Abstract
The marine environment is an invaluable natural goods and biomaterials resource. Sponges, abundant members of marine benthic ecosystems, are a significant source of bioactive secondary metabolites, including chitin, chitosan, ceramic, biosilica, and collagen. The sponge microbiome includes several different species of symbiotic bacteria. These symbiotic bacteria may produce the bioactive compounds found in marine sponges. In the laboratory, most prokaryotes are unculturable, and the metabolite productivity of the cultured bacteria is inadequate, quantity-wise. Consequently, metagenomics can be employed to analyze and produce bioactive substances. Using metagenome mining, discovering new natural product biosynthetic routes from different bacterial consortia is feasible. The basic technologies utilized are identifying the biosynthetic genes in the metagenome of sponge microbiomes and creating a metagenomic library. Separation of biosynthetic gene clusters that might eventually be utilized to generate sustainable natural product sources through heterologous expression. The expression of these genes in readily culturable bacteria results in higher yields of bioactive natural compounds. This review primarily emphasizes metagenomic technologies for using the metabolic pathways of symbiotic bacteria linked with marine sponges.
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References
Aakvik T, Degnes KF, Dahlsrud R, Schmidt F, Dam R, Yu L, Völker U, Ellingsen TE, Valla S (2009) A plasmid RK2-based broad-host-range cloning vector useful for transfer of metagenomic libraries to a variety of bacterial species. FEMS Microbiol Lett 296:149–158. https://doi.org/10.1111/j.1574-6968.2009.01639.x. PMID 19459950
Abdelmohsen UR, Pimentel-Elardo SM, Hanora A, Radwan M, Abou-El-Ela SH, Ahmed S, Hentschel U (2010) Isolation, phylogenetic analysis and anti-infective activity screening of marine sponge-associated actinomycetes. Mar Drugs 8(3):399–412. https://doi.org/10.3390/md8030399. PMID 20411105
Anbuchezhian R, Li Z (2014) Marine sponge Craniella australiensis-associated bacterial diversity. In: Encyclopedia of metagenomics. Springer, Berlin, pp 1–9
Andrianasolo EH, Gross H, Goeger D, Musafija-Girt M, McPhail K, Leal RM, Mooberry SL, Gerwick WH (2005) Isolation of swinholide A and related glycosylated derivatives from two field collections of marine cyanobacteria. Org Lett 7(7):1375–1378. https://doi.org/10.1021/ol050188x. PMID 15787510
Armstrong E, McKenzie JD, Goldsworthy GT (1999) Aquaculture of sponges on scallops for natural products research and antifouling. J Biotechnol 70:163–174
Baker DD, Chu M, Oza U, Rajgarhia V (2007) The value of natural products to future pharmaceutical discovery. Nat Prod Rep 24(6):1225–1244. https://doi.org/10.1039/b602241n. PMID 18033577
Baker PW, Kennedy J, Dobson AD, Marchesi JR (2009) Phylogenetic diversity and antimicrobial activities of fungi associated with Haliclona simulans isolated from Irish coastal waters. Mar Biotechnol (NY) 11(4):540–547. https://doi.org/10.1007/s10126-008-9169-7. PMID 19083060
Bayer K, Scheuermayer M, Fieseler L, Hentschel U (2013) Genomic mining for novel FADH2-dependent halogenases in marine sponge-associated microbial consortia. Mar Biotechnol 15:63–72
Becerro MA, Turon X, Uriz MJ (1997) Multiple functions for secondary metabolites in encrusting marine invertebrates. J Chem Ecol 23(6):1527–1547. https://doi.org/10.1023/B:JOEC.0000006420.04002.2e
