Genes Associated with the Peculiar Phenotypes of the Aerobic Anoxygenic Phototrophs

Advances in Botanical Research

Volumn 66, Issue , 2013, Pages 327-358

  Yurkov, Vladimir ^a   Hughes, Elizabeth ^a  

^a UNIVERSITY OF MANITOBA   (Canada)

Author keywords

Aerobic Anoxygenic Phototrophs; Bacteria; Phenotypes

Indexed keywords

EID: 84875179352     PISSN: 00652296     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-12-397923-0.00011-4     Document Type: Chapter

References (75)

1. Beatty J.T. On the natural selection and evolution of the aerobic phototrophic bacteria. Discoveries in photosynthesis 2005, 1099-1104. Springer. Govindjee, J.T. Beatty, H. Gest, J.F. Allen (Eds.).
2. Biebl H., Tindall B.J., Pukall R., Lünsdorf H., Allgaier M., Wagner-Döbler I. Hoeflea phototrophica sp. nov., a novel alphaproteobacterium that forms bacteriochlorophyll a. International Journal of Systematic and Evolutionary Microbiology 2006, 56:821-826.
3. Boldareva E.N., Tourova T.P., Kolganova T.V., Moskalenko A.A., Makhneva Z.K., Gorlenko V.M. Roseococcus suduntuyensis sp. nov., a new aerobic bacteriochlorophyll a-containing bacterium isolated from a low-mineralized soda Lake of Eastern Siberia. Microbiology 2009, 78(1):92-101.
4. Cho J.C., Stapels M.D., Morris R.M., Vergin M.S., Schwalbach M.S., Givan S.A., et al. Polyphyletic photosynthetic reaction centre genes in oligotrophic marine gammaproteobacteria. Environmental Microbiology 2007, 9:1456-1463.
5. Cottrell M.T., Ras J., Kirchman D. Bacteriochlorophyll and community structure of aerobic anoxygenic phototrophic bacteria in a particle-rich estuary. International Society of Microbial Ecology Journal: Multidisciplinary Journal of Microbial Ecology 2010, 4:945-954.
6. Csotonyi J., Stackebrandt E., Swiderski J., Schumann P., Yurkov V. Chromocurvus halotolerans gen. nov., sp. nov., a gammaproteobacterial obligately aerobic anoxygenic phototroph, isolated from a Canadian hypersaline spring. Archives of Microbiology 2011, 193(8):573-582.
7. Csotonyi J., Stackebrandt E., Swiderski J., Schumann P., Yurkov V. An alphaproteobacterium capable of both aerobic and anaerobic anoxygenic photosynthesis but incapable of photoautotrophy: Charonomicrobium ambiphototrophicum, gen. nov., sp. nov. Photosynthesis Research 2011, 107:257-268.
8. Csotonyi J.T., Swiderski J., Stackebrandt E., Yurkov V. A new environment for aerobic anoxygenic phototrophic bacteria: biological soil crusts. Environmental Microbiology Reports 2010, 2(5):651-656.
9. Denner E., Vybiral D., KoblíŽek M., Busse H.J., Velimirov B. Erythrobacter citreus sp. nov., a yellow pigmented bacterium that lacks bacteriochlorophyll a, isolated from the western Mediterranean Sea. International Journal of Systematic and Evolutionary Microbiology 2002, 52:1655-1661.
10. Eiler A., Beier S., Säwström C., Karlsson J., Bertilsson S. High ratio of bacteriochlorophyll biosynthesis genes to chlorophyll biosynthesis genes in bacteria of humic lakes. Applied and Environmental Microbiology 2009, 75(22):7221-7228.
11. Feng F., Jiao N., Du H., Zeng Y. Phylogenetic analysis of aerobic anoxygenic phototrophic bacteria and their relatives based on farnesyl pyrophosphate synthase gene. Acta Oceanologica Sinica 2010, 29(5):82-89.
12. 2. Microbial Biotechnology 2011, 4(1):74-81.
13. Fürch T., Preusse M., Tomasch J., Zech H., Wagner-Döbler I., Rabus R., et al. Metabolic fluxes in the central carbon metabolism of Dinoroseobacter shibae and Phaeobacter gallaeciensis, two members of the marine Roseobacter clade. BioMed Central Microbiology 2009, 9:209.
