Phylogenetic diversity of Gram-positive bacteria cultured from Antarctic deep-sea sponges

Polar Biology

Volumn 34, Issue 10, 2011, Pages 1501-1512

  Xin, Yanjuan ^a,b   Kanagasabhapathy, Manmadhan ^a   Janussen, Dorte ^d   Xue, Song ^a   Zhang, Wei ^a,c  

^a DALIAN INSTITUTE OF CHEMICAL PHYSICS   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c FLINDERS UNIVERSITY   (Australia)

^d SENCKENBERG RESEARCH INSTITUTE   (Germany)

Author keywords

16S rRNA; Antarctic porifera; Gram positive bacteria; PKS; Siliceous sponges

Indexed keywords

BACTERIUM; BIOASSAY; CULTIVATION; DEEP-SEA BENTHOS; PHYLOGENETICS; SECONDARY METABOLITE; SPONGE;

ACTINOBACTERIA; BACILLALES; BACTERIA (MICROORGANISMS); BRACHYBACTERIUM; BREVIBACTERIUM; DEMOSPONGIAE; DIETZIA; FIRMICUTES; HEXACTINELLIDA; HOMAXINELLA BALFOURENSIS; MYXILLA; NOCARDIOPSIS; NUDA; PORIFERA; POSIBACTERIA; PSEUDONOCARDIA; STREPTOMYCES;

EID: 85027950506     PISSN: 07224060     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00300-011-1009-y     Document Type: Article

References (77)

