Annals of Microbiology

, Volume 69, Issue 3, pp 253–265 | Cite as

Antimicrobial activity and diversity of bacteria associated with Taiwanese marine sponge Theonella swinhoei

  • Jimmy KuoEmail author
  • Yu-Ting Yang
  • Mei-Chin Lu
  • Tit-Yee Wong
  • Ping-Jung Sung
  • Yung-Sen Huang
Original Article


Marine sponges often rely on other epiphytes for protection from harmful predators. To understand the diversity and antimicrobial activity present among epiphytic bacteria isolated from marine sponge. We used both the 16S rRNA tag pyrosequencing method and the culture-based method to investigate the bacterial communities of Theonella swinhoei collected off the shore of southern Taiwan. Eight-hundred and eighteen operational taxonomic units (OTUs; 97% sequence similarity) were identified from 23,700 sponge-derived sequence tags. The bacteria associated with T. swinhoei were found to be highly diverse—as many as 12 different phyla of bacteria were identified. However, in terms of population evenness, the community was dominated by two phyla—Acidobacteria (71.54%) and Chloroflexi (19.60%). A total of 700 bacterial strains were isolated and cultured from samples of the sponge T. swinhoei. Within these culturable strains, only 12% were Actinomycetes. Despite the low percentage of Actinobacteria from the samples, among the 51 strains of culturable bacteria that showed high antimicrobial activity, a great majority (62%) were Actinomycetes (30 strains of Streptomyces and 1 strain each of Micromonospora and Brevibacterium). The remaining isolates that produced antimicrobial compounds were Gammaproteobacteria (10 strains of Pseudoalteromonas) and Firmicutes (8 and 1 strains of Bacillus and Paenibacillus, respectively). We speculated that many more Actinomycetes are yet to be isolated from T. swinhoei microbiota. Advanced techniques, such as high-throughput culture and culturome, should allow the isolation and purification of these medically important groups of bacteria from sponge.


Sponge-associated bacteria Antimicrobial activity Cytotoxic activity Metagenomic analysis 454 pyrosequencing 



This work was supported by intramural funding from the National Museum of Marine Biology and Aquarium.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

All procedures performed in studies involving animals were in accordance with the ethical standards of the institution or practice at which the studies were conducted.

Supplementary material

13213_2018_1414_MOESM1_ESM.xlsx (54 kb)
Supplementary File 1 Taxonomy assignments of the bacterial community associated with marine sponge Theonella swinhoei at different levels. (XLSX 53.9 kb)


