Diversity of Freshwater Thioploca Species and Their Specific Association with Filamentous Bacteria of the Phylum Chloroflexi

Microbial Ecology

Volumn 62, Issue 4, 2011, Pages 753-764

  Nemoto, Fumiko ^a   Kojima, Hisaya ^a   Fukui, Manabu ^a  

^a HOKKAIDO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; FRESH WATER; RNA 16S; RNA 23S;

ARTICLE; CHLOROFLEXI; CLASSIFICATION; DNA SEQUENCE; GENETICS; JAPAN; LAKE; MICROBIOLOGY; PHYLOGENY; PHYSIOLOGY; THIOTRICHACEAE;

CHLOROFLEXI; DNA, BACTERIAL; FRESH WATER; JAPAN; LAKES; PHYLOGENY; RNA, RIBOSOMAL, 16S; RNA, RIBOSOMAL, 23S; SEQUENCE ANALYSIS, DNA; THIOTRICHACEAE; WATER MICROBIOLOGY;

BACTERIA (MICROORGANISMS); CHLOROFLEXI; CHLOROFLEXI (CLASS); THIOPLOCA;

EID: 80255132918     PISSN: 00953628     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00248-011-9916-6     Document Type: Article

References (50)

1. Amann RI, Binder BJ, Olson RJ, Chisholm SW, Devereux R, Stahl DA (1990) Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl Environ Microbiol 56: 1919-1925.
2. Amann RI, Krumholz L, Stahl DA (1990) Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. J Bacteriol 172: 762-770.
3. Björnsson L, Hugenholtz P, Tyson GW, Blackall LL (2002) Filamentous Chloroflexi (green non-sulfur bacteria) are abundant in wastewater treatment processes with biological nutrient removal. Microbiol 148: 2309-2318.
4. Brock J, Schulz-Vogt HN (2011) Sulfide induces phosphate release from polyphosphate in cultures of a marine Beggiatoa strain. ISME J 5: 497-506.
5. Chávez FP, Lünsdorf H, Jerez CA (2004) Growth of polychlorinated-biphenyl-degrading bacteria in the presence of biphenyl and chlorobiphenyls generates oxidative stress and massive accumulation of inorganic polyphosphate. Appl Environ Microbiol 70: 3064-3072.
6. Chikita K, Hattori M, Hagiwara E (1985) A field study on river-induced currents-an intermountain lake, Lake Okotanpe, Hokkaido. Jpn J Limnol 46: 256-267.
7. Daims H, Bruhl A, Amann R, Schleifer KH, Wagner M (1999) The domain-specific probe EUB338 is insufficient for the detection of all Bacteria: development and evaluation of a more comprehensive probe set. Syst Appl Microbiol 22: 434-444.
8. Fossing H, Gallardo VA, Jørgensen BB, Hüttel M, Nielsen LP, Schulz H, Canfield DE, Forster S, Glud RN, Gundersen JK, Küver J, Ramsing NB, Teske A, Thamdrup B, Ulloa O (1995) Concentration and transport of nitrate by the mat-forming sulphur bacterium Thioploca. Nature 374: 713-715.
9. Fukui M, Teske A, Aßmus B, Muyzer G, Widdel F (1999) Physiology, phylogenetic relationships, and ecology of filamentous sulfate-reducing bacteria (genus Desulfonema). Arch Microbiol 172: 193-203.
10. Gich F, Garcia-Gil J, Overmann J (2001) Previously unknown and phylogenetically diverse members of the green nonsulfur bacteria are indigenous to freshwater lakes. Arch Microbiol 177: 1-10.
11. Girnth AC, Grünke LA, Felden J, Knittel K, Wenzhöfer F, de Beer D, Boetius A (2010) A novel, mat-forming Thiomargarita population associated with a sulfidic fluid flow from a deep-sea mud volcano. Environ Microbiol 13: 495-505.
12. Günther S, Trutnau M, Kleinsteuber S, Hause G, Bley T, Röske I, Harms H, Müller S (2009) Dynamics of polyphosphate-accumulating bacteria in wastewater treatment plant microbial communities detected via DAPI (4', 6'-diamidino-2-phenylindole) and tetracycline labeling. Appl Environ Microbiol 75: 2111-2121.
13. Hahn MW, Lünsdorf H, Wu Q, Schauer M, Höfle MG, Boenigk J, Stadler P (2003) Isolation of novel ultramicrobacteria classified as Actinobacteria from five freshwater habitats in Europe and Asia. Appl Environ Microbiol 69: 1442-1451.
