Life under extreme energy limitation: A synthesis of laboratory- and field-based investigations

FEMS Microbiology Reviews

Volumn 39, Issue 5, 2015, Pages 688-728

  Lever, Mark A ^a   Rogers, Karyn L ^b   Lloyd, Karen G ^c   Overmann, Jörg ^d   Schink, Bernhard ^e   Thauer, Rudolf K ^f   Hoehler, Tori M ^g   Jørgensen, Bo Barker ^a  

^a AARHUS UNIVERSITY   (Denmark)

^b Research Rensselaer Polytechnic Institute   (United States)

^c UNIVERSITY OF TENNESSEE   (United States)

^d LEIBNIZ INSTITUTE DSMZ GERMAN COLLECTION OF MICROORGANISMS AND CELL CULTURES   (Germany)

^e UNIVERSITY OF KONSTANZ   (Germany)

^f MAX PLANCK INSTITUTE FOR TERRESTRIAL MICROBIOLOGY   (Germany)

^g NASA AMES RESEARCH CENTER   (United States)

Author keywords

Adaptation; Energy limitation; Laboratory; Microbial life; Starvation; Subseafloor

Indexed keywords

AMINO ACID; MONOMER; SEA WATER;

AEROBE; ALPHAPROTEOBACTERIA; ANALYTICAL PARAMETERS; ANOXIC SEDIMENT; ARTHROBACTER; ARTHROBACTER GLOBIFORMIS; BACTERIAL GENOME; BACTERIAL STRAIN; BATCH REACTOR; BIOCHEMISTRY; BIOMASS ENERGY; BIOMASS PRODUCTION; BIOSYNTHESIS; BIOTECHNOLOGY; CARBOHYDRATE ANALYSIS; CATABOLISM; CAULOBACTER; CELL ADHESION; CELL C CONTENT; CELL CARBON CONTENT; CELL DAMAGE; CELL DIFFERENTIATION; CELL DIVISION; CELL MOTILITY; CELL SHAPE; CELL SIZE; CELL STRUCTURE; CELL VOLUME; CELLULAR DISTRIBUTION; CELLULAR PARAMETERS; CHEMOLITHOAUTOTROPH; CHEMOTAXIS ASSAY; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; CONTINUOUS FLOW REACTOR; DEMETHYLATION; DESULFOTOMACULUM; DESULFOTOMACULUM PUTEI; DNA CONTENT; DNA SEQUENCE; ECOLOGY; ENERGY CONSUMPTION; ENERGY EXPENDITURE; ENERGY LIMITATION; ENERGY METABOLISM; ENERGY RESOURCE; ENERGY YIELD; ESCHERICHIA COLI; EVOLUTIONARY ADAPTATION; FATTY ACID METABOLISM; FLOW CYTOMETRY; FLUORESCENCE ACTIVATED CELL SORTING; FLUORESCENCE IN SITU HYBRIDIZATION; GENE DUPLICATION; GENE EXPRESSION; GENE TRANSLOCATION; GENOME SIZE; GEOCHEMISTRY; GEOLOGICAL TIME; GEOLOGY; GROWTH CURVE; HALOFERAX VOLCANII; HETEROTROPHY; HORIZONTAL GENE TRANSFER; ION CYCLOTRON RESONANCE MASS SPECTROMETRY; KLEBSIELLA PNEUMONIAE; LIPID CONTENT; LOCOMOTION; MARINE ENVIRONMENT; MEMBRANE POTENTIAL; MEMBRANE TRANSPORT; METHYLOSINUS TRICHOSPORIUM; MICROBIAL BIOMASS; MICROBIAL COMMUNITY; MICROBIAL LIFE; MICROBIOLOGICAL PHENOMENA AND FUNCTIONS; MICROBIOLOGY; MICROFLUIDICS; MICROORGANISM; MOLECULAR BIOLOGY; MOORELLA THERMOACETICA; MORTALITY; MYXOCOCCUS XANTHUS; NANOTECHNOLOGY; NONHUMAN; NUTRIENT LIMITATION; OLIGOTROPH; ORGANISM COMMUNITY; ORGANISMS BY ENERGY SOURCE; OXIC SEDIMENT; OXIDATION REDUCTION REACTION; PHENOTYPIC PLASTICITY; POLYMERASE CHAIN REACTION; POLYMERIZATION; PROTEIN CONTENT; PROTEIN EXPRESSION; PROTEIN SYNTHESIS; PSEUDOALTEROMONAS HALOPLANKTIS; PURE CULTURE; RACEMIZATION; REVIEW; RNA ANALYSIS; SALMONELLA ENTERICA SEROVAR TYPHIMURIUM; SEDIMENT; SHEWANELLA ONEIDENSIS; SINORHIZOBIUM MELILOTI; SPHINGOMONAS; STAPHYLOCOCCUS AUREUS; STARVATION; SUBSTRATE CONCENTRATION; SULFATE REDUCER; TURNOVER TIME; VIBRIO; ZYMOMONAS; ZYMOMONAS ANAEROBIA; ZYMOMONAS MOBILIS; ADAPTATION; BACTERIAL PHENOMENA AND FUNCTIONS; ECOSYSTEM; RESEARCH; STANDARDS;

ADAPTATION, PHYSIOLOGICAL; BACTERIAL PHYSIOLOGICAL PHENOMENA; ECOSYSTEM; ENERGY METABOLISM; RESEARCH;

EID: 84947574394     PISSN: 01686445     EISSN: 15746976     Source Type: Journal    
DOI: 10.1093/femsre/fuv020     Document Type: Review

References (349)

