Biological characterisation of Haliclona (?gellius) sp.: Sponge and associated microorganisms

Microbial Ecology

Volumn 58, Issue 4, 2009, Pages 903-920

  Sipkema, Detmer ^a   Holmes, Bradley ^a   Nichols, Scott A ^b   Blanch, Harvey W ^a  

^a University of California   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMPHIMEDON; BACTERIA (MICROORGANISMS); CRENARCHAEOTA; GAMMAPROTEOBACTERIA; GELLIUS; HALICLONA; HEXAPODA; PROTEOBACTERIA;

ARCHAEAL DNA; BACTERIAL DNA; RIBOSOME DNA; RNA 18S;

ANIMAL; ARCHAEBACTERIUM; ARTICLE; BACTERIUM; CLASSIFICATION; GENE LIBRARY; GENETICS; HALICLONA; ISOLATION AND PURIFICATION; MICROBIOLOGY; PHYLOGENY; SPECIES DIFFERENCE; TRANSMISSION ELECTRON MICROSCOPY;

ANIMALS; ARCHAEA; BACTERIA; DNA, ARCHAEAL; DNA, BACTERIAL; DNA, RIBOSOMAL; GENOMIC LIBRARY; HALICLONA; MICROSCOPY, ELECTRON, TRANSMISSION; PHYLOGENY; RNA, RIBOSOMAL, 18S; SPECIES SPECIFICITY;

EID: 73349122019     PISSN: 00953628     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00248-009-9534-8     Document Type: Article

References (66)

