The renaissance of continuous culture in the post-genomics age (original) (raw)
Aboka FO, Heijnen JJ, van Winden WA (2009) Dynamic 13C-tracer study of storage carbohydrate pools in aerobic glucose-limited Saccharomyces cerevisiae confirms a rapid steady-state turnover and fast mobilization during a modest stepup in the glucose uptake rate. FEMS Yeast Res 9:191–201 ArticleCASPubMed Google Scholar
Agawin NSR, Rabouille S, Veldhuis MJW, Servatius L, Hol S, van Overzee MJ, Huisman J (2007) Competition and facilitation between unicellular nitrogen-fixing cyanobacteria and non-nitrogen-fixing phytoplankton species. Limnol Oceanogr 52:2233–2248 CAS Google Scholar
Alain K, Postec A, Grinsard E, Lesongeur F, Prieur D, Godfroy A (2010) Thermodesulfatator atlanticus sp. nov., a thermophilic, chemolithoautotrophic, sulfate-reducing bacterium isolated from a Mid-Atlantic Ridge hydrothermal vent. Int J Syst Evol Microbiol 60:33–38 ArticleCASPubMed Google Scholar
Ang CS, Vieth PD, Dashper SG, Reynolds EC (2008) Application of 16O/18O reverse proteolytic labeling to determine the effect of biofilm culture on the cell envelope proteome of Porphyyromonas gingivalis W50. Proteomics 8:1645–1660 ArticleCASPubMed Google Scholar
Arvas M, Pakula T, Lanthaler K, Saloheimo M, Valkonen M, Suortti T, Robson G, Pentilla M (2006) Common features and interesting differences in transcriptional responses to secretion stress in the fungi Trichoderma reesei and Saccharomyces cerevisiae. BMC Genomics 7:32 ArticlePubMedCAS Google Scholar
Avignone-Rossa C, White J, Kuiper A, Postma PW, Bibb MJ, Texeira de Mattos MJ (2002) Carbon flux distribution in chemostat cultures of Streptomyces lividans. Metab Eng 4:138–150 ArticleCASPubMed Google Scholar
Baart GJE, Zomer B, de Haan A, van der Pol LA, Beuvery EC, Tramper J, Martens DE (2007) Modeling Neisseria meningitidis metabolism: from genome to metabolic fluxes. Genome Biol 8:r136 ArticlePubMedCAS Google Scholar
Baart GJE, Willemsen M, Khatami E, de Haan A, Zomer B, Beuvery EC, Tramper J, Martens DE (2008) Modeling Neisseria meningitides B metabolism at different specific growth rates. Biotechnol Bioeng 101:1022–1035 ArticleCASPubMed Google Scholar
Babel W (2009) The auxiliary substrate concept: from simple considerations to heuristically valuable knowledge. Eng Life Sci 9:285–290 ArticleCAS Google Scholar
Baines SD, Saxton K, Freeman J, Wilcox MH (2006) Tigecycline does not induce proliferation or cytotoxin production by epidemic Clostridium difficile strains in human gut model. J Antimicrob Chemother 58:1062–1065 ArticleCASPubMed Google Scholar
Balagadde FK, You LK, Hansen CL, Arnold FH, Quake SR (2005) Long-term monitoring of bacteria undergoing programmed population control in a microchemostat. Science 309:137–140 ArticleCASPubMed Google Scholar
Bastidas-Oyanedel JR, Aceves-Lara CA, Ruiz-Filippi G, Steyer JP (2008) Thermodynamic analysis of energy transfer in acidogenic cultures. Eng Life Sci 8:487–498 ArticleCAS Google Scholar
Beste DJV, Peters J, Hooper C, Avignone–Rossa C, Bushell ME, McFadden JJ (2005) Compiling a molecular inventory for Mycobacterium bovis BCG at two growth rates: evidence for growth rate-mediated regulation of ribosome biosynthesis and lipid metabolism. J Bacteriol 187:1677–1684 ArticleCASPubMed Google Scholar
Beste DJV, Laing E, Bonde C, Avignone-Rossa C, Bushell ME, McFaddern JJ (2007) Transcriptomic analysis identifies growth rate modulation as a component of the adaptation of Mycobacteria to survival inside the macrophage. J Bacteriol 189:3969–3976 ArticleCASPubMed Google Scholar
Beste DJV, Hooper T, Stewart G, Bonde B, Avignone-Rossa C, Bushell M, Wheeler P, Klamt S, Kierzek AM, McFadden JJ (2007) GSMN-TB: a web-based genome scale network model of Mycobacterium tuberculosis metabolism. Genome Biol 8:r89 ArticlePubMedCAS Google Scholar
Beste DJV, Espasa M, Bonde B, Kierzek AM, Stewart GR, McFadden JJ (2009) The genetic requirements for fast and slow growth in mycobacteria. PLoS One 4:e5349 ArticlePubMedCAS Google Scholar
Bijmans MFM, Dopson M, Peeters TWT, Lens PNL, Bujisman CJN (2009) Sulfate reduction at pH 5 in a high-rate membrane bioreactor: reactor performance and microbial community analyses. J Microbiol Biotechnol 19:698–708 CASPubMed Google Scholar
Boer VM, Crutchfield CA, Bradley PH, Botstein D, Rabinowitz JD (2010) Growth-limiting intracellular metabolites in yeast growing under diverse nutrient limitations. Mol Biol Cell 21:198–211 ArticleCASPubMed Google Scholar
Boender LGM, de Huslster EAF, van Maris AJA, Daran-Lapujade PAS, Pronk JT (2009) Quantitative physiology of Saccharomyces cerevisiae at near-zero specific growth rates. Appl Environ Microbiol 75:5607–5614 ArticleCASPubMed Google Scholar
Bragg JG, Wagner A (2007) Protein carbon content evolves in response to carbon availability and may influence the fate of duplicated genes. Proc R Soc B 274:1063–1070 ArticleCASPubMed Google Scholar
Bragg JG, Wagner A (2009) Protein material costs: single atoms can make an evolutionary difference. Trends Genet 25:5–8 ArticleCASPubMed Google Scholar