1. 13C NMR and FTIR to investigate changes in the chemical composition of dissolved organic matter along an estuarine transect. Environ Sci Technol 2010;44: 8044-9.
2. Acha V, Meurens M, Naveau H, et al. ATR-FTIR sensor development for continuous on-line monitoring of chorinated aliphatic hydrocarbons in a fixed-bed bioreactor. Biotechnol Bioeng 2000;68:473-87.
3. Albertson NH, Nyström T, Kjelleberg S. Exoprotease activity of two marine bacteria during starvation. Appl Environ Microb 1990a;56:218-23.
4. Albertson NH, Nyström T, Kjelleberg S. Functional mRNA halflives in the marine Vibrio sp. S14 during starvation and recovery. J Gen Microbiol 1990b;136:2195-9.
5. Akram N, Palovaara J, Forsberg J, et al. Regulation of proteorhodopsin gene expression by nutrient limitation in the marine bacterium Vibrio sp. AND4. Environ Microbiol 2013;15:1400-15.
6. Amy PS, Durham C, Hall D, et al. Starvation-survival of deep subsurface isolates. Curr Microbiol 1993;26:345-52.
7. Amy PS, Morita RY. Starvation-survival patterns of sixteen freshly isolated open-ocean bacteria. Appl Environ Microb 1983;45:1109-15.
8. Andrews JH, Harris RF. r-and K-selection andmicrobial ecology. Adv Microb Ecol 1986;9:99-147.
9. Ashida N, Ishii S, Hayano S, et al. Isolation of functional single cells from environments using a micromanipulator: application to study denitrifying bacteria. Appl Microbiol Biot 2010;85:1211-7.
10. Bach W, Edwards KJ. Iron and sulfide oxidation within the basaltic ocean crust: implications for chemolithoautotrophic microbial biomass production. Geochim Cosmochim Acta 2003;67:3871-87.
11. Bada JL. Racemization of amino acids in nature. Interdiscipl Sci Rev 1982;7:30-46.
12. Bada JL, Miller S. Racemization and the origin of optically active organic compounds in living organisms. BioSystems 1987;20:21-6.
13. Belasco JG. All things must pass: contrasts and commonalities in eukaryotic and bacterial mRNA decay. Nat Rev Mol Cell Biol 2010;11:467-78.
14. Berg HC. The rotary motor of bacterial flagella. Biochem 2003;72:19-54.
15. Berg I, Kockelkorn D, Ramos-Vera HG, et al. Autotrophic carbon fixation in archaea. Nat Rev Microbiol 2010;10:1-14.
16. Berney M, Hammes F, Bosshard F, et al. Assessment and interpretation of bacterial viability by using the LIVE/DEAD BacLight kit in combination with flow cytometry. Appl Environ Microb 2007;73:3283-90.
17. Bevilacqua A, CerianiMC, Capaccioli S, et al. Post-transcriptional regulation of gene expression by degradation of messenger RNAs. J Cell Physiol 2003;195:356-72.
18. Biddle JF, Fitz-Gibbon S, Schuster SC, et al. Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment. P Natl Acad Sci USA 2008;105:10583-8.
19. Biddle JF, Lipp JS, Lever MA, et al. Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru. P Natl Acad Sci USA 2006;103:3846-51.
20. Blair CC, D'Hondt S, Spivack AJ, et al. Radiolytic hydrogen and microbial respiration in subsurface sediments. Astrobiology 2007;7:951-70.
21. Blom JF, Horňák K, Šimek K, et al. Aggregate formation in a freshwater bacterial strain induced by growth state and conspecific chemical cues. Environ Microbiol 2010;12: 2486-95.
22. Boender LGM, de Hulster EAF, van Maris AJA, et al. Quantitative Physiology of Saccharomyces cerevisiae at nearzero specific growth rates. Appl Environ Microb 2009;75: 5607-14.
23. Bölter M, Bloem J, Meiners K, et al. Enumeration and biovolume determination of microbial cells-a methodological review and recommendations for applications in ecological research. Biol Fert Soils 2002;36:249-59.
24. Børsheim KY. Bacterial biomass and production rates in the Gulf Stream front regions. Deep-Sea Res 1990;37:1297-309.
25. Bougdour A, Cunning C, Baptiste PJ, et al. Multiple pathways for regulation of σS (RpoS) stability in Escherichia coli via the action of multiple anti-adaptors. Mol Microbiol 2008;68: 298-313.
26. Boulos L, Prévost M, Barbeau B, et al. LIVE/DEAD® BacLightTM: application of a new rapid staining method for direct enumeration of viable and total bacteria in drinking water. J Microbiol Meth 1999;37:77-86.
27. Boylen CW, Ensign JC. Intracellular substrates for endogenous metabolism during long-term starvation of rod and spherical cells of Arthrobacter crystallopoietes. J Bacteriol 1970;103:578-87.
28. Boylen CW, Mulks MH. The survival of coryneform bacteria during periods of prolonged nutrient starvation. J Gen Microbiol 1978;105:323-34.
29. Brehm-Stecher BF, Johnson EA. Single-cell microbiology: tools, technologies, and applications. Microbiol Mol Biol Rev 2004;68:538-59.
30. Brocchieri L, Karlin S. Protein length in eukaryotic and prokaryotic proteomes. Nucleic Acids Res 2005;33:3390-400.
31. Burdige DJ. Preservation of organic matter in marine sediments: controls, mechanisms, and an imbalance in sediment organic carbon budgets? Chem Rev 2007;107:467-85.
32. Button DK, Robertson BR. Determination of DNA content of aquatic bacteria by flow cytometry. Appl Environ Microb 2001;67:1636-45.
33. Canfield DE, Jorgensen BB, Fossing H, et al. Pathways of organic carbon oxidation in three continental margin sediments. Mar Geol 1993;113:27-40.
34. Canfield DE, Raiswell R, Bottrell S. The reactivity of sedimentary iron minerals toward sulfide. Am J Sci 1992;292:659-83.
35. Carpousis AJ. The RNA degradosome of Escherichia coli: anmRNAdegrading machine assembled on RNase E. Annu RevMicrobiol 2007;61:71-87.
36. Carpousis AJ, Van Houwe G, Ehretsmann C, et al. Copurification of E. coli RNAse E and PNPase: evidence for a specific association between two enzymes important in RNA processing and degradation. Cell 1994;76:889-900.
37. Cavicchioli R, Ostrowski M, Fegatella F, et al. Life under nutrient limitation in oligotrophic marine environments: an eco/Physiological perspective of Sphingopyxix alaskensis (formerly Sphingomonas alaskensis). Microb Ecol 2003;45:203-17.
38. Chain PSG, Denef VJ, Konstantinidis KT, et al. Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility. P Natl Acad Sci USA 2006;103: 15280-7.
39. Chan CM, Zhou C, Huang RH. Reconstituting bacterial RNA repair and modification in vitro. Science 2009;326:247.
40. Chapman SJ, Gray TRG. Endogenous metabolism and macromolecular composition of Arthrobacter globiformis. Soil Biol Biochem 1981;13:11-8.
41. Cho J-C, Giovannoni SJ. Cultivation and growth characteristics of a diverse group of oligotrophic marine Gammaproteobacteria. Appl Environ Microb 2004;67:432-40.
42. Clarke S. Aging as war between chemical and biochemical processes: protein methylation and the recognition of agedamaged proteins for repair. Ageing Res Rev 2003;2:263-85.
43. Clements MO, Foster SJ. Starvation recovery of Staphylococcus aureus 8325-4. Microbiology 1998;144:1755-63.
44. Colwell FS, Boyd S, Delwiche ME, et al. Estimates of biogenic methane production rates in deep marine sediments at Hydrate Ridge, Cascadia Margin. Appl Environ Microb 2008;74:3444-52.
45. Crump BC, Armbrust EV, Baross JA. Phylogenetic analysis of particle-attached and free-living bacterial communities in the Columbia river, its estuary, and the adjacent coastal ocean. Appl Environ Microb 1999;65:3192-204.
46. D'Andrilli J, Dittmar T, Koch BP, et al. Comprehensive characterization of marine dissolved organic matter by Fourier transform ion cyclotron resonance mass spectrometry with electrospray and atmospheric pressure photoionization. Rapid Comm Mass Sp 2010;24:643-50.
47. D'Hondt S, Jørgensen BB, Miller DH, et al. Distributions of microbial activities in deep subseafloor sediments. Science 2004;306:2216-21.
48. D'Hondt S, Spivack AJ, Pockalny R, et al. Subseafloor sedimentary life in the South Pacific Gyre. P Natl Acad Sci USA 2009;106:11651-6.
49. Daniel SL, Keith ES, Yang H, et al. Utilization of methoxylated aromatic compounds by the acetogen Clostridum thermoaceticum: expression and specificity of the co-dependent O-demethylating activity. Biochem Bioph Res Co 1991;180: 416-22.
50. Davidson MM, Bisher ME, Pratt LM, et al. Sulfur isotope enrichment during maintenance metabolism in the thermophilic sulfate-reducing bacterium Desulfotomaculum putei. Appl Environ Microb 2009;75:5621-30.