  1. Abdelmohsen UR, Bayer K, Hentschel U (2014) Diversity, abundance and natural products of marine sponge-associated actinomycetes. Nat Prod Rep 31:381–399CrossRefGoogle Scholar
  2. Barns SM, Cain EC, Sommerville L, Kuske CR (2007) Acidobacteria phylum sequences in uranium-contaminated subsurface sediments greatly expand the known diversity within the phylum. Appl Environ Microbiol 73:3113–3116CrossRefGoogle Scholar
  3. Bayer K, Schmitt S, Hentschel U (2008) Physiology, phylogeny and in situ evidence for bacterial and archaeal nitrifiers in the marine sponge Aplysina aerophoba. Environ Microbiol 10:2942–2955CrossRefGoogle Scholar
  4. Bengtsson MM, Ovreas L (2010) Planctomycetes dominate biofilms on surfaces of the kelp Laminaria hyperborea. BMC Microbiol 10:261CrossRefGoogle Scholar
  5. Bewley CA, Holland ND, Faulkner DJ (1996) Two classes of metabolites from Theonella swinhoei are localized in distinct populations of bacterial symbionts. Experientia 52:716–722CrossRefGoogle Scholar
  6. Bredholdt H, Galatenko OA, Engelhardt K, Fjaervik E, Terekhova LP, Zotchev SB (2007) Rare actinomycete bacteria from the shallow water sediments of the Trondheim fjord, Norway: isolation, diversity and biological activity. Environ Microbiol 9:2756–2764CrossRefGoogle Scholar
  7. Breuker A, Koweker G, Blazejak A, Schippers A (2011) The deep biosphere in terrestrial sediments in the Chesapeake bay area, Virginia, USA. Front Microbiol 2:156CrossRefGoogle Scholar
  8. Burgess JG, Jordan EM, Bregu M, Mearns-Spragg A, Boyd KG (1999) Microbial antagonism: a neglected avenue of natural products research. J Biotechnol 70:27–32CrossRefGoogle Scholar
  9. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL (2009) BLAST+: architecture and applications. BMC Bioinformatics 10:421CrossRefGoogle Scholar
  10. Cardenas CA, Bell JJ, Davy SK, Hoggard M, Taylor MW (2014) Influence of environmental variation on symbiotic bacterial communities of two temperate sponges. FEMS Microbiol Ecol 88:516–527CrossRefGoogle Scholar
  11. Chen Y-H, Kuo J, Sung P-J et al (2012) Isolation of marine bacteria with antimicrobial activities from cultured and field-collected soft corals. World J Microbiol Biotechnol 28:3269–3279CrossRefGoogle Scholar
  12. Chen Y-H, Lu M-C, Chung H-M et al (2016) Bafilomycin M, a new cytotoxic bafilomycin produced by a Streptomyces sp. isolated from a marine sponge Theonella sp. Tetrahedron Lett 57:4863–4865CrossRefGoogle Scholar
  13. Closek CJ, Sunagawa S, DeSalvo MK et al (2014) Coral transcriptome and bacterial community profiles reveal distinct Yellow Band Disease states in Orbicella faveolata. ISME J 8:2411–2422CrossRefGoogle Scholar
  14. Cole JR, Chai B, Farris RJ et al (2005) The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res 33:D294–D296CrossRefGoogle Scholar
  15. Flatt PM, Gautschi JT, Thacker RW, Musafija-Girt M, Crews P, Gerwick WH (2005) Identification of the cellular site of polychlorinated peptide biosynthesis in the marine sponge Dysidea (Lamellodysidea) herbacea and symbiotic cyanobacterium Oscillatoria spongeliae by CARD-FISH analysis. Mar Biol 147:761–774CrossRefGoogle Scholar
  16. Flemer B, Kennedy J, Margassery LM, Morrissey JP, O’Gara F, Dobson AD (2012) Diversity and antimicrobial activities of microbes from two Irish marine sponges, Suberites carnosus and Leucosolenia sp. J Appl Microbiol 112:289–301CrossRefGoogle Scholar
  17. Gerwick WH, Moore BS (2012) Lessons from the past and charting the future of marine natural products drug discovery and chemical biology. Biol Chem 19:85–98CrossRefGoogle Scholar
  18. Graca AP, Bondoso J, Gaspar H et al (2013) Antimicrobial activity of heterotrophic bacterial communities from the marine sponge Erylus discophorus (Astrophorida, Geodiidae). PLoS One 8:e78992CrossRefGoogle Scholar