Brauer MJ, Huttenhower C, Airoldi EM, Rosenstein R, Matese JC, Gresham D, Boer VM, Troyanskaya OG, Botstein D (2008) Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast. Mol Biol Cell 19:352–367 ArticleCASPubMed Google Scholar
Breslauer DN, Lee PJ, Lee LP (2006) Microfluidics-based systems biology. Mol Bio Syst 2:97–112 ArticleCAS Google Scholar
Brown SW, Oliver SG (1982) Isolation of ethanol-tolerant mutants of yeast by continuous selection. Eur J Appl Microbiol Biotechnol 16:119–122 Article Google Scholar
Bull AT (1974) Microbial growth. In: Bull AT, Lagnado JR, Thomas JO, Tipton KF (eds) Companion to biochemistry–selected topics for further study. Longman, London, pp 415–442 Google Scholar
Bull AT (1983) Continuous culture for production. In: Hollaender A, Laskin AI, Rogers P (eds) Basic biology of new developments in biotechnology. Plenum, New York, pp 405–437 Google Scholar
Bull AT (1985) Mixed culture and mixed substrate systems. In: Bull AT, Dalton H (eds) Comprehensive biotechnology, vol 1. The principles of biotechnology: scientific fundamentals. Pergamon, Oxford, pp 281–299 Google Scholar
Bull AT, Brown CM (1979) Continuous culture applications to microbial biochemistry. In: Quayle JR (ed) International review of biochemistry, vol 21: microbial biochemistry. University Park Press, Baltimore, pp 177–226 Google Scholar
Bull AT, Trinci APJ (1977) The physiology and metabolic control of fungal growth. Adv Microbial Physiol 15:1–84 ArticleCAS Google Scholar
Bull DN, Young MD (1982) Enhanced product formation in continuous fermentations with microbial cell recycle. Biotechnol Bioeng 23:373–389 Article Google Scholar
Bushell ME, Kirk S, Zhao HJ, Avignone-Rossa C (2006) Manipulation of the physiology of clavulanic acid biosynthesis with the aid of metabolic flux analysis. Enzyme Microb Technol 39:149–157 ArticleCAS Google Scholar
Bushell ME, Sequeira SIP, Khannapho C, Zhao HJ, Chater KF, Butler MJ, Kierzek AJM, Avignone-Rossa C (2006) The use of genome scale metabolic flux variability analysis for process feed formulation based on an investigation of the effects of the zwf mutation on antibiotic production in Streptomyces coelicolor. Enzyme Microb Technol 39:1347–1353 ArticleCAS Google Scholar
Canelas AB, ten Pierick A, Ras C, Seifar RM, van Dam JC, van Gulik WM, Heijnen JJ (2009) Quantitative evaluation of intracellular metabolite extraction techniques for yeast metabolomics. Anal Chem 81:7379–7389 ArticleCASPubMed Google Scholar
Carlile MJ, Skehel JJ (eds) (1974) Evolution in the microbial world, pp i–x, 1–430, symposium 24 Soc Gen Microbiol, Cambridge University Press, Cambridge
Chrzanowski TH, Grover JP (2008) Element content of Pseudomonas fluorescens varies with growth rate and temperature: a replicated chemostat study addressing ecological stoichiometry. Limnol Oceanogr 53:1242–1251 CAS Google Scholar
Cipollina C, van den Brink J, Daran-Lapujade P, Pronk JT, Porro D, de Winde JH (2008) Saccharomyces cerevisiae SFP1: at the crossroads of central metabolism and ribosome biogenesis. Microbiology 154:1686–1699 ArticleCASPubMed Google Scholar
Clarke PH, Lilly MD (1969) The regulation of enzyme synthesis during growth. In: Meadows PM, Pirt SJ (eds) Microbial growth, symposium 19 Soc Gen Microbiol. Cambridge University Press, Cambridge, pp 113–159 Google Scholar
Codeco CT, Grover JP (2001) Competition along a spatial gradient of resource supply: a microbial experimental model. Am Nat 157:300–315 ArticleCASPubMed Google Scholar
Cooper DC, Copeland BJ (1973) Responses of continuous-series estuarine microecosytems to point source input variations. Ecol Monogr 43:213–236 Article Google Scholar
Cornejo OE, Rozen DE, May RM, Levin BR (2008) Oscillations in continuous cultures populations of Streptococcus pneumoniae: population dynamics and evolution of clonal suicide. Proc R Soc B 276:999–1008 Article Google Scholar
Crane KW, Grover JP (2010) Coexistence of mixotrophs, autotrophs, and heterotrophs in planktonic microbial communities. J Theor Biol 262:517–527 ArticlePubMed Google Scholar
Daran-Lapujade P, Jansen MLA, Daran JM, van Gulik W, de Winde JH, Pronk JT (2004) Role transcriptional regulation in controlling fluxes in central carbon metabolism of _Saccharomyces cerevisiae_–a chemostat study. J Biol Chem 279:9125–9138 ArticleCASPubMed Google Scholar
Daran-Lapujade P, Daran JM, van Maris AJA, de Winde JH, Pronk JT (2009) Chemostat-based micro-array analysis in baker’s yeast. Adv Microbial Physiol 54:257–311 ArticleCAS Google Scholar
Dashper SG, Ang CS, Veith PD, Mitchell HL, Lo AWH, Seers CA, Walsh KA, Slakeski N, Chen D, Lissel JP, Butler CA, O’Brien-Simpson NM, Barr IG, Reynolds EC (2009) Response of Porphyromonas gingivalis to heme limitation in continuous culture. J Bacteriol 191:1044–1055 ArticleCASPubMed Google Scholar
Dean ACR, Ellwood DC, Melling J, Robinson A (1976) The action of antibacterial agents on bacteria grown in continuous culture. In: Dean ACR, Ellwood DC, Evans CGT, Melling J (eds) Continuous culture 6: applications and new fields. Ellis Horwood, Chichester, pp 251–261 Google Scholar
de Crécy E, Metzgar D, Allen C, Pénicaud M, Lyons B, Hansen CJ, Crécy-Lagard V (2007) Development of a novel continuous culture devise for experimental evolution of bacterial populations. Appl Microbiol Biotechnol 77:489–496 ArticlePubMedCAS Google Scholar