51. Davis CL, Robb FT. Maintenance of different mannitol uptake systems during starvation in oxidative and fermentative marine bacteria. Appl Environ Microb 1985;50:743-8.
52. Dawes EA, Large PJ. Effect of starvation on the viability and cellular constituents of Zymomonas anaerobia and Zymomonas mobilis. J Gen Microbiol 1970;60:31-42.
53. Dawson MP, Humphrey BA, Marshall KC. Adhesion: a tactic in the survival strategy of a marine vibrio during starvation. Curr Microbiol 1981;6:195-9.
54. DeLong EF, Franks DG, Alldredge AL. Phylogenetic diversity of aggregate-attached vs. free-living marine bacterial assemblages. Limnol Oceanogr 1993;38:924-34.
55. DeLong EF, Preston CM, Mincer T, et al. Community genomics among stratified microbial assemblages in the ocean's interior. Science 2006;311:496-503.
56. Dice JF. Molecular determinants of protein half-lives in eukaryotic cells. FASEB J 1987;1:349-57.
57. Dittrich PS, Manz A. Single-molecule fluorescence detection in microfluidic channels-the Holy Grail in μTAS? Anal Bioanal Chem 2005;382:1771-82.
58. Drake HL, Küsel K, Matthies C. Acetogenic prokaryotes. In: Dworkin M, Falkow S, Rosenberg E, et al. (eds). The Prokaryotes, Vol. 2. New York, NY: Springer, 2006, 354-420.
59. Dressaire C, Picard F, Redon E, et al. Role ofmRNA stability during bacterial adaptation. PLoS One 2013;8:e59059.
60. Duclaux E. Traité de Microbiologie, Vol. 1. Paris: Masson, 1898. Dusenberry DB. Minimum size limit for useful locomotion by free-swimming microbes. P Natl Acad Sci USA 1997;94:10949-54.
61. Dusenberry DB. Fitness landscapes for effects of shape on chemotaxis and other behaviors of bacteria. J Bacteriol 1998;180:5978-83.
62. Edgcomb VP, Beaudoin D, Gast R, et al. Marine subsurface eukaryotes: the fungal majority. Environ Microbiol 2010;13:172-83.
63. Egli T. The ecological and Physiological significance of the growth of heterotrophic microorganisms with mixtures of substrates. Adv Microb Ecol 1995;14:305-86.
64. El Kasmi A, Rajasekharan S, Ragsdale SW. Anaerobic pathway for conversion of the methyl group of aromatic methyl ethers to acetic acid by Clostridium thermoaceticum. Biochem 1994;33:11217-24.
65. ElowitzMB, Levine AJ, Siggia ED, et al. Stochastic gene expression in a single cell. Science 2002;297:1183-6.
66. Elser JJ, BrackenMES, Cleland EE, et al. Global analysis of nitrogen and phosphorus limitation of primary producers in freshwater, marine and terrestrial ecosystems. Ecol Lett 2007;10:1135-42.
67. Engel MH, Zumberge JE, Nagy B. Kinetics of amino acid racemization in Sequoiadendron giganteum heartwood. Anal Biochem 1977;82:415-22.
68. Engelhardt T, Sahlberg M, Cypionka H, et al. Biogeography of Rhizobium radiobacter and distribution of associated temperate phages in deep subseafloor sediments. ISME J 2013;7:199-209.
69. Ensign JC. Long-term starvation survival of rod and spherical cells of Arthrobacter crystallopoietes. J Bacteriol 1970;103: 569-77.
70. Erce MA, Low JKK, Wilkins MR. Analysis of the RNA degradosome complex in Vibrio angustum S14. FEBS J 2010;277: 5161-73.
71. Evguenieva-Hackenberg E, Klug G. RNA degradation in Archaea and gram-negative bacteria different from Escherichia coli. Prog Mol Biol Transl 2009;85:275-317.
72. Evguenieva-Hackenberg E, Klug G. New aspects of RNA processing in prokaryotes. Curr Opin Microbiol 2011;14:587-92.
73. Fagerbakke KM, Heldal M, Norland S. Content of carbon, nitrogen, oxygen, sulfur and phosphorus in native aquatic and cultured bacteria. Aquat Microb Ecol 1996;10:15-27.
74. Farinas J, Chow AW, Wada HG. A microfluidic device for measuring cellular membrane potential. Anal Biochem 2001;295: 138-42.
75. Fenchel T. Eppur si muove: many water column bacteria are motile. Aquat Microb Ecol 2001;24:197-201.
76. Fenchel T. Microbial behavior in a heterogeneous world. Science 2002;296:1068-71.
77. Fenchel T. Motility of bacteria in sediments. Aquat Microb Ecol 2008;51:23-30.
78. Ferrari BC, Gillings MR. Cultivation of fastidious bacteria by viability staining and micromanipulation in a soil substrate membrane system. Appl Environ Microb 2009;75: 3352-4.
79. Ferrari BC, Vesey G, Weir C, et al. Comparison of Cryptosporidiumspecific and Giardia-specific monoclonal antibodies formonitoring water samples. Water Res 1999;33:1611-7.
80. Fida TT, Moreno-Forero SK, Heipieper HJ, et al. Physiology and transcriptome of the polycyclic aromatic hydrocarbondegrading Sphingomonas sp. LH128 after long-term starvation. Microbiol 2013;159:1807-17.
81. Finkel SE. Long-term stationary survival during stationary phase: evolution and the GASP phenotype. Nat Rev Microbiol 2006;4:113-20.
82. Finkel SE, Kolter R. Evolution of microbial diversity during prolonged starvation. P Natl Acad Sci USA 1999;96:4023-7.
83. Fisher AT, Wheat CG. Seamounts as conduits for massive fluid, heat, and solute fluxes on ridge flanks. Oceanography 2010;23:74-87.
84. Flärdh K, Cohen PS, Kjelleberg S. Ribosomes exist in large excess over the apparent demand for protein synthesis during carbon starvation in marine Vibrio sp. strain CCUG 15956. J Bacteriol 1992;174:6780-8.
85. Fletcher PDI, Haswell SJ, Zhang X. Monitoring of chemical reactions within microreactors using an inverted Raman microscopic spectrometer. Electrophoresis 2003;24:3239-45.
86. Foreman-Wykert AK, Weiss J, Elsbach P. Phospholipid synthesis by Staphylococcus aureus during (sub)lethal attach by mammalian 14-kilodalton group IIA phospholipase A2. Infect Immun 2000;68:1259-64.
87. 0 ATP synthase. FEBS J 2008;275:1999-2007.
88. Fuhrmann S, Overmann J, Pfennig N, et al. Influence of vitamin B12 and light on the formation of chlorosomes in green-and brown-colored Chlorobium species. Arch Microbiol 1993;160:193-8.
89. Fukuda R, Ogawa H, Nagata T, et al. Direct determination of carbon and nitrogen contents of natural bacterial assemblages in marine environments. Appl Environ Microb 1998;64: 3352-8.
90. Galdiereo E, Donnarumma G, de Martino L, et al. Effect of low-nutrient seawater on morphology, chemical composition, and virulence of Salmonella typhimurium. Arch Microbiol 1994;162:41-7.
91. Garcia CD, Liu Y, Anderson P, et al. Versatile 3-channel highvoltage power supply for microchip capillary electrophoresis. Lab Chip 2003;3:324-8.
92. Geesey GG, Morita RY. Capture of arginine at low concentrations by a marine psychrophilic bacterium. Appl Environ Microb 1979;38:1092-7.
93. Gevers D, Vandepoele K, Simillion C, et al. Gene duplication and biased functional retention of paralogs in bacterial genomes. Trends Microbiol 2004;12:148-54.
94. Giard J-C, Hartke A, Flahaut S, et al. Glucose starvation response in Enterococcus faecalis JH2-2: survival and protein analysis. Res Microbiol 1997;148:27-35.
95. Giovannoni SJ, Tripp HJ, Givan S, et al. Genome streamlining in a cosmopolitan oceanic bacterium. Science 2005;309: 1242-5.
96. Gómez-Consarnau L, Akram N, Lindell K, et al. Proteorhodopsin phototrophy promotes survival of marine bacteria during starvation. PLoS One 2010;8:e1000358.
97. Gonin M, Quardokus EM, O'Donnol D, et al. Regulation of stalk elongation by phosphate in Caulobacter crescentus. J Bacteriol 2000;182:337-47.
98. González JM, Fernández-Gómez B, Fernández-Guerra A, et al. Genome analysis of the proteorhodopsin-containing marine bacterium Polaribacter sp.MED152 (Flavobacteria). P Natl Acad Sci USA 2008;105:8724-9.
99. Gottschal JS, de Vries S, Kuenen JG. Competition between the facultatively chemolithotrophic Thiobacillus A2, and obligately chemolithotrophic Thiobacillus and a heterotrophic Spirillum for inorganic and organic substrates. Arch Microbiol 1979;121:241-9.
100. Greener J, Abbasi B, Kumacheva E. Attenuated total reflection Fourier transform infrared spectroscopy for on-chip monitoring of solute concentrations. Lab Chip 2012;10:1561-6. Grossart H-P, Riemann L, Azam F. Bacterial motility in the sea and its ecological implications. Aquat Microb Ecol 2001;25:247-58.
101. Grossart H-P, Riemann L, Azam F. Bacterial motility in the sea and its ecological implications. Aquat Microb Ecol 2001;25:247-58
