their symbiotic bacteria Buchnera. Annu Rev Entomol 43:17–37PubMedGoogle Scholar
  156. Driessen FM (1981) Protocooperation of yoghurt bacteria in continuous cultures. In: Buschell ME, Slater JH (eds) Mixed culture fermentations. Academic, London, pp 99–120Google Scholar
  157. Dubilier N, Giere O, Distel DL, Cavanaugh CM (1995) Characterization of chemoautotrophic bacterial symbionts in a gutless marine worm (Oligochaeta, Annelida) by phylogenetic 16S rRNA sequence analysis and in situ hybridization. Appl Environ Microbiol 61:2346–2350PubMedGoogle Scholar
  158. Dubinina GA, Leshcheva NV, Grabovich MY (1993) The colorless sulfur bacterium Thiodendron is actually a symbiotic association of spirochetes and sulfidogens. Microbiology 62:432–444Google Scholar
  159. Dubinina GA, Grabovich MY, Leshcheva NV, Rainey FA, Gavrish E (2011) Spirochaeta perfilievii sp. nov., an oxygen-tolerant, sulfide-oxidizing, sulfur- and thiosulfate-reducing spirochaete isolated from a saline spring. Int J Syst Evol Microbiol 61:110–117PubMedGoogle Scholar
  160. Dukan S, Nyström T (1998) Bacterial senescence: stasis results in increased and differential oxidation of cytoplasmic proteins leading to developmental induction of the heat shock regulon. Genes Dev 12:3431–3441PubMedGoogle Scholar
  161. Dunfield PF, Liesack W, Henckel T, Knowles R, Conrad R (1999) High-affinity methane oxidation by a soil enrichment culture containing a type II methanotroph. Appl Environ Microbiol 65:1009–1014PubMedGoogle Scholar
  162. Dwyer DF, Weeg-Aerssens E, Shelton DR, Tiedje JM (1988) Bioenergetic conditions of butyrate metabolism by a syntrophic, anaerobic bacterium in coculture with hydrogen oxidizing methanogenic and sulfidogenic bacteria. Appl Environ Microbiol 54:1354–1359PubMedGoogle Scholar
  163. Dykhuizen DE (1998) Santa Rosalia revisited: why are there so many species of bacteria? Antonie Van Leeuwenhoek 73:25–33PubMedGoogle Scholar
  164. Dykhuizen D, Davies M (1980) An experimental model: bacterial specialists and generalists competing in chemostats. Ecology 61:1213–1227Google Scholar
  165. Egland PG, Palmer RJ, Kolenbrander PE (2004) Interspecies communication in Streptococcus gordonii-Veillonella atypica biofilms: signaling in flow conditions requires juxtaposition. Proc Natl Acad Sci USA 101:16917–16922PubMedGoogle Scholar
  166. Egli T, Lindley ND, Quayle JR (1983) Regulation of enzyme synthesis and variation of residual methanol concentration during carbon limited growth of Kloeckera ap. 2201. on mixtures of methanol and glucose. J Gen Microbiol 129:1269–1281Google Scholar
  167. Eguchi M, Ostrowski M, Fegatella F, Bowman J, Nichols D, Nishino T, Cavicchioli R (2001) Sphingomonas alaskensis AFO1, an abundant oligotrophic ultramicrobacterium from the North Pacific. Appl Environ Microbiol 67:4945–4954PubMedGoogle Scholar
  168. Eichorst SA, Breznak JA, Schmidt TM (2007) Isolation and characterization of soil bacteria that define Terriglobus gen. nov., in the phylum Acidobacteria. Appl Environ Microbiol 73:2708–2717PubMedGoogle Scholar
  169. Eilers H, Pernthaler J, Peplies J, Glöckner FO, Gerdts G, Amann R (2001) Isolation of novel pelagic bacteria from the German Bight and their seasonal contributions to surface picoplankton. Appl Environ Microbiol 67:5134–5142PubMedGoogle Scholar
  170. Emde R, Schink B (1990) Oxidation of glycerol, lactate, and propionate by Propionibacterium freudenreichii in a poised-potential amperometric culture system. Arch Microbiol 153:506–512Google Scholar
  171. Emde R, Swain A, Schink B (1989) Anaerobic oxidation of glycerol by Escherichia coli in an amperometric poised-potential culture system. Appl Microbiol Biotechnol 32:170–175Google Scholar
  172. Epstein W (1986) Osmoregulation by potassium transport in Escherichia coli. FEMS Microbiol Rev 39:73–78Google Scholar
  173. Epstein W, Rothman-Denes LB, Hesse J (1975) Adenosine 3′:5′-cyclic monophosphate as mediator of catabolite repression in Escherichia coli. Proc Natl Acad Sci USA 72:2300–2304PubMedGoogle Scholar
  174. Esener AA, Roels JA, Kossen NW (1981) Fed batch culture: modelling and application in the study of microbial energetics. Biotechnol Bioeng 22:1851–1871Google Scholar
  175. Ettwig KF, Butler MK, LePaslier D, Pelletier E, Mangenot S, Kuypers MMM et al (2010) Nitrite-driven anaerobic methane oxidation by oxygenic bacteria. Nature 464:543–548PubMedGoogle Scholar
  176. Euzéby JP, Tindall BJ (2001) Nomenclatural type of orders: corrections necessary according to Rules 15 and 21a of the Bacteriological Code (1990 Revision), and designation of appropriate nomenclatural types of classes and subclasses. Request for an opinion. Int J Syst Evol Microbiol 51(Pt 2):725–727Google Scholar
  177. Euzéby JP (2012) List of bacterial names with standing in nomenclature. http://www.bacterio.cict.fr
  178. Evans CG, Herbert D, Tempest DW (1970) The continuous cultivation of microorganisms. 2. Construction of a chemostat. In: Norris JR, Ribbons DW (eds) Methods in microbiology, vol 2. Academic, London, pp 277–327Google Scholar
  179. Feller G (2007) Life at low temperatures: is disorder the driving force? Extremophiles 11:211–216PubMedGoogle Scholar
  180. Feller G, Narinx E, Arpigny JL, Zekhnini Z, Swings J, Gerday C (1994a) Temperature dependence of growth, enzyme secretion and activity of psychrophilic Antarctic bacteria. Appl Microbiol Biotechnol 41:477–479Google Scholar
  181. Feller G, Payan F, Theys F, Quian M, Haser R, Gerday C (1994b) Stability and structural analysis of α-amylase from the Antarctic psychrophile Alteromonas haloplanctis A23. Eur J Biochem 222:441–447PubMedGoogle Scholar
  182. Felske A, Wolterink A, van Lis R, Akkermans ADL (1998) Phylogeny of the main bacterial 16S rRNA sequences in Drentse A grassland soils (The Netherlands). Appl Environ Microbiol 64:871–879PubMedGoogle Scholar
  183. Felske A, Wolterink A, van Lis R, de Vos WM, Akkermans ADL (1999) Searching for predominant soil bacteria: 16S rDNA cloning versus strain cultivation. FEMS Microbiol Ecol 30:137–145PubMedGoogle Scholar
  184. Ferchichi M, Hemme D, Bouillaune C (1986) Influence of oxygen and pH on methanethiol production from l-methionine by Brevibacterium linens CNRZ 918. Appl Environ Microbiol 51:725–729PubMedGoogle Scholar
  185. Ferris MJ, Ruff-Roberts AL, Kopczynski ED, Bateson MM, Ward DM (1996) Enrichment culture and microscopy conceal diverse thermophilic Synechococcus populations in a single hot spring microbial mat habitat. Appl Environ Microbiol 62:1045–1050PubMedGoogle Scholar
  186. Filippini M, Kaech A, Ziegler U, Bagheri HC (2011) Fibrisoma limi gen. nov., sp. nov., a filamentous bacterium isolated from tidal flats. Int J Syst Evol Microbiol 61:1418–1424PubMedGoogle Scholar
  187. Fleming A (1929) On the antibacterial action of cultures of a Penicillium, with special reference to their use in the isolation of B. influenzae. Br J Exp Pathol 10:226–236Google Scholar
  188. Flint KP (1985) A note on a selective agar medium for the enumeration of Flavobacterium species in water. J Appl Bacteriol 59:561–566PubMedGoogle Scholar
  189. Fogg GE (1971) Extracellular products of algae in freshwater. Arch Hydrobiol Beih Ergebn Limnol 5:1–25Google Scholar
  190. Forsberg CW (1987) Production of 1,3-propanediol from glycerol by Clostridium acetobutylicum and other Clostridium species. Appl Environ Microbiol 53:639–643PubMedGoogle Scholar
  191. Francis CA, Tebo BM (2002) Enzymatic manganese(II) oxidation by metabolically dormant spores of diverse Bacillus species. Appl Environ Microbiol 68:874–880PubMedGoogle Scholar
  192. Franzmann PD, Höpfl P, Weiss N, Tindall BJ (1991) Psychrotrophic, lactic acid-producing bacteria from anoxic waters in Ace Lake, Antarctica: Carnobacterium funditum sp. nov. and Carnobacterium alterfunditum sp. nov. Arch Microbiol 156:255–262PubMedGoogle Scholar
  193. Franzmann PD, Springer N, Ludwig W, Conway de Macario E, Rohde M (1992) A methanogenic archaeon from Ace Lake, Antarctica: Methanococcoides burtonii sp. nov. Syst Appl Microbiol 15:573–581Google Scholar
  194. Franzmann PD, Liu Y, Balkwill DL, Aldrich HC, Conway de Macario E, Boone DR (1997) Methanogenium frigidum sp. nov., a psychrophilic H2-using methanogen from Ace Lake Antarctica. Int J Syst Bacteriol 47:1068–1072PubMedGoogle Scholar
  195. Fredrickson AG (1977) Behaviour of mixed cultures of microorganisms. Annu Rev Microbiol 31:63–87PubMedGoogle Scholar
  196. Fredrickson AG, Stephanopoulos G (1981) Microbial competition. Science 213:972–979PubMedGoogle Scholar
  197. Fritsche TR, Sobek D, Gautom RK (1998) Enhancement of in vitro cytopathogenicity by Acanthamoeba spp. following acquisition of bacterial endosymbionts. FEMS Microbiol Lett 166:231–236PubMedGoogle Scholar
  198. Fröhlich J, König H (1999) Rapid isolation of single microbial cells from mixed natural and laboratory populations with the aid of a micromanipulator. Syst Appl Microbiol 22:249–257PubMedGoogle Scholar
  199. Fröstl JM, Overmann J (1998) Physiology and tactic response of the phototrophic consortium “Chlorochromatium aggregatum”. Arch Microbiol 169:129–135PubMedGoogle Scholar
  200. Fröstl JM, Overmann J (2000) Phylogenetic affiliation of the bacteria that constitute phototrophic consortia. Arch Microbiol 174:50–58PubMedGoogle Scholar
  201. Fry JC (1990) Direct methods and biomass estimation. In: Grigorova R, Norris JR (eds) Methods in microbiology, vol 22. Academic, London, pp 41–85Google Scholar
  202. Fuhrman JA, McCallum K, Davis AA (1992) Novel major archaebacterial group from marine plankton. Nature 356:148–149PubMedGoogle Scholar
  203. Fuhrman JA, McCallum K, Davis AA (1993) Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific Oceans. Appl Environ Microbiol 59:1294–1302PubMedGoogle Scholar
  204. Funk HB, Krulwich TA (1964) Preparation of clear silica gels that can be streaked. J Bacteriol 88:1200–1201PubMedGoogle Scholar
  205. Fuqua C, Greenberg EP (1998) Self perception in bacteria: quorum sensing with acylated homoserine lactones. Curr Opin Microbiol 1:50–58Google Scholar
  206. Galinski EA, Trüper HG (1994) Microbial behaviour in salt-stressed ecosystems. FEMS Microbiol Rev 15:95–108Google Scholar
  207. Gangola P, Rosen BP (1987) Maintenance of intracellular calcium in Escherichia coli. J Biol Chem 262:12570–12574PubMedGoogle Scholar
  208. Ganzert L, Bajerski F, Mangelsdorf K, Lipski A, Wagner D (2011a) Arthrobacter livingstonensis sp. nov. and Arthrobacter cryotolerans sp. nov., salt-tolerant and psychrotolerant species from Antarctic soil. Int J Syst Evol Microbiol 61:979–984PubMedGoogle Scholar
  209. Ganzert L, Bajerski F, Mangelsdorf K, Lipski A, Wagner D (2011b) Leifsonia psychrotolerans sp. nov., a psychrotolerant species of the family Microbacteriaceae from Livingston Island, Antarctica. Int J Syst Evol Microbiol 61:1938–1943PubMedGoogle Scholar
  210. Garcia-Lara J, Shang LH, Rothfield LI (1996) An extracellular factor regulates expression of sdiA, a transcriptional activator of cell division genes in Escherichia coli. J Bacteriol 178:2742–2748PubMedGoogle Scholar
  211. Garnham CP, Gilbert JA, Hartman CP, Campbell RL, Laybourn-Parry J, Davies PL (2008) A Ca2+-dependent bacterial antifreeze protein domain has a novel β-helical ice-binding fold. Biochem J 411:171–180PubMedGoogle Scholar
  212. Garnham CP, Campbell RL, Dabies PL (2011) Anchored clathrate waters bind antifreeze proteins to ice. Proc Natl Acad Sci USA 108:7363–7367PubMedGoogle Scholar
  213. Gause GF (1934) The struggle for existence. Williams and Wilkins, BaltimoreGoogle Scholar
  214. Geissinger O, Herlemann DPR, Mörschel E, Maier UG, Brune A (2009) The ultramicrobacterium “Elusimicrobium minutum” gen. nov., sp. nov., the first cultivated representative of the termite group 1 phylum. Appl Environ Microbiol 75:2831–2840PubMedGoogle Scholar
  216. Gerhardt P, Murray RGE, Costilow RN, Nester EW, Wood WA, Krieg NR, Phillips GB (1981) Manual of methods for general bacteriology. American Society for Microbiology, Washington, DCGoogle Scholar
  217. Gherna RL, Reddy CA (2007) Culture preservation. In: Reddy CA (ed) Methods for general and molecular microbiology. ASM Press, Washington, DC, pp 1019–1033Google Scholar
  218. Gich F, Garcia-Gil J, Overmann J (2001) Previously unknown and phylogenetically diverse members of the green nonsulfur bacteria are indigenous to freshwater lakes. Arch Microbiol 177:1–10PubMedGoogle Scholar
  219. Gich F, Schubert K, Bruns A, Hoffelner H, Overmann J (2005) Specific detection, isolation and characterization of selected, previously uncultured members of freshwater bacterioplankton. Appl Environ Microbiol 71:5908–5919PubMedGoogle Scholar
  220. Giovannoni S, Stingl U (2007) The importance of culturing bacterioplankton in the ‘omics’ age. Nature 5:820–826Google Scholar
  221. Glöckner FO, Zaichikov E, Belkova N, Denissova L, Pernthaler J, Perthaler A, Amann R (2000) Comparative 16S rRNA analysis of lake bacterioplankton reveals globally distributed phylogenetic clusters including an abundant group of actinobacteria. Appl Environ Microbiol 66:5053–5065PubMedGoogle Scholar
  222. Gond O, Engasser JM, Matta-El-Amouri C, Petitdemange H (1986) The acetone butanol fermentation on glucose and xylose. II: Regulation and kinetics in fed batch cultures. Biotechnol Bioeng 28:167–175Google Scholar
  223. González JM, Mayer F, Moran MA, Hodson RE, Withman WB (1997) Sagittula stellata gen. nov., sp. nov., a lignin-transforming bacterium from a coastal environment. Int J Syst Bacteriol 47:773–780PubMedGoogle Scholar
  224. Goodfellow M (1992a) The family Nocardiaceae. In: Balows A, Trüper HG, Dworkin M, Schleifer K-H (eds) The prokaryotes, 2nd edn. Springer, New York, pp 1188–1213Google Scholar