de Crécy E, Jaronski S, Lyons B, Lyons TJ, Keyhani NO (2009) Directed evolution of a filamentous fungus for thermotolerance. BMC Biotechnol 9:74 ArticlePubMedCAS Google Scholar
Delneri D, Hoyle DC, Gkargkas K, Cross EJM, Rash B, Zeef L, Leong HS, Davey HM, Hayes A, Kell DB, Griffith GW, Oliver SG (2008) Identification and characterization of high-flux-control genes of yeast through competition analysis. Na Genet 40:113–117 ArticleCASPubMed Google Scholar
DellaGreca M, Zarelli A, Fergola P, Cerasuola M, Pollioi A, Pinto G (2010) Fatty acids released by Chlorella vulgaris and their role in interference with Pseudokirchneriella subcapita: experiments and modeling. J Chem Ecol 36:339–349 ArticleCASPubMed Google Scholar
De Nicola R, Hazelwood LA, De Hulster EAF, Walsh MC, Knijnenburg TA, Reinders MJT, Walker GM, Pronk JT, Daran JM, Daran-Lapujade (2007) Physiological and transcriptional responses of Saccharomyces cerevisiae to zinc-limitation in chemostat cultures. Appl Environ Microbiol 73:7680–7692 ArticlePubMedCAS Google Scholar
Diano A, Peeters J, Dynesen J, Nielsen J (2009) Physiology of Aspergillus niger in oxygen-limited continuous cultures: influence of aeration, carbon source concentration and dilution rate. Biotechnol Bioeng 103:956–965 ArticleCASPubMed Google Scholar
Droop MR (1968) Vitamin B12 and marine ecology. IV. The kinetics of uptake, growth and inhibition in Monochrysis butleri. J Protozool 48:689–733 CAS Google Scholar
Dye C, Williams BG (2010) The population dynamics and control of tuberculosis. Science 328:856861 ArticleCAS Google Scholar
Elias DA, Tollaksen SL, Kennedy DW, Mottaz HM, Giometti CS, McLean JS, Hill EA, Punchuk GE, Lipton MS, Fredrickson JK, Gorby YA (2008) The influence of cultivation methods on Shewanella oneidensis physiology and proteome expression. Arch Microbiol 189:313–324 ArticleCASPubMed Google Scholar
Ellwood DC, Hunter JR (1976) The mouth as a chemostat. In: Dean ACR, Ellwood DC, Evans CGT, Melling J (eds) Continuous culture 6: applications and new fields. Ellis Horwood, Chichester, pp 270–282 Google Scholar
Ferea TL, Botstein D, Brown PO, Rosenzweig RF (1999) Systematic changes in gene expression patterns following adaptive evolution in yeast. Proc Nat Acad Sci U S A 96:9721–9726 ArticleCAS Google Scholar
Ferenci T (1999) Growth of bacterial cultures 50 years on: towards an uncertainty principle instead of constants in bacterial growth kinetics. Res Microbiol 150:431–438 ArticleCASPubMed Google Scholar
Ferenci T (2008) Bacterial physiology, regulation and mutational adaptation in a chemostat environment. Adv Microbial Phyisol 53:22–169 Google Scholar
Fergola P, Cerasuolo M, Pollio A, Pinto G, DellaGreca M (2007) Allelopathy and competition between Chlorella vulgaris and Pseudokirchneriella subcapitata: experiments and mathematical model. Ecol Model 208:205–214 Article Google Scholar
Flynn KJ (2005) Castles built on sand: dysfunctionality in plankton models and the inadequacy of dialogue between biologists and modelers. J Plankton Res 27:1205–1210 ArticleCAS Google Scholar
Flynn KJ (2008) Use, abuse, misconceptions and insights from quota models–the droop cell quota model 40 years on. Oceanogr Mar Biol An Rev 46:1–23 Article Google Scholar
Gefen O, Balaban NQ (2008) The Moore’s Law of microbiology–towards bacterial culture miniaturization with the micro-Petri chip. Trends Biotechnol 26:345–347 ArticleCASPubMed Google Scholar
Gerhardt P (1946) Brucella suis in aerated broth culture, III. Continuous culture studies. J Bacteriol 52:283–292 CASPubMed Google Scholar
Gilbert A, Srienc F (2009) Optimized evolution in the cytostat: a Monte Carlo simulation. Biotechnol Bioeng 102:221–231 ArticleCASPubMed Google Scholar
Gilbert A, Sangurdekar DP, Scrienc F (2009) Rapid strain improvement through optimized evolution in the cytostat. Biotechnol Bioeng 103:500–512 ArticleCASPubMed Google Scholar
Golby P, Hatch KA, Bacon J, Cooney R, Riley P, Allnutt J, Hinds J, Nunez J, Marsh PD, Hewinson RG, Gordon SV (2007) Comparative transcriptomics reveals key gene expression differences between the human and bovine pathogens of the Mycobacterium tuberculosis complex. Microbiology 153:3323–3336 ArticleCASPubMed Google Scholar
Gresham D, Desai MM, Tucker CM, Jenq HT, Pai DA, Ward A, DeSevo CG, Botstein D, Dunham MJ (2008) The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast. PLOS Genet 4:e1000303 ArticlePubMedCAS Google Scholar
Groeneveld P, Stouthamer AH, Westerhoff HV (2009) Super life–how and why ‘cell selection’ leads to the fastest-growing eukaryote. FEBS J 276:254–270 ArticleCASPubMed Google Scholar
Groisman A, Lobo C, Campbell JK, Dufour YS, Stevens AM, Levchenko A (2005) A microfluidic chemostat for experiments with bacterial and yeast cells. Nat Methods 2:685–689 ArticleCASPubMed Google Scholar
Grover JP, Chrzanowski TH (2009) Dynamics and nutritional ecology of a nanoflagellate preying upon bacteria. Microb Ecol 58:231–243 ArticlePubMed Google Scholar
Guebel DV, Canovas M, Torres NV (2009) Analysis of the Escherichia coli response to glycerol pulse in continuous, high-cell density culture using a multivariate approach. Biotechnol Bioeng 102:910–922 ArticleCASPubMed Google Scholar