Béjà O, Aravind L, Koonin EV, Suzuki MT, Hadd A, Nguyen LP, Jovanovich SB, Gates CM, Feldman RA, Spudich JL, Spudich EN, DeLong EF (2000a) Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science 289(5486):1902–1906. https://doi.org/10.1126/science.289.5486.1902. PMID 10988064
Béjà O, Suzuki MT, Koonin EV, Aravind L, Hadd A, Nguyen LP, Villacorta R, Amjadi M, Garrigues C, Jovanovich SB, Feldman RA, DeLong EF (2000b) Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. Environ Microbiol 2(5):516–529. https://doi.org/10.1046/j.1462-2920.2000.00133.x. PMID 11233160
Belarbi EH, Contreras Gómez A, Chisti Y, García Camacho F, Molina Grima E (2003) Producing drugs from marine sponges. Biotechnol Adv 21(7):585–598. https://doi.org/10.1016/s0734-9750(03)00100-9. PMID 14516872
Brakhage AA (2013) Regulation of fungal secondary metabolism. Nat Rev Microbiol 11(1):21–32. https://doi.org/10.1038/nrmicro2916. PMID 23178386
Bringmann G, Gulder TA, Lang G, Schmitt S, Stöhr R, Wiese J, Nagel K, Imhoff JF (2007) Large-scale biotechnological production of the antileukemic marine natural product sorbicillactone A. Mar Drugs 5(2):23–30. https://doi.org/10.3390/md502023. PMID 18463724
Cortes J, Vahdat L, Blum JL, Twelves C, Campone M, Roché H, Bachelot T, Awada A, Paridaens R, Goncalves A, Shuster DE, Wanders J, Fang F, Gurnani R, Richmond E, Cole PE, Ashworth S, Allison MA (2010) Phase II study of the halichondrin B analog eribulin mesylate in patients with locally advanced or metastatic breast cancer previously treated with an anthracycline, a taxane, and capecitabine. J Clin Oncol 28(25):3922–3928. https://doi.org/10.1200/JCO.2009.25.8467. PMID 20679609
Costantino V, Fattorusso E, Imperatore C, Mangoni A (2001a) A biosynthetically significant new bacteriohopanoid present in large amounts in the Caribbean sponge Plakortis simplex. Tetrahedron 57(18):4045–4048. https://doi.org/10.1016/S0040-4020(01)00286-1
Costantino V, Fattorusso E, Imperatore C, Mangoni A (2001b) Plaxyloside from the marine sponge Plakortis simplex: an improved strategy for NMR structural studies of carbohydrate chains. Eur J Org Chem 2001:4457–4462
Courtois S, Cappellano CM, Ball M, Francou FX, Normand P, Helynck G, Martinez A, Kolvek SJ, Hopke J, Osburne MS, August PR, Nalin R, Guérineau 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(1):49–55. https://doi.org/10.1128/AEM.69.1.49-55.2003. PMID 12513976
Cueto M, Jensen PR, Kauffman C, Fenical W, Lobkovsky E, Clardy J (2001) Pestalone, a new antibiotic produced by a marine fungus in response to bacterial challenge. J Nat Prod 64(11):1444–1446. https://doi.org/10.1021/np0102713. PMID 11720529
Davidson SK, Allen SW, Lim GE, Anderson CM, Haygood MG (2001) Evidence for the biosynthesis of bryostatins by the bacterial symbiont ‘Candidatus Endobugula sertula’ of the bryozoan Bugula neritina. Appl Environ Microbiol 67(10):4531–4537. https://doi.org/10.1128/AEM.67.10.4531-4537.2001. PMID 11571152
Deane CD, Mitchell DA (2014) Lessons learned from the transformation of natural product discovery to a genomedriven endeavor. J Ind Microbiol Biotechnol 41(2):315–331. https://doi.org/10.1007/s10295-013-1361-8. PMID 24142337
Dharmaraj S (2010) Marine streptomyces as a novel source of bioactive substances. World J Microbiol Biotechnol 26(12):2123–2139. https://doi.org/10.1007/s11274-010-0415-6
Díez-Vives C, Moitinho-Silva L, Nielsen S, Reynolds D, Thomas T (2017) Expression of eukaryotic-like protein in the microbiome of sponges. Mol Ecol 26(5):1432–1451. https://doi.org/10.1111/mec.14003. PMID 28036141
Dobretsov S, Dahms HU, Qian PY (2005) Antibacterial and anti-diatom activity of Hong Kong sponges. Aquat Microb Ecol 38(2):191–201. https://doi.org/10.3354/ame038191