  225. Goodfellow M (1992b) The family Streptosporangiaceae. In: Balows A, Trüper HG, Dworkin M, Schleifer K-H (eds) The prokaryotes, 2nd edn. Springer, New York, pp 1115–1138Google Scholar
  226. Görtz H-D, Brigge T (1998) Intracellular bacteria in protozoa. Naturwissenschaften 85:359–368PubMedGoogle Scholar
  227. Gosink JJ, Staley JT (1995) Biodiversity of gas vacuolate bacteria from Antarctic sea ice and water. Appl Environ Microbiol 61:3486–3489PubMedGoogle Scholar
  228. Gosink JJ, Woese CR, Staley JT (1998) Polaribacter gen. nov., with three new species, P. irgensii sp. nov., P. franzmannii sp. nov. and P. filamentus so. nov., gas vacuolate polar marine bacteria of the Cytophaga-Flavobacterium-Bacteroides group and reclassification of “Flectobacillus glomeratus” as Polaribacter glomeratus comb. nov. Int J Syst Evol Microbiol 48:223–235Google Scholar
  229. Gottschal JC (1986) Mixed substrate utilization by mixed cultures. In: Leadbetter ER, Poindexter JS (eds) Bacteria in nature, vol 2. Plenum, New York, pp 261–292Google Scholar
  230. Gottschal JC (1990) Different types of continuous culture in ecological studies. In: Norris JR, Grigorova R (eds) Methods in microbiology, vol 22. Academic, London, pp 87–124Google Scholar
  231. Gottschal JC, Dijkhuizen L (1988) The place of the continuous culture in ecological research. In: Wimpenny JWT (ed) Handbook of laboratory model systems for microbial ecosystems, vol 1. CRC Press, Boca Raton, pp 19–79Google Scholar
  232. Gottschal JC, Kuenen JG (1980) Selective enrichment of facultatively chemolithotrophic thiobacilli and related organisms in continuous culture. FEMS Microbiol Lett 7:241–247Google Scholar
  233. Gottschal JC, Morris JG (1981) The induction of acetone and butanol production in cultures of Clostridium acetobutylicum by elevated concentrations of acetate and butyrate. FEMS Microbiol Lett 12:385–389Google Scholar
  234. Gottschal JC, de Vries S, Kuenen JG (1979) Competition between the facultatively chemolithotrophic Thiobacillus A2, an obligately chemolithotrophic Thiobacillus and a heterotrophic Spirillum for inorganic and organic substrates. Arch Microbiol 121:241–249Google Scholar
  235. Gottschal JC, Harder W, Prins RA (1991) Principles of enrichment, isolation, cultivation, and preservation. In: Balows A, Trüper HG, Dworkin M, Schleifer K-H (eds) The prokaryotes, 2nd edn. Springer, New York, pp 149–196Google Scholar
  236. Gottschalk G (1985) Bacterial metabolism. Springer, New YorkGoogle Scholar
  237. Gottwald M, Gottschalk G (1985) The internal pH of Clostridium acetobutylicum and its effect on the shift from acid to solvent formation. Arch Microbiol 143:42–46Google Scholar
  238. Graber JR, Breznak JA (2005) Folate cross-feeding supports symbiotic homoacetogenic spirochetes. Appl Environ Microbiol 71:1883–1889PubMedGoogle Scholar
  239. Graham AF, Lund BM (1983) The effect of alkaline pH on growth and metabolic products of a motile, yellow-pigmented Streptococcus sp. J Gen Microbiol 129:2429–2435Google Scholar
  240. Grant WD, Tindall BJ (1986) The alkaline saline environment. In: Herbert RA, Codd GA (eds) Microbes in extreme environments. Academic, London, pp 25–54Google Scholar
  241. Graumann P, Marahiel MA (1996) Some like it cold: response of microorganisms to cold shock. Arch Microbiol 166:293–300PubMedGoogle Scholar
  242. Gray ND, Howarth R, Pickup RW, Jones JG, Head IM (2000) Use of combined microautoradiography and fluorescence in situ hybridization to determine carbon metabolism in mixed natural communities of uncultured bacteria from the genus Achromatium. Appl Environ Microbiol 66:4518–4522PubMedGoogle Scholar
  243. Groeschel DHM (1982) The etiology of tuberculosis: a tribute to Robert Koch on the occasion of the centenary of his discovery of the tubercle bacillus. ASM News 48:248–250Google Scholar
  244. Gross CA (1996) Function and regulation of the heat shock proteins. In: Neidhardt FC (ed) Escherichia coli and Salmonella, 2nd edn. ASM Press, Washington, DC, pp 1382–1399Google Scholar
  245. Grosser RJ, Friedrich M, Ward DM, Inskeep WP (2000) Effect of model sorptive phases on phenanthrene biodegradation: different enrichment conditions influence bioavailability and selection of phenanthrene-degrading isolates. Appl Environ Microbiol 66:2695–2702PubMedGoogle Scholar
  246. Guan LL, Onuki H, Kamino K (2000) Bacteria growth stimulation with exogenous siderophore and synthetic N-acyl homoserine lactone autoinducers under iron-limited and low-nutrient conditions. Appl Environ Microbiol 66:2797–2803PubMedGoogle Scholar
  247. Guerin WF, Boyd SA (1997) Bioavailability of naphthalene associated with natural and synthetic sorbents. Water Res 51:1504–1512Google Scholar
  248. Guerrero R, Pedros-Alió C, Esteve I, Mas J, Chase D, Margulis L (1986) Predatory prokaryotes: predation and primary consumption evolved in bacteria. Proc Natl Acad Sci USA 83:2138–2142PubMedGoogle Scholar
  249. Hackstein JH, Akhmanova A, Boxma B, Harhangi HR, Voncken FG (1999) Hydrogenosomes: eukaryotic adaptations to anaerobic environments. Trends Microbiol 7:441–447PubMedGoogle Scholar
  250. Hahn MW (2003) Isolation of strains belonging to the cosmopolitan Polynucleobacter necessarius cluster from freshwater habitats located in three climatic zones. Appl Environ Microbiol 69:5248–5254PubMedGoogle Scholar
  251. Hahn MW (2009) Description of seven candidate species affiliated with the phylum Actinobacteria, representing planktonic freshwater bacteria. Int J Syst Evol Microbiol 59:112–117PubMedGoogle Scholar
  252. Hahn MW, Lünsdorf H, Wu Q, Schauer M, Höfle MG, Boenigk J, Stadler P (2003) Isolation of novel ultramicrobacteria classified as Actinobacteria from five freshwater habitats in Europe and Asia. Appl Environ Microbiol 69:1442–1451PubMedGoogle Scholar
  253. Hallam SJ, Mincer TJ, Schleper C, Preston CM, Roberts K, Richardson PM, DeLong EF (2006) Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota. PLoS Biol 4:e95PubMedGoogle Scholar
  254. Handelsmann J (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68:669–685Google Scholar
  255. Harder W, Dijkhuizen L (1982) Strategies of mixed substrate utilization in microorganisms. Philos Trans R Soc Lond B Biol Sci 297:459–480PubMedGoogle Scholar
  256. Harder W, Veldkamp H (1971) Competition of marine psychrophilic bacteria at low temperatures. Antonie Van Leeuwenhoek 37:51–63PubMedGoogle Scholar
  257. Harder W, Kuenen JG, Matin A (1977) Microbial selection in continuous culture. J Appl Bacteriol 43:1–24PubMedGoogle Scholar
  258. Hardin G (1960) The competitive exclusion principle. Science 131:1292–1297PubMedGoogle Scholar
  259. Harms H, Zehnder AJB (1995) Bioavailability of sorbed 3-chlorodibenzofuran. Appl Environ Microbiol 61:27–33PubMedGoogle Scholar
  260. Harris JE (1985) Gelrite as an agar substitute for the cultivation of mesophilic Methanobacterium and Methanobrevibacter species. Appl Environ Microbiol 50:1107–1109PubMedGoogle Scholar
  261. Harwood C, Buckley M (2008) The uncharted microbial world: microbes and their activities in the environment. A report from the American Academy of Microbiology. American Academy of Microbiology, Washington, DC, 37 pGoogle Scholar
  262. Hastings RC, Saunders JR, Hall GH, Pickup RW, McCarthy AJ (1998) Application of molecular biological techniques to a seasonal study of ammonia oxidation in a eutrophic freshwater lake. Appl Environ Microbiol 64:3674–3682PubMedGoogle Scholar
  263. Herbert RA (1986) The ecology and physiology of psychrophilic microorganisms. In: Herbert RA, Codd GA (eds) Microbes in extreme environments. Academic, London, pp 1–23Google Scholar
  264. Herbert D, Elsworth R, Telling RC (1956) The continuous culture of bacteria: a theoretical and experimental study. J Gen Microbiol 14:601–622PubMedGoogle Scholar
  265. Hespell RB, Bryant MP (1981) The genera Butyrivibrio, Succinivibrio, Lachnospira and Selenomonas. In: Starr MP, Stolp H, Trüper HG, Balows A, Schlegel HG (eds) The prokaryotes. Springer, New York, pp 1479–1494Google Scholar
  266. Hinrichs K-U, Hayes JM, Sylva SP, Brewer PG, DeLong EF (1999) Methane-consuming archaebacteria in marine sediments. Nature 398:802–805PubMedGoogle Scholar
  267. Hiorns WD, Methé BA, Nierzwicki-Bauer SA, Zehr JP (1997) Bacterial diversity in Adirondack Mountain lakes as revealed by 16S rRNA gene sequence analysis. Appl Environ Microbiol 63:2957–2960PubMedGoogle Scholar
  268. Hippe H (1991) Maintenance of methanogenic bacteria. In: Kirsop BE, Doyle A (eds) Maintenance of microorganisms and cultured cells, 2nd edn. Academic, London, pp 101–114Google Scholar
  269. Hirsch P (1984) Microcolony formation and consortia. In: Marshall KC (ed) Microbial adhesion and aggregation: Dahlem Konferenzen. Springer, New York, pp 373–393Google Scholar
  270. Hochachka PW, Moon TW, Mustafa T (1972) The adaptation of enzymes to pressure in abyssal and midwater fishes. In: Sleigh MA, Macdonald AG (eds) The effects of pressure on living organisms. Academic, London, pp 175–195Google Scholar
  271. Holmes AJ, Roslev P, McDonald IR, Iversen N, Henriksen K, Murrell JC (1999) Characterization of methanotrophic bacterial populations in soil showing atmospheric methane uptake. Appl Environ Microbiol 65:3312–3318PubMedGoogle Scholar
  272. Hommes RWJ, Postma PW, Tempest DW, Neijssel OM (1989) The influence of the culture pH value on the direct glucose oxidation pathway in Klebsiella pneumoniae NCTC 418. Arch Microbiol 151:261–267PubMedGoogle Scholar
  273. Hooke R (1665) Micrographia: or some physiological descriptions of minute bodies made by magnifying glasses with observations and inquiries thereupon. John Martyn and James Allestry, LondonGoogle Scholar
  274. Horikoshi K, Akiba T (1982) Alkalophilic microorganisms. Springer, New YorkGoogle Scholar
  275. Huang L, Forsberg CW, Gibbins LN (1986) Influence of external pH and fermentation products on Clostridium acetobutylicum intracellular pH and cellular distribution of fermentation products. Appl Environ Microbiol 51:1230–1234PubMedGoogle Scholar
  276. Hubalek Z (2003) Protectants used in the cryopreservation of microorganisms. Cryobiology 46:205–229PubMedGoogle Scholar
  277. Huber H, Hohn MJ, Rachel R, Fuchs T, Wimmer VC, Stetter KO (2002) A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nature 417:63–67PubMedGoogle Scholar
  278. Hugenholtz P (2002) Exploring prokaryotic diversity in the genomic era. Genome Biol Rev 3:0003.1–0003.8Google Scholar
  279. Hugenholtz P, Pitulle C, Hershberger KL, Pace NR (1998) Novel division level bacterial diversity in a yellowstone hot spring. J Bacteriol 180:366–376PubMedGoogle Scholar
  280. Humphry DR, George A, Black GW, Cummings SP (2001) Flavobacterium frigidarium sp. nov., an aerobic psychrophilic, xylanolytic and laminariolytic bacterium from Antarctica. Int J Syst Evol Microbiol 51:1235–1243PubMedGoogle Scholar
  281. Hungate RE (1950) The anaerobic mesophilic cellulolytic bacteria. Bacteriol Rev 14:1–49PubMedGoogle Scholar
  282. Hungate RE (1960) Microbial ecology of the rumen. Symposium: selected topics in microbial ecology. Bacteriol Rev 24:353–364PubMedGoogle Scholar
  283. Hungate RE (1966) The rumen and its microbes. Academic, New YorkGoogle Scholar
  284. Hungate RE (1969) A roll tube method for cultivation of strict anaerobes. In: Norris JR, Ribbons WD (eds) Methods in microbiology, vol 3B. Academic, London, pp 117–132Google Scholar
  285. Hungate RE (1985) Anaerobic biotransformations of organic matter. In: Leadbetter ER, Poindexter JS (eds) Bacteria in nature, vol 1. Plenum, New York, pp 39–96Google Scholar
  286. Huston AL, Krieger-Brockett BB, Deming JW (2000) Remarkably low temperature optima for extracellular enzyme activity form Arctic bacteria and sea ice. Environ Microbiol 2:383–388PubMedGoogle Scholar
  287. Ianotti EL, Kafkewitz D, Wolin MJ, Bryant MP (1973) Glucose fermentation products of Ruminococcus albus grown in continuous culture with Vibrio succinogenes. J Bacteriol 114:1231–1240Google Scholar
  288. Imhoff JF (1986) Osmoregulation and compatible solutes in eubacteria. FEMS Microbiol Rev 39:57–66Google Scholar
  289. Ingham CJ, Sprenkels A, Bomer J, Molenaar D, van der Berg A, van Hylckama Vlieg JET, de Vos WM (2007) The micro-Petri dish, a million-well growth chip for the culture and high-throughput screening of microorganisms. Proc Natl Acad Sci USA 104:18217–18222PubMedGoogle Scholar
  290. Ingraham JL (1962) Temperature relationships. In: Gunsalus IC, Stanier RY (eds) The bacteria, vol 4. Academic, New York, pp 265–296Google Scholar
  291. Ingraham JL, Marr AG (1996) Effect of temperature, pressure, pH, and osmotic stress on growth. In: Neidhardt FC (ed) Escherichia coli and Salmonella typhimurium. ASM Press, Washington, DC, pp 1570–1578Google Scholar
  292. Irgens RL, Gosink JJ, Staley JT (1996) Polaromonas vacuolata gen. nov., sp. nov., a psychrophilic, marine gas vacuolate bacterium from Antarctica. Int J Syst Evol Microbiol 46:822–826Google Scholar
  293. Isaksen MF, Jørgensen BB (1996) Adaptation of psychrophilic and psychrotrophic sulfate-reducing bacteria to permanently cold marine environments. Appl Environ Microbiol 62:408–414PubMedGoogle Scholar
  294. Ishii A, Sato T, Wachi M, Nagai K, Kato C (2004) Effects of high hydrostatic pressure on bacterial cytoskeleton FtsZ polymers in vivo and in vitro. Microbiology 150:1965–1972PubMedGoogle Scholar
  295. Jackson BE, McInerney MJ (2002) Anaerobic microbial metabolism can proceed close to thermodynamic limits. Nature 415:454–456PubMedGoogle Scholar