  19. Hardoim CC, Costa R (2014) Temporal dynamics of prokaryotic communities in the marine sponge Sarcotragus spinosulus. Mol Ecol 23:3097–3112CrossRefGoogle Scholar
  20. 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 35:305–312CrossRefGoogle Scholar
  21. 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 68:4431–4440CrossRefGoogle Scholar
  22. Hill M, Hill A, Lopez N, Harriott O (2006) Sponge-specific bacterial symbionts in the Caribbean sponge, Chondrilla nucula (Demospongiae, Chondrosida). Mar Biol 148:1221–1230CrossRefGoogle Scholar
  23. Hoffmann F, Radax R, Woebken D et al (2009) Complex nitrogen cycling in the sponge Geodia barretti. Environ Microbiol 11:2228–2243CrossRefGoogle Scholar
  24. Ivanitskaia LP, Singal EM, Bibikova MV, Vostrov SN (1978) Directed isolation of Micromonospora generic cultures on a selective medium with gentamycin. Antibiotiki 23:690–692Google Scholar
  25. Jensen PR, Gontang E, Mafnas C, Mincer TJ, Fenical W (2005) Culturable marine actinomycete diversity from tropical Pacific Ocean sediments. Environ Microbiol 7:1039–1048CrossRefGoogle Scholar
  26. Jetten MS (2008) The microbial nitrogen cycle. Environ Microbiol 10:2903–2909CrossRefGoogle Scholar
  27. Jin L, Liu F, Sun W, Zhang F, Karuppiah V, Li Z (2014) Pezizomycotina dominates the fungal communities of South China Sea sponges Theonella swinhoei and Xestospongia testudinaria. FEMS Microbiol Ecol 90:935–945CrossRefGoogle Scholar
  28. Kellogg CA, Ross SW, Brooke SD (2016) Bacterial community diversity of the deep-sea octocoral Paramuricea placomus. PeerJ 4:e2529CrossRefGoogle Scholar
  29. Kennedy J, Baker P, Piper C et al (2009) Isolation and analysis of bacteria with antimicrobial activities from the marine sponge Haliclona simulans collected from Irish waters. Mar Biotechnol 11:384–396CrossRefGoogle Scholar
  30. Keren R, Lavy A, Mayzel B, Ilan M (2015) Culturable associated-bacteria of the sponge Theonella swinhoei show tolerance to high arsenic concentrations. Front Microbiol 6:154CrossRefGoogle Scholar
  31. Kindaichi T, Yuri S, Ozaki N, Ohashi A (2012) Ecophysiological role and function of uncultured Chloroflexi in an anammox reactor. Water Sci Technol 66:2556–2561CrossRefGoogle Scholar
  32. Kiss H, Nett M, Domin N et al (2011) Complete genome sequence of the filamentous gliding predatory bacterium Herpetosiphon aurantiacus type strain (114-95(T)). Stand Genomic Sci 5:356–370CrossRefGoogle Scholar
  33. Lavy A, Keren R, Haber M, Schwartz I, Ilan M (2014) Implementing sponge physiological and genomic information to enhance the diversity of its culturable associated bacteria. FEMS Microbiol Ecol 87:486–502CrossRefGoogle Scholar
  34. Leal MC, Puga J, Serodio J, Gomes NC, Calado R (2012) Trends in the discovery of new marine natural products from invertebrates over the last two decades—where and what are we bioprospecting? PLoS One 7:e30580CrossRefGoogle Scholar
  35. Lin CH, Chuang CH, Twan WH et al (2016) Seasonal changes in bacterial communities associated with healthy and diseased Porites coral in southern Taiwan. Can J Microbiol 62:1021–1033CrossRefGoogle Scholar
  36. Lu M-C, Du Y-C, Chuu J-J et al (2009) Active extracts of wild fruiting bodies of Antrodia camphorata (EEAC) induce leukemia HL 60 cells apoptosis partially through histone hypoacetylation and synergistically promote anticancer effect of trichostatin A. Arch Toxicol 83:121–129CrossRefGoogle Scholar
  37. Mehbub MF, Lei J, Franco C, Zhang W (2014) Marine sponge derived natural products between 2001 and 2010: trends and opportunities for discovery of bioactives. Mar Drugs 12:4539–4577CrossRefGoogle Scholar