1. Althoff K, Schütt C, Steffen R, Batel R, Müller WEG (1998) Evidence for a symbiosis between bacteria of the genus Rhodobacter and the marine sponge Halichondria panicea: harbour also for putatively toxic bacteria? Mar Biol 130: 529-536.
2. Becerro MA (2008) Quantitative trends in sponge ecology research. Mar Ecol 29: 167-177.
3. Bewley CA, Holland ND, Faulkner DJ (1996) Two classes of metabolites from Theonella swinhoei are localized in distinct populations of bacterial symbionts. Experientia 52: 716-722.
4. Castresana J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17: 540-552.
5. Dawson SC, Pace NR (2002) Novel kingdom-level eukaryotic diversity in anoxic environments. Proc Natl Acad Sci 99: 8324-8329.
6. DeLong E (1992) Archaea in coastal marine environments. Proc Natl Acad Sci 89: 5685-5689.
7. De Weerdt WH (2002) Family Chalinidae Gray, 1867. In: Hooper JNA, van Soest RWM (eds) Systema Porifera. A guide to the classification of sponges. Kluwer/Pendulum, New York, pp 859-862.
8. Faulkner DJ (2002) Marine natural products. Nat Prod Rep 19: 1-48.
9. Felske A, Rheims H, Woltherink A, Stackebrandt E, Akkermans ADL (1997) Ribosome analysis reveals prominent activity of an uncultured member of the class Actinobacteria in grassland soils. Microbiol 143: 2983-2989.
10. Garson MJ (1994) The biosynthesis of sponge secondary metabolites: why it is important. In: van Soest RWM, van Kempen TMG, Braekman JC (eds) Sponges in time and space. Balkema, Rotterdam, pp 427-440.
11. Grozdanov L, Hentschel U (2007) An environmental genomics perspective on the diversity and function of marine sponge-associated microbiota. Curr Opin Microbiol 10: 215-220.
12. Hallam SJ, Mincer TJ, Schleper C, Preston CM, Roberts K, Richardson PM, DeLong EF (2006) Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analysis of marine Crenarchaeota. PLoS Biol 4: 520-536.
13. Hartman WD (1975) Phylum Porifera. In: Smith RI, Carlton JT (eds) Light's manual: intertidal invertebrates of the Central California coast. University of California Press, Berkeley, pp 32-64.
14. Hentschel U, Hopke J, Horn M, Friedrich AB, Wagner M, Hacker J, Moore BS (2002) Molecular evidence for a uniform microbial community in sponges from different oceans. Appl Environ Microbiol 68: 4431-4440.
15. Hentschel U, Fieseler L, Wehrl M, Gernert C, Steinert M, Hacker J, Horn M (2003) Microbial diversity of marine sponges. In: Müller WEG (ed) Marine Molecular Biotechnology. Springer, Berlin, pp 59-88.
16. Hentschel U, Usher KM, Taylor MW (2006) Marine sponges as microbial fermentors. FEMS Microbiol Ecol 55: 167-177.
17. Hill M, Hill A, Lopez N, Harriott O (2006) Sponge-specific bacterial symbionts in the Caribbean sponge, Chondrila nucula (Demospongia, Chondrosida). Mar Biol 148: 1221-1230.
18. Hoffmann F, Larsen O, Thiel V, Rapp HT, Pape T, Michaelis W, Reitner J (2005) An anaerobic world in sponges. Geomicrobiol J 22: 1-10.
19. Holmes BM (2006) Marine sponges: systematics, symbiosis and cell culture. PhD thesis, University of California Berkeley.
20. Holmes B, Blanch H (2007) Genus-specific associations of marine sponges with group I crenarchaeotes. Mar Biol 150: 759-772.
21. Hooper JNA, van Soest RWM (2006) A new species of Amphimedon (Porifera, Demospongiae, Haplosclerida, Niphatidae) from the Capricorn-Bunker Group of islands, Great Barrier Reef, Australia; target species for the 'sponge genome project'. Zootaxa 1314: 31-39.
22. Huber T, Faulkner G, Hugenholtz P (2004) Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20: 2317-2319.
23. Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.
24. Hurlbert S (1971) The nonconcept of species diversity: a critique and alternative parameters. Ecology 52: 577-586.
25. Ilan M, Abelson A (1995) The life of a sponge in a sandy lagoon. Biol Bull 189: 363-369.
26. Jensen PR, Mincer TJ, Williams PG, Fenical W (2005) Marine actinomycete diversity and natural product discovery. Antonie van Leeuwenhoek 87: 43-48.
27. Kennedy J, Codling CE, Jones BV, Dobson ADW, Marchesi JR (2008) Diversity of microbes associated with the marine sponge, Haliclona simulans, isolated from Irish waters and identification of polyketide synthase genes from the sponge metagenome. Environ Microbiol 10: 1888-1902.
28. Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellows M (eds) Nucleic acid techniques in bacterial systematics. Wiley, New York, pp 115-175.
29. Lee YK, Lee JH, Lee HK (2001) Microbial symbiosis in marine sponges. J Microbiol 39: 254-264.
30. Lee WL, Elvin DW, Reiswig HM (2007) The Sponges of California. A guide and key to the marine sponges of California, Monterey Bay Sanctuary Foundation, p. 111.
31. Li ZY, Liu Y (2006) Marine sponge Craniella australiensis-associated bacterial diversity revelation based on 16S rDNA library and biologically active Actinomycetes screening, phylogenetic analysis. Lett Appl Microbiol 43: 410-416.
32. Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar BA, Lai T, Steppi S, Jobb G, Forster W, Brettske I, Gerber S, Ginhart AW, Gross O, Grumann S, Hermann S, Jost R, Konig A, Liss T, Lussmann R, May M, Nonhoff B, Reichel B, Strehlow R, Stamatakis A, Stuckmann N, Vilbig A, Lenke M, Ludwig T, Bode A, Schleifer KH (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32: 1363-1371.
33. Margot H, Acebal C, Toril E, Amils R, Puentes JLF (2002) Consistent association of crenarchaeal Archaea with sponges of the genus Axinella. Mar Biol 140: 739-745.
34. Medlin L, Elwood HJ, Stickel S, Sogin ML (1988) The characterization of enzymatically amplified eukaryotic 16S-like rRNA coding regions. Gene 71: 491-499.