Esteves AIS, Amer N, Nguyen M, Thomas T (2016) Sample processing impacts the viability and cultivability of the sponge microbiome. Front Microbiol 7:499. https://doi.org/10.3389/fmicb.2016.00499. PMID 27242673
Fan L, Reynolds D, Liu M, Stark M, Kjelleberg S, Webster NS, Thomas T (2012) Functional equivalence and evolutionary convergence in complex communities of microbial sponge symbionts. Proc Natl Acad Sci U S A 109(27):E1878–E1887. https://doi.org/10.1073/pnas.1203287109. PMID 22699508
Faulkner DJ (2002) Marine natural products. Nat Prod Rep 19(1):1–48. https://doi.org/10.1039/b009029h. PMID 11902436
Felczykowska A, Krajewska A, Zielińska S, Łoś JM, Bloch SK, Nejman-Faleńczyk B (2015) The most widespread problems in the function-based microbial metagenomics. Acta Biochim Pol 62(1):161–166. https://doi.org/10.18388/abp.2014_917. PMID 25680374
Fieseler L, Horn M, Wagner M, Hentschel U (2004) Discovery of the novel candidate phylum Poribacteria in marine sponges. Appl Environ Microbiol 70(6):3724–3732
Fisch KM, Gurgui C, Heycke N, van der Sar SA, Anderson SA, Webb VL, Taudien S, Platzer M, Rubio BK, Robinson SJ, Crews P, Piel J (2009) Polyketide assembly lines of uncultivated sponge symbionts from structure-based gene targeting. Nat Chem Biol 5(7):494–501. https://doi.org/10.1038/nchembio.176. PMID 19448639
Freeman MF, Gurgui C, Helf MJ, Morinaka BI, Uria AR, Oldham NJ, Sahl HG, Matsunaga S, Piel J (2012) Metagenome mining reveals polytheonamides as post-translationally modified ribosomal peptides. Science 338(6105):387–390. https://doi.org/10.1126/science.1226121. PMID 22983711
Gabor EM, de Vries EJ, Janssen DB (2003) Efficient recovery of environmental DNA for expression cloning by indirect extraction methods. FEMS Microbiol Ecol 44(2):153–163. https://doi.org/10.1016/S0168-6496(02)00462-2. PMID 19719633
Gazave E, Lapébie P, Renard E, Vacelet J, Rocher C, Ereskovsky AV, Lavrov DV, Borchiellini C (2010) Molecular phylogeny restores the supra-generic subdivision of homoscleromorph sponges (Porifera, Homoscleromorpha). PLoS One 5(12):e14290. https://doi.org/10.1371/journal.pone.0014290. PMID 21179486
Gilbert JA, Jansson JK, Knight R (2014) The earth microbiome project: successes and aspirations. BMC Biol 12:69. https://doi.org/10.1186/s12915-014-0069-1. PMID 25184604
Gillespie DE, Brady SF, Bettermann AD, Cianciotto NP, Liles MR, Rondon MR, Clardy J, Goodman RM, Handelsman J (2002) Isolation of antibiotics turbomycin A and B from a metagenomic library of soil microbial DNA. Appl Environ Microbiol 68(9):4301–4306. https://doi.org/10.1128/AEM.68.9.4301-4306.2002. PMID 12200279
Ginolhac A, Jarrin C, Gillet B, Robe P, Pujic P, Tuphile K, Bertrand H, Vogel TM, Perrière 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(9):5522–5527. https://doi.org/10.1128/AEM.70.9.5522-5527.2004. PMID 15345440
Giovannoni SJ, Stingl U (2005) Molecular diversity and ecology of microbial plankton. Nature 437(7057):343–348. https://doi.org/10.1038/nature04158. PMID 16163344
Gloeckner V, Wehrl M, Moitinho-Silva L, Gernert C, Schupp P, Pawlik JR, Lindquist NL, Erpenbeck D, Wörheide G, Hentschel U (2014) The HMA-LMA dichotomy revisited: an electron microscopical survey of 56 sponge species. Biol Bull 227(1):78–88. https://doi.org/10.1086/BBLv227n1p78. PMID 25216505
Gomes ES, Schuch V, de Macedo Lemos EG (2013) Biotechnology of polyketides: new breath of life for the novel antibiotic genetic pathways discovery through metagenomics. Braz J Microbiol 44(4):1007–1034. https://doi.org/10.1590/s1517-83822013000400002. PMID 24688489