102. Grünberger A, Paczia N, Probst C, et al. A disposable picolitre bioreactor for cultivation and investigation of industrially relevant bacteria on the single cell level. Lab Chip 2012;12:2060-8.
103. Grünberger A, van Ooyen J, Paczia N, et al. Beyond growth rate 0.6: Corynebacterium glutamicum cultivated in highly diluted environments. Biotech Bioeng 2013;110:220-8.
104. Guckert JB, Hood MA, White DC. Phospholipid ester-linked fatty acid profile changes during nutrient deprivation of Vibrio cholerae: increases in the trans/cis ratio and proportions of cyclopropyl fatty acids. Appl Environ Microb 1986;52: 794-801.
105. Haller CM, Rölleke S, Vybiral D, et al. Investigation of 0.2 μm filterable bacteria from the Western Mediterranean Sea using amolecular approach: dominance of potential starvation forms. FEMS Microbiol Ecol 1999;31:153-61.
106. Hansen MT. Multiplicity of genome equivalents in the radiationresistant bacterium Micrococcus radiodurans. J Bacteriol 1978;134:71-5.
107. Hartke A, Giard J-C, Laplace J-M, et al. Survival of Enterococcus faecalis in an oligotrophic microcosm: changes in morphology, development of general stress resistance, and analysis of protein synthesis. Appl Environ Microb 1998;64: 4238-45.
108. Head IM, Jones DM, Larter SR. Biological activity in the deep subsurface and the origin of heavy oil. Nature 2003;426:344-52. Hedges JI, Keil RG. Sedimentary organic matter preservation: an assessment and speculative synthesis. Mar Chem 1995;49:81-115.
109. Hedges JI, Keil RG. Sedimentary organic matter preservation: an assessment and speculative synthesis. Mar Chem 1995;49:81-115
110. Heim S, Del Mar Lleo M, Bonato B, et al. The viable but nonculturable state and starvation are different stress responses of Enterococcus faecalis, as determined by proteome analysis. J Bacteriol 2002;184:6739-45.
111. Helmus RA, Liermann LJ, Brantley SL, et al. Growth advantage in stationary-phase (GASP) phenotype in long-term survival strains of Geobacter sulfurreducens. FEMS Microbiol Ecol 2011;79:218-28.
112. Hempfling WP, Mainzer SE. Effects of varying the carbon source limiting growth on yield and maintenance characteristics of Escherichia coli in continuous culture. J Bacteriol 1975;123:1076-87.
113. Herbert D, Elsworth R, Telling RC. The continuous culture of bacteria: a theoretical and experimental study. J Gen Microbiol 1956;14:601-22.
114. Herndl GJ. Ecology of amorphous aggregations (marine snow) in theNorthern Adriatic Sea. II. Microbial density and activity in marine snowand its implication to overall pelagic processes. Mar-Ecol Prog Ser 1988;48:265-75.
115. Hoefel D, Grooby WL, Monis PT, et al. Enumeration of waterborne bacteria using viability assays and flow cytometry: a comparison to culture-based techniques. J Microbiol Meth 2003;55:585-97.
116. Hoehler TM. Biological energy requirements as quantitative boundary conditions for life in the subsurface. Geobiology 2004;2:205-15.
117. Hoehler TM, Alperin MJ, Albert DM, et al. Thermodynamic control on hydrogen concentrations in anoxic sediments. Geochim Cosmochim Acta 1998;62:1745-56.
118. Hoehler TM, AlperinMJ, Albert DB, et al. Apparent minimum free energy requirements for methanogenic archaea and sulfatereducing bacteria in an anoxic marine sediment. FEMS Microbiol Ecol 2001;38:33-41.
119. Hoehler TM, Jørgensen BB. Microbial life under extreme energy limitation. Nat Rev Microbiol 2013;11:83-94.
120. Holden JF, Baross JA. Enhanced thermotolerance by hydrostatic pressure in the deep-sea hyperthermophile Pyrococcus strain ES4. FEMS Microbiol Ecol 1995;18:27-34.
121. Holm C, Jespersen L. A flow-cytometric Gram-staining technique for milk-associated bacteria. Appl Environ Microb 2003;69:2857-63.
122. Holmkvist L, Ferdelman TG, Jørgensen BB. A cryptic sulfur cycle driven by iron in the methane zone of marine sediment (Aarhus Bay, Denmark). Geochim Cosmochim Acta 2011;75:3581-99.
123. Holmquist L, Kjelleberg S. The carbon starvation stimulon in the marine Vibrio sp. S14 (CCUG 15956) includes three periplasmic space protein responders. J Gen Microbiol 1993;139:209-15.
124. Hood MA, Guckert JB, White DC, et al. Effect of nutrient deprivation on lipid, carbohydrate, DNA, RNA and protein levels in Vibrio cholerae. Appl Environ Microb 1986;52: 788-93.
125. Horsfield B, Schenk H, Zink K, et al. Living microbial ecosystems within the active zone of catagenesis: implications for feeding the deep biosphere. Earth Planet Sc Lett 2006;246:55-69.
126. Horvath P, Barrangou R. CRISPR/Cas, the immune system of bacteria and archaea. Science 2010;327:167-70.
127. Huang WE, Griffiths RI, Thompson IP, et al. Raman microscopic analysis of single microbial cells. Anal Chem 2004;76:4452-8.
128. Huang WE, Stoecker K, Griffiths R, et al. Raman-FISH: combining stable-isotope Raman spectroscopy and fluorescence in situ hybridization for the single cell analysis of identity and function. Environ Microbiol 2007;9:1878-89.
129. Hütz A, Schubert K, Overmann J. Thalassospira sp. isolated from the oligotrophic Eastern Mediterranean Sea exhibits chemotaxis toward inorganic phosphate during starvation. Appl Environ Microb 2011;77:4412-21
130. Imlay JA. The molecular mechanisms and Physiological consequences of oxidative stress: lessons from amodel bacterium. Nat Rev Microbiol 2013;11:443-54.
131. Ishii S, Tago K, Senoo K. Single-cell analysis and isolation formicrobiology and Biotechnology: methods and applications. Appl Microbiol Biot 2010;86:1281-92.
132. Ishikawa JK, Clarke S. A highly active protein repair enzyme from an extreme thermophile: the L-isoaspartyl methyltransferase from Thermotoga maritima. Arch Biochem Biophys 1998;358:222-31.
133. Ivleva NP, Wagner M, Horn H, et al. Towards a nondestructive chemical characterization of biofilm matrix by Raman microscopy. Anal Bioanal Chem 2009;393:197-206.
134. Jackson BE, McInerney MJ. Anaerobic microbial metabolism can proceed close to thermodynamic limits. Nature 2002;415: 454-6.
135. Jäger S, HebermehlM, Schiltz E, et al. Composition and activity of the Rhodobacter capsulatus degradosome vary under different oxygen concentrations. J Mol Microb Biotech 2004;7:148-54.
136. Jannasch HW. Growth of marine bacteria at limiting concentrations of organic carbon in seawater. Limnol Oceanogr 1967;12:264-71.
137. Jarrell KF, Albers S-V. The archaellum: an old motility structure with a new name. Trends Microbiol 2012;20:307-12.
138. Jetten MSM, Stams AJM, Zehnder AJB. Methanogenesis from acetate: a comparison of the acetate metabolism in Methanothrix soehngenii and Methanosarcina spp. FEMS Microbiol Rev 1992;88:181-98.
139. Johnson SS, Hebsgaard MB, Christensen TR, et al. Ancient bacteria show evidence of DNA repair. P Natl Acad Sci USA 2007;104:14401-5.
140. Johnstone BH, Jones RD. Physiological effects of long-term energy-source deprivation on the survival of a marine chemolithotrophic ammonium-oxidizing bacterium. Mar-Ecol Prog Ser 1988;49:295-303.
141. Jones KL, Rhodes-Roberts ME. The survival of marine bacteria under starvation conditions. J Appl Bacteriol 1981;50:247-58.
142. Jouper Jaan Å, Dahllöf B, Kjelleberg S. Changes in protein composition of three bacterial isolates from marine waters during short periods of energy and nutrient deprivation. Appl Environ Microb 1986;52:1419-21.
143. Jørgensen BB. Deep subseafloor microbial cells on Physiological standby. P Natl Acad Sci USA 2011;108:18193-4.
144. Jørgensen BB, Parkes RJ. Role of sulfate reduction and methane production by organic carbon degradation in eutrophic fjord sediments (Limfjorden, Denmark). Limnol Oceanogr 2010;55:1338-52.
145. Kallmeyer J, Pockalny R, Adhikari RR, et al. Global distribution of microbial abundance and biomass in subseafloor sediment. P Natl Acad Sci USA 2012;109:16213-6.
146. Kalyuzhnaya MG, Lidstrom ME, Chistoserdova L. Real-time detection of actively metabolizing microbes by redox sensing as applied to methylotroph populations in LakeWashington. ISME J 2008;2:696-706.
147. Karl DM. Solar energy capture and transformation in the sea. Elementa 2014;2:21.
148. Keene JD. RNA regulons: coordination of post-transcriptional events. Nat Rev Genet 2007;8:533-43.