35. Meyer B, Kuever J (2008) Phylogenetic diversity and spatial distribution of the microbial community associated with the Caribbean deep-water sponge Polymastia cf corticata by 16S rRNA, aprA, and amoA gene analysis. Microb Ecol 56: 306-321.
36. Mohamed NM, Enticknap JJ, Lohr JE, McIntosh SM, Hill RT (2008) Changes in bacterial communities of the marine sponge Mycale laxissima on transfer into aquaculture. Appl Environ Microbiol 74: 1209-1222.
37. Mohamed NM, Rao V, Hamann MT, Kelly M, Hill RT (2008) Monitoring bacterial diversity of the marine sponge Ircinia strobilina upon transfer into aquaculture. Appl Environ Microbiol 74: 4133-4143.
38. Nett M, König GM (2007) The chemistry of gliding bacteria. Nat Prod Rep 24: 1245-1261.
39. Osinga R, Tramper J, Wijffels RH (1999) Cultivation of marine sponges. Mar Biotechnol 1: 509-532.
40. Redmond NE, van Soest RWM, Kelly M, Raleigh J, Travers SAA, McCormack GP (2007) Reassessment of the classification of the order Haplosclerida (class Demospongiae, phylum Porifera) using 18S rRNA gene sequence data. Mol Phylogen Evol 43: 344-352.
41. Reiswig HM (1974) Water transport, respiration and energetics of three tropical marine sponges. J Exp Mar Biol Ecol 14: 231-249.
42. Ridley CP, Lee HY, Khosla C (2008) Evolution of polyketide synthases in bacteria. Proc Natl Acad Sci U S A 105: 4595-4600.
43. Ronquist F, Huelsenbeck JP, van der Mark O (2005) MrBayes 3. 1 manual. School of computational science, Florida State University, USA.
44. Schmitt S, Weisz JB, Lindquist N, Hentschel U (2007) Vertical transmission of a phylogenetically complex microbial consortium in the viviparous sponge Ircinia felix. Appl Environ Microbiol 73: 2067-2078.
45. Schleper C, DeLong EF, Preston CM, Feldman RA, Wu KY, Swanson RV (1998) Genomic analysis reveals chromosomal variation in natural populations of the uncultured psychrophilic archaeon Cenarchaeum symbiosum. J Bacteriol 180: 5003-5009.
46. Sharp KH, Eam B, Faulkner DJ, Haygood MG (2007) Vertical transmission of diverse microbes in the tropical sponge Corticium sp. Appl Environ Microbiol 73: 622-629.
47. Sipkema D, Franssen MCR, Osinga R, Tramper J, Wijffels RH (2005) Marine sponges as pharmacy. Mar Biotechnol 7: 142-162.
48. Sorokin DY, Tourova TP, Braker G, Muyzer G (2007) Thiohalomonas denitrificans gen. nov., sp. nov. and Thiohalomonas nitratireducens sp. nov., novel obligately chemolithoautotrophic, moderately halophilic, thiodenitrifying Gammaproteobacteria from hypersaline habitats. Int J Syst Evol Microbiol 57: 1585-1589.
49. Stackebrandt E, Ebers J (2006) Taxonomic parameters revisited: tarnished gold standards. Microbiol Today, Nov: 152-155.
50. Suzuki MT, Béjà O, Taylor LT, DeLong EF (2001) Phylogenetic analysis of ribosomal RNA operons from uncultivated coastal marine bacterioplankton. Environ Microbiol 3: 323-331.
51. Suzuki MT, Preston CM, Béjà O, De la Torre JR, Steward GF, DeLong EF (2004) Phylogenetic screening of ribosomal RNA gene-containing clones in bacterial artificial chromosome (BAC) libraries from different depths in Monterey Bay. Microb Ecol 48: 473-488.
52. Swofford DL (2003) Phylogenetic analysis using parsimony (*and other methods). Version 4. Sinauer Associates, Sunderland.
53. Taylor MW, Schupp PJ, Dahllöf I, Kjelleberg S, Steinberg PD (2004) Host specificity in marine sponge-associated bacteria and potential implications for marine microbial diversity. Environ Microbiol 6: 121-130.
54. Taylor MW, Radax R, Steger D, Wagner M (2007) Sponge-associated microorganisms: evolution, ecology and biotechnological potential. Microbiol Mol Biol Rev 71: 295-347.
55. Thiel V, Neulinger SC, Staufenberger T, Schmaljohann R, Imhoff JF (2007) Spatial distribution of sponge-associated bacteria in the Mediterranean sponge Tethya aurantium. FEMS Microbiol Ecol 59: 47-63.
56. Thiel V, Leininger S, Schmaljohann R, Brümmer F, Imhoff J (2007) Sponge-specific bacterial associations of the Mediterranean sponge Chondrilla nucula (Demospongiae, tetractinomorpha). Microb Ecol 54: 101-111.
57. Uriz MJ, Turon X, Galera J, Tur JM (1996) New light on the cell location of avarol within the sponge Dysidea avara (Dendroceratida). Cell Tissue Res 286: 519-527.
58. Vacelet J, Donadey C (1977) Electron microscopy study of the association between some sponges and bacteria. J Exp Mar Biol Ecol 30: 301-314.
59. Vacelet J, Fiala-Medioni A, Fisher CR, Boury-Esnault N (1996) Symbiosis between methane-oxidizing bacteria and a deep-sea carnivorous cladorhizid sponge. Mar Ecol Prog Ser 145: 77-85.
60. Webster NS, Wilson KJ, Blackall LL, Hill RT (2001) Phylogenetic diversity of bacteria associated with the marine sponge Rhopaloeides odorabile. Appl Env Microbiol 67: 434-444.
61. Webster NS, Negri AP, Munro MHG, Battershill CN (2004) Diverse microbial communities inhabit Antarctic sponges. Environ Microbiol 6: 288-300.
62. Webster NS, Cobb RE, Negri AP (2008) Temperature thresholds for bacterial symbiosis with a sponge. ISME J 2: 830-842.
63. Weisz JB, Hentschel U, Lindquist N, Martens CS (2007) Linking abundance and diversity of sponge-associated microbial communities to metabolic differences in host sponges. Mar Biol 152: 475-483.
64. Wichels A, Würtz S, Döpke H, Schütt C, Gerdts G (2006) Bacterial diversity in the breadcrumb sponge Halichondria panicea (Pallas). FEMS Microbiol Ecol 56: 102-118.
65. Wilkinson CR (1980) Nutrient translocation from green algal symbionts to the freshwater sponge Ephidatia fluviatilis. Hydrobiologia 75: 241-250.
66. Zwickl DJ (2006) Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. PhD thesis UT Austin, USA.