Gunasekera SP, Gunasekera M, Longley RE, Schulte GK (1990) Discodermolide: a new bioactive polyhydroxylated lactone from the marine sponge Discodermia dissoluta. J Org Chem 55(16):4912–4915. https://doi.org/10.1021/jo00303a029
Gurgui C, Piel J (2010) Metagenomic approaches to identify and isolate bioactive natural products from the microbiota of marine sponges. Methods Mol Biol 668:247–264. https://doi.org/10.1007/978-1-60761-823-2_17. PMID 20830569
Hardoim CCP, Cardinale M, Cúcio AC, Esteves AI, Berg G, Xavier JR, Cox CJ, Costa R (2014) Effects of sample handling and cultivation bias on the specificity of bacterial communities in keratose marine sponges. Front Microbiol 5:611. https://doi.org/10.3389/fmicb.2014.00611. PMID 25477868
He R, Wakimoto T, Egami Y, Kenmoku H, Ito T, Asakawa Y, Abe I (2012a) Heterologously expressed β-hydroxyl fatty acids from a metagenomic library of a marine sponge. Bioorg Med Chem Lett 22(24):7322–7325. https://doi.org/10.1016/j.bmcl.2012.10.082. PMID 23127887
He R, Wakimoto T, Takeshige Y, Egami Y, Kenmoku H, Ito T, Wang BC, Asakawa Y, Abe I (2012b) Porphyrins from a metagenomic library of the marine sponge Discodermia calyx. Mol Biosyst 8(9):2334–2338. https://doi.org/10.1039/c2mb25169h. PMID 22735778
He R, Wang B, Wakimoto T, Wang M, Zhu L, Abe I (2013) Cyclodipeptides from metagenomics library of a Japanese marine sponge. J Braz Chem Soc 24:1926–1932. https://doi.org/10.5935/0103-5053.20130240
Hellio C, Tsoukatou M, Maréchal JP, Aldred N, Beaupoil C, Clare AS, Vagias C, Roussis V (2005) Inhibitory effects of Mediterranean sponge extracts and metabolites on larval settlement of the barnacle Balanus amphitrite. Mar Biotechnol (NY) 7(4):297–305. https://doi.org/10.1007/s10126-004-3150-x. PMID 15971089
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(9):4431–4440. https://doi.org/10.1128/AEM.68.9.4431-4440.2002PMID 12200297
Hentschel U, Piel J, Degnan SM, Taylor MW (2012) Genomic insights into the marine sponge microbiome. Nat Rev Microbiol 10(9):641–654. https://doi.org/10.1038/nrmicro2839. PMID 22842661
Higgs MD, Faulkner DJ (1978) Plakortin, an antibiotic from Plakortis halichondrioides. J Org Chem 43(18):3454–3457. https://doi.org/10.1021/jo00412a006
Hochmuth T, Piel J (2009) Polyketide synthases of bacterial symbionts in sponges—evolution-based applications in natural products research. Phytochemistry 70(15–16):1841–1849. https://doi.org/10.1016/j.phytochem.2009.04.010. PMID 19443000
Hoffmann F, Larsen O, Thiel V, Rapp HT, Pape T, Michaelis W, Reitner J (2005) An anaerobic world in sponges. Geomicrobiol J 22(1–2):1–10. https://doi.org/10.1080/01490450590922505
Human Microbiome Project (2012) Structure, function and diversity of the healthy human microbiome. Nature 486(7402):207–214. https://doi.org/10.1038/nature11234. PMID 22699609
Jenke-Kodama H, Dittmann E (2009) Evolution of metabolic diversity: insights from microbial polyketide synthases. Phytochemistry 70(15–16):1858–1866. https://doi.org/10.1016/j.phytochem.2009.05.021. PMID 19619887
Jimeno J, López-Martín JA, Ruiz-Casado A, Izquierdo MA, Scheuer PJ, Rinehart K (2004) Progress in the clinical development of new marine-derived anticancer compounds. Anti Cancer Drugs 15(4):321–329. https://doi.org/10.1097/00001813-200404000-00003. PMID 15057135
Kaeberlein T, Lewis K, Epstein SS (2002) Isolating “uncultivable” microorganisms in pure culture in a simulated natural environment. Science 296(5570):1127–1129. https://doi.org/10.1126/science.1070633. PMID 12004133