  296. Jacobi CA, Aßmus B, Reichenbach H, Stackebrandt E (1997) Molecular evidence for association between the Sphingobacterium-like organism “Candidatus comitans” and the myxobacterium Chondromyces crocatus. Appl Environ Microbiol 63:719–723PubMedGoogle Scholar
  297. Jaenicke R (1988) Molecular mechanisms of adaptation of bacteria to extreme environments. Forum Microbiol 11:435–440Google Scholar
  298. Jannasch HW (1967a) Enrichment of aquatic bacteria in continuous culture. Arch Mikrobiol 59:165–173PubMedGoogle Scholar
  299. Jannasch HW (1967b) Growth of marine bacteria at limiting concentrations of organic carbon in seawater. Limnol Oceanogr 12:264–271Google Scholar
  300. Jannasch HW, Mateles RI (1974) Experimental bacterial ecology studied in continuous culture. Adv Microb Physiol 11:165–212Google Scholar
  301. Jannasch HW, Taylor CD (1984) Deep-sea microbiology. Annu Rev Microbiol 38:487–514PubMedGoogle Scholar
  302. Jannasch HW, Wirsen CO, Taylor CD (1976) Undecompressed microbial populations from the deep sea. Appl Environ Microbiol 32:360–367PubMedGoogle Scholar
  303. Jannasch HW, Wirsen CO, Doherty KW (1996) A pressurized chemostat for the study of marine barophilic and oligotrophic bacteria. Appl Environ Microbiol 62:1593–1596PubMedGoogle Scholar
  304. Janssen PH, Schuhmann A, Mörschel E, Rainey FA (1997) Novel anaerobic ultramicrobacteria belonging to the Verrucomicrobiales lineage of bacterial decent isolated by dilution culture from anoxic rice paddy soil. Appl Environ Microbiol 63:1382–1388PubMedGoogle Scholar
  305. Janssen PH, Yates PS, Grinton BE, Taylor PM, Sait M (2002) Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia. Appl Environ Microbiol 68:2391–2396PubMedGoogle Scholar
  306. Jaspers E, Nauhaus K, Cypionka H, Overmann J (2001) Multitude and temporal variability of ecological niches as indicated by the diversity of cultivated bacterioplankton. FEMS Microbiol Ecol 36:153–164PubMedGoogle Scholar
  307. Jensen PR, Williams PG, Oh DC, Zeigler L, Fennical W (2007) Species-specific secondary metabolite production in marine actinomycetes of the genus Salinispora. Appl Environ Microbiol 73:1146–1152PubMedGoogle Scholar
  308. Jetten MSM, Strous M, van de Pas-Schoonen KT, Schalk J, van Dongen UGJM, van de Graaf AA, Logemann S, Muyzer G, van Loosdrecht MCM, Kuenen JG (1998) The anaerobic oxidation of ammonium. FEMS Microbiol Rev 22:421–437PubMedGoogle Scholar
  309. Jones AK (1982) The interaction of algae and bacteria. In: Bull AT, Slater JH (eds) Microbial interactions and communities. Academic, London, pp 189–247Google Scholar
  310. Jones SL, Drouin P, Wilkinson BJ, Morse PD (2002) Correlation of long-range membrane order with temperature-dependent growth characteristics of parent and a cold-sensitive, branched-chain-fatty-acid-deficient mutant of Listeria monocytogenes. Arch Microbiol 177:217–222PubMedGoogle Scholar
  311. Jørgensen BB (1982) Ecology of the bacteria of the sulphur cycle with special reference to anoxic-oxic interface environments. Philos Trans R Soc Lond B Biol Sci 298:543–561PubMedGoogle Scholar
  312. Jost JL, Drake JF, Fredrickson AG, Tsuchiya HM (1973) Interactions of Tetrahymena pyriformis, Escherichia coli, Azotobacter vinelandii and glucose in a minimal medium. J Bacteriol 113:834–840PubMedGoogle Scholar
  313. Jung L, Jost R, Stoll E, Zuber H (1974) Metabolic differences in Bacillus stearothermophilus grown at 55°C and 37°C. Arch Microbiol 95:125–138Google Scholar
  314. Junge K, Eicken H, Deming JW (2004) Bacterial activity at −2 to −20°C in Arctic wintertime sea ice. Appl Environ Microbiol 70:550–557PubMedGoogle Scholar
  315. Kaeberlein T, Lewis K, Epstein SS (2002) Isolating the “uncultivable” microorganisms in pure culture in a simulated natural environment. Science 296:1127–1129PubMedGoogle Scholar
  316. Kalmbach S, Manz W, Szewyk U (1997) Isolation of new bacterial species from drinking water biofilms and proof of their in situ dominance with highly specific 16S rRNA probes. Appl Environ Microbiol 63:4164–4170PubMedGoogle Scholar
  317. Kämpfer P, Rainey FA, Andersson MA, Nurmiaho Lassila EL, Ulrych U, Busse HJ, Weiss N, Mikkola R, Salkinoja-Salonen M (2000) Frigoribacterium faeni gen. nov., sp. nov., a novel psychrophilic genus of the family Microbacteriaceae. Int J Syst Evol Microbiol 50:355–363PubMedGoogle Scholar
  318. Kämpfer P, Buczolits S, Albrecht A, Busse H-J, Stackebrandt E (2003) Towards a standardized format for the description of a novel species (of an established genus): Ochrobactrum gallinifaecis sp. nov. Int J Syst Evol Microbiol 53:893–896PubMedGoogle Scholar
  319. Kane MD, Poulsen LK, Stahl DA (1993) Monitoring the enrichment and isolation of sulfate-reducing bacteria by using oligonucleotide probes designed from environmentally derived 16S rRNA sequences. Appl Environ Microbiol 59:682–686PubMedGoogle Scholar
  320. Kaneda T (1991) Iso-fatty and anteiso-fatty acids in bacteria-biosynthesis, function, and taxonomic significance. Microbiol Rev 55:288–302PubMedGoogle Scholar
  321. Kaprelyants AS, Kell DB (1993) Dormancy in stationary-phase cultures of Micrococcus luteus—flow cytometric analysis of starvation and resuscitation. Appl Environ Microbiol 59:3187–3196PubMedGoogle Scholar
  322. Kaprelyants AS, Mukamolova GV, Kell DB (1994) Estimation of dormant Micrococcus luteus cells by penicillin lysis and by resuscitation in cell free spent culture medium at high dilution. FEMS Microbiol Lett 115:347–352Google Scholar
  323. Kaprelyants AS, Mukamolova GV, Davey HM, Kell DB (1996) Quantitative analysis of the physiological heterogeneity within starved cultures of Micrococcus luteus by flow cytometry and cell sorting. Appl Environ Microbiol 62:1311–1316PubMedGoogle Scholar
  324. Karl DM, Bird DF, Björkman K, Houlihan T, Shackelford R, Tupas L (1999) Microorganisms in the accreted ice of Lake Vostok, Antarctica. Science 286:2144–2147PubMedGoogle Scholar
  325. Karner M, Fuhrman JA (1997) Determination of active bacterioplankton: a comparison of universal 16S rRNA probes, autoradiography, and nucleoid staining. Appl Environ Microbiol 63:1208–1213PubMedGoogle Scholar
  326. Kato Y, Sakala RM, Hayashidani H, Kiuchi A, Kaneuchi C, Ogawa M (2000) Lactobacillus algidus sp. nov., a psychrophilic lactic acid bacterium isolated from vacuum-packaged refrigerated beef. Int J Syst Evol Microbiol 50:1143–1149PubMedGoogle Scholar
  327. Kawato M, Shinobu R (1959) On Streptomyces herbaricolor nov. sp.; supplement: a simple technique for the microscopical observation. Mem Osaka Univ Lib Arts Educ 8:114Google Scholar
  328. Keith SM, Herbert RA (1985) The application of compound bi-directional flow diffusion chemostats to the study of microbial interactions. FEMS Microbiol Ecol 31:239–248Google Scholar
  329. King GM (1984) Utilization of hydrogen, acetate, and “noncompetitive” substrates by methanogenic bacteria in marine sediments. Geomicrobiol J 3:275–306Google Scholar
  330. King D, Nedwell DB (1984) Changes in the nitrate-reducing community of an anaerobic saltmarsh sediment in response to seasonal selection by temperature. J Gen Microbiol 130:2935–2941Google Scholar
  331. Kjaergaard L, Jørgensen BB (1979) Redox potential as a state variable in fermentation systems. Biotechnol Bioeng Symp 9:85–94Google Scholar
  332. Kjelleberg S, Humphrey BA, Marshall KC (1982) Effect of interfaces on small, starved bacteria. Appl Environ Microbiol 43:1166–1172PubMedGoogle Scholar
  333. Kjelleberg S, Flardh KBG, Nystrom T, Moriarty DJW (1993) Growth limitation and starvation in bacteria. In: Ford TE (ed) Aquatic microbiology: an ecological approach. Blackwell, Oxford, pp 298–320Google Scholar
  334. Kluyver AJ, Donker HJL (1926) Unity in biochemistry. Chem Zelle Gewebe 13:134–190Google Scholar
  335. Knoblauch C, Jørgensen BB (1999) Effect of temperature on sulphate reduction, growth rate and growth yield in five psychrophilic sulphate-reducing bacteria from Arctic sediments. Environ Microbiol 1:457–467PubMedGoogle Scholar
  336. Knoblauch C, Jørgensen BB, Harder J (1999) Community size and metabolic rates of psychrophilic sulfate-reducing bacteria in arctic marine sediments. Appl Environ Microbiol 65:4230–4233PubMedGoogle Scholar
  337. Koch IH, Gich F, Dunfield PF, Overmann J (2008) Edaphobacter modestus gen. nov., sp. nov., and Edaphobacter aggregans sp. nov., two novel acidobacteria isolated from alpine and forest soils. Int J Syst Evol Bacteriol 58:1114–1122Google Scholar
  338. Kogure K, Simidu U, Taga N (1979) A tentative direct microscopic method for counting living marine bacteria. Can J Microbiol 25:415–420PubMedGoogle Scholar
  339. Kole MM, Draper I, Gerson DF (1988) Protease production by Bacillus subtilis in oxygen controlled, glucose fed-batch fermentations. Appl Microbiol Biotechnol 28:404–408Google Scholar
  340. Kolenbrander PE, London J (1993) Adhere today, here tomorrow: oral bacterial adherence. J Bacteriol 175:3247–3252PubMedGoogle Scholar
  341. Kolter R, Siegele DA, Tormo A (1993) The stationary phase of the bacterial life cycle. Annu Rev Microbiol 47:855–874PubMedGoogle Scholar
  342. Könneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB, Stahl DA (2005) Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437:543–645PubMedGoogle Scholar
  343. Krembs C, Juhl AR, Long RA, Azam F (1998) Nanoscale patchiness of bacteria in lake water studied with the spatial information preservation method. Limnol Oceanogr 43:307–314Google Scholar
  344. Kristjansson JR, Schönheit P, Thauer RK (1982) Different Km values for hydrogen of methanogenic bacteria and sulfate reducing bacteria: an explanation for the apparent inhibition of methanogenesis by sulfate. Arch Microbiol 131:278–282Google Scholar
  345. Krulwich TA, Guffanti AA (1983) Physiology of acidophilic and alkalophilic bacteria. Adv Microb Physiol 24:173–214PubMedGoogle Scholar
  346. Krulwich TA, Guffanti AA (1989) Alkalophilic bacteria. Annu Rev Microbiol 43:435–463PubMedGoogle Scholar
  347. Kuenen JG, Gottschal JC (1982) Competition among chemolithotrophs and methylotrophs and their interactions with heterotrophic bacteria. In: Bull AT, Slater JH (eds) Microbial interactions and communities, vol 1. Academic, London, pp 153–187Google Scholar
  348. Kuenen JG, Harder W (1982) Microbial competition in continuous culture. In: Burns RG, Slater JH (eds) Experimental microbial ecology. Blackwell, Oxford, pp 342–367Google Scholar
  349. Kuenen JG, Robertson LA (1984) Competition among chemolithotrophic bacteria under aerobic and anaerobic conditions. In: Klug MJ, Reddy CA (eds) Current perspectives in microbial ecology. ASM Press, Washington, DC, pp 306–313Google Scholar
  350. Kuenen JG, Robertson LA, van Gemerden H (1985) Microbial interactions among aerobic and anaerobic sulfur-oxidizing bacteria. Adv Microbiol Ecol 8:1–59Google Scholar
  351. Kushner DJ (1978) Life in high salt and solute concentrations: halophilic bacteria. In: Kushner DJ (ed) Microbial life in extreme environments. Academic, London, pp 318–368Google Scholar
  352. Kuske CR, Barns SM, Busch JD (1997) Diverse uncultivated bacterial groups from soils of the arid southwestern United States that are present in many geographical regions. Appl Environ Microbiol 63:3614–3621PubMedGoogle Scholar
  353. Kuznetsov SI, Dubinina GA, Laptev NA (1979) Biology of oligotrophic bacteria. Annu Rev Microbiol 33:377–387PubMedGoogle Scholar
  354. Laanbroek HJ, Veldkamp H (1982) Microbial interactions in sediment communities. Philos Trans R Soc Lond B Biol Sci 297:533–550PubMedGoogle Scholar
  355. Laanbroek HJ, Smit AJ, Klein Nulend G, Veldkamp H (1979) Competition for l-glutamate between specialized and versatile Clostridium species. Arch Microbiol 120:61–66PubMedGoogle Scholar
  356. Laanbroek HJ, Geerlings HJ, Peynenburg AACM, Siesling J (1983) Competition for l-lactate between Desulfovibrio, Veillonella, and Acetobacterium species isolated from anaerobic intertidal sediments. Microb Ecol 9:341–354Google Scholar
  357. Laanbroek HJ, Geerlings HJ, Sijtsma L, Veldkamp H (1984) Competition for sulfate and ethanol among Desulfobacter, Desulfobulbus, and Desulfovibrio species isolated from intertidal sediments. Appl Environ Microbiol 47:329–334PubMedGoogle Scholar
  358. Lange W (1971) Enhancement of algal growth in cyanophyta-bacteria systems by carbonaceous compounds. Can J Microbiol 17:303–314PubMedGoogle Scholar
  359. Lange R, Hengge-Aronis R (1991) Identification of a central regulator of stationary-phase gene expression in Escherichia coli. Mol Microbiol 5:49–59PubMedGoogle Scholar
  360. Langworthy TA (1978) Microbial life in extreme pH values. In: Kushner DJ (ed) Microbial life in extreme environments. Academic, New York, pp 279–317Google Scholar
  361. Lapierre L, Undeland P, Cox LJ (1992) Lithium chloride-sodium propionate agar for the enumeration of bifidobacteria in fermented dairy products. J Dairy Sci 75:1192–1196PubMedGoogle Scholar
  362. Larsen H (1986) Halophilic and halotolerant microorganisms—an overview and historical perspective. FEMS Microbiol Rev 39:3–7Google Scholar
  363. Law AT, Button DK (1977) Multiple-carbon-source-limited growth kinetics of a marine coryneform bacterium. J Bacteriol 129:115–123PubMedGoogle Scholar
  364. Leadbetter JR, Schmidt TM, Graber JR, Breznak JA (1999) Acetogenesis from H2 Plus CO2 by Spirochetes from Termite Guts. Science 283:686–689PubMedGoogle Scholar
  365. Lee IH, Fredrickson AG, Tsuchiya HM (1976) Dynamics of mixed cultures of Lactobacillus plantarum and Propionibacterium shermanii. Biotechnol Bioeng 18:513–526PubMedGoogle Scholar