14. Hügler M., Sievert S.M. Beyond the Calvin cycle: autotrophic carbon fixation in the ocean. Annual Review of Marine Science 2011, 3:261-289.
15. Igarashi N., Harada J., Nagashima S., Matsuura K., Shimada K., Nagashima K.V.P. Horizontal transfer of the photosynthesis gene cluster and operon rearrangement in purple bacteria. Journal of Molecular Evolution 2001, 52:333-341.
16. Ivanova E.P., Bowmanc J.P., Lysenkod A.M., Zhukovae N.V., Gorshkovab N.M., Kuznetsovab T.A., et al. Erythrobacter vulgaris sp. nov., a novel organism isolated from the marine invertebrates. Systematic and Applied Microbiology 2005, 28:123-130.
17. Jaschke P.R., Hardjasa A., Digby E.L., Hunter C.N., Beatty J.T. A BchD (Mg-chelatase) mutant of Rhodobacter sphaeroides synthesizes zinc-bacteriochlorophyll through novel zinc-containing intermediates. Journal of Biological Chemistry 2011, 286:20313-20322.
18. Jiang H., Dong H., Yu B., Lv G., Deng S., Wu Y., et al. Abundance and diversity of aerobic anoxygenic phototrophic bacteria in saline lakes on the Tibetan plateau. FEMS Microbiology Ecology 2009, 67:268-278.
19. Jiao N., Zhang R., Zheng Q. Coexistence of two different photosynthetic operons in Citromicrobium bathyomarinum JL354 as revealed by whole-genome sequencing. Journal of Bacteriology 2010, 192(4):1169-1170.
20. Jiao N.Z., Zhang Y., Zeng Y.H., Hong N., Liu R.L., Chen F., Wang P.X. Distinct distribution pattern of abundance and diversity of aerobic anoxygenic phototrophic bacteria in the global ocean. Environmental Microbiology 2007, 9:3091-3099.
21. Jung Y.T., Park S., Oh T.K., Yoon J.H. Erythrobacter marinus sp. nov., isolated from seawater of the Yellow Sea in Korea. International Journal of Systematic and Evolutionary Microbiology 2011, http://dx.doi.org/10.1099/ijs.0.034702-0.
22. Kim B.C., Park J.R., Bae J.W., Rhee S.K., Kim K.H., Oh J.W., et al. Stappia marina sp. nov., a marine bacterium isolated from the Yellow Sea. International Journal of Systematic and Evolutionary Microbiology 2006, 56:75-79.
23. Klassen J. Pathway evolution by horizontal transfer and positive selection is accommodated by relaxed negative selection upon upstream pathway genes in purple bacterial carotenoid biosynthesis. Journal of Bacteriology 2009, 191(24):7500-7508.
24. KoblíŽek M., JanouŠkovec J.J., Oborník M., Johnson J.H., Ferriera S., Falkowski P.G. Genome sequence of the marine photoheterotrophic bacterium erythrobacter sp. strain NAP1. Journal of Bacteriology 2011, 193(20):5881-5882.
25. Kortluke C., Breese K., Gad'on N., Labahn A., Drews G. Structure of the puf operon of the obligately aerobic, bacteriochlorophyll a-containing bacterium Roseobacter denitrificans OCh114 and its expression in a Rhodobacter capsulatus puf puc deletion mutant. Journal of Bacteriology 1997, 179:5247-5258.
26. Labrenz M., Lawson P.A., Tindall B.J., Hirsch P. Roseibaca ekhonensis gen. nov., sp. nov., an alkilitolerant and aerobic bacteriochlorophyll a-producing alphaproteobacterium from hypersaline Ekho Lake. International Journal of Systematic and Evolutionary Microbiology 2009, 59:1935-1940.
27. Lee Y.S., Lee D.H., Kahng H.Y., Kim E.M., Jung J.S. Erythrobacter gangjinensis sp. nov., a marine bacterium isolated from seawater. International Journal of Systematic and Evolutionary Microbiology 2010, 60:1413-1417.