14. Holmkvist L, Arning ET, Küster-Heins K, Vandieken V, Peckmann J, Zabel M, Jørgensen BB (2010) Phosphate geochemistry, mineralization processes, and Thioploca distribution in shelf sediments off central Chile. Marine Geol 277: 61-72.
15. Høgslund S, Nielsen JL, Nielsen LP (2010) Distribution, ecology and molecular identification of Thioploca from Danish brackish water sediments. FEMS Microbiol Ecol 73: 110-120.
16. Høgslund S, Revsbech NP, Kuenen JG, Jørgensen BB, Gallardo VA, van de Vossenberg J, Nielsen JL, Holmkvist L, Arning ET, Nielsen LP (2009) Physiology and behaviour of marine Thioploca. ISME J 3: 647-657.
17. Jaspers E, Overmann J (2004) Ecological significance of microdiversity: identical 16S rRNA gene sequences can be found in bacteria with highly divergent genomes and ecophysiologies. Appl Environ Microbiol 70: 4831-4839.
18. Jørgensen BB (1977) Distribution of colorless sulfur bacteria (Beggiatoa spp.) in coastal marine sediment. Mar Biol 41: 19-28.
19. Jørgensen BB, Gallardo VA (1999) Thioploca spp.: filamentous sulfur bacteria with nitrate vacuoles. FEMS Microbiol Ecol 28: 301-313.
20. Kojima H, Koizumi Y, Fukui M (2006) Community structure of bacteria associated with sheaths of freshwater and brackish Thioploca species. Microb Ecol 52: 765-773.
21. Kojima H, Nakajima T, Fukui M (2007) Carbon source utilization and accumulation of respiration-related substances by freshwater Thioploca species. FEMS Microbiol Ecol 59: 23-31.
22. Kojima H, Teske A, Fukui M (2003) Morphological and phylogenetic characterizations of freshwater Thioploca species from Lake Biwa, Japan, and Lake Constance, Germany. Appl Environ Microbiol 69: 390-398.
23. Kornberg A, Rao NN, Ault-Riché D (1999) Inorganic polyphosphate: a molecule of many functions. Annu Rev Biochem 68: 89-125.
24. Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, New York, pp 115-147.
25. Manz W, Amann R, Ludwig W, Vancanneyt M, Schleifer KH (1996) Application of a suite of 16S rRNA specific oligonucleotides designed to investigate bacteria of the phylum Cytophaga-Flavobacter-Bacteroides in the natural environment. Microbiology 142: 1097-1106.
26. Manz W, Amann R, Ludwig W, Wagner M, Schleifer KH (1992) Phylogenetic oligodeoxynucleotide probes for the major subclasses of Proteobacteria: problems and solutions. Syst Appl Microbiol 15: 593-600.
27. Meyer B, Küver J (2007) Molecular analysis of the diversity of sulfate-reducing and sulfur-oxidizing prokaryotes in the environment, using aprA as functional marker gene. Appl Environ Microbiol 73: 7664-7679.
28. Moriarty TF, Mullan A, McGrath JW, Quinn JP, Elborn JS, Tunney MM (2006) Effect of reduced pH on inorganic polyphosphate accumulation by Burkholderia cepacia complex isolates. Lett Appl Microbiol 42: 617-623.
29. Muyzer G, de Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59: 695-700.
30. Mußmann M, Hu FZ, Richter M, de Beer D, Preisler A, Jørgensen BB, Huntemann M, Glöckner FO, Amann R, Koopman WJH, Lasken RS, Janto B, Hogg J, Stoodley P, Boissy R, Ehrlich GD (2007) Insights into the genome of large sulfur bacteria revealed by analysis of single filaments. PLoS Biol 5: 1923-1937.
31. Nishino M, Fukui M, Nakajima T (1998) Dense mats of Thioploca, gliding filamentous sulfur-oxidizing bacteria in Lake Biwa, central Japan. Water Res 32: 953-957.
32. Olson FCW (1950) Quantitative estimates of filamentous algae. Trans Amer Microsc Soc 59: 272-279.