Hall BG (1985) Enzyme evolution. In: Bull AT, Dalton H (eds) Comprehensive biotechnology vol 1, the principles of biotechnology: scientific fundamentals. Pergamon, Oxford, pp 553–566 Google Scholar
Hamer G (1984) Continuous culture kinetics and activated sludge processes. In: Dean ACR, Ellwood DC, Evans CGT (eds) Continuous culture 8: biotechnology, medicine and the environment. Ellis Horwood, Chichester, pp 169–184 Google Scholar
Hamilton IR, Ellwood DC (1978) Effects of fluoride on carbohydrate metabolism by washed cells of Streptococcus mutans grown at various pH values in a chemostat. Infect Immun 19:434–442 CASPubMed Google Scholar
Harder W, Dijkhuisen L (1976) Mixed substrate utilization. In: Dean ACR, Ellwood DC, Evans CGT, Melling J (eds) Continuous culture 6: applications and new fields. Ellis Horwood, Chichester, pp 297–314 Google Scholar
Hardman DJ, Huxley M, Bull AT, Slater JH, Bates R (1997) Generation of environmentally enhanced products: clean technology for paper chemicals. J Chem Technol Biotechnol 70:60–66 ArticleCAS Google Scholar
Harris DM, van der Krogt ZA, Klaasen P, Raamsdonk LM, Hage S, van den Berg MA, Bovenberg RAL, Pronk JT, Daran JM (2009) Exploring and dissecting genome-wide gene expression responses of Penicillium chrysogenum to phenylacetic acid and penicillin G. BMC Genomics 10:75 ArticlePubMedCAS Google Scholar
Harrison DEF (1972) Physiological effects of dissolved oxygen tension and redox potential on growing populations of micro-organisms. In: Dean ACR, Pirt SJ, Tempest DW (eds) Continuous culture 5: environmental control of cell synthesis and function. Academic, London, pp 417–440 Google Scholar
Harrison DEF, Topiwala HH, Hamer G (1972) Yield and productivity in single-cell protein production from methane and methanol. In: Terui G (ed) Proc IV Int Ferment Symp Fermentation Technology Today, pp 491–495
Harrison DEF, Wikinson TG, Wren SJ, Harwood JH (1976) Mixed bacterial cultures as a basis for continuous production of SCP from C1 compounds. In: Dean ACR, Ellwood DC, Evans CGT, Melling J (eds) Continuous culture 6: applications and new fields. Ellis Horwood, Chichester, pp 122–134 Google Scholar
Hazelwood LA, Walsh MC, Luttik MAH, Daran-Lapujade P, Pronk JT, Daran JM (2009) Identity of the growth-limiting nutrient strongly affects storage carbohydrate accumulation in anaerobic chemostat cultures of Saccharomyces cerevisiae. Appl Environ Microbiol 75:6876–6885 ArticleCASPubMed Google Scholar
Hendrickson EL, Haydock AK, Moore BC, Whitman WB, Leigh JA (2007) Functionally distinct genes regulated by hydrogen limitation and growth rate in methanogenic Archaea. Proc Nat Acad Sci U S A 104:8930–8934 ArticleCAS Google Scholar
Hendrickson EL, Liu Y, Rosas-Sandoval G, Porat I, Soll D, Whitman WB, Leigh JA (2008) Global responses of Methanococcus maripaludis to specific nutrient limitations and growth rate. J Bacteriol 190:2198–2205 ArticleCASPubMed Google Scholar
Herbert D (1976) Stoichiometric aspects of microbial growth. In: Dean ACR, Ellwood DC, Evans CGT, Melling J (eds) Continuous culture 6: applications and new fields. Ellis Horwood, Chichester, pp 1–30 Google Scholar
Herbert D, Elsworth R, Telling RC (1956) The continuous culture of bacteria: a theoretical and experimental study. J Gen Microbiol 14:601–622 CASPubMed Google Scholar
Hospodka J (1966) Industrial application of continuous fermentation. In: Malék I, Fencl Z (eds) Theoretical and methodological basis of continuous culture of microorganisms. Czech Acad Sci, Prague, pp 493–645 Google Scholar
Hough JS, Keevil CW, Maric C, Philliskirk G, Young TW (1976) Continuous culture brewing. In: Dean ACR, Ellwood DC, Evans CGT, Melling J (eds) Continuous culture 6: applications and new fields. Ellis Horwood, Chichester, pp 226–237 Google Scholar
Huisman J, Matthijs HCP, Visser PM, Balke H, Sigon CAM, Passarge J, Weissing FJ, Mur LR (2002) Principles of the light-limited chemostat: theory and ecological applications. Antonie van Leeuwen 81:117–133 ArticleCAS Google Scholar
Ingham CJ, Sprenkels A, Bomer J, Molenaar D, van den Berg A, Vlieg JETV, de Vos WM (2007) The micro-Petri dish, a million-well growth chip for the culture and high-throughput screening of microorganisms. Proc Nat Acad Sci U S A 104:18217–18222 ArticleCAS Google Scholar
Ishii N et al (2007) Multiple high-throughput analyses monitor the response of E. coli to perturbations. Science 316: 593–597 Google Scholar
Ives PR, Bushell ME (1997) Manipulation of the physiology of clavulanic acid production in Streptomyces clavuligerus. Microbiol 143:3573–3579 ArticleCAS Google Scholar
Jansen MLA, Diderich JA, Mashego M, Hassane A, de Winde JH, Daran-Lapujade P, Pronk JT (2005) Prolonged selection in aerobic, glucose-limited chemostat cultures of Saccharomyces cerevisiae causes a partial loss of glycolytic capacity. Microbiology 151:1657–1669 ArticleCASPubMed Google Scholar
Johri AK, Margarit I, Broenstrup M, Buttoni C, Hua L, Gygi SP, Telford JL, Grandi G, Paoletii LC (2007) Transcriptional and proteomic profiles of group B Streptococcus type V reveal potential adherence proteins associated with highlevel invasion. Infect Immun 75:1473–1483 ArticleCASPubMed Google Scholar