28. Lehours A.-C., Cottrell M.T., Dahan O., Kirchman D.L., Jeanthon C. Summer distribution and diversity of aerobic anoxygenic phototrophic bacteria in the Mediterranean Sea in relation to environmental variables. FEMS Microbiology Ecology 2010, 74:397-409.
29. Liebetanz R., Hornberger U., Drews G. Organization of the genes coding for the reaction-centre L and M subunits and B870 antenna polypeptides α and β from the aerobic photosynthetic bacterium Erythrobacter species OCh114. Molecular Microbiology 1991, 5:1459-1468.
30. Liotenberg S., Steunou A.S., Picaud M., Reiss-Husson F., Astier C., Ouchane S. Organization and expression of photosynthesis genes and operons in anoxygenic photosynthetic proteobacteria. Environmental Microbiology 2008, 10:2267-2276.
31. Marrs B. Mobilization of the genes for photosynthesis from Rhodopseudomonas capsulata by a promiscuous plasmid. Journal of Bacteriology 1981, 146:1003-1012.
32. Oh H.-M., Giovannoni S.J., Ferriera S., Johnson J., Cho J.-C. Complete genome sequence of Erythrobacter litoralis HTCC2594. Journal of Bacteriology 2009, 191(7):2419-2420.
33. Ponnampalam S.N., Elsen S., Bauer C.E. Aerobic repression of the Rhodobacter capsulatus bchC promoter involves cooperative interactions between crtJ bound to neighbouring palindromes. Journal of Biological Chemistry 1998, 273(46):30757-30761.
34. Rathgeber C., Alric J., Hughes E., Vermeglio A., Yurkov V. The photosynthetic apparatus and photoinduced electron transfer in the aerobic phototrophic bacteria Roseicyclus mahoneyensis and Porphyrobacter meromictius. Photosynthesis Research 2012, 110(3):193-203.
35. Rathgeber C., Beatty J.T., Yurkov V. Aerobic phototrophic bacteria: new evidence for the diversity, ecological importance and applied potential of this previously overlooked group. Photosynthesis Research 2004, 81:113-128.
36. Rathgeber C., Yurkova N., Stackebrandt E., Schumann P., Beatty J.T., Yurkov V. Roseicyclus mahoneyensis gen nov., sp. nov., an aerobic phototrophic bacterium isolated from a meromictic lake. International Journal of Systematic and Evolutionary Microbiology 2005, 55:1597-1603.
37. Rathgeber C., Yurkova N., Stackebrandt E., Schumann P., Humphrey E., Beatty J.T., et al. Porphyrobacter meromictius sp. nov., an appendaged bacterium, that produces bacteriochlorophyll a. Current Microbiology 2007, 55:356-361.
38. Raymond J., Blankenship R.E. Biosynthetic pathways, gene replacement and the antiquity of life. Geobiology 2004, 22:199-203.
39. Salka I., Cuperova Z., Masin M., Koblizek M., Grossart H.-P. Rhodoferax-related pufM gene cluster dominates the aerobic anoxygenic phototrophic communities in German freshwater lakes. Environmental Microbiology 2011, 13(11):2865-2875.
40. Sato-Takabe Y., Hamasaki K., Suzuki K. Photosynthetic characteristics of marine aerobic anoxygenic bacteria Roseobacter and Erythrobacter strains. Archives of Microbiology 2011, http://dx.doi.org/10.1007/s00203-011-0761-2.
41. Shiba T. Roseobacter litoralis gen. nov., sp. nov., and Roseobacter denitrificans sp. nov., aerobic pink-pigmented bacteria which contain bacteriochlorophyll a. Systematic and Applied Microbiology 1991, 14(2):140-145.
42. Shiba T., Simidu U. Erythrobacter longus gen. nov., sp. nov., an aerobic bacterium which contains bacteriochlorophyll a. International Journal of Systematic Bacteriology 1982, 32:211-217.
43. Shiba T., Simidu U., Taga N. Distribution of aerobic bacteria which contain bacteriochlorophyll a. Applied and Environmental Microbiology 1979, 38:43-45.