33. Otte S, Kuenen JG, Nielsen LP, Paerl HW, Zopfi J, Schulz HN, Teske A, Strotmann B, Gallardo VA, Jørgensen BB (1999) Nitrogen, carbon and sulfur metabolism in natural Thioploca samples. Appl Environ Microbiol 65: 3148-3157.
34. Petri R, Podgorsek L, Imhoff JF (2001) Phylogeny and distribution of the soxB gene among thiosulfate-oxidizing bacteria. FEMS Microbiol Lett 197: 171-178.
35. Rabus R, Fukui M, Wilkes H, Widdel F (1996) Degradative capacities and 16S rRNA-targeted whole-cell hybridization of sulfate-reducing bacteria in an anaerobic enrichment culture utilizing alkylbenzenes from crude oil. Appl Environ Microbiol 62: 3605-3613.
36. Sagi T (1966) Determination of ammonia in the sea water by the indophenol method and its application to the coastal and offshore waters. Oceanogr Mag 18: 43-51.
37. Sahl JW, Gary MO, Harris JK, Spear JR (2011) A comparative molecular analysis of water-filled limestone sinkholes in north-eastern Mexico. Environ Microbiol 13: 226-240.
38. Salman V, Amann R, Girnth AC, Polerecky L, Bailey JV, Høgslund S, Jessen G, Pantoja S, Schulz-Vogt HN (2011) A single-cell sequencing approach to the classification of large, vacuolated sulfur bacteria. System Appl Microbiol 34: 243-259.
39. Schulz HN, Schulz HD (2005) Large sulfur bacteria and the formation of phosphorite. Science 307: 416-418.
40. Stahl DA, Amann R (1991) Development and application of nucleic acid probes. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, New York, pp 205-248.
41. Takeda M, Suzuki I, Koizumi J (2004) Balneomonas flocculans gen. nov., sp. nov., a new cellulose-producing member of the α-2 subclass of Proteobacteria. System Appl Microbiol 27: 139-145.
42. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4. 0. Mol Biol Evol 24: 1596-1599.
43. Tamura H, Goto K, Yotsuyanagi T, Nagayama M (1974) Spectrophotomeric determination of iron(II) with 1, 10-phenanthroline in the presence of large amount of iron(III). Talanta 21: 314-318.
44. Teske A, Jørgensen BB, Gallardo VA (2009) Filamentous bacteria inhabiting the sheaths of marine Thioploca spp. on the Chilean continental shelf. FEMS Microbiol Ecol 68: 164-172.
45. Teske A, Ramsing NB, Küver J, Fossing H (1995) Phylogeny of Thioploca and related filamentous sulfide-oxidizing bacteria. System Appl Microbiol 18: 517-526.
46. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24: 4876-4882.
47. Yamada T, Imachi H, Ohashi A, Harada H, Hanada S, Kamagata Y, Sekiguchi Y (2007) Bellilinea caldifistulae gen. nov., sp. nov. and Longilinea arvoryzae gen. nov., sp. nov., strictly anaerobic, filamentous bacteria of the phylum Chloroflexi isolated from methanogenic propionate-degrading consortia. Int J Syst Evol Microbiol 57: 2299-2306.
48. Yamada T, Sekiguchi Y, Hanada S, Imachi H, Akiyoshi O, Harada H, Kamagata Y (2006) Anaerolinea thermolimosa sp. nov., Levilinea saccharolytica gen. nov., sp. nov. and Leptolinea tardivitalis gen. nov., sp. nov., novel filamentous anaerobes, and description of the new classes Anaerolineae classis nov. and Caldilineae classis nov. in the bacterial phylum Chloroflexi. Int J Syst Evol Microbiol 56: 1331-1340.
49. Ward DM, Ferris MJ, Nold SC, Bateson MM (1998) A natural view of microbial biodiversity within hot spring cyanobacterial mat communities. Microbiol Mol Biol Rev 62: 1353-1370.
50. Wirsen CO, Brinkhoff T, Küver J, Muyzer G, Molyneaux S, Jannasch HW (1998) Comparison of a new Thiomicrospira strain from the Mid-Atlantic Ridge with known hydrothermal vent isolates. Appl Environ Microbiol 64: 4057-4059.