  38. Mohamed NM, Saito K, Tal Y, Hill RT (2010) Diversity of aerobic and anaerobic ammonia-oxidizing bacteria in marine sponges. ISME J 4:38–48Google Scholar
  39. Montalvo NF, Davis J, Vicente J, Pittiglio R, Ravel J, Hill RT (2014) Integration of culture-based and molecular analysis of a complex sponge-associated bacterial community. PLoS One 9:e90517CrossRefGoogle Scholar
  40. Ng JC, Chan Y, Tun HM, Leung FC, Shin PK, Chiu JM (2015) Pyrosequencing of the bacteria associated with Platygyra carnosus corals with skeletal growth anomalies reveals differences in bacterial community composition in apparently healthy and diseased tissues. Front Microbiol 6:1142Google Scholar
  41. Nithyanand P, Manju S, Karutha Pandian S (2011) Phylogenetic characterization of culturable actinomycetes associated with the mucus of the coral Acropora digitifera from Gulf of Mannar. FEMS Microbiol Lett 314:112–118CrossRefGoogle Scholar
  42. O’Connor-Sanchez A, Rivera-Dominguez AJ, Santos-Briones Cde L, Lopez-Aguiar LK, Pena-Ramirez YJ, Prieto-Davo A (2014) Acidobacteria appear to dominate the microbiome of two sympatric Caribbean sponges and one Zoanthid. Biol Res 47:67CrossRefGoogle Scholar
  43. Osinga R, Armstrong E, Grant Burgess J, Hoffmann F, Reitner J, Schumann-Kindel G (2001) Sponge–microbe associations and their importance for sponge bioprocess engineering. Hydrobiologia 461:55–62CrossRefGoogle Scholar
  44. Piel J, Hui D, Wen G, Butzke D, Platzer M, Fusetani N, Matsunaga S (2004) Antitumor polyketide biosynthesis by an uncultivated bacterial symbiont of the marine sponge Theonella swinhoei. Proc Natl Acad Sci U S A 101:16222–16227CrossRefGoogle Scholar
  45. Pimentel-Elardo S, Wehrl M, Friedrich AB, Jensen PR, Hentschel U (2003) Isolation of planctomycetes from Aplysina sponges. Aquat Microb Ecol 33:239–245CrossRefGoogle Scholar
  46. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glockner FO (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35:7188–7196CrossRefGoogle Scholar
  47. Reveillaud J, Maignien L, Eren AM, Huber JA, Apprill A, Sogin ML, Vanreusel A (2014) Host-specificity among abundant and rare taxa in the sponge microbiome. ISME J 8:1198–1209CrossRefGoogle Scholar
  48. Rodriguez-R LM, Konstantinidis KT (2014) Nonpareil: a redundancy-based approach to assess the level of coverage in metagenomic datasets. Bioinformatics 30:629–635CrossRefGoogle Scholar
  49. Santos OC, Pontes PV, Santos JF, Muricy G, Giambiagi-deMarval M, Laport MS (2010) Isolation, characterization and phylogeny of sponge-associated bacteria with antimicrobial activities from Brazil. Res Microbiol 161:604–612CrossRefGoogle Scholar
  50. Schloss PD, Westcott SL, Ryabin T et al (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75Google Scholar
  51. Schloss PD, Gevers D, Westcott SL (2011) Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS One 6:e27310CrossRefGoogle Scholar
  52. Schmidt EW, Obraztsova AY, Davidson SK, Faulkner DJ, Haygood MG (2000) Identification of the antifungal peptide-containing symbiont of the marine sponge Theonella swinhoei as a novel δ-proteobacterium, “Candidatus Entotheonella palauensis”. Mar Biol 136:969–977CrossRefGoogle Scholar
  53. Schmitt S, Deines P, Behnam F, Wagner M, Taylor MW (2011) Chloroflexi bacteria are more diverse, abundant, and similar in high than in low microbial abundance sponges. FEMS Microbiol Ecol 78:497–510CrossRefGoogle Scholar
  54. Schmitt S, Hentschel U, Taylor MW (2012) Deep sequencing reveals diversity and community structure of complex microbiota in five Mediterranean sponges. Hydrobiologia 687:341–351CrossRefGoogle Scholar
  55. Simister R, Taylor MW, Tsai P, Fan L, Bruxner TJ, Crowe ML, Webster N (2012) Thermal stress responses in the bacterial biosphere of the Great Barrier Reef sponge, Rhopaloeides odorabile. Environ Microbiol 14:3232–3246CrossRefGoogle Scholar