44. Sieracki M.E., Gilg I.C., Their E.C., Poulton N.J., Goericke R. Distribution of planktonic aerobic photoheterotrophic bacteria in the northwest Atlantic. Limnology and Oceanography 2006, 51:38-46.
45. Spring S., Lunsdorf H., Fuchs B.M., Tindall B.J. The photosynthetic apparatus and its regulation in the aerobic gammaproteobacterium Congregibacter litoralis gen. nov., sp. nov. PLoS One 2009, 4(3):e4866.
46. Swingley W.D., Sadekar S., Mastrian S.D., Matthies H.J., Hao J., Ramos H., et al. The complete genome sequence of Roseobacter denitrificans reveals a mixotrophic rather than photosynthetic metabolism. Journal of Bacteriology 2007, 189:683-690.
47. Tang K.H., Feng X., Tang Y.J., Blankenship R.E. Carbohydrate metabolism and carbon fixation in Roseobacter denitrificans Och114. PLoS One 2009, 4(10):e7233.
48. Tang K.-H., Tang Y., Blankenship R.E. Carbon metabolic pathways in phototrophic bacteria and their broader evolutionary implications. Frontiers in Microbiology 2011, 2(165). http://dx.doi.org/10.3389/fmicb.2011.00165.
49. Tang K., Zong R., Zhang F., Xiao N., Jiao N. Characterization of the photosynthetic apparatus and proteome of Roseobacter denitrificans. Current Microbiology 2010, 60:124-133.
50. Venkata Ramana V., Sasikala C., Takaichi S., Ramana C.V. Roseomonas aestuarii sp. nov., a bacteriochlorophyll-a containing alphaproteobacterium isolated from an estuarine habitat of India. Systematic and Applied Microbiology 2010, 33:198-203.
51. Wakao N., Yokoi N., Isoyama N., Hiraishi A., Shimada K., Kobayashi M., et al. Discovery of natural photosynthesis using Zn-containing bacteriochlorophyll in an aerobic bacterium Acidiphilium rubrum. Plant Cell Physiology 1996, 37:889-896.
52. Woese C.R. Bacterial evolution. Microbiology Reviews 1987, 51:221-271.
53. Wu H.X., Lai P.Y., Lee O.O., Zhou X.J., Miao L., Wang H., et al. Erythrobacter pelagi sp. nov., a member of the family Erythrobacteraceae isolated from the Red Sea. International Journal of Systematic and Evolutionary Microbiology 2012, 62:1348-1353.
54. Xu M., Xin Y., Yu Y., Zhang J., Zhou Y., Liu H., et al. Erythrobacter nanhaisediminis sp. nov., isolated from marine sediment of the South China Sea. International Journal of Systematic and Evolutionary Microbiology 2010, 60:2215-2220.
55. Yoon J.-H., Kang K.H., Oh T.K., Park Y.H. Erythrobacter aquimaris sp. nov., isolated from sea water of a tidal flat of the Yellow Sea in Korea. International Journal of Systematic and Evolutionary Microbiology 2004, 54:1981-1985.
56. Yoon J.-H., Kang K.H., Yeo S.H., Oh T.-K. Erythrobacter luteolus sp. nov., isolated from a tidal flat of the Yellow Sea in Korea. International Journal of Systematic and Evolutionary Microbiology 2005, 55:1167-1170.
57. Yoon J.-H., Kim H., Kim I.G., Kang K.H., Park Y.H. Erythrobacter flavus sp. nov., a slight halophile from the East Sea in Korea. International Journal of Systematic and Evolutionary Microbiology 2003, 53:1169-1174.
58. Yoon B.J., Lee D.H., Oh D.C. Erythrobacter jejuensis 1 sp. nov., isolated from seawater. International Journal of Systematic and Evolutionary Microbiology 2012, 10.1099/ijs.0.038349-0.
59. Yoon J.-H., Oh T.-K., Park Y.H. Erythrobacter seohaensis sp. nov. and Erythrobacter gaetbuli sp. nov., isolated from a tidal flat of the Yellow Sea in Korea. International Journal of Systematic and Evolutionary Microbiology 2005, 55:71-75.
60. Yurkov, V. (1990). Academy of Sciences, Ph.D. thesis. Moscow, Russia.