1. Ayuso-Sacido A, Genilloud O (2005) New PCR primers for the screening of NRPS and PKS-I systems in actinomycetes: detection and distribution of these biosynthetic gene sequences in major taxonomic groups. Microb Ecol 49: 10-24.
2. Barthel D, Tendal OS (1994) Antarctic hexactinellida. In: Wägele JW, Sieg J (eds) Synopses of the Antarctic benthos, vol 6. Koeltz Scientific Books, Koenlgstein, p 154.
3. Barthel D, Gutt J, Tendal OS (1991) New information on the biology of Antarctic deep-water sponges derived from underwater photography. Mar Ecol Prog Ser 69: 303-307.
4. Bavestrello G, Arillo A, Calcinai B, Cattaneo-Vietti R, Cerrano C, Gaino E et al (2000) Parasitic diatoms inside antarctic sponges. Biol Bull 198: 29-33.
5. Bérdy J (2005) Bioactive microbial metabolites. J Antibiot 58: 1-26.
6. Brandt A, Brix S, Brökeland W, Cedhagen T, Choudhury M, Cornelius N, Danis B, Mesel I De, Diaz R, Gillan D, Hilbig B, Howe J, Janussen D, Kaiser S, Linse K, Malyutina M, Brandao S, Pawlowski J, Raupach M, Gooday A, vanreusel A (2007) The Southern Ocean deep sea: first insights into biodiversity and biogeography. Nature 447: 307-311 (+Suppl.).
7. Brown MV, Bowman JP (2001) A molecular phylogenetic survey of sea-ice microbial communities (SIMCO). FEMS Microbiol Ecol 35: 267-275.
8. Burja AM, Hill RT (2001) Microbial symbionts of the Australian Great Barrier Reef sponge, Candidaspongia flabellate. Hydrobilolgia 461: 41-47.
9. Cattaneo-Vietti R, Bavestrello G, Cerrano C, Gaino E, Mazzella L, Pansini M, Sarà M (1999) The role of sponges in the Terra Nova ecosystem. In: Faranda F, Guglielmo L, Ianora A (eds) Ross Sea ecology italiantartide expeditions (1987-1995). Springer, New York, pp 539-549.
10. Cerrano C, Arillo A, Bavestrello G, Calcinai B, Cattaneo-Vietti R, Penna A (2000a) Diatom invasion in the antarctic hexactinellid sponge Scolymastra joubini. Polar Biol 23: 441-444.
11. Cerrano C, Bavestrello G, Calcinai B, Cattaneo-Vietti R, Sarà A (2000b) Asteroids eating sponges from Tethys Bay, East Antarctica. Antarctic Sci 12: 425-426.
12. Chun J (1995) Computer-assisted classification and identification of actinomycetes. Ph. D Thesis, Univ Newcastle, Newcastle upon Tyne, UK.
13. Connon SA, Giovannoni SJ (2002) High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates. Appl Environ Microbiol 68: 3878-3885.
14. Courtois S, Cappellano CM, Ball M, Francou FX, Normand P, Helynck G, Martinez A, Kolvek SJ, Hopke J, Osburne MS, August PR, Nalin R, Guerineau M, Jeannin P, Simonet P, Pernodet JL (2003) Recombinant environmental libraries provide access to microbial diversity for drug discovery from natural products. Appl Environ Microbiol 69: 49-55.
15. Dayton PK (1989) Interdecadal variation in an Antarctic sponge and its predators from oceanographic climate shifts. Science 245: 1484-1486.
16. Felsenstein J (1993) PHYLIP (Phylogeny inference package), version 3. 5c. Department of Genetics, University of Washington, Seattle, WA, USA.
17. Ginolhac A, Jarrin C, Gillet B, Robe P, Pujic P, Tuphile K, Bertrand H, Vogel TM, Perriere G, Simonet P, Nalin R (2004) Phylogenetic analysis of polyketide synthase I domains from soil metagenomic libraries allows selection of promising clones. Appl Environ Microbiol 70: 5522-5527.
18. Gontang EA, Fenical W, Paul R, Jensen PR (2007) Phylogenetic diversity of gram-positive bacteria cultured from marine sediments. Appl Environ Microbiol 73: 3272-3282.
19. Gontang EA, Gaudêncio SP, Fenical W, Jensen PR (2010) Sequence-based analysis of secondary-metabolite biosynthesis in marine actinobacteria. Appl Environ Microbiol 76: 2487-2499.
20. Goodfellow M, Williams ST, Mordarski M (1983) Introduction to and importance of actinomycetes. In: Goodfellow M, Mordarski M, Williams ST (eds) The biology of the actinomycetes. Academic Press Inc., London, pp 1-6.
21. Gordon DA, Priscu J, Giovannoni S (2000) Origin and phylogeny of microbes living in permanent Antarctic lake ice. Microb Ecol 39: 197-202.
22. Governal RA, Yahya MT, Gerba CP, Shadman F (1991) Oligotrophic bacteria in ultra-pure water systems: media selection and process component evaluations. J Ind Microbiol Biotechnol 8: 223-227.
23. Hayakawa M, Nonomura H (1987) Humic acid-vitamin agar, a new medium for the selective isolation of soil actinomycetes. J Ferment Technol 65: 501-509.
24. Hentschel U, Schmid M, Wagner M, Fieseler L, Gernert C, Hacker J (2001) Isolation and phylogenetic analysis of bacteria with antimicrobial activities from the Mediterranean sponges Aplysina aerophoba and Aplysina cavernicola. FEMS Microbiol Ecol 35: 305-312.
25. Hentschel U, Hopke J, Horn M, Friedrich AB, Wagner M, Hacker J (2002) Molecular evidence for a uniform microbial community in sponges from different oceans. Appl Environ Microbiol 68: 4431-4440.