Kato Y, Fusetani N, Matsunaga S, Hashimoto K, Fujita S, Furuya T (1986) Bioactive marine metabolites. Part 16. Calyculin A. A novel antitumor metabolite from the marine sponge Discodermia calyx. J Am Chem Soc 108(10):2780–2781. https://doi.org/10.1021/ja00270a061
Katz M, Hover BM, Brady SF (2016) Culture-independent discovery of natural products from soil metagenomes. J Ind Microbiol Biotechnol 43(2–3):129–141. https://doi.org/10.1007/s10295-015-1706-6. PMID 26586404
Kennedy J, Marchesi JR, Dobson ADW (2007) Metagenomic approaches to exploit the biotechnological potential of the microbial consortia of marine sponges. Appl Microbiol Biotechnol 75(1):11–20. https://doi.org/10.1007/s00253-007-0875-2. PMID 17318533
Kennedy J, Marchesi JR, Dobson ADW (2008) Marine metagenomics: strategies for discovering novel enzymes with biotechnological applications from marine environments. Microb Cell Fact 7(27):27. https://doi.org/10.1186/1475-2859-7-27. PMID 18717988
Kennedy J, Flemer B, Jackson SA, Lejon DPH, Morrissey JP, O’Gara F, Dobson ADW (2010) Marine metagenomics: new tools for studying and exploiting marine microbial metabolism. Mar Drugs 8(3):608–628. https://doi.org/10.3390/md8030608. PMID 20411118
Khan ST, Komaki H, Motohashi K, Kozone I, Mukai A, Takagi M, Shin-Ya K (2011) Streptomyces associated with a marine sponge Haliclona sp.; biosynthetic genes for secondary metabolites and products. Environ Microbiol 13(2):391–403. https://doi.org/10.1111/j.1462-2920.2010.02337.x. PMID 20849448
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. https://doi.org/10.1111/j.1462-2920.2005.00716.x. PMID 15816928
Kimura M, Wakimoto T, Egami Y, Tan KC, Ise Y, Abe I (2012) Calyxamides A and B, cytotoxic cyclic peptides from the marine sponge Discodermia calyx. J Nat Prod 75(2):290–294. https://doi.org/10.1021/np2009187. PMID 22276742
Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, Glöckner FO (2013) Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res 41(1):e1. https://doi.org/10.1093/nar/gks808. PMID 22933715
Knappe TA, Linne U, Zirah S, Rebuffat S, **e X, Marahiel MA (2008) Isolation and structural characterization of capistruin, a lasso peptide predicted from the genome sequence of Burkholderia thailandensis E264. J Am Chem Soc 130(34):11446–11454. https://doi.org/10.1021/ja802966g. PMID 18671394
Kodzius R, Gojobori T (2015) Marine metagenomics as a source for bioprospecting. Mar Genomics 24(1):21–30. https://doi.org/10.1016/j.margen.2015.07.001. PMID 26204808
Kurnia NM, Uria AR, Kusnadi Y, Dinawati L, Zilda DS, Hadi TA, Setyahadi S, Felix F (2017) Metagenomic survey of potential symbiotic bacteria and polyketide synthase genes in an Indonesian marine sponge. HAYATI J Biosci 4(1):6–15. https://doi.org/10.1016/j.hjb.2017.04.004
Lane AL, Moore BS (2012) A sea of biosynthesis: marine natural products meet the molecular age. Nat Prod Rep 28(2):411–428
Laroche M, Imperatore C, Grozdanov L, Costantino V, Mangoni A, Hentschel U, Fattorusso E (2007) Cellular localisation of secondary metabolites isolated from the Caribbean sponge Plakortis simplex. Mar Biol 151(4):1365–1373. https://doi.org/10.1007/s00227-006-0572-1
Lee YK, Lee JH, Lee HK (2001) Microbial symbiosis in marine sponges. J Microbiol 39:254–264
Lee OO, Lau SCK, Qian PY (2006) Defense against epibiosis in the sponge Mycale adhaerens: modulating the bacterial community associated with its surface. Aquat Microb Ecol 43:55–65. https://doi.org/10.3354/ame043055
Li ZY, Wang YZ, He LM, Zheng HJ (2014) Metabolic profiles of prokaryotic and eukaryotic communities in deep-sea sponge Neamphius huxleyi indicated by metagenomics. Sci Rep 4:3895. https://doi.org/10.1038/srep03895. PMID 24463735