  366. Lee N, Nielsen PH, Andrasen KH, Juretschko S, Nielsen JL, Schleifer K-H, Wagner M (1999) Combination of fluorescent in situ hybridization and microautoradiography—a new tool for structure: function analyses in microbial ecology. Appl Environ Microbiol 65:1289–1297PubMedGoogle Scholar
  367. Lee KC-Y, Dunfield PF, Morgan XC, Crowe MA, Houghton KM, Vyssotski M, Ryan JLJ, Lagutin K, McDonald IR, Stott MB (2011) Chthonomonas calidirosea gen. nov., sp. nov., an aerobic, pigmented, thermophilic micro-organism of a novel bacterial class, Chthonomonadetes classis nov., of the newly described phylum Armatimonadetes originally designated candidate division OP10. Int J Syst Evol Microbiol 61:2482–2490PubMedGoogle Scholar
  368. Leedle JAZ, Hespell RB (1980) Differential carbohydrate media and anaerobic replica plating technique in delineating carbohydrate utilizing subgroups in rumen bacterial populations. Appl Environ Microbiol 39:709–719PubMedGoogle Scholar
  369. Legan JD, Owens JD (1988) Bacterial competition for methylamine: computer simulation of a three-strain continuous culture supplied continuously or alternatively with two nutrients. FEMS Microbiol Ecol 53:307–314Google Scholar
  370. Legan JD, Owens JD, Chilvers GA (1987) Competition between specialist and generalist methylotrophic bacteria for an intermittent supply of methylamine. J Gen Microbiol 133:1061–1073Google Scholar
  371. Lengeler JW, Drews G, Schlegel HG (1999) Biology of the prokaryotes. Thieme, New YorkGoogle Scholar
  372. Li L, Kato C, Nogi Y, Horikoshi K (1998) Distribution of the pressure-regulated operons in deep-sea bacteria. FEMS Microbiol Lett 159:159–166PubMedGoogle Scholar
  373. Licht TR, Tolker-Nielsen T, Holmstrøm K, Krogfelt KA, Molin S (1999) Inhibition of Escherichia coli precursor-16S rRNA processing by mouse intestinal contents. Environ Microbiol 1:23–32PubMedGoogle Scholar
  374. Liesack W, Janssen PH, Rainey FA, Ward-Rainey NL, Stackebrandt E (1997) Microbial diversity in soil: the need for a combined approach using molecular and cultivation techniques. In: van Elsas JD, Trevors JT, Wellington EMH (eds) Modern soil microbiology. Marcel Dekker, New York, pp 375–439Google Scholar
  375. Lilburn TG, Kim KS, Ostrom NE, Byzek KR, Leadbetter JR, Breznak JA (2001) Nitrogen fixation by symbiotic and free-living spirochetes. Science 292:2495–2498PubMedGoogle Scholar
  376. Lins U, Farina M (1999) Organization of cells in magnetotactic multicellular aggregates. Microbiol Res 154:9–13Google Scholar
  377. Little B, Gerchakov S, Udey L (1987) A method for sterilization of natural seawater. J Microbiol Methods 7:193–200Google Scholar
  378. Loewen PC, Hengge-Aronis R (1994) The role of the sigma factor σ6 (Kat F) in bacterial global regulation. Annu Rev Microbiol 48:53–80PubMedGoogle Scholar
  379. Loewen PC, Hu B, Stutinsky J, Sparling R (1998) Regulation in the rpoS regulon of Escherichia coli. Can J Microbiol 44:707–717PubMedGoogle Scholar
  380. Long RA, Azam F (2001) Antagonistic interactions among marine pelagic bacteria. Appl Environ Microbiol 67:4975–4983PubMedGoogle Scholar
  381. Lonhienne T, Gerday C, Feller G (2000) Psychrophilic enzymes: revisiting the thermodynamic parameters of activation may explain local flexibility. Biochim Biophys Acta 1543:1–10PubMedGoogle Scholar
  382. Loomis WD, Durst RW (1992) Chemistry and biology of boron. Biofactors 3:229–239PubMedGoogle Scholar
  383. Loveland-Curtze J, Sheridan PP, Gutshall KR, Brenchley JE (1999) Biochemical and phylogenetic analyses of psychrophilic isolates belonging to the Arthrobacter subgroup and description of Arthrobacter psychrolactophilus, sp. nov. Arch Microbiol 171:355–363PubMedGoogle Scholar
  384. Lovitt RW, Wimpenny JWT (1981) The gradostat: a bidirectional compound chemostat and its application in microbiological research. J Gen Microbiol 127:261–268PubMedGoogle Scholar
  385. Lovley DR, Blunt-Harris EL (1999) Role of humic-bound iron as an electron transfer agent in dissimilatory Fe(III) reduction. Appl Environ Microbiol 65:4252–4254PubMedGoogle Scholar
  386. Lovley DR, Dwyer DF, Klug MJ (1982) Kinetic analysis of competition between sulfate reducers and methanogens for hydrogen in sediments. Appl Environ Microbiol 43:1373–1379PubMedGoogle Scholar
  387. Lovley DR, Coates JD, Blunt-Harris EL, Phillips EJP, Woodward JC (1996a) Humic substances as electron acceptors for microbial respiration. Nature 382:445–448Google Scholar
  388. Lovley DR, Woodward JC, Chapelle FH (1996b) Rapid anaerobic benzene oxidation with a variety of chelated Fe(III) forms. Appl Environ Microbiol 62:288–291PubMedGoogle Scholar
  389. Lovley DR, Fraga JL, Coates JD, Blunt-Harris EL (1999) Humics as an electron donor for anaerobic respiration. Environ Microbiol 1:89–98PubMedGoogle Scholar
  390. Ludwig W, Bauer SH, Bauer H, Held I, Kirchhof G, Schulze R, Huber I, Spring S, Hartmann A, Schleifer K-H (1997) Detection and in situ identification of representatives of a widely distributed bacterial phylum. FEMS Microbiol Lett 153:181–190PubMedGoogle Scholar
  391. Lum KT, Meers PD (1989) Boric acid converts urine into an effective bacteriostatic transport medium. J Infect 18:51–58PubMedGoogle Scholar
  392. MacDonald AG (1984) The effects of pressure on the molecular structure and physiological functions of cell membranes. Philos Trans R Soc Lond B Biol Sci 304:47–68PubMedGoogle Scholar
  393. Macy JM, Snellen JE, Hungate RE (1972) Use of syringe methods for anaerobiosis. Am J Clin Nutr 25:1318–1323PubMedGoogle Scholar
  394. Madigan MT (1998) Isolation and characterization of psychrophilic purple bacteria from Antarctica. In: Peschek GA, Löffelhardt W, Schmetterer G (eds) The phototrophic prokaryotes. Kluwer/Plenum, New York, pp 699–706Google Scholar
  395. Madigan MT, Martinko JM, Parker J (2000a) Biology of microorganisms. Prentice-Hall International, Upper Saddle RiverGoogle Scholar
  396. Madigan MT, Jung DO, Woese CR, Achenbach LA (2000b) Rhodoferax antarcticus sp. nov., a moderately psychrophilic purple nonsulfur bacterium isolated from an Antarctic microbial mat. Arch Microbiol 173:269–277PubMedGoogle Scholar
  397. Malone AS, Shellhammer TH, Courtney PD (2002) Effects of high pressure on the viability, morphology, lysis and cell wall hydrolase activity of Lactococcus lactis subsp. cremoris. Appl Environ Microbiol 68:4357–4363PubMedGoogle Scholar
  398. Mannisto MK, Schumann P, Rainey FA, Kampfer P, Tsitko I, Tiirola MA, Salkinoja-Salonen MS (2000) Subtercola boreus gen. nov., sp. nov., and Subtercola frigoramans sp. nov., two new psychrophilic actinobacteria isolated from boreal groundwater. Int J Syst Evol Microbiol 50:1731–1739PubMedGoogle Scholar
  399. Margesin R, Spröer C, Zhang DC, Busse HJ (2011) Polaromonas glacialis sp. nov. and Polaromonas cryoconiti sp. nov., two novel bacteria from alpine glacier cryoconite. Int J Syst Evol Microbiol. doi:10.1099/ijs.0.037556-0Google Scholar
  400. Margesin R, Zhang DC, Busse HJ (2012) Sphingomonas alpina sp. nov., a psychrophilic bacterium isolated from alpine soil. Int J Syst Evol Microbiol 62:1558–1563Google Scholar
  401. Margulis L (1981) Symbiosis in cell evolution. Freeman, San FranciscoGoogle Scholar
  402. Marquis RE (1976) High pressure microbial physiology. Adv Microb Physiol 14:159–239PubMedGoogle Scholar
  403. Marquis RE, Matsumura P (1978) Microbial life under pressure. In: Kushner DJ (ed) Microbial life in extreme environments. Academic, London, pp 105–158Google Scholar
  404. Marschall E, Jogler M, Henssge U, Overmann J (2010) Large scale distribution and activity patterns of an extremely low-light adapted population of green sulfur bacteria in the Black Sea. Environ Microbiol 12:1348–1362PubMedGoogle Scholar
  405. Martens-Habbena W, Berube PM, Urakawa H, de la Torre JR, Stahl DA (2009) Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria. Nature 461:976–979PubMedGoogle Scholar
  406. Martin GA, Hempfling WP (1976) A method for the regulation of microbial population density during continuous culture at high growth rates. Arch Microbiol 107:41–47PubMedGoogle Scholar
  407. Martin SE, Flowers RS, Ordal ZJ (1976) Catalase: its effect on microbial enumeration. Appl Environ Microbiol 32:731–734PubMedGoogle Scholar
  408. Maruyama A, Honda D, Yamamoto H, Kitamura K, Higashihara T (2000) Phylogenetic analysis of psychrophilic bacteria isolated from the Japan Trench, including a description of the deep-sea species Psychrobacter pacificensis sp. nov. Int J Syst Evol Microbiol 50:835–846PubMedGoogle Scholar
  409. Mason CA, Egli T (1993) Dynamics of microbial growth in the decelerating and stationary phase of batch culture. In: Kjelleberg S (ed) Starvation in bacteria. Plenum, New York, pp 81–98Google Scholar
  410. Matin A (1981) Regulation of enzyme synthesis as studied in continuous culture. In: Calcott PH (ed) Continuous culture of cells, vol 2. CRC Press, Boca Raton, pp 69–97Google Scholar
  411. Matin A (1990) Keeping a neutral cytoplasm: the bioenergetics of obligate acidophiles. FEMS Microbiol Rev 75:307–318Google Scholar
  412. Matin A, Veldkamp H (1978) Physiological basis of the selective advantage of a Spirillum sp. in a carbon-limited environment. J Gen Microbiol 105:187–197PubMedGoogle Scholar
  413. Mazur P (1980) Limits to life at low temperatures and at reduced water contents and water activities. Orig Life 10:137–159PubMedGoogle Scholar
  414. McDougald D, Kjelleberg S (1999) New perspectives on the viable but nonculturable response. Biologia 54:617–623Google Scholar
  415. McInerney MJ, Bryant MD, Pfennig N (1979) Anaerobic bacterium that degrades fatty acids in syntrophic association with methanogens. Arch Microbiol 122:129–135Google Scholar
  416. McInerney MJ, Bryant MP, Hespell RB, Costerton JW (1981) Syntrophomonas wolfei gen. nov. sp. nov., an anaerobic, syntrophic, fatty acid-oxidizing bacterium. Appl Environ Microbiol 41:1029–1039PubMedGoogle Scholar
  417. Meers JL (1973) Growth of bacteria in mixed cultures CRC. Crit Rev Microbiol 2:139–184Google Scholar
  418. Megee RD 3rd, Drake JF, Fredrickson AG, Tsuchiya HM (1972) Studies in intermicrobial symbiosis. Saccharomyces cerevisiae and Lactobacillus casei. Can J Microbiol 18:1733–1742PubMedGoogle Scholar
  419. Meldrum FC, Heywood BR, Mann S, Frankel RB, Bazylinski DA (1993) Electron microscopy study of magnetosomes in a cultured coccoid magnetotactic bacterium. Proc R Soc Lond B Biol Sci 251:231–236Google Scholar
  420. Meyer JS, Tsuchiya HM, Fredrickson AG (1975) Dynamics of mixed populations having complementary metabolism. Biotechnol Bioeng 17:1065–1081Google Scholar
  421. Michels PAM, Michels JPJ, Boonstra J, Konings WN (1979) Generation of an electrochemical proton gradient in bacteria by the excretion of metabolic end-products. FEMS Microbiol Lett 5:357–364Google Scholar
  422. Mikx FJM, van der Hoeven JS (1975) Symbiosis of Streptococcus mutans and Veillonella alcalescens in mixed continuous cultures. Arch Oral Biol 20:407–410PubMedGoogle Scholar
  423. Miller TL, Wolin MJ (1974) A serum bottle modification of the Hungate technique for cultivating obligate anaerobes. Appl Microbiol 27:985–987PubMedGoogle Scholar
  424. Miura Y, Tanaka H, Okazaki M (1980) Stability analysis of commensal and mutual relations with competitive assimilation in continuous mixed culture. Biotechnol Bioeng 22:929–948Google Scholar
  425. Miyamoto-Shinohara Y, Sukenobe J, Imaizumi T, Nakahara T (2006) Survival curves for microbial species stored by freeze-drying. Cryobiology 52:27–32PubMedGoogle Scholar
  426. Mizunoe Y, Wai SN, Takade A, Yoshida S (1999) Restoration of culturability of starvation-stressed and low-temperature-stressed Escherichia coli O157 cells using H2O2-degrading compounds. Arch Microbiol 172:63–67PubMedGoogle Scholar
  427. Moench TT, Zeikus JG (1983) An improved preparation method for a titanium (III) media reductant. J Microbiol Methods 1:199–202Google Scholar
  428. Moissl C, Rudolph C, Huber R (2002) Natural communities of novel archaea and bacteria with a string-of-pearls-like morphology: molecular analysis of the bacterial partners. Appl Environ Microbiol 68:933–937PubMedGoogle Scholar
  429. Monod J (1942) Recherches sur la croissance des cultures bacteriennes. Hermann, ParisGoogle Scholar
  430. Monod J (1950) La technique de culture continue: théorie et applications. Ann Inst Pasteur 79:390–410Google Scholar
  431. Morita RY (1975) Psychrophilic bacteria. Bacteriol Rev 39:144–167PubMedGoogle Scholar
  432. Morita RY (1982) Starvation—survival of heterotrophs in the marine environment. Adv Microbiol Ecol 6:171–198Google Scholar
  433. Morita RY (1986) Pressure as an extreme environment. In: Herbert RA, Codd GA (eds) Microbes in extreme environments. Academic, London, pp 171–185Google Scholar
  434. Morotomi M, Nagai F, Watanabe Y (2011) Parasutterella secunda sp. nov., isolated from human faeces and proposal of Sutterellaceae fam. nov. in the order Burkholderiales. Int J Syst Evol Microbiol 61:637–643PubMedGoogle Scholar
  435. Mossel DAA, Veldman A, Eelderink I (1980) Comparison of the effects of liquid medium repair and the incorporation of catalase in Macconkey type media on the recovery of Enterobacteriaceae sublethally stressed by freezing. J Appl Bacteriol 49:405–419PubMedGoogle Scholar
  436. Mountfort DO, Asher RA (1986) Isolation from a methanogenic ferulate degrading consortium of an anaerobe that converts methoxyl groups of aromatic acids to volatile fatty acids. Arch Microbiol 144:55–61Google Scholar
  437. Mountfort DO, Bryant MP (1985) Isolation and characterization of an anaerobic syntrophic benzoate degrading bacterium from sewage sludge. Arch Microbiol 133:249–256Google Scholar
