Fingerprinting the genetic diversity of the biotin carboxylase gene (accC) in aquatic ecosystems as a potential marker for studies of carbon dioxide assimilation in the dark

Environmental Microbiology

Volumn 10, Issue 10, 2008, Pages 2527-2536

  Auguet, Jean Christophe ^a   Borrego, Carles M ^b   Bañeras, Lluís ^b   Casamayor, Emilio O ^a  

^a CENTRE D ESTUDIS AVANÇATS DE BLANES CEAB CSIC   (Spain)

^b Institut d'Ecologia Aquatica   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEAL DNA; ARCHAEAL PROTEIN; BACTERIAL DNA; BACTERIAL PROTEIN; BIOTIN CARBOXYLASE; CARBON DIOXIDE; LIGASE; PRIMER DNA;

AMINO ACID SEQUENCE; ARTICLE; CLUSTER ANALYSIS; DNA DENATURATION; DNA FINGERPRINTING; DNA SEQUENCE; ECOSYSTEM; GENETIC POLYMORPHISM; GENETICS; METABOLISM; METHODOLOGY; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYACRYLAMIDE GEL ELECTROPHORESIS; POLYMERASE CHAIN REACTION; SEQUENCE ALIGNMENT;

AMINO ACID SEQUENCE; ARCHAEAL PROTEINS; BACTERIAL PROTEINS; CARBON DIOXIDE; CARBON-NITROGEN LIGASES; CLUSTER ANALYSIS; DNA FINGERPRINTING; DNA PRIMERS; DNA, ARCHAEAL; DNA, BACTERIAL; ECOSYSTEM; ELECTROPHORESIS, POLYACRYLAMIDE GEL; MOLECULAR SEQUENCE DATA; NUCLEIC ACID DENATURATION; PHYLOGENY; POLYMERASE CHAIN REACTION; POLYMORPHISM, GENETIC; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; WATER MICROBIOLOGY;

ARCHAEA; BACTERIA (MICROORGANISMS); CRENARCHAEOTA;

EID: 51649106372     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2008.01677.x     Document Type: Article

References (46)