Lipko IA, Kalyuzhnaya OV, Kravchenko OS, Parfenova VV (2012) Identification of polyketide synthase genes in genome of Pseudomonas fluorescens strain 28Bb-06 from freshwater sponge Baikalospongia bacillifera. Mol Biol 46(4):609–611. https://doi.org/10.1134/S0026893312040073
Lipton AP, Pramitha VS, Selvin J, Huxley AJ (2006) Bioactivity profile of sponge-associated bacteria isolated from marine sponges, Callyspongia sp. and Sigmadocia sp. In: 7th international sponge symposium, vol 2006, Buzios-Rio de Janeiro, Brazil, p 250
Maldonado M, Aguilar R, Bannister R, Bell J, Conway K, Dayton P et al (2015) Sponge grounds as key marine habitats: a synthetic review of types, structure, functional roles and conservation concerns. In: Rossi S, Bramanti L, Gori A, Orejas C (eds) Marine animal forests. Springer, Cham, pp 1–39
Manzo E, Ciavatta ML, Villani G, Varcamonti M, Sayem SM, van Soest R, Gavagnin M (2011) Bioactive terpenes from Spongia officinalis. J Nat Prod 74(5):1241–1247. https://doi.org/10.1021/np200226u. PMID 21548580
Martinez A, Kolvek SJ, Yip CLT, Hopke J, Brown KA, MacNeil IA, Osburne MS (2004) Genetically modified bacterial strains and novel bacterial artificial chromosome shuttle vectors for constructing environmental libraries and detecting heterologous natural products in multiple expression hosts. Appl Environ Microbiol 70(4):2452–2463. https://doi.org/10.1128/AEM.70.4.2452-2463.2004. PMID 15066844
Matroodi S, Siitonen V, Baral B, Yamada K, Akhgari A, Metsä-Ketelä M (2020) Genoty**-guided discovery of Persiamycin a from sponge-associated halophilic Streptomonospora sp. PA3. Front Microbiol 11:1237. https://doi.org/10.3389/fmicb.2020.01237. PMID 32582127
McClintock JB, Amsler CD, Baker BJ, Van Soest RWM (2005) Ecology of Antarctic marine sponges: an overview. Integr Comp Biol 45(2):359–368. https://doi.org/10.1093/icb/45.2.359. PMID 21676781
Medema MH, Blin K, Cimermancic P, de Jager V, Zakrzewski P, Fischbach MA, Weber T, Takano E, Breitling R (2011) AntiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res 39(Web Server issue):W339–W346. https://doi.org/10.1093/nar/gkr466. PMID 21672958
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(8):4539–4577. https://doi.org/10.3390/md12084539. PMID 25196730
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):1–6. https://doi.org/10.1111/j.1574-6968.1999.tb08770.x. PMID 10547437
Milshteyn A, Schneider JS, Brady SF (2014) Mining the metabiome: identifying novel natural products from microbial communities. Chem Biol 21(9):1211–1223. https://doi.org/10.1016/j.chembiol.2014.08.006. PMID 25237864
Mocali S, Benedetti A (2010) Exploring research frontiers in microbiology: the challenge of metagenomics in soil microbiology. Res Microbiol 161(6):497–505. https://doi.org/10.1016/j.resmic.2010.04.010. PMID 20452420
Moitinho-Silva L, Díez-Vives C, Batani G, Esteves AI, Jahn MT, Thomas T (2017a) Integrated metabolism in sponge-microbe symbiosis revealed by genome-centered metatranscriptomics. ISME J 11(7):1651–1666. https://doi.org/10.1038/ismej.2017.25. PMID 28338677
Moitinho-Silva L, Nielsen S, Amir A, Gonzalez A, Ackermann GL, Cerrano C, Astudillo-Garcia C, Easson C, Sipkema D, Liu F, Steinert G, Kotoulas G, McCormack GP, Feng G, Bell JJ, Vicente J, Björk JR, Montoya JM, Olson JB, Reveillaud J, Steindler L, Pineda MC, Marra MV, Ilan M, Taylor MW, Polymenakou P, Erwin PM, Schupp PJ, Simister RL, Knight R, Thacker RW, Costa R, Hill RT, Lopez-Legentil S, Dailianis T, Ravasi T, Hentschel U, Li Z, Webster NS, Thomas T (2017b) The sponge microbiome project. Gigascience 6(10):1–7. https://doi.org/10.1093/gigascience/gix077. PMID 29020741