149. Kefford B, Humphrey BA, Marshall KC. Adhesion: a possible survival strategy for leptospires under starvation conditions. Curr Microbiol 1986;13:247-50.
150. Kieft TL, McCuddy SM, Onstott TC, et al. Geochemically generated, energy-rich substrates and indigenous microorganisms in deep, ancient groundwater. Geomicrobiol J 2005;22: 325-35.
151. Kieft TL, Ringelberg DB, White DC. Changes in ester-linked phospholipid fatty acid profiles of subsurface bacteria during starvation and desiccation in a porous medium. Appl Environ Microb 1994;60:3292-9.
152. Kieft TL, Wilch E, O'Connor K, et al. Survival and phospholipid fatty acid profiles of surface and subsurface bacteria in natural sedimentmicrocosms. Appl EnvironMicrob 1997;63:1531-42.
153. King AV, Welter BH, Koushlik AB, et al. A genome-wide overexpression screen identifies genes involved in phagocytosis in the human protozoan parasite, Entamoeba histolytica. PLoS One 2012;7:e43025.
154. Kirchman DL, Hansen TE. Bioenergetics of photoheterotrophic bacteria in the oceans. Environ Microbiol Rep 2013;5:188-99.
155. 2 degassing from the active fault zone. J Geophys Res 1982;87: 789-95.
156. Kjelleberg S, Albertson N, Flärdh K, et al. How do nondifferentiating bacteria adapt to starvation? Anton Leeuw 1993;63:333-41.
157. Kjelleberg S, Hermansson M. Starvation-induced effects on bacterial surface characteristics. Appl Environ Microb 1984;48:497-503.
158. Kjelleberg S, Humphrey BA, Marshall KC. Effect of interfaces on small, starved marine bacteria. Appl Environ Microb 1982;43:1166-72.
159. Kjelleberg S, Humphrey BA, Marshall KC. Initial phases of starvation and activity of bacteria at surfaces. Appl EnvironMicrob 1983;46:978-84.
160. Klappenbach JA, Dunbar JM, Schmidt TM. rRNA operon copy number reflects ecological strategies of bacteria. Appl Environ Microb 2000;66:1328-33.
161. Komaki K, Ishikawa H. Intracellular bacterial symbionts of aphids possess many genomic copies per bacterium. J Mol Evol 1999;48:717-22.
162. Könneke M, Bernhard AE, de la Torre J, et al. Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 2005;437:543-6.
163. Konstantinidis KT, Tiedje JM. Trends between gene content and genome size in prokaryotic species with larger genomes. P Natl Acad Sci USA 2004;101:3160-5.
164. Kragelund L, Nybroe O. Culturability and expression of outer membrane proteins during carbon, nitrogen, or phosphorus starvation of Pseudomonas fluorescens DF57 and Pseudomonas putida DF14. Appl Environ Microb 1994;60:2944-8.
165. Kriausakul N, Mitterer RM. Isoleucine epimerization in peptides and proteins: kinetic factors and application to fossil proteins. Science 1978;201:1011-4.
166. Krisko A, Radman M. Protein damage and death by radiation in Escherichia coli and Deinococcus radiodurans. P Natl Acad Sci USA 2010;107:14373-7.
167. Laflamme C, Ho J, Veillette M, et al. Flow cytometry analysis of germinating Bacillus spores, using membrane potential dye. Arch Microbiol 2005;183:107-12.
168. Lalaouna D, Simoeau-Roy M, Lafontaine D, et al. Regulatory RNAs and target mRNA decay in prokaryotes. Biochim Biophys Acta 2013;1829:742-7.
169. Lappin-Scott HM, Cusack F, Costerton JW. Nutrient resuscitation and growth of starved cells in sandstone cores: a novel approach to enhanced oil recovery. Appl Environ Microb 1988;54:1373-82.
170. LaRowe DE, Helgeson HC. Quantifying the energetics of metabolic reactions in diverse biogeochemical systems: electron flow and ATP synthesis. Geobiology 2007;5:153-68.
171. LaRowe DE, Van Cappellen P. Degradation of natural organic matter: a thermodynamic analysis. Geochim Cosmochim Acta 2011;75:2030-42.
172. Lauro FM, Dougald D, Thomas T, et al. Genomic basis of trophic strategy in marine bacteria. P Natl Acad Sci USA 2009;106:15527-33.
173. Le J, Wehr JD, Campbell L. Uncoupling of bacterioplankton and phytoplankton production in fresh waters is affected by inorganic nutrient limitation. Appl EnvironMicrob 1994;60:2086-93.
174. Lebaron P, Servais P, Agogué H, et al. Does the high nucleic acid content of individual bacterial cells allow us to discriminate between active cells and inactive cells in aquatic systems? Appl Environ Microb 2001;67:1775-82.
175. Lee H, Popodi E, Tang H, et al. Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing. P Natl Acad Sci USA 2012;109:E2774-83.
176. Lee KS, Boccazzi P, Sinskey AJ, et al. Microfluidic chemostat and turbidostat with flow rate, oxygen, and temperature control for dynamic continuous culture. Lab Chip 2011;11:1730-9.
177. Leloup J, Fossing H, Kohls K, et al. Sulfate-reducing bacteria in marine sediment (Aarhus Bay, Denmark): abundance and diversity related to geochemical zonation. Environ Microbiol 2009;11:1278-91.
178. Leloup J, Loy A, KnabNJ, et al. Diversity and abundance of sulfatereducing microorganisms in the sulfate and methane zones of a marine sediment, Black Sea. EnvironMicrobiol 2007;9:131-42.
179. Leman L, Orgel L, Ghadiri MR. Carbonyl sulfide-mediated prebiotic formation of peptides. Science 2004;306:283-6.
180. Lennon JT, Jones SE. Microbial seed banks: the ecological and evolutionary implications of dormancy. Nat Rev Microbiol 2011;9:119-30.
181. LeverMA. Acetogenesis in the energy-starved deep biosphere-a paradox? Front Microbiol 2012;2:18.
182. Lever MA, Rouxel OJ, Alt J, et al. Evidence for microbial carbon and sulfur cycling in deeply buried ridge flank basalt. Science 2013;339:1305-8.
183. Lever MA, Valiela I. Response of microphytobenthic biomass to experimental nutrient enrichment and grazer exclusion at different land-derived nitrogen loads. Mar-Ecol Prog Ser 2005;294:117-29.
184. Li D, He M, Jiang SC. Detection of infectious adenoviruses in environmentalwaters by fluorescence-activated cell sorting assay. Appl Environ Microb 2010;76:1442-8.
185. Li G, Tang JX. Low flagellar motor torque and high swimming efficiency of Caulobacter crescentus swarmer cells. Biophys J 2006;91:2726-34.
186. Lin B, Westerhoff HV, Röling WFM. How Geobacteraceae may dominate subsurface biodegradation: physiology of Geobacter metallireducens in slow-growth habitat-simulating retentostats. Environ Microbiol 2009;11:2425-33.
187. Lin H-T, Cowen JP, Olson EJ, et al. Inorganic chemistry, gas compositions and dissolved organic carbon in fluids from sedimented young basaltic crust on the Juan de Fuca Ridge flanks. Geochim Cosmochim Acta 2012a;85: 213-27.
188. Lin L-H, Hall J, Lippmann-Pipke J, et al. Radiolytic H2 in continental crust: nuclear power for deep subsurface microbial communities. Geochem Geophy Geosy 2005;6:1-13.
189. Lin Y-S, Heuer VB, Goldhammer T, et al. Towards constraining H2 concentration in subseafloor sediment: a proposal for combined analysis by two distinct approaches. Geochim Cosmochim Acta 2012b;77:186-201.
190. Lindahl T. Instability and decay of the primary structure of DNA. Nature 1993;362:709-15.
191. Lindahl T, Nyberg B. Rate of depurination of native deoxyribonucleic acid. Biochem 1972;11:3610-8.
192. Lipp JS, Morono Y, Inagaki F, et al. Significant contribution of Archaea to extant biomass in marine subsurface sediments. Nature 2008;454:991-4.
193. Liu Y, Karnauchow TM, Jarrell KF, et al. Description of two new thermophilic Desulfotomaculum spp., Desulfotomaculum putei sp. nov., from a deep terrestrial subsurface, and Desulfotomaculum luciae sp. nov., from a hot spring. Int J Syst Evol Micr 1997;47:615-21.
194. Lloyd KG, May MK, Kevorkian RT, et al. Meta-analysis of quantification methods shows that Archaea and Bacteria have similar abundances in the subseafloor. Appl Environ Microb 2013;79:7790-9.
195. Lomstein BA, Langerhuus AT, D'Hondt S, et al. Endospore abundance, microbial growth and necromass turnover in deep sub-seafloor sediment. Nature 2012;484:101-4.
196. Lovley DR, Goodwin S. Hydrogen concentrations as an indicator of the predominant terminal electron-accepting reactions in aquatic sediments. Geochim Cosmochim Acta 1988;52:2993-3003.
197. Luscombe BM, Gray TRG. Characteristics of Arthrobacter grown in continuous culture. J Gen Microbiol 1974;82: 213-22.