1. Agogué, H., Casamayor, E.O., Joux, F., Obernosterer, I., Dupuy, C., Lantoine, F., et al. (2004) Comparison of samplers for the biological characterization of the sea surface microlayer. Limnol Oceanogr Methods 2 : 213 225.
2. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. Lipman, D.J. (1990) Basic local alignment search tool. J Mol Biol 215 : 403 410.
3. Auguet, J.C. Casamayor, E.O. (2008) A hotspot for cold crenarchaeota in the neuston of high mountain lakes. Environ Microbiol 10 : 1080 1086.
4. Berg, I.A., Kockelkorn, D., Buckel, W. Fuchs, G. (2007) A 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in archaea. Science 318 : 1782 1786.
5. Bruns, A., Nübel, U., Cypionka, H. Overmann, J. (2003) Effect of signal compounds and incubation conditions on the culturability of freshwater bacterioplankton. Appl Environ Microbiol 69 : 1980 1989.
6. Calvin, M. Bassham, J.A. (1962) The Photosynthesis of Carbon Compounds. New York, USA : W.A. Benjamin Publications.
7. Casamayor, E.O., Schafer, H., Bañeras, L., Pedrós- Alió, C. Muyzer, G. (2000) Identification of and spatio-temporal differences between microbial assemblages from two neighboring sulfurous lakes: comparison by microscopy and Denaturing Gradient Gel Electrophoresis. Appl Environ Microbiol 66 : 499 508.
8. Casamayor, E.O., Mas, J. Pedrós-Alió, C. (2001a) In situ assessment on the physiological state of purple and green sulfur bacteria through the analyses of pigment and 5S rRNA content. Microb Ecol 42 : 427 437.
9. Casamayor, E.O., Muyzer, G. Pedrós-Alió, C. (2001b) Composition and temporal dynamics of planktonic archaeal assemblages from anaerobic sulfurous environments studied by 16S rDNA denaturing gradient gel electrophoresis and sequencing. Aquat Microb Ecol 25 : 237 246.
10. Casamayor, E.O., Pedrós-Alió, C., Muyzer, G. Amann, R. (2002) Microheterogeneity in 16S rDNA-defined bacterial populations from a stratified planktonic environment is related to temporal changes and to ecological adaptations. Appl Environ Microbiol 68 : 1706 1714.
11. Casamayor, E.O., Ferrera, I., Cristina, X., Borrego, C. Gasol, J.M. (2007) Flow cytometric identification and enumeration of photosynthetic sulfur bacteria and potential for ecophysiological studies at the single cell level. Environ Microbiol 9 : 1969 1985.
12. Casamitjana, X., Colomer, J., Roget, E. Serra, T. (2006) Physical limnology in Lake Banyoles. Limnetica 25 : 181 188.
13. Catalan, J., Camarero, L., Felip, M., Pla, S., Ventura, M., Buchaca, T., et al. (2006) High mountain lakes: extreme habitats and witnesses of environmental changes. Limnetica 25 : 551 584.
14. Chuakrut, S., Arai, H., Ishii, M. Igarashi, Y. (2003) Characterization of a bifunctional archaeal acyl coenzyme A carboxylase. J Bacteriol 185 : 938 947.
15. DeLong, E.F. (1992) Archaea in coastal marine environments. Proc Nat Acad Sci 89 : 5685 5689.
16. DeLong, E.F., King, L.L., Massana, R., Cittone, H., Murray, A., Schleper, C. Wakeham, S.G. (1998) Dibiphytanyl ether lipids in nonthermophilic crenarchaeotes. Appl Environ Microbiol 64 : 1133 1138.
17. Dumestre, J.F., Casamayor, E.O., Massana, R. Pedrós-Alió, C. (2002) Changes in bacterial and archaeal assemblages in an equatorial river induced by the water eutrophication of Petit Saut dam reservoir (French Guiana). Aquat Microb Ecol 26 : 209 221.
18. Francis, C.A., Beman, J.M. Kuypers, M.M.M. (2007) New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation. ISME J 1 : 19 27.
19. Fuhrman, J.A., McCallum, K. Davis, A.A. (1992) Novel major archaebacterial group from marine plankton. Nature 356 : 148 149.
20. 2 incorporation among guilds of microorganisms in lakes with oxic/anoxic interfaces and estimation of in situ specific growth rates. Microb Ecol 50 : 230 241.
21. Guerrero, R., Pedrós-Alió, C., Esteve, I. Mas, J. (1987) Communities of phototrophic sulfur bacteria in lakes of the Spanish Mediterranean region. Act Acad Aboensis 47 : 125 151.
22. Hall, T.A. (1999) BioEdit: a user-friendly biological sequence alingment editor and analysis program for Windows 95/98/NT. Nucleic Acid Symp Ser 41 : 95 98.
23. Hallam, S.J., Mincer, T.J., Schleper, C., Preston, C.M., Roberts, K., Richardson, P.M. DeLong, E.F. (2006) Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine crenarchaeota. Plos Biol 4 : 520 536.