  438. Mountfort DO, Rainey FA, Burghardt J, Kaspar HF, Stackebrandt E (1997) Clostridium vincentii sp. nov., a new anaerobic, saccharolytic, psychrophilic bacterium isolated from low-salinity pond sediment of the McMurdo ice shelf, Antarctica. Arch Microbiol 167:54–60PubMedGoogle Scholar
  439. Mountfort DO, Rainey FA, Burghardt J, Kaspar HF, Stackebrandt E (1998) Psychromonas antarcticus gen. nov., sp. nov., a new aerotolerant anaerobic, halophilic psychrophile isolated from pond sediment of the McMurdo ice shelf, Antarctica. Arch Microbiol 169:231–238PubMedGoogle Scholar
  440. Mukamolova GV, Kaprelyants AS, Young DI, Young M, Kell DB (1998) A bacterial cytokine. Proc Natl Acad Sci USA 95:8916–8921PubMedGoogle Scholar
  441. Müller RH, Babel W (1996) Measurement of growth at very low rates (μ ≧ 0), an approach to study the energy requirement for the survival of Alcaligenes eutrophus JMP 134. Appl Environ Microbiol 62:147–151PubMedGoogle Scholar
  442. Munro PM, Flatau GN, Clément RL, Gauthier MJ (1995) Influence of the RpoS (KatF) sigma factor on maintenance of viability and culturability of Escherichia coli and Salmonella typhimurium in seawater. Appl Environ Microbiol 61:1853–1858PubMedGoogle Scholar
  443. Mur LR, Gons HJ, van Liere L (1977) Some experiments on the competition between green algae and blue-green bacteria in light-limited environments. FEMS Microbiol Lett 1:335–338Google Scholar
  444. Murray DR (1989) Biology of food radiation. Wiley, ChichesterGoogle Scholar
  445. Myers J, Clark LB (1944) Culture conditions and the development of the photosynthetic mechanism. II: an apparatus for the continuous culture of Chlorella. J Gen Physiol 28:103–112PubMedGoogle Scholar
  446. Nakamura I, Ogimoto K, Izumu H (1995) ATP-dependent calcium release from binding site in Streptococcus bovis: bound versus free pools. J Gen Appl Microbiol 41:389–398Google Scholar
  447. Nakasone K, Ikegami A, Kato C, Usami R, Horikoshi K (1998) Mechanisms of gene expression controlled by pressure in deep-sea microorganisms. Extremophiles 2:149–154PubMedGoogle Scholar
  448. National Center for Biotechnology Information (2012) http://www.ncbi.nlm.nih.gov/genomes/MICROBES/microbial_growth.html
  449. Nedwell DB (1984) The input and mineralization of organic carbon in anaerobic aquatic sediments. Adv Microbiol Ecol 7:93–131Google Scholar
  450. Nedwell DB, Rutter M (1994) Influence of temperature on growth rate and competition between two psychrotolerant Antarctic bacteria: low temperature diminishes affinity for substrate uptake. Appl Environ Microbiol 60:1984–1992PubMedGoogle Scholar
  451. Neidhardt FC, Umbarger HE (1996) Chemical composition of Escherichia coli. In: Neidhardt FC (ed) Escherichia coli and Salmonella, 2nd edn. ASM Press, Washington, DC, pp 13–16Google Scholar
  452. Nelson DC, Jørgensen BB, Revsbech NP (1986) Growth pattern and yield of a chemoautotrophic Beggiatoa sp. in oxygen-sulfide microgradients. Appl Environ Microbiol 52:225–233PubMedGoogle Scholar
  453. Neuhard J, Kelln RA (1996) Biosynthesis and conversions of pyrimidines. In: Neidhardt FC (ed) Escherichia coli and Salmonella, 2nd edn. ASM Press, Washington, DC, pp 580–599Google Scholar
  454. Nichols DS, Greenhill AR, Shadbolt CT, Ross T, McMeekin TA (1999) Physicochemical parameters for growth of the sea ice bacteria Glaciecola punicea ACAM 611T and Gelidibacter sp. strain IC158. Appl Environ Microbiol 65:3757–3760PubMedGoogle Scholar
  455. Nichols D, Lewis K, Orjala J, Mo S, Ortenberg R, O’Connor P, Zhao C, Vouros P, Kaeberlein T, Epstein SS (2008) Short peptide induces an “uncultivable” microorganism to grow in vitro. Appl Environ Microbiol 74:4889–4897PubMedGoogle Scholar
  456. Niehaus F, Hantke K, Unden G (1991) Iron content and FNR-dependent gene regulation in Escherichia coli. FEMS Microbiol Lett 84:319–324Google Scholar
  457. Nielsen PH, de Muro MA, Nielsen JL (2000) Studies on the in situ physiology of Thiothrix spp. present in activated sludge. Environ Microbiol 2:389–398PubMedGoogle Scholar
  458. Nogales B, Guerrero R, Esteve I (1997) A heterotrophic bacterium inhibits growth of several species of the genus Chlorobium. Arch Microbiol 167:396–399Google Scholar
  459. Nogales B, Moore ERB, Abraham WR, Timmis KN (1999) Identification of the metabolically active members of a bacterial community in a polychlorinated biphenyl-polluted moorland soil. Environ Microbiol 1:199–212PubMedGoogle Scholar
  460. Norland S, Fagerbakke KM, Heldal M (1995) Light element analysis of individual bacteria by X-ray microanalysis. Appl Environ Microbiol 61:1357–1362PubMedGoogle Scholar
  461. Norris JR, Ribbons DW (1970) Methods in microbiology, vol 3. Academic, New York, pp 1–506Google Scholar
  462. Notley L, Ferenci T (1996) Induction of RpoS-dependent functions in glucose-limited continuous culture: what levels of nutrient limitation induces the stationary phase of Escherichia coli. J Bacteriol 178:1465–1468PubMedGoogle Scholar
  463. Novick A, Szilard L (1950) Description of the chemostat. Science 112:715–716PubMedGoogle Scholar
  464. Nozhevnikova AN, Simankova MV, Parshina SN, Kotsyurbenko OR (2001) Temperature characteristics of methanogenic archaea and acetogenic bacteria isolated from cold environments. Water Sci Technol 44:41–48PubMedGoogle Scholar
  465. Nurmikko V (1956) Biochemical factors affecting symbiosis among bacteria. Experientia 12:245–249PubMedGoogle Scholar
  466. Oerther DB, Pernthaler J, Schramm A, Amann R, Raskin L (2000) Monitoring precursor 16S rRNAs of Acinetobacter spp. in activated sludge wastewater treatment systems. Appl Environ Microbiol 66:2154–2165PubMedGoogle Scholar
  467. Ohmura N, Matsumoto N, Sasaki K, Saiki H (2002) Electrochemical regeneration of Fe(III) to support growth on anaerobic iron respiration. Appl Environ Microbiol 68:405–407PubMedGoogle Scholar
  468. Okada T, Ueyama K, Niya S, Kanazawa H, Futai M, Tsuchiya T (1981) Role of inducer exclusion in preferential utilization of glucose over melibiose in diauxic growth of Escherichia coli. J Bacteriol 146:1030–1037PubMedGoogle Scholar
  469. Oliver JD (1995) The viable but non-culturable state in the human pathogen Vibrio vulnificus. FEMS Microbiol Lett 133:203–208PubMedGoogle Scholar
  470. Olsen RA, Bakken LR (1987) Viability of soil bacteria: optimization of plate-counting technique and comparison between total counts and plate counts within different size groups. Microb Ecol 13:59–74Google Scholar
  471. Oltmann LF, Schoenmaker GS, Reijnders WNM, Stouthamer AH (1978) Modification of the pH auxostat culture method for the mass cultivation of bacteria. Biotechnol Bioeng 20:921–925PubMedGoogle Scholar
  472. Orcutt KM, Rasmussen U, Webb EA, Waterbury JB, Gundersen K, Bergman B (2002) Characterization of Trichodesmium spp. by genetic techniques. Appl Environ Microbiol 68:2236–2245PubMedGoogle Scholar
  473. Oremland RS (1988) Biogeochemistry of methanogenic bacteria. In: Zehnder AJB (ed) Biology of anaerobic microorganisms. Wiley, New York, pp 641–706Google Scholar
  474. Oremland RS, Hoeft SE, Santini JM, Bano N, Hollibough RA (2002) Anaerobic oxidation of arsenite in Mono Lake water and by a facultative, arsenite-oxidizing chemoautotroph, strain MLHE-1. Appl Environ Microbiol 68:4795–4802PubMedGoogle Scholar
  475. Oren A (1986) Intracellular salt concentrations of the halophilic eubacteria Haloaerobium praevalens and Halobacteroides halobius. Can J Microbiol 32:4–9Google Scholar
  476. Oren A (1999) Bioenergetic aspects of halophilism. Microbiol Mol Biol Rev 63:334–348PubMedGoogle Scholar
  477. Ostrowski M, Cavicchioloi R, Blaauw M, Gottschal JC (2001) Specific growth rate plays a critical role in hydrogen peroxide resistance of the marine oligotrophic ultramicrobacterium Sphingomonas alaskensis strain RB2256. Appl Environ Microbiol 67:1292–1299PubMedGoogle Scholar
  478. Ott JA, Novak R, Schiemer F, Hentschel U, Nebelsiek M, Polz M (1991) Tackling the sulfide gradient: a novel strategy involving marine nematodes and chemoautotrophic ectosymbionts. Mar Ecol 12:261–279Google Scholar
  479. Otto R, Hugenholtz J, Konings WN, Veldkamp H (1980) Increase of molar growth yield of Streptococcus cremoris for lactose as a consequence of lactate consumption by Pseudomonas stutzeri in mixed culture. FEMS Microbiol Lett 9:85–88Google Scholar
  480. Ouverney CC, Fuhrman JA (1999) Combined microautoradiography—16S rRNA probe technique for determination of radioisotope uptake by specific microbial cell types in situ. Appl Environ Microbiol 65:1746–1752PubMedGoogle Scholar
  481. Ouverney CC, Fuhrman JA (2000) Marine planktonic Archaea take up amino acids. Appl Environ Microbiol 66:4829–4833PubMedGoogle Scholar
  482. Overmann J (2002a) Phototrophic consortia: a tight cooperation between non-related eubacteria. In: Seckbach J (ed) Symbiosis. Mechanisms and model systems. Kluwer, Dordrecht, pp 239–255Google Scholar
  483. Overmann J (2002b) Principles of enrichment, isolation, cultivation, and preservation of bacteria. In: Dworkin M et al (eds) The prokaryotes: an evolving electronic resource for the microbiological community, 3rd edn (latest update release 3.11, September 2002). Springer, New York. http://ep.springer-ny.com:6336/contents/ or http://141.150.157.117:8080/prokPROD/index.htm
  484. Overmann J (2005) Chemotaxis and behavioural physiology of not-yet-cultivated microbes, vol 397, Methods in enzymology. Elsevier, San Diego, pp 133–147, Chap II.8Google Scholar
  485. Overmann J, Pfennig N (1989) Pelodictyon phaeoclathratiforme sp. nov., a new brown-colored member of the Chlorobiaceae forming net-like colonies. Arch Microbiol 152:401–406Google Scholar
  486. Overmann J, Pfennig N (1992) Continuous chemotrophic growth and respiration of Chromatiaceae species at low oxygen concentrations. Arch Microbiol 158:59–67Google Scholar
  487. Overmann J, Schubert K (2002) Phototrophic consortia: model systems for symbiotic interrelations between prokaryotes. Arch Microbiol 177:201–208PubMedGoogle Scholar
  488. Overmann J, van Gemerden H (2000) Microbial interactions involving sulfur bacteria: implications for the ecology and evolution of bacterial communities. FEMS Microbiol Rev 24:591–599PubMedGoogle Scholar
  489. Overmann J, Lehmann S, Pfennig N (1991) Gas vesicle formation and buoyancy regulation in Pelodictyon phaeoclathratiforme (green sulfur bacteria). Arch Microbiol 157:29–37Google Scholar
  490. Overmann J, Beatty JT, Hall KJ (1996) Purple sulfur bacteria control the growth of aerobic heterotrophic bacterioplankton in a meromictic salt lake. Appl Environ Microbiol 62:3251–3258PubMedGoogle Scholar
  491. Overmann J, Tuschak C, Fröstl J, Sass H (1998) The ecological niche of the consortium “Pelochromatium roseum”. Arch Microbiol 169:120–128PubMedGoogle Scholar
  492. Padan E, Schuldinger S (1986) Intracellular pH regulation in bacterial cells. Methods Enzymol 125:337–352PubMedGoogle Scholar
  493. Paerl H (1978) Role of heterotrophic bacteria in promoting N2-fixation by Anabaena in aquatic habitats. Microb Ecol 4:215–231Google Scholar
  494. Paerl HW (1982) Interactions with bacteria. In: Carr NG, Whitton NG (eds) The biology of cyanobacteria. University of California Press, Los Angeles, pp 441–461Google Scholar
  495. Pankratov TA, Dedysh SN (2011) Granulicella paludicola gen. nov., sp. nov., Granulicella pectinivorans sp. nov., Granulicella aggregans sp. nov. and Granulicella rosea sp. nov., acidophilic, polymer-degrading acidobacteria from Sphagnum peat bogs. Int J Syst Evol Microbiol 60:2951–2959Google Scholar
  496. Parkes RJ, Senior E (1988) Multistage chemostats and other models for studying anoxic ecosystems. In: Wimpenny JWT (ed) Handbook of laboratory model systems for microbial ecosystems, vol 1. CRC Press, Boca Raton, pp 51–71Google Scholar
  497. Pastan I, Perlman R (1969) Repression of β-galactosidase synthesis by glucose in phosphotransferase mutants of Escherichia coli. Repression in the absence of glucose phosphorylation. J Biol Chem 244:5836–5842PubMedGoogle Scholar
  498. Pasteur L (1862) Mémoire sur les corpuscules qui existent dans l’atmosphère: examen de la doctrine des génerations spontanées. Ann Chém Phys 64:5–110Google Scholar
  499. Pernthaler J, Posch T, Simek K, Vrba J, Pernthaler A, Glöckner FO, Nübel U, Psenner R, Amann R (2001) Predator-specific enrichment of Actinobacteria from a cosmopolitan freshwater clade in mixed continuous culture. Appl Environ Microbiol 67:2145–2155PubMedGoogle Scholar
  500. Pfennig N (1980) Syntrophic mixed cultures and symbiotic consortia with phototrophic bacteria: a review. In: Gottschalk G, Pfennig N, Werner HH (eds) Anaerobes and anaerobic infections. Fischer, Stuttgart, pp 127–131Google Scholar
  501. Pfennig N (1993) Reflections of a microbiologist, or how to learn from the microbes. Annu Rev Microbiol 47:1–29PubMedGoogle Scholar
  502. Pfennig N, Trüper HG (1989) Anoxygenic phototrophic bacteria. In: Staley JT, Bryant MP, Pfennig N, Holt JG (eds) Bergey’s manual of systematic bacteriology, vol 3. Williams and Wilkins, Baltimore, pp 1635–1709Google Scholar
  503. Pietzsch O (1967) Ein Nährboden zur Schwärmhemmung und gleichzeitigen Unterscheidung der Proteuskeime von Salmonellen. Fleischwirtschaft 1:31–32Google Scholar
  504. Pinhassi J, Berman T (2003) Differential growth response of colony-forming α- and γ-Proteobacteria in dilution culture and nutrient addition experiments from Lake Kinneret (Israel), the Eastern Mediterranean Sea, and the Gulf of Eilat. Appl Environ Microbiol 69:199–211PubMedGoogle Scholar
  505. Pinhassi J, Zweifel UL, Hagström Å (1997) Dominant marine bacterioplankton species found among colony-forming bacteria. Appl Environ Microbiol 63:3359–3366PubMedGoogle Scholar