Jones LE, Ellner SP (2008) Effects of rapid prey evolution on predator-prey cycles. J Math Biol 55:541–573 Article Google Scholar
Kacmar J, Gilbert A, Cockrell J, Srienc (2006) The cytostat: a new way to study cell physiology in a precisely defined environment. J Biotechnol 125:163–172 ArticleCAS Google Scholar
Khannapho C, Zhao H, Bonde BK, Kierzek AM, Avignone-Rossa CA, Bushell ME (2008) Selection of objective function in genome scale flux balance analysis for process feed development in antibiotic production. Metab Eng 10:227–233 ArticleCASPubMed Google Scholar
King T, Seeto S, Ferenci T (2006) Genotype-by-environment interactions influencing the emergence of rpoS mutations in Escherichia coli populations. Genetics 172:2071–2079 ArticleCASPubMed Google Scholar
Kirk S, Avignone-Rossa CA, Bushell ME (2000) Growth limiting substrate affects antibiotic production and associated metabolic fluxes in Streptomyces clavuligerus. Biotechnol Lett 22:1803–1809 ArticleCAS Google Scholar
Kisand V, Rocker D, Simon M (2008) Significant decomposition of riverine humic-rich DOC by marine but not estuarine bacteria assessed in sequential chemostat experiments. Aquatic Microbial Ecol 53:151–160 Article Google Scholar
Kleijn RJ, Liu F, van Winden WA, van Gulik WA, Ras C, Heijnen JJ (2007) Cytosolic NADPH metabolism in penicillin-G producing and non-producing chemostat cultures of Penicillium chrysogenum. Metab Eng 9:12–123 ArticleCAS Google Scholar
Knijnenburg TA, de Winde JH, Daran JM, Daran-Lapujade, Pronk JT, Reinders MJT, Wessels LFA (2007) Exploiting combinatorial cultivation conditions to infer regulation. BMC Genomics 8:25 ArticlePubMedCAS Google Scholar
Koetsier MJ and 10 other authors (2010) The Penicillium chrysogenum aclA gene encodes a broad-substrate-specificity acyl-coenzyme A ligase involved in activation of adipic acid, a side-chain precursor for cephem antibiotics. Fungal Genet Biol 47: 33-42 Google Scholar
Kolkman A, Daran-Lapujade P, Fullaondo A, Oisthoorn MMA, Pronk JT, Slijper M, Heck AJR (2006) Proteome analysis of yeast response to various nutrient limitations. Mol Syst Biol 2:026 ArticleCAS Google Scholar
Kubitschek HE (1970) Introduction to research with continuous cultures. Prentice-Hall, Englewood Cliffs, pp iix, 1–195
Kuenen JG, Gottschahl JC (1982) Competition among chemolithotrophs and methylotrophs and their interactions with heterotrophic bacteria. In: Bull AT, Slater JH (eds) Microbial interactions and communities. Academic, London, pp 153–187 Google Scholar
Lambert PA (1984) The role of the bacterial envelop in antibiotic resistance. In: Dean ACR, Ellwood DC, Evans CGT (eds) Continuous culture 8: biotechnology, medicine and the environment. Ellis Horwood, Chichester, pp 38–54 Google Scholar
Lennon JT, Martiny JBH (2008) Rapid evolution buffers ecosystem impacts of viruses in a microbial food web. Ecol Lett 11:1178–1188 PubMed Google Scholar
Li BZ, Cheng JS, Qiao B, Yuan YJ (2010) Genome-wide transcriptional analysis of Saccharomyces cereviseae during industrial bioethanol fermentation. J Ind Microbiol Biotechnol 37:43–55 ArticlePubMedCAS Google Scholar
Lin B, Westerhoff, Roling WFM (2009) How Geobacteriaceae may dominate subsurface biodegradation: physiology of Geobacter metallireducens in slow growth habitat-simulating retentostats. Environ Microbiol 11:2425–2433 ArticleCASPubMed Google Scholar
Linton JD, Drozd JW (1982) Microbial interactions and communities in biotechnology. In: Bull AT, Slater JH (eds) Microbial interactions and communities. Academic, London, pp 357–406 Google Scholar
Lo AW, Seers CA, Boyce JD, Dashper SG, Slakeski N, Lissel JP, Reynolds EC (2009) Comparative transcriptomic analysis of Porphyromonas gingivalis biofilm and planktonic cells. BMC Microbiol 9:18 ArticlePubMedCAS Google Scholar
Lovitt RW, Wimpenny JWT (1981) The gradostat: a bidirectional compound chemostat, and its application in microbiological research. J Gen Microbiol 127:261–268 CASPubMed Google Scholar
Luders S, Fallet C, Franco-Lara E (2009) Proteome analysis of the Escherichia coli heat shock response under steady-state conditions. Proteome Sci 7:36 ArticlePubMedCAS Google Scholar
Luscombe BM, Gray TRG (1974) Characteristics of Arthrobacter grown in continuous culture. J Gen Microbiol 82:213–222 Google Scholar
Macfarlane GT, Macfarlane S, Gibson G (1998) Validation of a three-stage compound continuous culture system for investigating the effect of retention time on the ecology and metabolism of bacteria in the human gut. Microbial Ecol 35:180–187 ArticleCAS Google Scholar
Macfarlane GT, Macfarlane LE (2009) Acquisition, evolution and maintenance of the normal gut microbiota. Digestive Dis 27:90–98 Article Google Scholar
Maharjan R, Seeto S, Notley-McRobb L, Ferenci T (2006) Clonal adaptive radiation in a constant environment. Science 313:514–517 ArticleCASPubMed Google Scholar
Major NC, Bull AT (1989) The physiology of lactate production by Lactobacillus delbreuckii in a chemostat with cell recycle. Biotechnol Bioeng 34:592–599 ArticleCASPubMed Google Scholar