24. Herndl, G.J., Reinthaler, T., Teira, E., van Aken, H., Veth, C., Pernthaler, A. Pernthaler, J. (2005) Contribution of Archaea to total prokaryotic production in the deep Atlantic Ocean. Appl Environ Microbiol 71 : 2303 2309.
25. Hugler, M., Krieger, R.S., Jahn, M. Fuchs, G. (2003a) Characterization of acetyl-CoA/propionyl-CoA carboxylase in Metallosphaera sedula- carboxylating enzyme in the 3-hydroxypropionate cycle for autotrophic carbon fixation. Europ J Biochem 270 : 736 744.
26. 2 fixation pathways in archaea (Crenarchaeota). Arch Microbiol 179 : 160 173.
27. Ingalls, A.E., Shah, S.R., Hansman, R.L., Aluwihare, L.I., Santos, G.M., Druffel, E.R. Pearson, A. (2006) Quantifying archaeal community autotrophy in the mesopelagic ocean using natural radiocarbon. Proc Natl Acad Sci USA 103 : 6442 6447.
28. Ishii, M., Chuakrut, S., Arai, H. Igarashi, Y. (2004) Occurrence, biochemistry and possible biotechnological application of the 3-hydroxypropionate cycle. Appl Microbiol Biotech 64 : 605 610.
29. Jensen, E.C., Schrader, H.S., Rieland, B., Thompson, T.L., Lee, K.W., Nickerson, K.W. Kokjohn, T.A. (1998) Prevalence of broad-host-range lytic bacteriophages of Sphaerotilus natans, Escherichia coli, and Pseudomonas aeruginosa. Appl Environ Microbiol 64 : 575 580.
30. Karner, M.B., DeLong, E.F. Karl, D.M. (2001) Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature 409 : 507 510.
31. Konneke, M., Bernhard, A.E., de la Torre, J.R., Walker, C.B., Waterbury, J.B. Stahl, D.A. (2005) Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437 : 543 546.
32. Kuypers, M.M.M., Blokker, P., Erbacher, J., Kinkel, H., Pancost, R.D., Schouten, S. Damsté, J.S.S. (2001) Massive expansion of marine archaea during a Mid-Cretaceous oceanic anoxic event. Science 293 : 92 95.
33. Massana, R., Murray, A., Preston, C. DeLong, E.F. (1997) Vertical distribution and phylogenetic characterization of marine planktonic Archaea in the Santa Barbara Channel. Appl Environ Microbiol 63 : 50 56.
34. Menéndez, C., Bauer, Z., Huber, H., Gad'on, N., Stetter, K.-O. Fuchs, G. (1999) Presence of Acetyl Coenzyme A (CoA) Carboxylase and Propionyl-CoA Carboxylase in autotrophic Crenarchaeota and indication for operation of a 3-Hydroxypropionate cycle in autotrophic carbon fixation. J Bacteriol 181 : 1088 1098.
35. Moss, J. Lane, M.D. (1971) Biotin-dependent enzymes. Adv Enzymol Relat Areas Mol Biol 35 : 321 442.
36. Nicol, G.W. Schleper, C. (2006) Ammonia-oxidizing Crenarchaeota: important players in the nitrogen cycle? TRENDS Microbiol 14 : 207 212.
37. Ouverney, C.C. Fuhrman, J.A. (2000) Marine planktonic Archaea take up amino acids. Appl Environ Microbiol 66 : 4829 4833.
38. Øvreas, L., Forney, L., Daae, F.L. Torsvik, V. (1997) Distribution of bacterioplankton in meromictic Lake Saelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. Appl Environ Microbiol 63 : 3367 3373.
39. Pearson, A.A.P., McNichol, A.P., Benitez-Nelson, B.-C., Hayes, J.M. Eglington, T.I. (2001) Origins of lipid biomarkers in Santa Monica Basin surface sediment: a case study using compound-specific 14C analysis. Geochem Cosmochim Acta 65 : 3123 3137.
40. Reche, I., Pulido-Villena, E., Morales-Baquero, R. Casamayor, E.O. (2005) Does ecosystem size determine aquatic bacterial richness? Ecology 86 : 1715 1722.
41. 2 by bacterial flora of water. Mikrobiologiya 33 : 610 613.
42. Samols, D., Thornton, C.G., Murtif, V.L., Kumar, G.K., Haase, F.C. Wood, H.G. (1988) Evolutionary conservation among biotin enzymes. J Biol Chem 263 : 6461 6464.
43. Schmidt, H.A., Strimmer, K., Vingron, M. von Haeseler, A. (2002) TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18 : 502 504.
44. Schouten, S., Hopmans, E.C., Pancost, R.D. Damsté, J.S.S. (2000) Widespread occurrence of structurally diverse tetraether membrane lipids: evidence for the ubiquitous presence of low-temperature relatives of hyperthermophiles. Proc Nat Acad Sci 97 : 14421 14426.
45. Thauer, R.K. (2007) Microbiology - a fifth pathway of carbon fixation. Science 318 : 1732 1733.
46. Wuchter, C., Schouten, S., Boschker, H.T.S. Damsté, J.S.S. (2003) Bicarbonate uptake by marine Crenarchaeota. FEMS Microbiol Lett 219 : 203 207.