26. Imhoff JF, Stoehr R (2003) Sponge-associated bacteria: general overview and special aspects of bacteria associated with Halichondria panicea. In: Mueller WEG (ed) Sponges (Porifera). Springer, Heidelberg, pp 35-57.
27. Janssen PH, Yates PS, Grinton BE, Taylor PM, Sait M (2002) Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia. Appl Environ Microbiol 68: 2391-2396.
28. Janussen D (2006) Collection of Porifera (sponges) during ANDEEP III. Rep Polar Mar Res 533: 174-178.
29. Janussen D (2008) Diversity of sponges west and east of the Antarctic Peninsula. Rep Polar Mar Res 569: 41-48 (hdl: 10013/epic. 28679).
30. Janussen D, Tendal OS (2007) Diversity and distribution of porifera in the bathyal and abyssal Weddell Sea and adjacent areas. Deep-Sea Res II 54(16/17): 1864-1875.
31. Jiang SM, Sun W, Chen MJ, Dai SK, Zhang L, Liu YH, Lee KJ, Li X (2007) Diversity of culturable actinobacteria isolated from marine sponge Haliclona sp. Antonie van Leeuwenhoek 92: 405-416.
32. Jiang SM, Li X, Zhang L, Sun W, Dai SK, Xin LW, Liu YH, Lee KJ (2008) Cutlurable actinobacteria isolated from marine sponge Iotrochota sp. Mar Biol 153: 945-952.
33. Joseph SJ, Hugenholtz P, Sangwan P, Osbone CA, Janssen PH (2003) Laboratory cultivation of widespread and previously uncultured soil bacteria. Appl Environ Microbiol 69: 7210-7215.
34. Kennedy J, Baker P, Piper C, Cotter PD, Walsh M, Mooij MJ, Bourke MB, Rea MC, O'Connor PM, Ross RP, Hill C, O'Gara F, Marchesi JR, Dobson ADW (2009) Isolation and analysis of bacteria with antimicrobial activities from the marine sponge Haliclona simulans collected from Irish waters. Mar Biotechnol 11: 384-396.
35. Ketela MM, Halo L, Manukka E, Hakala J, Mantsala P, Ylihonko K (2002) Molecular evolution of aromatic polyketides and comparative sequence analysis of polyketide ketosynthase and 16S ribosomal DNA genes from various Streptomyces species. Appl Environ Microbiol 68: 4472-4479.
36. Kim TK, Garson MJ, Fuerst JA (2005) Marine actinomycetes related to the 'Salinospora' group from the Great Barrier Reef sponge Pseudoceratina clavata. Environ Microbiol 7(4): 509-518.
37. Lafi FF, Garson MJ, Fuerst JA (2005) Culturable bacterial symbionts isolated from two distinct sponge species (Pseudoceratina clavata and Rhabdastrella globostellata) from the Great Barrier Reef display similar phylogenetic diversity. Microb Ecol 50: 213-220.
38. Laiz L, Pinãr G, Lubitz W, Saiz-Jimenez C (2003) Monitoring the colonization of monuments by bacteria: cultivation versus molecular methods. Environ Microbiol 5: 72-74.
39. Lee YK, Kim HW, Liu CL, Lee HK (2003) A simple method for DNA extraction from marine bacteria that produce extracellular materials. J Microbiol Methods 52: 245-250.
40. Li SK, Xiao X, Yin XB, Wang FP (2006) Bacterial community along a historic lake sediment core of Ardley Island, west Antarctica. Extremophiles 10: 461-467.
41. Linse K, Brandt A, Bohn J, Danis B, De Broyer C, Ebbe B, Heterier V, Janussen D, López González PJ, Schüller M, Schwabe E, Thomson MRA (2007) Macro- and megabenthic assemblages in the bathyal and abyssal Weddell Sea (Southern Ocean). Deep-Sea Res II 54(16/17): 1848-1863.
42. Liu W, Ahlert J, Gao Q, Pienkowski EW, Shen B, Thorson JS (2003) Rapid PCR amplification of minimal enediyne polyketide synthase cassettes leads to a predictive familial classification model. Proc Natl Acad Sci 100: 11959-11963.
43. Maldonado LA, Stach JEM, Pathom-aree W, Ward AC, Bull AT, Goodfellow M (2005) Diversity of cultivable Actinobacteria in geographically widespread marine sediments. Antonie van Leeuwenhoek 87: 11-18.
44. Mangano S, Michaud L, Caruso C, Brilli M, Bruni V, Fani R, Giudice AL (2009) Antagonistic interactions between psychrotrophic cultivable bacteria isolated from Antarctic sponges: a preliminary analysis. Res Microbiol 160: 27-37.
45. McClintock JB, Amsler CD, Baker BJ, Rob WMVS (2005) Ecology of Antarctic marine sponges: an overview. Integr Comp Bilo 45: 359-368.
46. Merriman PR, Price RD, Baker FK, Kollmorgen JF, Piggott T, Ridge ED (1977) Effect of Bacillus and Streptomyces spp. applied to seed. In: Bruehl E (ed) Biology and control of soil-borne plant pathogens. American Phytopathological Society, St. Paul, pp 130-133.
47. Metsä-Ketelä M, Salo V, Halo L, Hautala A, Hakala J, Mäntsälä P, Ylihonko K (1999) An efficient approach for screening minimal PKS genes from Streptomyces. FEMS Microbiol Lett 180: 1-6.
48. Mincer TJ, Jensen PR, Kauffman CA, Fenical W (2002) Widespread and persistent populations of a major new marine actinomycete taxon in ocean sediments. Appl Environ Microbiol 68: 5005-5011.
49. Montalvo NF, Mohamed NM, Enticknap JJ, Hill RT (2005) Novel actinobacteria from marine sponge. Antonie van Leeuwenhoek 87: 29-36.
50. Murray AE, Preston CM, Massana R, Taylor LT, Blakis A, Wu K (1998) Seasonal and spatial variability of bacterial and archaeal assemblages in the coastal waters near Anvers Island, Antarctica. Appl Environ Microbiol 64: 2585-2595.