  56. Simister R, Taylor MW, Rogers KM, Schupp PJ, Deines P (2013) Temporal molecular and isotopic analysis of active bacterial communities in two New Zealand sponges. FEMS Microbiol Ecol 85:195–205CrossRefGoogle Scholar
  57. Stern NJ, Svetoch EA, Eruslanov BV et al (2006) Isolation of a Lactobacillus salivarius strain and purification of its bacteriocin, which is inhibitory to Campylobacter jejuni in the chicken gastrointestinal system. Antimicrob Agents Chemother 50:3111–3116CrossRefGoogle Scholar
  58. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739CrossRefGoogle Scholar
  59. Taylor MW, Radax R, Steger D, Wagner M (2007) Sponge-associated microorganisms: evolution, ecology, and biotechnological potential. Microbiol Mol Biol Rev 71:295–347CrossRefGoogle Scholar
  60. Terekhova LP, Galatenko OA, Alferova IV, Preobragenskaya TP (1991) Comparative estimation of some bacterial growth inhibitors as selective agents for isolation of soil actinomycetes. Antibiot Chemother 36:5–8Google Scholar
  61. Thomas TRA, Kavlekar DP, LokaBharathi PA (2010) Marine drugs from sponge-microbe association—a review. Mar Drugs 8:1417–1468CrossRefGoogle Scholar
  62. Thoms C, Horn M, Wagner M, Hentschel U, Proksch P (2003) Monitoring microbial diversity and natural product profiles of the sponge Aplysina cavernicola following transplantation. Mar Biol 142:685–692CrossRefGoogle Scholar
  63. Unson MD, Faulkner DJ (1993) Cyanobacterial symbiont biosynthesis of chlorinated metabolites from Dysidea herbacea (Porifera). Experientia 49:349–353CrossRefGoogle Scholar
  64. Unson MD, Holland ND, Faulkner DJ (1994) A brominated secondary metabolite synthesized by the cyanobacterial symbiont of a marine sponge and accumulation of the crystalline metabolite in the sponge tissue. Mar Biol 119:1–11CrossRefGoogle Scholar
  65. Ward NL, Challacombe JF, Janssen PH et al (2009) Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils. Appl Environ Microbiol 75:2046–2056CrossRefGoogle Scholar
  66. 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 138:843–851Google Scholar
  67. Webster NS, Taylor MW (2012) Marine sponges and their microbial symbionts: love and other relationships. Environ Microbiol 14:335–346CrossRefGoogle Scholar
  68. Wilkinson CR, Fay P (1979) Nitrogen fixation in coral reef sponges with symbiotic cyanobacteria. Nature 279:527–529CrossRefGoogle Scholar
  69. Wilkinson CR, Nowak M, Austin B, Colwell RR (1981) Specificity of bacterial symbionts in Mediterranean and Great Barrier Reef sponges. Microb Ecol 7:13–21CrossRefGoogle Scholar
  70. Wilson GS, Raftos DA, Corrigan SL, Nair SV (2010) Diversity and antimicrobial activities of surface-attached marine bacteria from Sydney Harbour, Australia. Microbiol Res 165:300–311CrossRefGoogle Scholar
  71. Ye Q, Wu Y, Zhu Z, Wang X, Li Z, Zhang J (2016) Bacterial diversity in the surface sediments of the hypoxic zone near the Changjiang Estuary and in the East China Sea. MicrobiologyOpen 5:323–339CrossRefGoogle Scholar
  72. Zhang W, Li Z, Miao X, Zhang F (2009) The screening of antimicrobial bacteria with diverse novel nonribosomal peptide synthetase (NRPS) genes from South China Sea sponges. Mar Biotechnol 11:346–355CrossRefGoogle Scholar

Copyright information

© Università degli studi di Milano 2019

Authors and Affiliations

  1. 1.Department of Planning and ResearchNational Museum of Marine Biology and AquariumPingtungTaiwan
  2. 2.Graduate Institute of Marine BiologyNational Dong Hwa UniversityPingtungTaiwan
  3. 3.Department of Biological SciencesUniversity of MemphisMemphisUSA
  4. 4.Department of Life SciencesNational University of KaohsiungKaohsiungTaiwan

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