Novel observations of Thiobacterium, a sulfur-storing Gammaproteobacterium producing gelatinous mats

ISME Journal

Volumn 4, Issue 8, 2010, Pages 1031-1043

  Grünke, Stefanie ^a,b   Lichtschlag, Anna ^b   Beer, Dirk De ^b   Kuypers, Marcel ^b   Lösekann Behrens, Tina ^c   Ramette, Alban ^b   Boetius, Antje ^a,b  

^a ALFRED WEGENER INSTITUTE FOR POLAR AND MARINE RESEARCH   (Germany)

^b MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY   (Germany)

^c STANFORD UNIVERSITY   (United States)

Author keywords

gelatinous mats; microsensor; sulfur oxidizer; Thiobacterium

Indexed keywords

GELATIN; SULFUR;

BACTERIUM; BIOGEOCHEMISTRY; DEEP WATER; GENETIC ANALYSIS; GROWTH RATE; HABITAT TYPE; HYBRIDIZATION; HYDROGEN SULFIDE; MARINE ENVIRONMENT; OXYGEN; PHYLOGENETICS; SEAFLOOR; SPECIES DIVERSITY; SPECIES OCCURRENCE; SULFUR;

ARTICLE; CLASSIFICATION; GAMMAPROTEOBACTERIA; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY; MOLECULAR GENETICS; PHYLOGENY; SEDIMENT; THIOTRICHACEAE;

GAMMAPROTEOBACTERIA; GELATIN; GEOLOGIC SEDIMENTS; MOLECULAR SEQUENCE DATA; PHYLOGENY; SULFUR; THIOTRICHACEAE; WATER MICROBIOLOGY;

BACTERIA (MICROORGANISMS); CETACEA; GAMMAPROTEOBACTERIA; THIOBACTERIUM;

EID: 77954834533     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2010.23     Document Type: Article

References (62)