Majors PD, McLean JS, Scholten JCM (2008) NMR bioreactor development for live in situ microbial functional analysis. J Magn Reson 192:159–166 ArticleCASPubMed Google Scholar
Málek I (1976) Physiological state of continuously grown microbial cultures. In: Dean ACR, Ellwood DC, Evans CGT, Melling J (eds) Continuous Culture 6: Applications and New Fields. Ellis Horwood, Chichester, pp 31–39 Google Scholar
Málek I, Fencl Z (eds) (1966) Theoretical and methodological basis of continuous culture of microorganisms. Czech Acad Sci, Prague, pp 1–655 Google Scholar
Massie TM, Blasius B, Weithoff G, Gaedke U, Fussmann GF (2010) Cycles, phase synchronization, and entrainment in single-species phytoplankton populations. Proc Nat Acad Sci U S A 107:4236–4241 ArticleCAS Google Scholar
McFadden J (2010) Systems biology and the TB bacillus. Microbiology Today 17:16–19 Google Scholar
McIntyre JJ, Bunch AW, Bull AT (1999) Vancomycin production is enhanced in chemostat culture with biomass-recycle. Biotechnol Bioeng 62:576–582 ArticleCASPubMed Google Scholar
M’Kendrick AG, Pai MK (1911) The rate of multiplication of microorganisms, a mathematical study. Proc R Soc Edinb 31:649–655 Google Scholar
Middelboe M, Holmfeldt K, Riemann L, Nybroe O, Haaber J (2009) Ba24 bacteriophages drive strain diversification in a marine Flavobacterium: implications for phage resistance. Environ Microbiol 11:1971–1982 ArticleCASPubMed Google Scholar
Minnikin DE, Abdolrahimzadeh H, Baddiley J (1972) Variation of polar lipid composition of Bacillus subtilis (Marburg) with different growth conditions. FEBS Lett 27:16–18 ArticleCASPubMed Google Scholar
Mitchell HL, Dashper SG, Catmull DV, Paolini RA, Cleal SM, Slakeski N, Tan KH, Reynolds EC (2010) Treponema denticola biofilm-induced expression of a bacteriophage, toxin-antitoxin systems and transposases. Microbiology 156:774–788 ArticleCASPubMed Google Scholar
Monod J (1949) The growth of bacterial cultures. Ann Rev Microbiol 3:371–394 ArticleCAS Google Scholar
Monod J (1950) La technique de culture continuée. Theorie et application. Ann Inst Pasteur (Paris) 79:390–410 CAS Google Scholar
Muñoz-Aguayo J, Lang JK, LaPara TM, González G, Singer RS (2007) Evaluating the effects of chlortetracycline on the proliferation of antibiotic- resistant bacteria in a simulated river water ecosystem. Appl Environ Microbiol 73:5421–5425 ArticlePubMedCAS Google Scholar
Nakhu R, Valgepea K, Lahtvee PJ, Erm S, Abner K, Adamberg K, Vilu R (2010) Specific growth rate dependent transcriptome profiling of Escherichia coli K12 MG1655 in accelerostat cultures. J Biotechnol 145:60–65 ArticleCAS Google Scholar
Nanchen A, Schicker A, Revelles O, Sauer U (2008) Cyclic AMP-dependent catabolite repression is the dominant control mechanism of metabolic fluxes under glucose limitation in Escherichia coli. J Bacteriol 190:2323–2330 ArticleCASPubMed Google Scholar
Neijssel OM, Tempest DW (1976) Role of energy-spilling reactions in growth of Klebsiella aerogenes NCTC-418 in aerobic chemostat culture. Arch Microbiol 110:305–311 ArticleCASPubMed Google Scholar
Nicholls HA, Osborn DW, Buchan L, Melmed LN, Pitman AR (1984) Biological removal of phosphorus and nitrogen from waste water. In: Dean ACR, Ellwood DC, Evans CGT (eds) Continuous culture 8: biotechnology, medicine and the environment. Ellis Horwood, Chichester, pp 185–204 Google Scholar
Nishikawa T, Guilbahce N, Motter AE (2008) Spontaneous reaction silencing in metabolic optimization. PLoS Comput Biol 4:e1000236 ArticlePubMedCAS Google Scholar
Novick A, Szilard L (1950) Experiments with the chemostat on spontaneous mutations of bacteria. Proc Nat Acad Sci U S A 36:708–719 ArticleCAS Google Scholar
Parkes RJ (1982) Methods for enriching, isolating, and analysing microbial communities in laboratory systems. In: Bull AT, Slater JH (eds) Microbial interactions and communities. Academic, London, pp 45–102 Google Scholar
Parkes RJ, Wellsbury P (2004) Deep biospheres. In: Bull AT (ed) Microbial diversity and bioprospecting. ASM, Washington, DC, pp 120–129 Google Scholar
Partridge JD, Scott C, Tang Y, Poole RK, Green J (2006) Escherichia coli transcriptome dynamics during the transition from anaerobic to aerobic conditions. J Biol Chem 281:27806–27815 ArticleCASPubMed Google Scholar
Pickell LD, Wells ML, Trick CG, Cochlan WP (2009) A sea-going continuous culture system for investigating phytoplankton community response to macro- and micro-nutrient manipulations. Limnol Oceanogr Methods 7:21–32 CAS Google Scholar
Pir P, Kirdar B, Hayes A, Onsan ZI, Ulgen KO, Oliver SG (2008) Exometabolic and transcriptional response in relation to phenotype and gene copy number in respiration-related deletion mutants of S. cerevisiae. Yeast 25:661–672 ArticleCASPubMed Google Scholar
Pirt SJ (1965) The maintenance energy of bacteria in growing cultures. Proc R Soc B 163:224–231 ArticleCAS Google Scholar
Pirt SJ (1975) Principles of microbe and cell culture. Blackwell, Oxford, pp i–x, 1–274
Pirt SJ, Kurowski WM (1970) Extension of theory of chemostat with feedback of organisms - its experimental realization with a yeast culture. J Gen Microbiol 63:357–366 CASPubMed Google Scholar