198. Lysak LV, Lapygina EV, Konova IA, et al. Population density and taxonomic composition of bacterial nanoforms in soils of Russia. Eur Soil Sci 2010;43:765-70.
199. McCarthy MD, Beaupré SR, Walker BD, et al. Chemosynthetic origin of 14C-depleted dissolved organic matter in a ridge-flank hydrothermal system. Nature Geosci 2010;4:32-6.
200. McCollom TM, Amend JP. A thermodynamic assessment of energy requirements for biomass synthesis by chemolithoautotrophic micro-organisms in oxic and anoxic environments. Geobiology 2005;3:135-44.
201. McCollom TM, Seewald JS. Abiotic synthesis of organic compounds in deep-sea hydrothermal environments. Chem Rev 2007;107:382-401.
202. MacLeod FA, Lappin-ScottHM, Costerton JW. Plugging of amodel rock system by using starved bacteria. Appl Environ Microbiol 1988;54:1365-72.
203. McMillan DGG, Ferguson SA, Dey D, et al. A1Ao-ATP synthase of Methanobrevibacterium ruminantium couples sodium ions for ATP synthesis under physiological conditions. J Biol Chem 2011;46:39382-892.
204. Magge A, Setlow B, Cowan AE, et al. Analysis of dye binding by and membrane potential in spores of Bacillus species. J Appl Microbiol 2009;106:814-24.
205. Malfatti F, Azam F. Atomic force microscopy reveals microscale networkds and possible symbioses among pelagic marine bacteria. Aquat Microb Ecol 2009;58:2-14.
206. Malmcrona-Friberg K, Goodman A, Kjelleberg S. Chemotactic responses of marine Vibrio sp. Strain S14 (CCUG 15956) to lowmolecular-weight substances under starvation and recovery conditions. Appl Environ Microb 1990;56:3699-704.
207. Mao X, Nawaz AA, Lin SS, et al. An integrated, multiparametric flow cytometry chip using 'microfluidic drifting' based three-dimensional hydrodynamic focusing. Biomicrofluidics 2012;6:24113-9.
208. Mardén P, Nyström T, Kjelleberg S. Uptake of leucine by a marine Gram-negative heterotrophic bacterium during exposure to starvation conditions. FEMS Microbiol Lett 1987;45:233-41.
209. Marouga R, Kjelleberg S. Synthesis of immediate upshift (Iup) proteins during recovery of marine Vibrio sp. strain S14 subjected to long-term carbon starvation. J Bacteriol 1996;178:817-22.
210. Marschall E, JoglerM, HessgeU, et al. Large-scale distribution and activity patterns of an extremely low-light-adapted population of green sulfur bacteria in the Black Sea. EnvironMicrobiol 2010;12:1348-62.
211. Martin JH, Fitzwater SE. Iron deficiency limits phytoplankton growth in the north-east Pacific subarctic. Nature 1988;33:341-3.
212. Maurelli AT, Fernandez RE, Bloch CA et al.'Black holes' and bacterial pathogenicity: a large genome deletion that enhances the virulence of Shigella spp. and enteroinvasive Escherichia coli. P Natl Acad Sci USA 1998;95:3943-8.
213. Mayer F, Müller V. Adaptations of anaerobic archaea to life under extreme energy limitation. FEMS Microbiol Rev 2014;38:449-72.
214. Mendell JE, Clements KD, Choat JH, et al. Extreme polyploidy in a large bacterium. P Natl Acad Sci USA 2008;105: 6730-4.
215. Mira A, Ochman H, Moran NA. Deletional bias and the evolution of bacterial genomes. Genetics 2001;17:589-96.
216. Mitchell JG. The energetics and scaling of search strategies in Bacteria. Am Nat 2002;160:727-40.
217. Mitchell JG, Okubo A, Fuhrman JA. Microzones surrounding phytoplankton form the basis for a stratified marine microbial ecosystem. Nature 1985;316:58-9.
218. Mitchell JG, Pearson L, Dillon S, et al. Natural assemblages of marine bacteria exhibiting high-speed motility and large accelerations. Appl Environ Microb 1995;61:4436-40.
219. Mongodin EF, Shapir N, Daugherty SC, et al. Secrets of soil survival revealed by the genome sequence of Arthrobacter aurescens TC1. PLOS Genet 2006;2:2094-106.
220. Monod J. Recherches sur la Croissance Bacteriennes. Paris: Masson, 1942.
221. Moran MA, Buchan A, González JM, et al. Genome sequence of Silicibacter pomeroyi reveals adaptations to marine environment. Nature 2004;432:910-3.
222. Morita R, Nakane S, Shimada A, et al. Molecular mechanisms of the whole DNA repair system: comparison of bacterial and eukaryotic systems. J Nucleic Acids 2010;2010:179594.
223. Morita RY. The starvation-survival state of microorganisms in nature and its relationship to the bioavailable energy. Experientia 1990;46:813-7.
224. Morita RY. Bacteria in Oligotrophic Environments. New York, NY: Chapman & Hall, 1997.
225. Morono Y, Terada T, Masui N, et al. Discriminative detection and enumeration of microbial life in marine subsurface sediments. ISME J 2009;3:503-11.
226. Morton DS, Oliver JD. Induction of carbon starvation-induced proteins in Vibrio vulnificus. Appl Environ Microb 1994;60: 3653-9.
227. Moyer CL, Morita RY. Effect of growth rate and starvationsurvival on the viability and stability of a psychrophilic marine bacterium. Appl Environ Microb 1989a;55: 1122-7.
228. Moyer CL, Morita RY. Effect of growth rate and starvationsurvival on cellular DNA, RNA, and protein of a psychrophilic marine bacterium. Appl Environ Microb 1989b;55:2710-6.
229. Mukhopadhyay B, Johnson EF, Wolfe RS. A novel pH2 control on the expression of flagella in the hyperthermophilic strictly hydrogenotrophic methanarchaeaon Methanococcus jannaschii. P Natl Acad Sci USA 2000;97:11522-7.
230. Musat N, Foster R, Vagner T, et al. Detecting metabolic activities in single cells, with emphasis on nanoSIMS. FEMS Microbiol Rev 2012;36:486-511.
231. Neidhardt FC, Ingraham JL, Schaechter M. Physiology of the Bacterial Cell: A Molecular Approach. Sunderland, MA: Sinauer Associates, 1990, 520.
232. Nelson DR, Zusman DR. Evidence for long-lived mRNA during fruiting body formation in Myxococcus xanthus. P Natl Acad Sci USA 1983;80:1467-71.
233. 4 by weathering of olivine at temperatures between 30 and 70°C. Geochem T 2011;12:6.
234. Nielsen KM, Calamai L, Pietramellara G. 7. Stabilization of extracellular DNA and proteins by transient binding to various soil components. In: Nannipieri P, Smalla K (eds). Soil Biology: Nucleic Acids and Proteins in Soil., Vol. 8. Berlin-Heidelberg: Springer, 2006, 141-57.
235. Nilsson G, Belasco JG, Cohen SN, et al. Growth-rate dependent regulation of mRNA stability in Escherichia coli. Nature 1984;312:75-7.
236. Nissen H. Long term starvation of a marine bacterium, Alteromonas denitrificans, isolated from a Norwegian fjord. FEMS Microbiol Ecol 1987;45:173-83.
237. Nordström K, Dasgupta S. Copy-number control of the Escherichia coli chromosome: a plasmidologist's view. EMBO Rep 2006;7:484-9.
238. Norland S, Fagerbakke KM, Heldal M. Light element analysis of individual bacteria by x-ray microanalysis. Appl Environ Microb 1995;61:1357-62.
239. Novitsky JA, Morita RY. Morphological characterization of small cells resulting from nutrient starvation of a psychrophilic marine vibrio. Appl Environ Microb 1976;32:617-22.
240. Nyström T, Albertson N, Kjelleberg S. Synthesis of membrane and periplasmic proteins during starvation of a marine Vibrio sp. J Gen Microbiol 1988;134:1645-51.
241. Nyström T, Olsson RM, Kjelleberg S. Survival, stress resistance, and alteration in protein expression in the marine Vibrio sp. strain S14 (VIBRIO ANGUSTUM) during starvation for different individual nutrients. Appl Environ Microb 1992;58:55-65.
242. Oliver JD. The viable but nonculturable state in bacteria. J Microbiol 2005;43:93-100.
243. Oliver JD, Nilsson L, Kjelleberg S. Formation of nonculturable Vibrio vulnificus cells and its relationship to the starvation state. Appl Environ Microb 1991;57:2640-4.
244. Oliver JD, Stringer WF. Lipid composition of a psychrophilic marine Vibrio sp. during starvation-induced morphogenesis. Appl Environ Microb 1984;47:461-6.
245. Onstott TC, Magnabosco C, Aubrey AD, et al. Does aspartic acid racemization constrain the depth limit of the subsurface biosphere? Geobiology 2013;12:1-19.
246. Onuchic JN, Luthey-Schulten Z, Wolynes PG. Theory of protein folding: the energy landscape perspective. Annu Rev Phys Chem 1997;48:545-600.
247. Paerl HW. Factors limiting productivity of freshwater ecosystems. Adv Microb Ecol 1982;6:75-110.
248. Paik WK, Paik DC, Kim S. Historical review: the field of protein methylation. Trends Biochem Sci 2007;32:146-62.