61. Yurkov V., Beatty J.T. Aerobic anoxygenic phototrophic bacteria. Microbiology and Molecular Biology Reviews 1998, 62:695-724.
62. Yurkov V., Csotonyi J. New light on aerobic anoxygenic photosynthesis. The purple phototrophic bacteria 2009, 31-55. Springer Science + Business Media B.V. C. Neil Hunter, F. Daldal, M.C. Thurnauer, J.T. Beatty (Eds.).
63. Yurkov V.V., Gorlenko V.M. Erythrobacter sibiricus sp. nov., a new freshwater aerobic bacterial species containing bacteriochlorophyll a. Microbiology (New York) 1990, 59(1):120-126.
64. Yurkov V.V., Gorlenko V.M. A new genus of freshwater aerobic bacteriochlorophyll a-containing bacteria, Roseococcus gen. nov. Microbiology (New York) 1992, 60(5):902-907.
65. Yurkov V.V., Gorlenko V.M. New species of aerobic bacteria from the genus Erythromicrobium containing bacteriochlorophyll a. Microbiology (New York) 1992, 61(2):248-255.
66. Yurkov V.V., Gorlenko V.M., Kompantseva E.I. A new type of freshwater aerobic orange colored bacterium Erythromicrobium gen. nov., containing bacteriochlorophyll a. Microbiology (New York) 1993, 61(2):256-260.
67. Yurkov V., Krieger S., Stackebrandt E., Beatty J.T. Citromicrobium bathyomarinum, a novel aerobic bacterium isolated from deep-sea hydrothermal vent plume waters that contains photosynthetic pigment-protein complexes. Journal of Bacteriology 1999, 181:4517-4525.
68. Yurkov V.V., Lysenko A.M., Gorlenko V.M. Hybridization analysis of the classification of bacteriochlorophyll a-containing freshwater aerobic bacteria. Microbiology (New York) 1991, 60(3):518-523.
69. Yurkov V., Stackebrandt E., Buss O., Verméglio A., Gorlenko V., Beatty J.T. Reorganization of the genus Erythromicrobium: description of " Erythromicrobium sibiricum" as Sandaracinobacter sibiricus gen. nov., sp. nov., and of " Erythromicrobium ursincola" as Erythromonas ursincola gen. nov., sp. nov. International Journal of Systematic Bacteriology 1997, 47:1172-1178.
70. Yurkov V., Stackebrandt E., Holmes A., Fuerst J.A., Hugenholtz P., Golecki J., et al. Phylogenetic positions of novel aerobic, bacteriochlorophyll a-containing bacteria and description of Roseococcus thiosulfatophilus gen. nov., sp. nov., Erythromicrobium ramosum gen nov., sp. nov., and Erythrobacter litoralis sp. nov. International Journal of Systematic Bacteriology 1994, 44:427-434.
71. Yurkov V., Van Germeden H. Impact of light/dark regimen on growth rate, biomass formation and bacteriochlorophyll synthesis in Erythromicrobium hydrolyticum. Archives of Microbiology 1993, 159:84-89.
72. Yutin N., Suzuki M.T., Rosenberg M., Rotem D., Madigan M.T., Suling J., et al. BchY-based degenerate primers target all types of anoxygenic photosynthetic bacteria in a single PCR. Applied and Environmental Microbiology 2009, 75(23):7556-7559.
73. Yu Y., Yan S.L., Li H.R., Zhang X.H. Roseicitreum antarcticum gen. nov., sp. nov., an aerobic bacteriochlorophyll a-containing alphaproteobacterium isolated from Antarctic sandy intertidal sediment. International Journal of Systematic and Evolutionary Microbiology 2011, 61:2173-2179.
74. Zeng Y., Shen W., Jiao N. Genetic diversity of aerobic anoxygenic photosynthetic bacteria in open ocean surface water and upper twilight zones. Marine Biology 2009, 156:425-437.
75. Zheng Q., Zhang R., KoblíŽek M., Boldareva E.N., Yurkov V., Yan S., et al. Diverse arrangement of photosynthetic gene clusters in aerobic anoxygenic phototrophic bacteria. PLoS One 2011, 6(9):e25050. http://dx.doi.org/10.1371/journal.pone.0025050.