Postec A, Lesongeur F, Oignet P, Ollivier B, Querellou J, Godfroy A (2007) Continuous enrichment cultures: insights into prokaryotic diversity and metabolic interactions in deep-sea vent chimneys. Extremophiles 11:747–757 ArticlePubMed Google Scholar
Primrose SB, Derbyshire P, Jones IM, Robinson A, Ellwood DC (1984) The application of continuous culture to the study of plasmid stability. In: Dean ACR, Ellwood DC, Evans CGT (eds) Continuous culture 8: biotechnology, medicine and the environment. Ellis Horwood, Chichester, pp 213–238 Google Scholar
Pullan ST, Monk CE, Lee L, Poole RK (2008) Microbial responses to nitric oxide and nitrosative stress: growth, “omic”, and physiological methods. Methods Enzymol 437:499–519 ArticleCASPubMed Google Scholar
Rautio JJ, Smit BA, Wiebe M, Pentilla M, Saloheimo M (2006) Transcriptional monitoring of steady state and effects of anaerobic phases in chemostat cultures of the fungus Trichoderma reesei. BMC Genomics 7:247 ArticlePubMedCAS Google Scholar
Revilla T, Weissing FJ (2008) Nonequilibrium coexistence in a competition model with nutrient storage. Ecology 89:865–877 ArticlePubMed Google Scholar
Robinson A, Gorringe AR, Keevil CW (1984) Expression of virulence determinants in Bordetella pertusis and Neisseria gonorrhoeae. In: Dean ACR, Ellwood DC, Evans CGT (eds) Continuous culture 8: biotechnology, medicine and the environment. Ellis Horwood, Chichester, pp 22–37 Google Scholar
Rokem JS, Laantz AE, Nielsen J (2007) Systems biology of antibiotic production by microorganisms. Nat Prod Rep 24:1262–1287 ArticleCASPubMed Google Scholar
Rowley BI, Bull AT (1973) Chemostat for the cultivation of moulds. Lab Prac, April: 286–289
Russell JB (2007) The energy spilling reactions of bacteria and other organisms. J Mol Microbiol Biotechnol 13:1–11 ArticleCASPubMed Google Scholar
Russell DG, Barry CE, Flynn JL (2010) Tuberculosis: what we don’t know can, and does, hurt us. Science 328:852–856 ArticleCASPubMed Google Scholar
Saxton K, Baines SD, Freeman J, O’Connor R, Wilcox MH (2008) Effects of exposure of Clostridium difficile PCRF ribotypes 027 and 001 to fluoroquinolones in a human gut model. Antimicrob Agents Chemother 53: 412-420 Google Scholar
Schaub J, Reuss M (2008) In vivo dynamics of glycolysis in Escherichia coli shows need for growth-rate dependent metabolome analysis. Biotechnol Prog 24:1401–1407 Article Google Scholar
Senior E, Bull AT, Slater JH (1976) Enzyme evolution in a microbial community growing on the herbicide Dalapon. Nature 263:476–479 ArticleCASPubMed Google Scholar
Senior PJ (1984) Polyhydroxybutyrate, a speciality polymer of microbial origin. In: Dean ACR, Ellwood DC, Evans CGT (eds) Continuous culture 8: biotechnology, medicine and the environment. Ellis Horwood, Chichester, pp 266–271 Google Scholar
Shah D, Dang MD, Hasbun R, Koo HL, Jiang ZD, DuPont HL, Garey KW (2010) Clostridium difficile infection: update on emerging antibiotic treatment options and antibiotic resistance. Expert Rev Anti Infect Ther 8:555–564 ArticleCASPubMed Google Scholar
Shimono N, Morici L, Casal N, Cantrell S, Sidders B, Ehrt S, Riley LW (2003) Hypervirulent mutant of Mycobacterium tuberculosis resulting from disruption of the mce1 operon. Proc Natl Acad Sci U S A 100:15918–15923 ArticleCASPubMed Google Scholar
Shockley KR, Scott KL, Conners SB, Johnson MR, Montero CI, Wolfinger RD, Kelly RM (2005) Genome-wide transcriptional variation within and between steady states for continuous growth of the hyperthermophile Thermatoga maritima. Appl Environ Microbiol 71:5572–5576 ArticleCASPubMed Google Scholar
Sikyta B (1991) Directed selection of microorganisms in continuous culture. Academia, Prague, pp 1–134
Smith SRL (1980) Single cell protein. In: Brenner S, Hartley BS, Rodgers PJ (eds) New horizons in industrial microbiology. The Royal Society, London, pp 63–76 Google Scholar
Smith VH, Foster BL, Grover JP, Holt RD, Leibold MA, deNoyelles F (2005) Phytoplankton species richness scales consistently from laboratory microcosms to the world’s oceans. Proc Nat Acad Sci USA 102:4393–4396 ArticleCAS Google Scholar
Snoep JL, Mrwebi M, Schuurmans JM, Rohwer JM, de Mattos MJT (2009) Control of specific growth rate in Saccharomyces cerevisiae. Microbiology 155:1699–1707 ArticleCASPubMed Google Scholar
Stejskal A (1966) Fundamental advantages of continuous cultivation of pathogenic microorganisms. In: Malék I, Fencl Z (eds) (1966) Theoretical and methodological basis of continuous culture of microorganisms. Czech Acad Sci, Prague, pp 418–442
Sterner RW, Elser JJ (2002) Ecological stoichiometry. Princeton University Press, Princeton Google Scholar
Stomp M, van Dijk MA, van Overzee HMJ, Wortel MT, Sigon CAM, Egas M, Hoogveld H, Gons HJ, Huisman J (2008) The timescale of phenotypic plasticity and its impact on competetion in fluctuating environments. American Naturalist 172:E169–E185 Article Google Scholar
Stouthamer AH (1979) The search for correlation between theoretical and experimental growth yields. In: Quayle JR (ed) International review of biochemistry vol 21, microbial biochemistry. University Park Press, Baltimore, pp 1–47 Google Scholar