  506. Pirt SJ (1974) The theory of fed batch culture with reference to the penicillin fermentation. J Appl Chem Biotechnol 24:415–4224Google Scholar
  507. Pirt SJ (1975) Principles of microbe and cell cultivation. Blackwell, OxfordGoogle Scholar
  508. Ploug H, Grossart HP, Azam F, Jørgensen BB (1999) Photosynthesis, respiration, and carbon turnover in sinking marine snow from surface waters of Southern California Bight: implications for the carbon cycle in the ocean. Mar Ecol Prog Ser 179:1–11Google Scholar
  509. Poindexter JS (1992) Dimorphic protshecate bacteria: the genera Caulobacter, Asticcacaulis, Hyphomicrobium, Pedomicrobium, Hyphomonas, and Thiodendron. In: Balows A, Trüper HG, Dworkin M, Schleifer K-H (eds) The prokaryotes, 2nd edn. Springer, New York, pp 2176–2196Google Scholar
  510. Poindexter JS, Leadbetter ER (1986) Enrichment cultures in bacterial ecology. In: Poindexter JS, Leadbetter ER (eds) Bacteria in nature, vol 2. Plenum, New York, pp 229–260Google Scholar
  511. Porter JR (1976) Antony van Leeuwenhoek: tercentenary of is discovery of bacteria. Microbiol Rev 40:260–269Google Scholar
  512. Pörtner R, Märkl H (1998) Dialysis cultures. Appl Microbiol Biotechnol 50:403–414PubMedGoogle Scholar
  513. Postgate JR, Hunter JR (1963) Acceleration of bacterial death by growth substrates. Nature 198:273–280PubMedGoogle Scholar
  514. Postgate JR, Hunter JR (1964) Accelerated death of Aerobacter aerogenes starved in the presence of growth-limiting substrates. J Gen Microbiol 34:459–473PubMedGoogle Scholar
  515. Powell EO (1958) Criteria for the growth of contaminants and mutants in continuous culture. J Gen Microbiol 18:259–268PubMedGoogle Scholar
  516. Pratuangdejkul J, Dharmsthiti S (2000) Purification and characterization of lipase from psychrophilic Acinetobacter calcoaceticus LP009. Microbiol Res 155:95–100PubMedGoogle Scholar
  517. Price B (2000) A habitat for psychrophiles in deep Antarctic ice. Proc Natl Acad Sci USA 97:1247–1251PubMedGoogle Scholar
  518. Pringault O, de Wit R, Caumette P (1996) A benthic gradient chamber for culturing phototrophic sulfur bacteria on reconstituted sediments. FEMS Microbiol Ecol 20:237–250Google Scholar
  519. Pruesse E, Quast C, Knittel K, Fuchs B, Ludwig W, Peplies J, Glöckner FO (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35:7188–7196PubMedGoogle Scholar
  520. Puskas A, Greenberg EP, Kaplan S, Schaefer AL (1997) A quorum-sensing system in the free-living photosynthetic bacterium Rhodobacter sphaeroides. J Bacteriol 179:7530–7537PubMedGoogle Scholar
  521. Radajewski S, Ineson P, Parekh NR, Murrell JC (2000) Stable-isotope probing as a tool in microbial ecology. Nature 403:646–649PubMedGoogle Scholar
  522. Rappe MS, Connon SA, Vergin KL, Giovannoni SJ (2002) Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418:630–633PubMedGoogle Scholar
  523. Ratkowsky PA, Lowry RR, McMeekin TA, Stokes AN, Chandler RE (1983) Model for bacterial culture growth rate throughout the entire biokinetic temperature range. J Bacteriol 154:1222–1226PubMedGoogle Scholar
  524. Reddy GS, Aggarwal RK, Matsumoto GI, Shivaji S (2000) Arthrobacter flavus sp. nov., a psychrophilic bacterium isolated from a pond in McMurdo Dry Valley, Antarctica. Int J Syst Evol Microbiol 50:1553–1561PubMedGoogle Scholar
  525. Reed RH, Walsby AE (1985) Changes in turgor pressure in response to increases in external NaCl concentration in the gas-vacuolate cyanobacterium Microcystis sp. Arch Microbiol 143:290–296Google Scholar
  526. Reichenbach H (1984) Myxobacteria: a most peculiar group of social prokaryotes. In: Rosenberg E (ed) Myxobacteria: development and cell interactions. Springer, New York, pp 1–50Google Scholar
  527. Reisch CR, Stoudemayer MJ, Varaljay VA, Amster IJ, Moran MA, Whitman WB (2011) Novel pathway for assimilation of dimethylsulphoniopropionate widespread in marine bacteria. Nature 12:208–211Google Scholar
  528. Renesto P, Crapoulet N, Ogata H, La Scola B, Vestris G, Claveri J-M, Raoult D (2003) Genome-based design of a cell-free culture medium for Tropheryma whipplei. Lancet 362:447–449PubMedGoogle Scholar
  529. Reusse U, Meyer A (1972) Der “Pril-Mannit-Agar” in der Salmonellen-Diagnostik. Zbl Bakteriol I Abt Orig 219:555–557Google Scholar
  530. Revsbech NP, Jørgensen BB (1986) Microelectrodes: their use in microbial ecology. Adv Microbiol Ecol 9:293–352Google Scholar
  531. Rhee GY (1972) Competition between an algae and an aquatic bacterium for phosphate. Limnol Oceanogr 17:505–514Google Scholar
  532. Ricica J, Dobersky P (1981) Complex systems. In: Calcott PH (ed) Continuous cultures of cells, vol 1. CRC Press, Boca Raton, pp 63–96Google Scholar
  533. Robinson JA, Tiedje JM (1984) Competition between sulfate-reducing and methanogenic bacteria for H2 under resting and growing conditions. Arch Microbiol 137:26–32Google Scholar
  534. Roesch LFW, Fulthorpe RR, Riva A, Casella G, Hadwin AKM, Kent AD, Daroub SH, Camargo FAO, Farmerie WG, Triplett EW (2007) Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J 1:283–290PubMedGoogle Scholar
  535. Roeßler M, Müller V (1998) Quantitative and physiological analyses of chloride dependence of growth of Halobacillus halophilus. Appl Environ Microbiol 64:3813–3817PubMedGoogle Scholar
  536. Roeßler M, Müller V (2002) Chloride, a new environmental signal molecule involved in gene regulation in a moderately halophilic bacterium, Halobacillus halophilus. J Bacteriol 184:6207–6215PubMedGoogle Scholar
  537. Rose AH, Evison LM (1965) Studies on the biochemical basis of the minimum temperature for growth of certain psychrophilic and mesophilic microorganisms. J Gen Microbiol 38:131–141PubMedGoogle Scholar
  538. Rosenberg E, Keller KH, Dworkin M (1977) Cell-density dependent growth of Myxococcus xanthus on casein. J Bacteriol 129:770–777PubMedGoogle Scholar
  539. Roslev P, Iversen N (1999) Radioactive fingerprinting of microorganisms that oxidize atmospheric methane in different soils. Appl Environ Microbiol 65:4064–4070PubMedGoogle Scholar
  540. Roszak DB, Colwell RR (1987) Survival strategies of bacteria in the natural environment. Microbiol Rev 51:365–379PubMedGoogle Scholar
  541. Rouf MA (1964) Spectrochemical analysis of inorganic elements in bacteria. J Bacteriol 88:1545–1549PubMedGoogle Scholar
  542. Ruger HJ, Fritze D, Sproer C (2000) New psychrophilic and psychrotolerant Bacillus marinus strains from tropical and polar deep-sea sediments and emended description of the species. Int J Syst Evol Microbiol 50:1305–1313PubMedGoogle Scholar
  543. Russel NJ (1984) Mechanisms of thermal adaptation in bacteria: blueprints for survival TIBS. Trends Biol Sci 9:108–112Google Scholar
  544. Russel NJ (2000) Toward a molecular understanding of cold activity of enzymes from psychrophiles. Extremophiles 4:83–90Google Scholar
  545. Russel NJ, Fukunaga N (1990) A comparison of thermal adaptation of membrane lipids in psychrophilic and thermophilic bacteria. FEMS Microbiol Rev 74:171–182Google Scholar
  546. Russell EJ (1923) The micro-organisms of the soil. Longmans, Green, LondonGoogle Scholar
  547. Sambanis A, Fredrickson AG (1987) Long-term studies of ciliate-bacterial interactions: use of a chemostat fed with bacteria grown in a separate chemostat. J Gen Microbiol 133:1619–1630Google Scholar
  548. Sánchez O, van Gemerden H, Mas J (1996) Description of a redox-controlled sulfidostat fro the growth of sulfide-oxidizing phototrophs. Appl Environ Microbiol 62:3640–3645PubMedGoogle Scholar
  549. Sandaa R-A, Torsvik V, Enger Ø, Daae FL, Castberg T, Hahn D (1999) Analysis of bacterial communities in heavy metal-contaminated soils at different levels of resolution. FEMS Microbiol Ecol 30:237–251PubMedGoogle Scholar
  550. Sass A, Sass H, Coolen MJL, Cypionka H, Overmann J (2001) Microbial communities in the chemocline of a hypersaline deep-sea basin (Urania Basin, Mediterranean Sea). Appl Environ Microbiol 67:5392–5402PubMedGoogle Scholar
  551. Schauer NL, Brown DP, Ferry JG (1982) Kinetics of formate metabolism in Methanobacterium formicicum and Methanospirillum hungatei. Appl Environ Microbiol 44:549–554PubMedGoogle Scholar
  552. Schink B (1991) Syntrophism among prokaryotes. In: Balows A, Trüper HG, Dworkin M, Schleifer K-H (eds) The prokaryotes, 2nd edn. Springer, New York, pp 276–299Google Scholar
  553. Schink B (1997) Energetics of syntrophic cooperation in methanogenic degradation. Microbiol Mol Biol Rev 61:262–280PubMedGoogle Scholar
  554. Schink B, Friedrich M (2000) Phosphite oxidation by sulphate reduction. Nature 406:37PubMedGoogle Scholar
  555. Schink B, Thiemann V, Laue H, Friedrich MW (2002) Desulfotignum phosphitoxidans sp. nov., a new marine sulfate reducer that oxidizes phosphite to phosphate. Arch Microbiol 177:381–391PubMedGoogle Scholar
  556. Schlegel HG, Jannasch HW (1967) Enrichment cultures. Annu Rev Microbiol 21:49–70PubMedGoogle Scholar
  557. Schlesner H (1986) Pirellula marina sp. nov., a budding peptidoglycanless bacterium from brackish water. Syst Appl Microbiol 8:177–180Google Scholar
  558. Schlesner H (1994) The development of media suitable for the microorganisms morphologically resembling Planctomyces spp., Pirellula spp., and other Planctomycetales from various aquatic habitats using dilute media. Syst Appl Microbiol 17:135–145Google Scholar
  559. Schloss PD, Handelsman J (2004) Status of the microbial census. Microbiol Mol Biol Rev 68:686–691PubMedGoogle Scholar
  560. Schmid M, Schmitz-Esser S, Jetten M, Wagner M (2001) 16S–23S rDNA intergenic spacer and 23S rDNA of anaerobic ammonium-oxidizing bacteria: implications for phylogeny and in situ detection. Environ Microbiol 3:450–459PubMedGoogle Scholar
  561. Schmidt GB, Rosano CL, Hurwitz C (1971) Evidence for a magnesium pump in Bacillus cereus T. J Bacteriol 105:150–155PubMedGoogle Scholar
  562. Schober A, Günther R, Schwienhorst A, Döring M, Lindemann BF (1993) Accurate high-speed liquid handling of very small biological samples. Biotechniques 15:324–329PubMedGoogle Scholar
  563. Scholten JCM, Conrad R (2000) Energetics of syntrophic propionate oxidation in defined batch and chemostat cultures. Appl Environ Microbiol 66:2934–2942PubMedGoogle Scholar
  564. Schopfer P, Brennicke A (1999) Pflanzenphysiologie, 5th edn. Springer, New YorkGoogle Scholar
  565. Schramm A, de Beer D, van den Heuvel JC, Ottengraf S, Amann R (1999) Microscale distribution of populations and activities of Nitrosospira and Nitrospira spp. along a macroscale gradient in a nitrifying bioreactor: quantification by in situ hybridization and the use of microsensors. Appl Environ Microbiol 65:3690–3696PubMedGoogle Scholar
  566. Schulten HR, Plage B, Schnitzer M (1991) A chemical structure for humic substances. Naturwissenschaften 78:31–312Google Scholar
  567. Schulz E, Lüdemann H-D, Jaenicke R (1976) High-pressure equilibrium studies on the dissociation-association of E. coli ribosomes. FEBS Lett 64:40–43PubMedGoogle Scholar
  568. Schumann P, Zhang DC, Redzic M, Margesin R (2012) Alpinimonas psychrophila gen. nov., sp. nov., a novel actinobacterium of the family Microbacteriaceae isolated from alpine lacier cryoconite. Int J Syst Evol Microbiol. doi:10.1099/ijs.0.036160-0Google Scholar
  569. Schut F, de Vries EJ, Gottschal JC, Robertson BR, Harder W, Prins RA, Button DK (1993) Isolation of typical marine bacteria by dilution culture: growth, maintenance, and characteristics of isolates under laboratory conditions. Appl Environ Microbiol 59:2150–2160PubMedGoogle Scholar
  570. Schut F, Jansen M, Pedro Gomes TM, Gottschal JC, Harder W, Prins RA (1995) Substrate uptake and utilization by a marine ultramicrobacterium. Microbiology 141:351–361PubMedGoogle Scholar
  571. Schut F, Prins RA, Gottschal JC (1997) Oligotrophy and pelagic marine bacteria: facts and fiction. Aquat Microb Ecol 12:177–202Google Scholar
  572. Scott DT, McKnight DM, Blunt-Harris EL, Kolesar SE, Lovley DR (1998) Quinone moieties act as electron acceptors in the reduction of humic substances by humic-reducing microorganisms. Environ Sci Technol 32:2984–2989Google Scholar
  573. Seitz AP, Nielsen TH, Overmann J (1993) Physiology of purple sulfur bacteria forming macroscopic aggregates in Great Sippewissett Salt Marsh, Massachusetts. FEMS Microbiol Ecol 12:225–236Google Scholar
  574. Sekiguchi Y, Takahashi H, Kamagata Y, Ohashi A, Harada H (2001) In situ detection, isolation, and physiological properties of a thin filamentous microorganism abundant in methanogenic granular sludges: a novel isolate affiliated with a clone cluster, the green non-sulfur bacteria, subdivision I. Appl Environ Microbiol 67:5740–5749PubMedGoogle Scholar
  575. Shilo M (1984) Bdellovibrio as a predator. In: Klug MJ, Reddy CA (eds) Current perspectives in microbial ecology. ASM Press, Washington, DC, pp 334–339Google Scholar
  576. Shindler DB, Wydro RM, Kushner DJ (1977) Cell-bound cations in the moderately halophilic bacterium Vibrio costicola. J Bacteriol 130:698–703PubMedGoogle Scholar
  577. Shockey WL, Dehority BA (1989) Comparison of two methods for enumeration of anaerobe numbers on forages and evaluation of ethylene oxide treatment for forage sterilization. Appl Environ Microbiol 55:1766–1768PubMedGoogle Scholar
  578. Siebert J, Hirsch P (1988) Characterization of 15 selected coccal bacteria isolated from Antarctic rock and soil samples from the McMurdo-Dry Valleys (South-Victoria Land). Polar Biol 9:37–44PubMedGoogle Scholar