Monks NR, Lerner C, Henriques AT, Farias FM, Schapoval EES, Suyenaga ES, da Rocha AB, Schwartsmann G, Mothes B (2002) Anticancer, antichemotactic and antimicrobial activities of marine sponges collected off the coast of Santa Catarina, southern Brazil. J Exp Mar Biol Ecol 281(1–2):1–12. https://doi.org/10.1016/S0022-0981(02)00380-5
Mori T, Cahn JKB, Wilson MC, Meoded RA, Wiebach V, Martinez AFC, Helfrich EJN, Albersmeier A, Wibberg D, Dätwyler S, Keren R, Lavy A, Rückert C, Ilan M, Kalinowski J, Matsunaga S, Takeyama H, Piel J (2018) Single-bacterial genomics validates rich and varied specialized metabolism of uncultivated Entotheonella sponge symbionts. Proc Natl Acad Sci U S A 115(8):1718–1723. https://doi.org/10.1073/pnas.1715496115. PMID 29439203
Newman DJ, Cragg GM, Snader KM (2000) The influence of natural products upon drug discovery. Nat Prod Rep 17(3):215–234. https://doi.org/10.1039/a902202c. PMID 10888010
Ng TB, Cheung RCF, Wong JH, Bekhit AA, Ael-D B (2015) Antibacterial products of marine organisms. Appl Microbiol Biotechnol 99(10):4145–4173. https://doi.org/10.1007/s00253-015-6553-x. PMID 25874533
Nikolouli K, Mossialos D (2012) Bioactive compounds synthesized by nonribosomal peptide synthetases and type-I polyketide synthases discovered through genome-mining and metagenomics. Biotechnol Lett 34(8):1393–1403. https://doi.org/10.1007/s10529-012-0919-2. PMID 22481301
Ogram A, Sayler GS, Barkay T (1987) The extraction and purification of microbial DNA from sediments. J Microbiol Methods 7(2–3):57–66. https://doi.org/10.1016/0167-7012(87)90025-X
Osinga R, Tramper J, Wijffels RH (1998) Cultivation of marine sponges for metabolite production: applications for biotechnology? Trends Biotechnol 16(3):130–134. https://doi.org/10.1016/S0167-7799(97)01164-5
Ouyang Y, Dai S, **e L, Ravi Kumar MSR, Sun W, Sun H, Tang D, Li X (2010) Isolation of high molecular weight DNA from marine sponge bacteria for BAC library construction. Mar Biotechnol (NY) 12(3):318–325. https://doi.org/10.1007/s10126-009-9223-0. PMID 19685098
Passarini MRZ, Miqueletto PB, de Oliveira VM, Sette LD (2015) Molecular diversity of fungal and bacterial communities in the marine sponge Dragmacidon reticulatum. J Basic Microbiol 55(2):207–220. https://doi.org/10.1002/jobm.201400466. PMID 25213208
Penesyan A, Kjelleberg S, Egan S (2010) Development of novel drugs from marine surface associated microorganisms. Mar Drugs 8(3):438–459. https://doi.org/10.3390/md8030438. PMID 20411108
Piel J (2004) Metabolites from symbiotic bacteria. Nat Prod Rep 21(4):519–538. https://doi.org/10.1039/b310175b. PMID 15282634
Piel J (2010) Biosynthesis of polyketides by trans-AT polyketide synthases. Nat Prod Rep 27(7):996–1047. https://doi.org/10.1039/b816430b. PMID 20464003
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(46):16222–16227. https://doi.org/10.1073/pnas.0405976101. PMID 15520376
Pimentel-Elardo SM, Grozdanov L, Proksch S, Hentschel U (2012) Diversity of nonribosomal peptide synthetase genes in the microbial metagenomes of marine sponges. Mar Drugs 10(6):1192–1202. https://doi.org/10.3390/md10061192. PMID 22822366
Pineda MC, Duckworth A, Webster N (2015) Appearance matters: sedimentation effects on different sponge morphologies. J Mar Biol Assoc 96:481–492