1. Ahmad A, Barry JP, Nelson DC. (1999). Phylogenetic affinity of a wide, vacuolate, nitrate-accumulating Beggiatoa sp. from Monterey Canyon, California, with Thioploca spp. Appl Environ Microbiol 65: 270-277.
2. Ahmad A, Kalanetra KM, Nelson DC. (2006). Cultivated Beggiatoa spp. define the phylogenetic root of morphologically diverse, noncultured, vacuolate sulfur bacteria. Can J Microbiol 52: 591-598.
3. Amann R, Fuchs BM. (2008). Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques. Nat Rev Microbiol 6: 339-348.
4. 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.
5. Anagnostidis K. (1968). Untersuchungen uber die Salz- und Susswasser-Thiobioconosen (Sulphuretum) Griechenlands. Wissenschaftliches Jahrbuch der Physiko- Mathematischen Fakultat Aristoteles-Universitat, vol.10. Thessaloniki. pp 551-552.
6. Ashelford KE, Chuzhanova NA, Fry JC, Jones AJ, Weight- man AJ. (2005). At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies. Appl Environ Microbiol 71: 7724-7736.
7. Ashelford KE, Chuzhanova NA, Fry JC, Jones AJ, Weightman AJ. (2006). New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras. Appl Environ Microbiol 72: 5734-5741.
8. Caldwell DE, Caldwell SJ. (1974). The response of littoral communities of bacteria to variations in sulfide and thiosulfate. Abstracts Ann Meeting Am Soc Microbiol 74: 59.
9. Dahlgren TG, Wiklund H, Kallstrom B, Lundalv T, Smith CR, Glover AG. (2006). A shallow-water whale-fall experiment in the north Atlantic. Cah Biol Mar 47: 385-389.
10. 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.
11. de Beer D, Sauter E, Niemann H, Kaul N, Foucher J-P, Witte U et al. (2006). In situ fluxes and zonation of microbial activity in surface sediments of the Hakon Mosby Mud Volcano. Limnol Oceanogr 51: 1315-1331.
12. de Beer D, Schramm A, Santegoeds CM, Kuhl M. (1997). A nitrite microsensor for profiling environmental biofilms. Appl Environ Microbiol 63: 973-977.
13. Devide Z. (1952). Zwei neue farblose Schwefelbakterien: Thiogloea ruttneri n.gen., n.sp. und Thiogloea ragusina n.sp. Schweiz Z Hydrol 14: 446-455.
14. Duperron S, de Beer D, Zbinden M, Boetius A, Schipani V, Kahil N et al. (2009). Molecular characterization of bacteria associated with the trophosome and the tube of Lamellibrachia sp., a siboglinid annelid from cold seeps in the eastern Mediterranean. FEMS Microb Ecol 69: 395-409.
15. Eller G, Stubner S, Frenzel P. (2001). Group-specific 16S rRNA targeted probes for the detection of type I and type II methanotrophs by fluorescence in situ hybridisation. FEMS Microbiol Lett 198: 91-97.
16. Fjerdingstad E. (1979). Sulfur bacteria. Am Soc Test Mat p 77.
17. Fossing H, Gallardo VA, Jorgensen BB, Huttel M, Nielsen LP, Schulz H et al. (1995). Concentration and transport of nitrate by the mat-forming sulphur bacterium Thioploca. Nature 374: 713-715.
18. Girnth A-C, Grirnke S, Lichtschlag A, Felden J, Knittel K, Wenzhofer F et al. (submitted) A novel, mat-forming Thiomargarita population associated with a sulfidic fluid flow from a deep-sea mud volcano.
19. Glover AG, Kallstrom B, Smith CR, Dahlgren TG. (2005). World-wide whale worms? A new species of Osedax from the shallow north Atlantic. Proc R Soc B 272: 2587-2592.
20. Gonzalez-Toril E, Llobet-Brossa E, Casamayor EO, Amann R, Amils R. (2003). Microbial ecology of an extreme acidic environment, the Tinto River. Appl Environ Microbiol 69: 4853-4865.
21. Gugliandolo C, Maugeri TL. (1993). Chemolithotrophic, sulfur-oxidizing bacteria from a marine, shallow hydrothermal vent of Vulcano (Italy). Geomicrobiol J 11: 109-120.
22. Gulledge J, Ahmad A, Steudler PA, Pomerantz WJ, Cavanaugh CM. (2001). Family- and genus-level 16S rRNA-targeted oligonucleotide probes for ecological studies of methanotrophic bacteria. Appl Environ Microbiol 67: 4726-4733.
23. Hedoin H, Coute A, Kaiser P, Laugier R. (1996). Nature and occurrence of sulfoxidizing bacteria in Baregine developing in sulfurated thermal waters at Bareges (France). Hydrobiologia 323: 75-81.
24. Huettel M, Forster S, Kloser S, Fossing H. (1996). Vertical migration in the sediment-dwelling sulfur bacteria Thioploca spp. in overcoming diffusion limitations. Appl Environ Microbiol 62: 1863-1872.
25. Jeroschewski P, Steuckart C, Kuhl M. (1996). An ampero- metric microsensor for the determination of H2S in aquatic environments. Anal Chem 68: 4351-4357.
26. Kalanetra KM, Huston SL, Nelson DC. (2004). Novel, attached, sulfur-oxidizing bacteria at shallow hydro- thermal vents possess vacuoles not involved in respiratory nitrate accumulation. Appl Environ Microbiol 70: 7487-7496.
27. Kanagawa T, Kamagata Y, Aruga S, Kohno T, Horn M, Wagner M. (2000). Phylogenetic analysis of and oligonucleotide probe development for Eikelboom type 021N filamentous bacteria isolated from bulking activated sludge. Appl Environ Microbiol 66: 5043-5052.
28. 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.
29. Kuenen JG. (2005). Genus V. Thiobacterium (ex Janke 1924) la Riviere and Kuenen 1989b, 496VP (Effective publication: la Riviere and Kuenen 1989a, 1838). In: Brenner DJ, Krieg NR, Staley JT, Garrity GM (eds). Bergey's Manual of Systematic Bacteriology, 2nd edn. Springer: New York, NY. p 169.
30. Lackey JB, Lackey EW. (1961). The habitat and description of a new genus of sulphur bacterium. J Gen Microbiol 26: 29-39.
31. Lackey JB, Lackey EW, Morgan GB. (1965). Taxonomy and ecology of the sulfur bacteria. Florida Engineering Industrial Experimentation Station, State University of Florida, Bulletin Series No 119, Gainesville, FL 29: 1-23.