  580. Simankova MV, Kotsyurbenko OR, Stackebrandt E, Kostrikina NA, Lysenko AM, Osipov GA, Nozhevnikova AN (2000) Acetobacterium tundrae sp. nov., a new psychrophilic acetogenic bacterium from tundra soil. Arch Microbiol 174:440–447PubMedGoogle Scholar
  581. Simek K, Vrba J, Pernthaler J, Posch T, Hartman P, Nedoma J, Psenner R (1997) Morphological and compositional shifts in an experimental bacterial community influenced by protists with contrasting feeding modes. Appl Environ Microbiol 63:587–595PubMedGoogle Scholar
  582. Sitnikov DM, Schineller JB, Baldwin TO (1996) Control of cell division in Escherichia coli: regulation of transcription of ftsQA involves both rpoS and SdiA-mediated autoinduction. Proc Natl Acad Sci USA 93:336–341PubMedGoogle Scholar
  583. Skerman VDB (1968) A new type of micromanipulator and microforge. J Gen Microbiol 54:287–297PubMedGoogle Scholar
  584. Skulachev VP (1987) Bacterial sodium transport: bioenergetic functions of sodium ions. In: Rosen BP, Silver S (eds) Ion transport in prokaryotes. Academic, New York, pp 131–164Google Scholar
  585. Slater JH, Bull AT (1978) Interactions between microbial populations. In: Bull AT, Meadow PM (eds) Companion to microbiology. Longman, London, pp 181–206Google Scholar
  586. Slonczewski J, Foster JW (1996) pH-regulated genes and survival at extreme pH. In: Neidhardt FC (ed) Escherichia coli and Salmonella, 2nd edn. ASM Press, Washington, DC, pp 1539–1549Google Scholar
  587. Sly LI, Arunpairojana V (1987) Isolation of manganese-oxidizing Pedomicrobium cultures from water by micromanipulation. J Microbiol Methods 6:177–182Google Scholar
  588. Soendergaard M, Riemann B, Jörgensen NOG (1985) Extracellular organic carbon (EOC) released by phytoplankton and bacterial production. Oikos 45:323–332Google Scholar
  589. Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, Neal PR, Arrieta JM, Herndl GJ (2006) Microbial diversity in the deep sea and the underexplored “rare biosphere”. Proc Natl Acad Sci USA 103:12115–12120PubMedGoogle Scholar
  590. Somero GN (1992) Adaptations to high hydrostatic pressure. Annu Rev Physiol 54:557–577PubMedGoogle Scholar
  591. Spring S, Amann R, Ludwig W, Schleifer K-H, van Gemerden H, Petersen N (1993) Dominating role of an unusual magnetotactic bacterium in the micraerobic zone of a freshwater sediment. Appl Environ Microbiol 59:2397–2403PubMedGoogle Scholar
  592. Spring S, Schulze R, Overmann J, Schleifer K-H (2000) Identification and characterization of ecologically significant prokaryotes in the sediment of freshwater lakes: molecular and cultivation studies. FEMS Microbiol Rev 24:573–590PubMedGoogle Scholar
  593. Stal LJ, van Gemerden H, Krumbein WE (1985) Structure and development of a benthic marine microbial mat. FEMS Microbiol Ecol 31:111–125Google Scholar
  594. Staley JT, Fuerst JA, Giovannoni SJ, Schlesner H (1992) The order Planctomycetales and the genera Planctomyces, Pirellula, gemmata and Isosphaera. In: Balows A, Dworkin M, Harder W, Schleifer K-H, Trüper HG (eds) The prokaryotes. Springer, New York, pp 3710–3731Google Scholar
  595. Stanton TB, Canale-Parola E (1979) Enumeration and selective isolation of rumen spirochetes. Appl Environ Microbiol 38:965–973PubMedGoogle Scholar
  596. Stetter KO (2001) Genus III: Pyrolobus. In: Boone DR, Castenholz RW (eds) Bergey’s manual of systematic bacteriology, vol 1. Springer, New York, pp 186–197Google Scholar
  597. Stevens TO (1995) Optimization of media for enumeration and isolation of aerobic heterotrophic bacteria from the deep terrestrial subsurface. J Microbiol Methods 21:293–303Google Scholar
  598. Stewart CS, Bryant MP (1988) The rumen bacteria. In: Hobson PN (ed) The rumen microbial ecosystem. Elsevier Applied Science, London, pp 21–75Google Scholar
  599. Stolp H, Starr MP (1963) Bdellovibrio bacteriovorus gen. et sp. n., a predatory ectoparasitic and bacteriolytic microorganism. Antonie Van Leeuwenhoek 29:217–248PubMedGoogle Scholar
  600. Stolp H, Starr MP (1965) Bacteriolysis. Annu Rev Microbiol 19:79–104PubMedGoogle Scholar
  601. Stringfellow WT, Aitken MD (1994) Comparative physiology of phenanthrene degradation by two dissimilar pseudomonads isolated from a creosote-contaminated soil. Can J Microbiol 40:432–438PubMedGoogle Scholar
  602. Sugio T, Kuwano H, Negishi A, Maeda T, Takeuchi F, Kamimura K (2001) Mechanism of growth inhibition by tungsten in Acidithiobacillus ferrooxidans. Biosci Biotechnol Biochem 65:555–562PubMedGoogle Scholar
  603. Suh DH, Becker TC, Sands JA, Montenecourt BS (1988) Effects of temperature on xylanase secretion by Trichoderma reesei. Biotechnol Bioeng 32:821–825PubMedGoogle Scholar
  604. Suzuki K, Sasaki J, Uramoto M, Nakase T, Komagata K (1997a) Cryobacterium psychrophilum gen. nov., sp. nov., nom. rev., comb. nov., an obligately psychophilic actinomycete to accommodate “Curtobacterium psychrophilum”, Inoue and Komagata 1976. Int J Syst Evol Microbiol 47:474–478Google Scholar
  605. Suzuki MT, Rappé MS, Haimberger ZW, Winfield H, Adair N, Ströbel J, Giovannoni SJ (1997b) Bacterial diversity among small-subunit rRNA gene clones and cellular isolates from the same seawater sample. Appl Environ Microbiol 63:983–989PubMedGoogle Scholar
  606. Sweerts JPRA, de Beer D (1989) Microelectrode measurements of nitrate gradients in the littoral and profundal sediments of a meso-eutrophic lake (Lake Vechten, The Netherlands). Appl Environ Microbiol 55:754–757PubMedGoogle Scholar
  607. Swift ST, Najita IY, Ohtaguchi K, Fredrickson AG (1982) Continuous culture of the ciliate Tetrahymena pyriformis on Escherichia coli. Biotechnol Bioeng 24:1953–1964PubMedGoogle Scholar
  608. Szewzyk U, Schink B (1989) Degradation of hydroquinone, gentisate, and benzoate by a fermenting bacterium in pure or defined mixed culture. Arch Microbiol 15:541–545Google Scholar
  609. Talamoto S, Yamada K, Ezura Y (1994) Producing of bacteriolytic enzymes during the growth of a marine bacterium Alteromonas sp. no. 8-R. J Gen Appl Microbiol 40:499–508Google Scholar
  610. Tamaki H, Sekiguchi Y, Hanada S, Nakamura K, Nomura N, Matsumara M, Kamagata Y (2005) Comparative analysis of bacterial diversity in freshwater sediment of a shallow eutrophic lake by molecular and improved cultivation-based techniques. Appl Environ Microbiol 71:2162–2169PubMedGoogle Scholar
  611. Tamaki H, Tanaka Y, Matsuzawa H, Muramatsu M, Meng X, Hanada S, Mori K, Kamagata Y (2011) Armatimonas rosea gen. nov., sp. nov., of a novel bacterial phylum, Armatimonadetes phyl. nov., formally called the candidate phylum OP10. Int J Syst Evol Microbiol 61:1442–1447PubMedGoogle Scholar
  612. Tang W-C, White JC, Alexander M (1998) Utilization of sorbed compounds by microorganisms specifically isolated for that purpose. Appl Microbiol Biotechnol 49:117–121PubMedGoogle Scholar
  613. Tappe W, Tomaschewski C, Rittershaus S, Groeneweg J (1996) Cultivation of nitrifying bacteria in the retentostat, a simple fermenter with internal biomass retention. FEMS Microbiol Ecol 19:47–52Google Scholar
  614. Tappe W, Laverman A, Bohland M, Braster M, Rittershaus S, Groeneweg J, van Versefeld HW (1999) Maintenance energy demand and starvation recovery dynamics of Nitrosomonas europaea and Nitrobacter winogradskyi cultivated in a retentostat with complete biomass retention. Appl Environ Microbiol 65:2471–2477PubMedGoogle Scholar
  615. Tarin JJ, Trounson AO (1993) Effect of stimulation or inhibition of lipid peroxidation on freezing-thawing of mouse embryos. Biol Reprod 49:1362–1368PubMedGoogle Scholar
  616. Teather RM (1982) Maintenance of laboratory strains of obligately anaerobic rumen bacteria. Appl Environ Microbiol 44:499–501PubMedGoogle Scholar
  617. Tempest DW (1970) The continuous culture in microbial research. Adv Microb Physiol 4:223–250Google Scholar
  618. Tempest DW, Neyssel OM (1978) Eco-physiological aspects of microbial growth in aerobic nutrient limited environments. Adv Microbiol Ecol 2:105–153Google Scholar
  619. Tempest DW, Herbert F, Phipps PJ (1967) Studies on the growth of Aerobacter aerogenes at low dilution rates in a chemostat. In: Powell EO, Evans CGT, Strange RE, Tempest DW (eds) Microbial physiology and continuous culture. HMSO, London, pp 240–254Google Scholar
  620. Thauer RK, Käufer B, Fuchs G (1975) The active species of “CO2” utilized by reduced ferredoxin: CO2 oxidoreductase from Clostridium pasteurianum. Eur J Biochem 27:282–290Google Scholar
  621. Thauer RK, Jungermann K, Decker K (1977) Energy conservation in chemotrophic anaerobic bacteria. Bacteriol Rev 41:100–180PubMedGoogle Scholar
  622. Thiele JH, Zeikus JG (1988) Control of interspecies electron flow during anaerobic digestion: significance of formate transfer versus hydrogen transfer during syntrophic methanogenesis in flocs. Appl Environ Microbiol 54:20–29PubMedGoogle Scholar
  623. Thiele JH, Chartrain M, Zeikus JG (1988) Control of interspecies electron flow during anaerobic digestion: role of floc formation in syntrophic methanogenesis. Appl Environ Microbiol 54:10–19PubMedGoogle Scholar
  624. Thompson LA, Nedwell DB, Balba MT, Banat IM, Senior E (1983) The use of multiple vessel, open flow systems to investigate carbon flow in anaerobic microbial communities. Microb Ecol 9:189–199Google Scholar
  625. Tindall BJ (2007) Vacuum-drying and cryopreservation of prokaryotes. In: Day JG, Stacey GN (eds) Cryopreservation and freeze-drying protocols, vol 368, 2nd edn, Methods in molecular biology. Humana Press, Totowa, pp 73–97Google Scholar
  626. Tomczak MM, Hincha DK, Crowe JH, Harding MM, Haymet ADJ (2003) The effect of hydrophobic analogues of the type I winter flounder antifreeze protein on lipid bilayers. FEBS Lett 551:13–19PubMedGoogle Scholar
  627. Torella F, Morita RY (1981) Microcultural study of bacterial size changes and microcolony and ultramicrocolony formation by heterotrophic bacteria in seawater. Appl Environ Microbiol 41:518–527Google Scholar
  628. Trimbur DE, Gutshall KR, Prema P, Brenchley JE (1994) Characterization of a psychrotrophic Arthrobacter gene and its cold-active β-galactosidase. Appl Environ Microbiol 60:4544–4552PubMedGoogle Scholar
  629. Tripp HJ, Kitner JB, Schwalbach MS, Dacey JW, Wilhelm LJ, Giovannoni SJ (2008) SAR11 marine bacteria require exogenous reduced sulphur for growth. Nature 452:741–744PubMedGoogle Scholar
  630. Trüper HG, Pfennig N (1971) Family of phototrophic green sulfur bacteria: Chlorobiaceae Copeland, the correct family name; rejection of Chlorobacterium Lauterborn; and the taxonomic situation of the consortium-forming species. Int J Syst Bacteriol 21:8–10Google Scholar
  631. Tuschak C, Glaeser J, Overmann J (1999) Specific detection of green sulfur bacteria by in situ hybridization with a fluorescent labeled oligonucleotide probe. Arch Microbiol 171:265–272PubMedGoogle Scholar
  632. Uphoff HU, Felske A, Fehr W, Wagner-Döbler I (2001) The microbial diversity in picoplankton enrichment cultures: a molecular screening of marine isolates. FEMS Microbiol Ecol 35:249–258PubMedGoogle Scholar
  633. Urakawa H, Kita-Tsukamoto K, Steven SE, Ohwada K, Colwell RR (1998) A proposal to transfer Vibrio marinus (Russell 1891) to a new genus Moritella gen. nov. as Moritella marina comb. nov. FEMS Microbiol Lett 165:373–378PubMedGoogle Scholar
  634. Urbach E, Vergin KL, Giovannoni SJ (1999) Immunochemical detection and isolation of DNA from metabolically active bacteria. Appl Environ Microbiol 65:1207–1213PubMedGoogle Scholar
  635. Usui K, Hiraishi T, Kawamoto J, Kurihara T, Nogi Y, Kato C, Abe F (2012) Eicosapentaenoic acid plays a role in stabilizing dynamic membrane structure in the deep-sea piezophile Shewanella violacea: a study employing high-pressure time-resolved fluorescence anisotropy measurement. Biochim Biophys Acta 1818:574–583PubMedGoogle Scholar
  636. Van den Ende FPL, Laverman AM, van Gemerden H (1996) Coexistence of aerobic chemotrophic and anaerobic phototrophic sulfur bacteria under oxygen limitations. FEMS Microbiol Ecol 19:141–151Google Scholar
  637. Van den Ende FP, Meier J, van Gemerden H (1997) Syntrophic growth of sulfate-reducing bacteria and colorless sulfur bacteria during oxygen limitation. FEMS Microbiol Ecol 23:65–80Google Scholar
  638. van der Meer MTJ, Schouten S, van Dongen BE, Rijpstra WIC, Fuchs G, Sinninghe Damsté JS, de Leeuw JW, Ward DM (2001) Biosynthetic controls on the 13C contents of organic components in the photoautotrophic bacterium Chloroflexus aurantiacus. J Biol Chem 276:10971–10976PubMedGoogle Scholar
  639. Van der Wielen PWJJ, Lipman LJA, van Knapen F, Biesterveld S (2002) Competitive exclusion of Salmonella enterica serovar enteritidis by Lactobacillus crispatus and Clostridium lactatifermentans in a sequencing fed-batch culture. Appl Environ Microbiol 68:555–559PubMedGoogle Scholar
  640. van Gemerden H (1974) Coexistence of organisms competing for the same substrate: an example among purple sulfur bacteria. Microb Ecol 1:104–110Google Scholar
  641. van Gemerden H, Mas J (1995) Ecology of phototrophic sulfur bacteria. In: Blankenship RE, Madigan MT, Bauer CE (eds) Anoxygenic phototrophic bacteria. Kluwer, Dordrecht, pp 49–85Google Scholar
  642. van Gemerden H, Tughan CS, De Witz R, Herbert RA (1989) Laminated microbial ecosystems on sheltered beaches in Scapa Flow, Orkney Islands. FEMS Microbiol Ecol 62:87–102Google Scholar
  643. Van Iterson G Jr, Den Dooren de Jong LE, Kluyver AJ (1940) Martinus Willem Beijerinck, his life and work. Martinus Nijhoff, The HagueGoogle Scholar
  644. Van Niel CB (1930) Contributions to marine biology. Stanford University Press, Stanford, pp 161–169Google Scholar
  645. Van Niel CB (1967) Prefatory chapter. The education of a microbiologist: some reflections. Annu Rev Microbiol 21:1–30Google Scholar