249. Parkes RJ, Cragg BA, Bale SJ, et al. Deep bacterial biosphere in Pacific Ocean sediments. Nature 1994;371:410-3.
250. Parkes RJ, Linnane CD, Webster G, et al. Prokaryotes stimulate mineral H2 formation for the deep biosphere and subsequent thermogenic activity. Geology 2011;39:219-22.
251. Parkes RJ, Webster G, Cragg BA, et al. Deep sub-seafloor prokaryotes stimulated at interfaces over geological time. Nature 2005;436:390-4.
252. Penning H, Conrad R. Effect of inhibition of acetoclastic methanogenesis on growth of archaeal populations in an anoxic model environment. Appl Environ Microb 2006;72:178-84.
253. Pino S, Costanzo G, Giorgi A, et al. Sequence complementaritydriven nonenzymatic ligation of RNA. Biochemistry 2011;50:2994-3003.
254. Pirt SJ.Maintenance energy of bacteria in growing cultures. P Roy Soc Lond B Bio 1965;163:224-31.
255. Pirt SJ. Maintenance energy: a general model for energylimited and energy-sufficient growth. Arch Microbiol 1982;133: 300-2.
256. Pogoryelov D, Klyszejko AL, Krasnoselska GO, et al. Engineering rotor ring stoichiometries in the ATP synthase. P Natl Acad Sci USA 2012;109:1599-608.
257. Poindexter JS. Oligotrophy, feast and famine existence. Adv Microb Ecol 1981;5:63-89.
258. Poindexter JS, Cohen-Bazire G. The fine structure of stalked bacteria belonging to the family Caulbacteraceae. J Cell Biol 1964;23:587-97.
259. Poli A, Di Donato P, Abbamondi GR, et al. Synthesis, production, and biotechnological applications of exopolysaccharides and polyhydroxyalkanoates by Archaea. Archaea 2011;2011:693253.
260. Polz MF, Hunt DE, Preheim SP, et al. Patterns and mechanisms of genetic and phenotypic differentiation in marine microbes. Philos T Roy Soc B 2006;361:2009-21.
261. Porwollik S, Wong RMY, Helm RA, et al. DNA amplification and rearrangements in archival Salmonella enterica serovar typhimurium LT2 cultures. J Bacteriol 2004;186:1678-82.
262. Powner MW, Gerland B, Sutherland JD. Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions. Nature 2009;459:239-42.
263. Price PB, Sowers T. Temperature dependence of metabolic rates for microbial growth, maintenance, and survival. P Natl Acad Sci USA 2004;101:4631-6.
264. Py B, Causton H, Mudd EA, et al. A protein complex mediating mRNA degradation in Escherichia coli. Mol Microbiol 1994;14:717-29.
265. Rabus R, Hansen TA, Widdel F. Dissimilatory sulfate-and sulfurreducing prokaryotes. In: Dworkin M, Falkow S, Rosenberg Eet al. (eds). The Prokaryotes, Vol. 2. New York, NY: Springer, 2006, 659-768.
266. Rappé MS, Connon SA, Vergin KL, et al. Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 2002;418:630-3.
267. Rasmussen H, Jørgensen BB. Microelectrode studies of seasonal oxygen uptake in a coastal sediment: role of molecular diffusion. Mar-Ecol Prog Ser 1992;81:289-303.
268. Ravenschlag K, Sahm K, Knoblauch C, et al. Community structure, cellular rRNA content, and activity of sulfate-reducting bacteria in marine Arctic sediments. Appl Environ Microb 2000;66:3592-602.
269. Redon E, Loubiere P, Cocaign-BousquetM. Role ofmRNA stability during genome-wide adaptation of Lactococcus lactis to carbon starvation. J Biol Chem 2005;280:36380-5.
270. Reimers CE. An in situ microprofiling instrument for measuring interfacial pore water gradients: methods and oxygen profiles from the North Pacific Ocean. Deep-Sea Res II 1987;34:2019-35.
271. Rice SA, Oliver JD. Starvation response of the marine barophile CNPT-3. Appl Environ Microb 1992;58:2432-7.
272. Riedel TE, BerelsonWM, Nealson KH, et al. Oxygen consumption rates of bacteria under nutrient-limited conditions. Appl Environ Microb 2013;79:4921-31.
273. Riedinger N, Formolo MJ, Lyons TW, et al. An inorganic geochemical argument for coupled anaerobic oxidation of methane and iron reduction in marine sediments. Geobiology 2014;12:172-81.
274. Riemann L, Winding A. Community dynamics of free-living and particle-associatedbacterial assemblages during a freshwater phytoplankton bloom. Microb Ecol 2001;42:274-85.
275. Robertson JG, Batt RD. Survival of Nocardia corallina and degradation of constituents during starvation. J Gen Microbiol 1973;78:109-17.
276. Röling WFM, Head IM, Larter SR. The microbiology of hydrocarbon degradation in subsurface petroleum reservoirs: perspectives and prospects. Res Microbiol 2003;154:321-8.
277. Romanova ND, Sazhin AF. Relationships between the cell volume and the carbon content of bacteria. Oceanology 2010;50:556-65.
278. Romeo T, Vakulskas CA, Babitzke P. Post-transcriptional regulation on a global scale: form and function of Csr/Rsm systems. Environ Microbiol 2013;15:313-24.
279. Roslev P, King GM. Survival and recovery of methanotrophic bacteria starved under oxic and anoxic conditions. Appl Environ Microb 1994;60:2602-8.
280. Rother M, Metcalf WW. Anaerobic growth of Methanosarcina acetivorans C2A on carbonmonoxide: an unusualway of life for a methanogenic archaeon. P Natl Acad Sci USA 2004;101:16929-34.
281. Russell MJ, Martin W. The rocky roots of the acetyl-CoA pathway. Trends Biochem Sci 2004;29:358-63.
282. Røy H, Kallmeyer J, Adhikari RR, et al. Aerobic microbial respiration in 86-million-year-old deep-sea red clay. Science 2012;336:922-7.
283. Sahm K, MacGregor BJ, Jørgensen BB, et al. Sulfate reduction and vertical distribution of sulfate-reducing bacteria quantified by rRNA slot-blot hybridization in a coastal marine sediment. Environ Microbiol 1999;1:65-74.
284. Saini G, Nasholm N, Wood BD. Implications of growth and starvation conditions in bacterial adhesion and transport. J Adhes Sci Technol 2011;25:2281-97.
285. Schäfer G, Engelhard M, Müller V. Bioenergetics of Archaea. Microbiol Mol Biol R 1999;63:570-620.
286. Scherer CG, Boylen CW.Macromolecular synthesis and degradation in Arthrobacter during periods of nutrient deprivation. J Bacteriol 1977;132:584-9.
287. Schimz K-L, Overhoff B. Investigations of the influence of carbon starvation on the carbohydrate storage compounds (trehalose, glycogen), viability, adenylate pool, and adenylate energy charge in Cellulomonas sp. (DSM20108). FEMS Microbiol Lett 1987;40:333-7.
288. Schink B. Energetics of syntrophic cooperation in methanogenic degradation. Microbiol Mol Biol R 1997;61:262-80.
289. Schink B, Stams AJM. Syntrophism among prokaryotes. In: Dworkin M, Falkow S, Rosenberg E, et al. (eds). The Prokaryotes, New York, NY: Springer, 2013, 471-93.
290. Schut F, Prins RA, Gottschal JC. Oligotrophy and pelagic marine bacteria: facts and fiction. Aquat Microb Ecol 1997;12:177-202.
291. Shipboard Scientific Party. Controls on microbial communities in deeply buried sediments, Eastern Equatorial Pacific and Peru Margin sites. In: D'Hondt SL, Jørgensen BB, Miller DJ, et al. (eds). Proceedings of the Ocean Drilling Program, Initial Reports. College Station, TX: Ocean Drilling Program, 2003, 1225-31.
292. Shock EL. Geochemistry at the biotic fringe. Geochim Cosmochim Acta 2009;;73:A1215.
293. Sleep NH, ZobackMD. Did earthquakes keep the early crust habitable? Astrobiology 2007;7:1023-32.
294. Smith DC, Simon M, Alldredge AL, et al. Intense hydrolytic enzyme activity on marine aggregates and implications for rapid particle dissolution. Nature 1992;359:139-42.
295. Smith KS, Ingram-Smith C. Methanosaeta, the forgotten methanogen? Trends Microbiol 2007;15:150-5.
296. Steen AD, Jørgensen BB, Lomstein BA. Abiotic racemization kinetics of amino acids in marine sediments. PLoS One 2013;8:e71648.
297. Steindler L, Schwalbach MS, Smith DP, et al. Energy starved Candidatus Pelagibacter Ubique substitutes light-mediated ATP production for endogenous carbon respiration. PLoS One 2011;6:e19725.
298. Stingl U, Desiderio RA, Cho JC, et al. The SAR92 clade: an abundant coastal clade of culturable marine bacteria possessing proteorhodopsin. Appl Environ Microb 2007;73:2290-6.
299. Stocker R. Marine microbes see a sea of gradients. Science 2012;338:628-33.
300. Stocker R, Seymour JR, Samadani A, et al. Rapid chemotactic response enables marine bacteria to exploit ephemeral microscale nutrient patches. Science 2008;105:4209-14.