Stouthamer AH, Bulthius BA, van Verseveld HW (1990) Energetics of growth at low growth rates and its relevance for the maintenance concept. In: Poole RK, Bazin MJ, Keevil CW (eds) Microbial growth dynamics. IRL, Oxford, pp 85–102 Google Scholar
Sutherland IW, Ellwood DC (1979) Microbial exopolysaccharides–industrial polymers of current and future potential. In: Bull AT, Ellwood DC, Ratledge C (eds) Microbial technology: current state, future prospects, symposium 29 Soc Gen Microbiol. Cambridge University Press, Cambridge, pp 107–150 Google Scholar
Tai SL, Daran-Lapujade P, Walsh MC, Pronk JT (2007) Acclimation of Saccharomyces cerevisiae to low temperature: a chemostat-based transcriptome analysis. Mol Biol Cell 18:5100–5112 ArticleCASPubMed Google Scholar
Tanji Y, Hattori K, Suzuki K, Miyanaga K (2008) Spontaneous deletion of a 209-kilobase-pair fragment from the Escherichia coli genome occurs with acquisition of resistance to an assortment of infectious phages. Appl Environ Microbiol 74:4256–4263 ArticleCASPubMed Google Scholar
Tarantola A (2006) Popper, Bayes and the inverse problem. Nat Phys 2:492–494 ArticleCAS Google Scholar
Tarkiainen V, Kotiaho T, Mattila I, Virkajarvi L, Aristidou A, Ketola RA (2005) On-line monitoring of continuous beer fermentation process using automatic membrane inlet mass spectrometric system. Talanta 65:1254–1263 ArticleCASPubMed Google Scholar
Tempest DW, Herbert D, 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) Continuous culture 3: microbial physiology and continuous culture. Her Majesty’s Stationery Office, London, pp 240–254
Tempest DW (1969) Quantitative relationships between inorganic cations and anionic polymers in growing bacteria. In: Meadows PM, Pirt SJ (eds) Microbial growth, symposium 19 Soc Gen Microbiol. Cambridge University Press, Cambridge, pp 87–111 Google Scholar
Tempest DW, Neijssel OM, Zevenboom W (1983) Properties and performance of microorganisms in laboratory culture: their relevance to growth in natural ecosystems. In: Slater JH, Whittenbury R, Wimpenny JWT (eds) Microbes in their natural environments, symposium 34 Soc Gen Microbiol. Cambridge University Press, Cambridge, pp 119–152
Teusink B, Wiersma A, Molenaar D, Francke C, de Vos WM, Siezen RJ, Smid EJ (2006) Analysis of growth of Lactobacillus plantarum WCFS1 on a complex medium using a genome-scale metabolic model. J Biol Chem 281:40041–40048 ArticleCASPubMed Google Scholar
Trinci AJP (1994) Evolution of the Quorn® myco-protein fungus, Fusarium graminearum A3/5. Microbiology 140:2181–2188 ArticleCASPubMed Google Scholar
van Bodegom P (2007) Microbial maintenance. A critical review on its quantification. Microbial Ecol 53:513–523 Article Google Scholar
van Eunen K, Bouwman J, Daran-Lapujade P, Postmus J, Canelas AB, Mensonides FIC, Orij R, Tuzun I, van den Brink J, Smits JG, van Gulik WM, Brul S, Heijnen JJ, de Winde JH, Teixeira de Mattos MJ, Kettner C, Nielsen J, Westerhoff HV, Bakker BM (2010) Measuring enzyme activities under standardized in vivo-like conditions for systems biology. FEBS J 277:749–760 Google Scholar
van der Brink J, Akeroyd M, van der Hoeven R, Pronk JT, de Winde JH, Daran-Lapujade P (2009) Energetic limits to metabolic flexibility: responses of Saccharomyces cerevisiae to glucose-galactose transitions. Microbiology 155:1340–1350 ArticlePubMedCAS Google Scholar
van der Greef J, Martin S, Juhsz P (2007) The art and practice of systems biology in medicine: Mapping patterns of relationships. J Proteome Res 6:1540–1559 ArticlePubMedCAS Google Scholar
van der Stap I, Vos M, Kooi BW, Mulling BTM, van Donk E, Mooij WM (2009) Algal defenses, population stability, and the risk of herbivore extinctions: a chemostat model and experiment. Ecol Res 24:1145–1153 Article Google Scholar
Veldkamp H, Jannasch HW (1972) Mixed culture studies with the chemostat. J appl Chem Biotechnol 22:105–123 ArticleCAS Google Scholar
Way JC, Silver PA (2007) Why we need systems biology. Complexity 13:22–29 Article Google Scholar
Wiebe MG, Robson GD, B, SG, Trinci AJP (1993) Periodic selection in long-term continuous-flow cultures of the filamentous fungus Fusarium graminearum J Gen Microbiol 139: 2811–2817
Zeng AP, Sun J (2010) Continuous culture. In: Baltz RH, Demain AL, Davies JE (eds) Manual of industrial microbiology and biotechnology, 3rd edn. ASM, Washington DC, pp 685–699 Google Scholar
Zhang Z, Boccazzi P, Choi HG, Perozziello G, Sinskey AJ, Jensen KF (2006) Microchemostat–microbial continuous culture in a polmer-based, instrumented microbioreactor. Lab Chip 6:906–913 ArticleCASPubMed Google Scholar
Zhong S, Khodursky A, Dykhuizen DE, Dean AM (2004) Evolutionary genomics of ecological specialization. Proc Nat Acad Sci U S A 101:11719–11724 ArticleCAS Google Scholar
Zhong S, Miller SP, Dykhuisen DE, Dean AM (2009) Transcription, translation, and the evolution of specialists and generalists. Molecular Biol Evol 26:2661–2678 ArticleCAS Google Scholar
Zilm PS, Bagley CJ, Rogers AH, Milne IR (2007) The proteomic profile of Fusobacterium nucleatum is regulated by growth pH. Microbiology 153:148–159 ArticleCASPubMed Google Scholar
Zilm PS, Rogers AH (2007) Co-adhesion and biofilm formation by Fusobacterium nucleatum in response to growth pH. Anaerobe 13:146–152 ArticleCASPubMed Google Scholar