51. Muscholl-Silberhorn A, Thiel V, Imhoff JF (2008) Abundance and bioactivity of cultured sponge-associated bacteria from the Mediterranean Sea. Microb Ecol 55: 94-106.
52. Nold SC, Kopczynski ED, Ward DM (1996) Cultivation of aerobic chemoorganotrophic proteobacteria and gram-positive bacteria from a hot spring microbial mat. Appl Environ Microbiol 62: 3917-3921.
53. Pathom-aree W, Nogi Y, Sutcliffe IC, Ward AC, Horikoshi K, Bull AT, Goodfellow M (2006) Dermacoccus abyssi sp. nov., a piezotolerant actinomycete isolated from the Mariana Trench. Int J Syst Evol Microbiol 56: 1233-1237.
54. Plotkin AS, Janussen D (2008) Polymastiidae and Suberitidae (Porifera: Demospongiae: Hadromerida) of the deep Weddell Sea, Antarctic. Zootaxa 1866: 95-135.
55. Priest FG (1989) Products and applications. In: Harwood CR (ed) Bacillus. Plenum Press, New York, pp 293-320.
56. Radwan M, Hanora A, Zan J, Mohamed NM, Abo-Elmatty DM, Abou-El-Ela SD, Hill RT (2010) Bacterial community analyses of two Red Sea sponges. Mar Biotechnol 12: 350-360.
57. Reysenbach A-L, Giver LJ, Wickham GS, Pace NR (1992) Differential amplification of rRNA genes by polymerase chain reaction. Appl Environ Microbiol 58: 3417-3418.
58. Sait M, Hugenholtz P, Janssen PH (2002) Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys. Environ Microbiol 4: 654-666.
59. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-425.
60. Schaal KP (1977) Nocardia, actinomadura and streptomyces. In: Seligson D, von Graevenitz A (eds) CRC handbook series in clinical laboratory science, section E, clinical microbiology. CRC Press, Cleveland, pp 131-158.
61. Stevens H, Brinkhoff T, Rink B, Vollmers J, Simon M (2007) Diversity and abundance of gram positive bacteria in a tidal flat ecosystem. Environ Microbiol 9: 1810-1822.
62. Sun W, Dai SK, Jiang SM, Wang GH, Liu GH, Wu HB, Li X (2010) Culture-dependent and culture-independent diversity of Actinobacteria associated with the marine sponge Hymeniacidon perleve from the South China Sea. Antonie van Leeuwenhoek 98: 65-75.
63. Suzuki S, Takahashi K, Okuda T, Komatsubara S (1998) Selective isolation of Actinobispora on gellan gum plates. Can J Microbiol 44: 1-5.
64. Tabares P, Pimentel-Elardo SM, Schirmeister T, Hünig T, Hentschel U (2011) Anti-protease and immunomodulatory activities of bacteria associated with Caribbean sponges. Mar Biotechnol. doi: 10. 1007/s10126-010-9349-0.
65. Tamaki H, Sekiguchi Y, Hanada S, Nakamura K, Nomura N, Matsumura M, Kamagata Y (2005) Comparative analysis of bacterial diversity in freshwater sediment of a shallow eutrophic lake by molecular and improved cultivation-based techniques. Appl Environ Microbiol 71: 2162-2169.
66. Taylor MW, Mohamed NM, Enticknap JJ, Hill RT (2007) Sponge-associated microorganisms: evolution, ecology, and biotechnological potential. Microbiol Mol Biol Rev 71: 295-347.
67. 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 Acid Res 24: 4876-4882.
68. To Isaacs L, Kan J, Nguyen L, Videau P, Anderson MA, Wright TL, Hill RT (2009) Comparison of the bacterial communities of wild and captive sponge Clathria prolifera from the Chesapeake Bay. Mar Biotechnol 11: 758-770.
69. Vickers JC, Williams ST, Ross GW (1984) A taxonomic approach to selective isolation of streptomycetes from soil. In: Ortiz-Ortiz L, Bojalil LF, Yakoleff V (eds) Biological, biochemical and biomedical aspects of actinomycetes. Academic Press, Orlando, pp 553-561.
70. Webster NS, Hill RT (2001) The culturable microbial community of the Great Barrier Reef sponge Rhopaloeides odorabile is dominated by an alpha-Proteobacterium. Mar Biol 138: 843-851.
71. Webster NS, Wilson K, Blackall LL, Hill RT (2001a) Phylogentic diversity of the bacterial communities associated with the marine sponge, Rhopaloeides odorabile. Appl Environ Microbiol 67: 434-444.
72. Webster NS, Watts JEM, Hill RT (2001b) Detection and phylogenetic analysis of novel crenarchaeote and euryarchaeote sequences from a Great Barrier Reef sponge. Mar Biotech 3: 600-608.
73. Webster NS, Negri AP, Munro MMHG, Battershill CN (2004) Diverse microbial communities inhabit Antarctic sponges. Environ Microbiol 6: 288-300.
74. Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Baceriol 173: 697-703.
75. Zhang HT, Lee YK, Zhang W, Lee HK (2006) Culturable actinobacteria from the marine sponge Hymeniacidon perleve: isolation and phylogenetic diversity by 16S rRNA gene-RFLP analysis. Antonie van Leeuwenhoek 90: 159-169.
76. Zhang HT, Zhang W, Jin Y, Jin MF, Yu XJ (2008) A comparative study on the phylogenetic diversity of culturable actinomycetes isolated from five marine sponge species. Antonie van Leeuwenhoek 93: 241-248.
77. Zhu P, Li QZ, Wang GY (2008) Unique microbial signatures of the alien Hawaiian marine sponge Suberites zeteki. Microb Ecol 55: 406-414.