  646. Van Verseveld HW, Chesbro WR, Braster M, Stouthamer AH (1984) Eubacteria have 3 growth modes keyed to nutrient-flow—consequences for the concept of maintenance and maximal growth yield. Arch Microbiol 137:176–184PubMedGoogle Scholar
  647. Vancanneyt M, Schut F, Snauwaert C, Goris J, Swings J, Gottschal JC (2001) Sphingomonas alaskensis sp. nov., a dominant bacterium from a marine oligotrophic environment. Int J Syst Evol Microbiol 51:73–79PubMedGoogle Scholar
  648. Varon M, Shilo M (1980) Ecology of aquatic Bdellovibrios. Adv Aquat Microbiol 2:1–48Google Scholar
  649. Veldkamp H (1965) Enrichment cultures—history and prospects. In: Schlegel HG, Kröger E (eds) Anreicherungskultur und Mutantenauslese: zentralbl. Bakteriol. Parasitenkd. Infektionskrankh. Hygiene I. Abteilung Gustav. Fischer, Stuttgart, Supplement 1, pp 1–13Google Scholar
  650. Veldkamp H (1977) Ecological studies with the chemostat. Adv Microbiol Ecol 1:59–94Google Scholar
  651. Veldkamp H, Jannasch HW (1972) Mixed culture studies with the chemostat. J Appl Chem Biotechnol 22:105–123Google Scholar
  652. Veldkamp H, Kuenen JG (1973) The chemostat as a model system for ecological studies. Bull Ecol Res Commun 17:347–355Google Scholar
  653. Veldkamp H, van Gemerden H, Harder W, Laanbroek HJ (1984) Microbial competition. In: Klug MJ, Reddy CA (eds) Current perspectives in microbial ecology. ASM Press, Washington, DC, pp 279–290Google Scholar
  654. Vester F, Ingvorsen K (1998) Improved most-probable-number method to detect sulfate-reducing bacteria with natural media and a radiotracer. Appl Environ Microbiol 64:1700–1707PubMedGoogle Scholar
  655. Visscher PT, Prins RA, van Gemerden H (1992a) Rates of sulfate reduction and thiosulfate consumption in a marine microbial mat. FEMS Microbiol Ecol 86:283–294Google Scholar
  656. Visscher PT, van den Ende FP, Schaub BEM, van Gemerden H (1992b) Competition between anoxygenic phototrophic bacteria and colorless sulfur bacteria in a microbial mat. FEMS Microbiol Ecol 101:51–58Google Scholar
  657. Vobis G (1992) The genus, Actinoplanes and related genera. In: Balows A, Trüper HG, Dworkin M, Schleifer K-H (eds) The prokaryotes, 2nd edn. Springer, New York, pp 1029–1060Google Scholar
  658. Vogl K, Glaeser J, Pfannes KR, Wanner G, Overmann J (2006) Chlorobium chlorochromatii sp. nov., a symbiotic green sulfur bacterium isolated from the phototrophic consortium “Chlorochromatium aggregatum”. Arch Microbiol 185:363–372PubMedGoogle Scholar
  659. Wachenheim DE, Hespell RB (1984) Inhibitory effects of titanium (III) citrate on enumeration of bacteria from rumen contents. Appl Environ Microbiol 48:444–445PubMedGoogle Scholar
  660. Wagner M, Nielsen PH, Loy A, Nielsen JL, Daims H (2006) Linking microbial community structure with function: fluorescence in situ hybridization-microautoradiography and isotope arrays. Curr Opin Biotechnol 17:1–9Google Scholar
  661. Walderhaug MO, Dosch DC, Epstein W (1987) Potassium transport in bacteria. In: Rosen BP, Silver S (eds) Ion transport in prokaryotes. Academic, New York, pp 85–130Google Scholar
  662. Walker GC (1996) The SOS response of Escherichia coli. In: Neidhardt FC (ed) Escherichia coli and Salmonella, vol 1. ASM Press, Washington, DC, pp 1400–1416Google Scholar
  663. Wang X, de Boer PAJ, Rothfield LI (1991) A factor that positively regulates cell division by activating transcription of the major cluster of essential cell division genes of Escherichia coli. EMBO J 10:3363–3372PubMedGoogle Scholar
  664. Ward DM, Bateson MM, Weller R, Ruff-Roberts AL (1992) Ribosomal RNA analysis of microorganisms as they occur in nature. Adv Microbiol Ecol 12:219–286Google Scholar
  665. Warthmann R, Cypionka H, Pfennig N (1992) Photoproduction of H2 from acetate by syntrophic cocultures of green sulfur bacteria and sulfur-reducing bacteria. Arch Microbiol 157:343–348Google Scholar
  666. Waterbury JB (1991) The cyanobacteria—isolation, purification, and identification. In: Balows A, Trüper HG, Dworkin M, Schleifer K-H (eds) The prokaryotes, 2nd edn. Springer, New York, pp 149–196Google Scholar
  667. Waterbury JB, Calloway CB, Turner RD (1983) A cellulolytic nitrogen-fixing bacterium cultured from the gland of Deshayes in shipworms (Bivalvia: Terebrenidae). Science 221:1401–1403PubMedGoogle Scholar
  668. Watson TG (1969) Steady state operation of a continuous culture at maximum growth rate by control of carbon-dioxide production. J Gen Microbiol 59:83–89PubMedGoogle Scholar
  669. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, Starr MP, Trüper HG (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464Google Scholar
  670. Weimer PJ, Zeikus JG (1977) Fermentation of cellulose and cellobiose by Clostridium thermocellum in the absence and presence of Methanobacterium thermoautotrophicum. Appl Environ Microbiol 33:289–297PubMedGoogle Scholar
  671. Weise W, Rheinheimer G (1978) Scanning electron microscopy and epifluorescence investigation of bacterial colonization of marine sand sediments. Microb Ecol 4:175–188Google Scholar
  672. Welch TJ, Farewell A, Neidhardt FC, Bartlett D (1993) Stress response of Escherichia coli to elevated hydrostatic pressure. J Bacteriol 175:7170–7177PubMedGoogle Scholar
  673. Westermann P, Ahring BK, Mah RA (1989) Temperature compensation in Methanosarcina barkeri by modulation of hydrogen and acetate affinity. Appl Environ Microbiol 55:1262–1266PubMedGoogle Scholar
  674. White RH (1984) Hydrolytic stability of biomolecules at high temperatures and its implications for life at 250°C. Nature 310:430–432PubMedGoogle Scholar
  675. Whitesides MD, Oliver JD (1997) Resuscitation of Vibrio vulnificus from the viable but non-culturable state. Appl Environ Microbiol 63:1002–1005PubMedGoogle Scholar
  676. Widdel F (1988) Microbiology and ecology of sulfate-and sulfur-reducing bacteria. In: Zehnder AJB (ed) Biology of anaerobic microorganisms. Wiley, New York, pp 469–585Google Scholar
  677. Widdel F, Bak F (1992) Gram-negative mesophilic sulfate-reducing bacteria. In: Balows A, Trüper HG, Dworkin M, Schleifer K-H (eds) The prokaryotes, 2nd edn. Springer, New York, pp 3352–3378Google Scholar
  678. Widdel F, Kohring G-W, Mayer F (1983) Studies on dissimilatory sulfate-reducing bacteria that decompose fatty acids. III: characterization of the filamentous gliding Desulfonema limicola gen. nov. sp. nov., and Desulfonema magnum sp. nov. Arch Microbiol 134:286–294Google Scholar
  679. Wiegel J (1990) Temperature spans for growth: hypothesis and discussion. FEMS Microbiol Rev 75:155–170Google Scholar
  680. Wiegel J, Ljungdahl LG (1986) The importance of thermophilic bacteria in biotechnology CRC. Crit Rev Biotechnol 3:39–107Google Scholar
  681. Wilkinson TG, Topiwala HH, Hamer G (1974) Interactions in a mixed bacterial population growing on methane in continuous culture. Biotechnol Bioeng 16:41–59PubMedGoogle Scholar
  682. Winogradsky S (1949) Microbiologie du sol: oeuvres complèetes. Marson, ParisGoogle Scholar
  683. Wirsen CO, Jannasch HW (1978) Physiological and morphological observations on Thiovulum sp. J Bacteriol 136:765–774PubMedGoogle Scholar
  684. Wirsen CO, Molyneaux SJ (1999) A study of deep-sea natural microbial populations and barophilic pure cultures using a high-pressure chemostat. Appl Environ Microbiol 65:5314–5321PubMedGoogle Scholar
  685. Wirsen CO, Jannasch HW, Wakeham SG, Cannel EA (1987) Membrane lipids of a psychrophilic and barophilic deep-sea bacterium. Curr Microbiol 14:319–322Google Scholar
  686. Wolfe RS, Pfennig N (1977) Reduction of sulfur by Spirillum 5175 and syntrophism with Chlorobium. Appl Environ Microbiol 33:427–433PubMedGoogle Scholar
  687. Wolin MJ (1982) Hydrogen transfer in microbial communities. In: Bull AT, Slater JH (eds) Microbial interactions and communities, vol 1. Academic, London, pp 323–356Google Scholar
  688. Wolter K (1982) Bacterial incorporation of organic substances released by natural phytoplankton populations. Mar Ecol Prog Ser 7:287–295Google Scholar
  689. Xiao J, Luo Y, Xu J, Xie S, Xu J (2011) Modestobacter marinus sp. nov., a psychrotolerant actinobacterium from deep-sea sediment, and emended description of the genus Modestobacter. Int J Syst Evol Microbiol 61:1710–1714PubMedGoogle Scholar
  690. Xu HS, Roberts N, Singleton FL, Attwell RW, Grimes DJ, Colwell RR (1982) Survival and viability of nonculturable Escherichia coli and Vibrio cholerae in the estuarine and marine environment. Microbiol Ecol 8:313–323Google Scholar
  691. Xu M, Xin Y, Tian J, Dong K, Yu Y, Zhang J, Liu H, Zhou Y (2011) Flavobacterium sinopsychrotolerans sp. nov., isolated from a glacier. Int J Syst Evol Microbiol 61:20–24PubMedGoogle Scholar
  692. Yabe S, Aiba Y, Sakai Y, Hazaka M, Yokota A (2011) Thermogemmatispora onikobensis gen. nov., sp. nov. and Thermogemmatispora foliorum sp. nov., isolated from fallen leaves on geothermal soils, and description of Thermogemmatisporaceae fam. nov. and Thermogemmatisporales ord. nov. within the class Ktedonobacteria. Int J Syst Evol Microbiol 61:903–910PubMedGoogle Scholar
  693. Yamamoto Y, Fukui K, Koujin N, Ohya H, Kimura K, Kamio Y (2004) Regulation of the intracellular free iron pool by Dpr provides oxygen tolerance to Streptococcus mutans. J Bacteriol 186:5997–6002PubMedGoogle Scholar
  694. Yancey PH, Clark ME, Hand SC, Bowlus RD, Somero GN (1982) Living with water stress: evolution of osmolyte systems. Science 217:1214–1227PubMedGoogle Scholar
  695. Yarza P, Richter M, Peplies J, Euzeby J, Amann R, Schleifer K-H, Ludwig W, Glöckner FO, Rosselo-Mora R (2008) The all-species living tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 31:241–250PubMedGoogle Scholar
  696. Yasumoto-Hirose M, Nishijima M, Ngirchechol MK, Kanoh K, Shizuri Y, Miki W (2006) Isolation of marine bacteria by in situ culture on media-supplemented polyurethane foam. Mar Biotechnol 8:227–237PubMedGoogle Scholar
  697. Yayanos AA (1978) Recovery and maintenance of live amphipods at a pressure of 580 bars from an ocean depth of 5700 meters. Science 200:1056–1059PubMedGoogle Scholar
  698. Yayanos AA (1986) Evolutional and ecological implications of the properties of deep-sea barophilic bacteria. Proc Natl Acad Sci USA 83:9542–9546PubMedGoogle Scholar
  699. Yoshida F, Yamane T, Nakamoto K (1973) Fed-batch hydrocarbon fermentation with colloidal emulsion feed. Biotechnol Bioeng 15:257–270Google Scholar
  700. Yu Y, Li H-R, Zeng Y-Y (2011) Colwellia chukchiensis sp. nov., a psychrotolerant bacterium isolated from the Arctic Ocean. Int J Syst Evol Microbiol 61:850–853PubMedGoogle Scholar
  701. Yumoto I, Yamazaki K, Hishinuma M, Nodasaka Y, Nakajima K, Inoue N, Kawasaki K (2001) Pseudomonas alcaliphila sp. nov., a novel facultatively psychrophilic alkaliphile isolated from seawater. Int J Syst Evol Microbiol 51:349–355PubMedGoogle Scholar
  702. Yumoto I, Nakamura A, Iwata H, Kusumoto K, Nodasaka Y, Matsuyama H (2002) Dietzia psychralcaliphila sp. nov., a novel, facultatively psychrophilic alkaliphile that grows on hydrocarbons. Int J Syst Evol Microbiol 52:85–90PubMedGoogle Scholar
  703. Zehnder AJB, Stumm W (1988) Geochemistry and biogeochemistry of anaerobic habitats. In: Zehnder AJB (ed) Biology of anaerobic microorganisms. Wiley, New York, pp 1–38Google Scholar
  704. Zehnder AJB, Wuhrman K (1976) Titanium (III) citrate as a non-toxic oxidation-reduction buffering system for the culture of obligate anaerobes. Science 194:1165–1166PubMedGoogle Scholar
  705. Deutsche Sammlung für Mikroorganismen und Zellkulturen (2012) Bacterial nomenclature up-to-date. http://www.dsmz.de/bacterial-diversity/bacterial-nomenclature-up-to-date.html
  706. Zengler K, Richnow HH, Rosselló-Mora R, Michaelis W, Widdel F (1999) Methane formation from long-chain alkanes by anaerobic microorganisms. Nature 401:266–269PubMedGoogle Scholar
  707. Zengler K, Toledo G, Rappe M, Elkins J, Mathur EJ, Short JM, Keller M (2002) Cultivating the uncultured. Proc Natl Acad Sci USA 99:15681–15686PubMedGoogle Scholar
  708. Zhang DC, Rezic M, Schinner F, Margesin R (2011a) Glaciimonas immobilis gen. nov., sp. nov., a member of the family Oxalobacteraceae isolated from alpine glacier cryoconite. Int J Syst Evol Microbiol 61:2186–2190PubMedGoogle Scholar
  709. Zhang DC, Busse H-J, Liu H-C, Zhou Y-G, Schinner F, Margesin R (2011b) Hymenobacter psychrophilus sp. nov., a psychrophilic bacterium isolated from soil. Int J Syst Evol Microbiol 61:859–863PubMedGoogle Scholar
  710. Zhang DC, Redzic M, Liu HC, Zhou YG, Schinner F, Margesin R (2012) Devosia psychrophila sp. nov. and Devosia glacialis sp. nov., two novel bacteria from alpine glacier cryoconite. Int J Syst Evol Microbiol 62:710–715Google Scholar
  711. Zhou Z, Jiang F, Wang S, Peng F, Dai J, Li W, Fang C (2012) Pedobacter arcticus sp. nov., a facultative psychrophile isolated from Arctic soil and emended descriptions of the genus Pedobacter, P. heparinus, P. daechungensis, P. terricola, P. glucosidilyticus and P. lentus. Int J Syst Evol Microbiol 62:1963–1969Google Scholar
  712. Zinder SH, Koch M (1984) Non-aceticlastic methanogenesis from acetate: acetate oxidation by a thermophilic syntrophic coculture. Arch Microbiol 138:263–272Google Scholar
  713. ZoBell CE (1941) Studies on marine bacteria. J Mar Res 4:42–75Google Scholar
  714. Zobell CE, Johnson FH (1949) The influence of hydrostatic pressure on the growth and viability of terrestrial and marine bacteria. J Bacteriol 57:179–189PubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  1. 1.Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbHBraunschweigGermany

Personalised recommendations

Cite entry