301. Stouthamer AH. A theoretical study on the amount of ATP required for synthesis of microbial cell material. Anton Leeuw 1973;39:545-65.
302. Stouthamer AH, Bettenheimer C. Utilization of energy for growth and maintenance in continuous and batch cultures of microorganisms. A reevaluation of the method for the determination of ATP production by measuring molar growth yields. Biochim Biophys Acta 1973;301:53-70.
303. Süss J, Herrmann K, Seidel M, et al. Two distinct Photobacterium populations thrive in ancient Mediterranean sapropels. Microb Ecol 2008;55:371-83.
304. Tännler S, Decasper S, Sauer U. Maintenance metabolism and carbon fluxes in Bacillus species. Microb Cell Fact 2008;7:19. Takahashi K, Hattori A, Suzuki I, et al. Non-destructive on-chip cell sorting system with real-time microscopic image processing. J Nanobiotechnol 2004;2:5.
305. Takahashi K, Hattori A, Suzuki I, et al. Non-destructive on-chip cell sorting system with real-time microscopic image processing. J Nanobiotechnol 2004;2:5
306. Takano Y, Chikaraishi Y, Ogawa NO, et al. Sedimentary membrane lipids recycled by deep-sea benthic archaea. Nature Geosci 2010;3:858-61.
307. Tappe W, Laverman A, Bohland M, et al. Maintenance energy demand and starvation recovery dynamics of Nitrosomonas europaea and Nitrobacter winogradskyi cultivated in a retentostat with complete biomass retention. Appl Environ Microb 1999;65:2471-7.
308. Tappe W, Tomaschewski C, Rittershaus S, et al. Cultivation of nitrifying bacteria in the retentostat, a simple fermenter with internal biomass retention. FEMS Microbiol Ecol 1996;19: 47-52.
309. Tarpgaard IH. Dual kinetics of marine sulfate reduction. Ph.D. Dissertation. Aarhus University 2013.
310. Taylor JR, Stocker R. Trade-offs of chemotactic foraging in turbulent water. Science 2012;;338:675-9.
311. Thauer RK, Kaster A-K, Seedorf H, et al. Methanogenic archaea: ecologically relevant differences in energy conservation. Nat Rev Microbiol 2008;6:579-91.
312. Thauer RK, Morris G. Metabolism of chemotrophic anaerobes: old views and new aspects. In: Florkin M, Mason HS (eds). The Microbe, Part II, Prokaryotes and Eukaryotes. New York, NY: Cambridge University Press, 1984, 123-68.
313. Thorne SH, Williams HD. Adaptation to nutrient starvation in Rhizobium leguminosarum bv. phaseoli: analysis of survival, stress resistance, and changes in macromolecular synthesis during entry to and exit from stationary phase. J Bacteriol 1997;179:6894-901.
314. Tijhuis L, van Loosdrecht MCM, Heijnen JJ. A thermodynamically based correlation for maintenance Gibbs energy requirements in aerobic and anaerobic chemotrophic growth. Biotechnol Bioeng 1993;42:509-19.
315. Tobiason DM, Seifert HS. Genomic content of Neisseria species. J Bacteriol 2010;192:2160-8.
316. Torrella F, Morita RY. Microcultural study of bacterial size changes and microcolony and ultramicrocolony formation by heterotrophic bacteria in seawater. Appl Environ Microb 1981;41:518-27.
317. Torrella F, Morita RY. Starvation induced morphological changes, motility, and chemotaxis patterns in a psychrophilic marine vibrio. Publ Cent Natl Exploit Oceans Actes Colloq 1982;13:45-60.
318. Tran QH, Unden G. Changes in the proton potential and the cellular energetics of Escherichia coli during growth by aerobic and anaerobic respiration or by fermentation. Eur J Biochem 1998;251:538-43.
319. Troussellier M, Bouvy M, Courties C, et al. Variation of carbon content among bacterial species under starvation condition. Aquat Microb Ecol 1997;13:113-9.
320. Trucksis M, Michalski J, Deng YK, et al. The Vibrio cholerae genome contains two unique circular chromosomes. P Natl Acad Sci USA 1998;95:14464-9.
321. Umehara S, Hattori A, Inoue I, et al. Asynchrony in the growth and motility responses to environmental changes by individual bacterial cells. Biochem Bioph Res Co 2007;356: 464-9.
322. Vågbø CB, Svaasand EK, Aas PA, et al. Methylation damage to RNA induced in vivo in Escherichia coli is repaired by endogenous AlkB as part of the adaptive response. DNA Repair 2013;12:188-95.
323. Vancanneyt M, Schut F, Snauwaert C, et al. Sphingomonas alaskensis sp. nov., a dominant bacterium froma marine oligotrophic environment. Int J Syst Evol Micr 2001;51:73-9.
324. Vitousek PM, Howarth RW. Nitrogen limitation on land and in the sea. How can it occur? Biogeochemistry 1991;13:87-115.
325. Vrede K, Heldal M, Norland S, et al. Elemental composition (C, N, P) and cell volume of exponentially growing and nutrientlimited bacterioplankton. Appl Environ Microb 2002;68:2965-71.
326. Wagner JK, Setayeshgar S, Sharon LA, et al. A nutrient uptake role for acterial cell envelope extensions. P Natl Acad Sci USA 2006;103:11772-7.
327. Wagner M. Single-cell ecoPhysiology of microbes as revealed by Raman microspectroscopy or secondary ion mass spectrometry imaging. Annu Rev Microbiol 2009;63:411-29.
328. Wang G, Spivack AJ, Rutherford S, et al. Quantification of cooccurring reaction rates in deep subseafloor sediments. Geochim Cosmochim Acta 2008;72:3479-88.
329. Wang Y, Hammes F, Boon N, et al. Isolation and characterization of low nucleic acid (LNA)-content bacteria. ISME J 2009;3:889-902.
330. Watson SW, Novitsky TJ, Quinby HL, et al. Determination of bacterial number and biomass in the marine environment. Appl Environ Microb 1977;33:940-6.
331. Weber CA. Aufbau und Vegetation der Moore Norddeutschlands. Beiblatt zu den Botanischen Jahrbüchern 1907;90:19-34.
332. Wei X, Bauer WD. Starvation-induced changes in motility, chemotaxis, and flagellation of Rhizobium meliloti. Appl Environ Microb 1998;64:1708-14.
333. Weiss MS, Abele U, WeckesSer J, et al. Molecular architecture and electrostatic properties of a bacterial porin. Science 1991;254:1627-30.
334. Whitman WB, Coleman DC, Wiebe WJ. Prokaryotes: the unseen majority. P Natl Acad Sci USA 1998;95:6578-83.
335. Wikström M, Hummer G. Stoichiometry of proton translocation by respiratory complex I and its mechanistic implications. P Natl Acad Sci USA 2012;109:4431-6.
336. Wilusz CJ, Wormington M, Peltz SW. The cap-to-tail guide to mRNA turnover. Nat Rev Mol Cell Bio 2001;2:237-46.
337. Wrangstadh M, Conway PL, Kjelleberg S. The production and release of an extracellular polysaccharide during starvation of a marine Pseudomonas sp. and the effect thereof on adhesion. Arch Microbiol 1986;145:220-7.
338. Wrangstadh M, Szewzyk U, Ostling J, et al. Starvation-specific formation of a peripheral exopolysaccharide by a marine Pseudomonas sp., strain S9. Appl Environ Microb 1990;56:2065-72.
339. Wurtmann EJ, Wolin SL. RNA under attack: cellular handling of RNA damage. Crit Rev Biochem Mol 2009;44:34-49.
340. Xie S, Lipp JS, Wegener G, et al. Turnover of microbial lipids in the deep biosphere and growth of benthic archaeal populations. P Natl Acad Sci USA 2013;110:6010-4.
341. Yam EM, Tang KW. Effects of starvation on aggregate colonization and motility of marine bacteria. Aquat Microb Ecol 2007;48:207-15.
342. Yeo LY, Chang H-C, Chan PPY, et al. Microfluidic devices for bioapplications. Small 2011;7:12-48.
343. Yin H, Marshall D. Microfluidics for single cell analysis. Curr Opin Biotech 2012;23:110-9.
344. 13C NMR heterospectral correlation spectroscopy to characterize extracellular polymeric substances in biofilms produced during composting. Environ Science Technol 2011;45:9224-31.
345. Zaera F. Probing liquid/solid interfaces at the molecular level. Chem Rev 2012;112:2920-86.
346. Zambrano MM, Siegele DA, Almíron M, et al. Microbial competition: Escherichia coli mutants that take over stationary phase cultures. Science 1993;259:1757-60.
347. Zevenhuizen LP. Levels of trehalose and glycogen in Arthrobacter globiformis under conditions of nutrient starvation and osmotic stress. Anton Leuuw 1992;61:61-8.
348. Zhou XX, Wang YB, Pan YJ, et al. Differences in amino acids composition and coupling patterns between mesophilic and thermophilic proteins. Amino Acids 2008;34:25-33.
349. Zinser ER, Kolter R. Mutations enhancing amino acid catabolism confer a growth advantage in stationary phase. J Bacteriol 1999;181:5800-7.