32. Lichtschlag A, Felden J, Bruchert V, Boetius A, de Beer D. (2010). Geochemical processes and chemosynthetic primary production in different thiotrophic mats of the Hakon Mosby Mud Volcano (Barents Sea) Limnol Oceanogr XX.
33. Limnol Oceanogr XX. Losekann T, Robador A, Niemann H, Knittel K, Boetius A, Dubilier N. (2008). Endosymbioses between bacteria and deep-sea siboglinid tubeworms from an Arctic cold seep (Haakon Mosby Mud Volcano, Barents Sea). Environ Microbiol 10: 3237-3254.
34. Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar et al. (2004). ARB: a software environment for sequence data. Nucleic Acids Res 32: 1363-1371.
35. 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.
36. Mills HJ, Martinez RJ, Story S, Sobecky PA. (2004). Identification of members of the metabolically active microbial populations associated with Beggiatoa species mat communities from Gulf of Mexico cold- seep sediments. Appl Environ Microbiol 70: 5447-5458.
37. Miyoshi M. (1897). Studien uber die Schwefelrasenbil- dung und die Schwefelbacterien der Thermen von Yumoto bei Nikko. J College Sci, Imp Univ, Japan, Tokyo 10: 143-173.
38. Molisch H. (1912). Neue farblose Schwefelbakterien. Zentralblatt fur Bakteriologie, Parasitenkunde, Infek- tionskrankheiten und Hygiene, Abt 2 33: 55-62.
39. Mosso MA, Sanchez MC, de la Rosa MC. (2002). Microbial diversity of the mineral water springs of Alhama de Granada Spa town. Anal Real Acad Nac Farm 68: 46-75.
40. Mufimann M, Schulz HN, Strotmann B, Kjsr T, Nielsen LP, Rossello-Mora RA et al. (2003). Phylogeny and distribution of nitrate-storing Beggiatoa spp. in coastal marine sediments. Environ Microbiol 5: 523-533.
41. 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.
42. Muyzer G, Teske A, Wirsen CO, Jannasch HW. (1995). Phylogenetic relationships of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electro- phoresis of 16S rDNA fragments. Arch Microbiol 164: 165-172.
43. Naganuma T, Ikemoto E, Sukizaki S, Tsuji Y, Hotta H. (1990). Sulfur bacteria originating from the water and organisms in a hydrothermally active area of the Mid- Okinawa Trough. J Oceanograph Soc Japan 46:111-117.
44. Narvaez-Zapata JA, Rodrfguez-Avila N, Ortega-Morales BO. (2005). Method for recovery of intact DNA for community analysis of marine intertidal microbial biofilms. Mol Biotechnol 30: 51-56.
45. Nielsen LP, Risgaard-Petersen N, Fossing H, Christensen PB, Sayama M. (2008). Electric currents in marine sediment. The 12th International Symposium on Microbial Ecology-ISME12: Microbial Diversity- Sustaining the Blue Planet Cairns, Australia.
46. Nussbaumer AD, Fisher CR, Bright M. (2006). Horizontal endosymbiont transmission in hydrothermal vent tubeworms. Nature 441: 345-348.
47. Peccia J, Marchand EA, Silverstein J, Hernandez M. (2000). Development and application of small-subunit rRNA probes for assessment of selected Thiobacillus species and members of the genus Acidiphilium. Appl Environ Microbiol 66: 3065-3072.
48. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J et al. (2007). SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35: 7188-7196.
49. Ravenschlag K, Sahm K, Amann R. (2001). Quantitative molecular analysis of the microbial community in marine arctic sediments (Svalbard). Appl Environ Microbiol 67: 387-395.
50. Revsbech NP, Ward DM. (1983). Oxygen microelectrode that is insensitive to medium chemical composition: use in an acid microbial mat dominated by Cyanidium caldarium. Appl Environ Microbiol 45: 755-759.
51. Sayama M, Risgaard-Petersen N, Nielsen LP, Fossing H, Christensen PB. (2005). Impact of bacterial NO3 transport on sediment biogeochemistry. Appl Environ Microbiol 71: 7575-7577.
52. Scheminzky F, Klas Z, Job C. (1972). Uber das Vorkommen von Thiobacterium bovista in Thermalwassern. Int Revue ges Hydrobiol 57: 801-813.
53. Schulz HN. (2006). The Genus Thiomargarita. In: Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E (eds). The Prokaryotes, 3rd edn. Springer: New York. pp 1156-1163.
54. Seki H, Naganuma T. (1989). Growth characteristics of Thiobacterium sp. from the plume of hydrothermal vents of the North Fiji Basin. Mar Ecol Prog Ser 54: 199-202.
55. Snaidr J, Amann R, Huber I, Ludwig W, Schleifer KH. (1997). Phylogenetic analysis and in situ identification of bacteria in activated sludge. Appl Environ Microbiol 63: 2884-2896.
56. Teske A, Nelson DC. (2006). The Genera Beggiatoa and Thioploca. In: Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E (eds). The Prokaryotes, 3rd edn. Springer: New York. pp 784-810.
57. Teske A, Ramsing NB, Kuver J, Fossing H. (1995). Phylogeny of Thioploca and related filamentous sulfide-oxidizing bacteria. Syst Appl Microbiol 18: 517-526.
58. Vouk V, Klas Z, Scheminzky F. (1967). Krenobiologische Untersuchungen an der Gasteiner Therme I. Die Schwefelbakterien des Allophan-Hydrogels. Sitz ber Osterr Akad Wiss, Math nat Kl, Abt 1176: 21-43.
59. Wagner M, Amann R, Kampfer P, Assmus B, Hartmann A, Hutzler P et al. (1994). Identification and in situ detection of gram-negative filamentous bacteria in activated sludge. Syst Appl Microbiol 17: 405-417.
60. Wallner G, Amann R, Beisker W. (1993). Optimizing fluorescent in situ hybridization with rRNA-targeted oligonucleotide probes for flow cytometric identification of microorganisms. Cytometry 14: 136-143. (Pubitemid 23042736)
61. Wang Q, Garrity GM, Tiedje JM, Cole JR. (2007). Na'ive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73: 5261-5267.
62. Yang E, Schaperdoth I, Albrecht H, Freeman KH, Macalady JL. (2008). Geomicrobiology and hopanoid content of sulfidic subsurface vent biofilms, Little Salt Spring, Florida. Abstr Eos Trans AGU, 89 (53), Fall Meet Suppl, abstr B53C-0517.