Pita L, Turon X, López-Legentil S, Erwin PM (2013) Hosts. Host rules: spatial stability of bacterial communities associated with marine sponges (Ircinia spp.) in the Western Mediterranean Sea. FEMS Microbiol Ecol 86(2):268–276. https://doi.org/10.1111/1574-6941.12159. PMID 23837533
Pomponi SA (1999) The bioprocess—technological potential of the sea. J Biotechnol 70(1–3):5–13. https://doi.org/10.1016/S0168-1656(99)00053-X
Preston CM, Wu KY, Molinski TF, DeLong EF (1996) A psychrophilic crenarchaeon inhabits a marine sponge: Cenarchaeum symbiosum gen. nov., sp. nov. Proc Natl Acad Sci U S A 93(13):6241–6246. https://doi.org/10.1073/pnas.93.13.6241. PMID 8692799
Proksch P, Edrada RA, Ebel R (2002) Drugs from the sea—current status and microbiological implications. Appl Microbiol Biotechnol 59(2–3):125–134. https://doi.org/10.1007/s00253-002-1006-8. PMID 12111137
Rifai S, Fassouane AF, Kijjoa A, Van Soest R (2004) Antimicrobial activity of Untenospongin B, a metabolite from the marine sponge Hippospongia communis collected from the Atlantic Coast of Morocco. Mar Drugs 2(3):147–153. https://doi.org/10.3390/md203147
Rocha-Martin J, Harrington C, Dobson ADW, O’Gara F (2014) Emerging strategies and integrated systems microbiology technologies for biodiscovery of marine bioactive compounds. Mar Drugs 12(6):3516–3559. https://doi.org/10.3390/md12063516. PMID 24918453
Rohde S, Nietzer S, Schupp PJ (2015) Prevalence and mechanisms of dynamic chemical defenses in tropical sponges. PLoS One 10(7):e0132236. https://doi.org/10.1371/journal.pone.0132236. PMID 26154741
Scherlach K, Hertweck C (2009) Triggering cryptic natural product biosynthesis in microorganisms. Org Biomol Chem 7(9):1753–1760. https://doi.org/10.1039/b821578b. PMID 19590766
Schloss PD, Handelsman J (2003) Biotechnological prospects from metagenomics. Curr Opin Biotechnol 14(3):303–310. https://doi.org/10.1016/s0958-1669(03)00067-3. PMID 12849784
Schmeisser C, Steele H, Streit WR (2007) Metagenomics, biotechnology with non-culturable microbes. Appl Microbiol Biotechnol 75(5):955–962. https://doi.org/10.1007/s00253-007-0945-5. PMID 17396253
Selvin J, Gandhimathi R, Kiran GS, Priya SS, Ravji TR, Hema TA (2009) Culturable heterotrophic bacteria from the marine sponge Dendrilla nigra: isolation and phylogenetic diversity of actinobacteria. Helgol Mar Res 63(3):239–247. https://doi.org/10.1007/s10152-009-0153-z
Selvin J, Ninawe AS, Kiran GS, Lipton AP (2010) Sponge microbial interactions: ecological implications and bioprospecting avenues. Crit Rev Microbiol 36(1):82–90. https://doi.org/10.3109/10408410903397340. PMID 20088685
Siegl A, Kamke J, Hochmuth T, Piel J, Richter M, Liang C, Dandekar T, Hentschel U (2011) Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges. ISME J 5(1):61–70. https://doi.org/10.1038/ismej.2010.95. PMID 20613790
Singh BK, MacDonald CA (2010) Drug discovery from uncultivable microorganisms. Drug Discov Today 15(17–18):792–799. https://doi.org/10.1016/j.drudis.2010.07.002. PMID 20656054
Sipkema D, Schippers K, Maalcke WJ, Yang Y, Salim S, Blanch HW (2011) Multiple approaches to enhance the cultivability of bacteria associated with the marine sponge Haliclona (Gellius) sp. Appl Environ Microbiol 77(6):2130–2140. https://doi.org/10.1128/AEM.01203-10. PMID 21296954
Skinnider MA, Dejong CA, Rees PN, Johnston CW, Li H, Webster ALH, Wyatt MA, Magarvey NA (2015) Genomes to natural products PRediction informatics for secondary metabolomes (PRISM). Nucleic Acids Res 43(20):9645–9662. https://doi.org/10.1093/nar/gkv1012. PMID 26442528
Sleator RD, Shortall C, Hill C (2008) Metagenomics. Lett Appl Microbiol 47(5):361–366. https://doi.org/10.1111/j.1472-765X.2008.02444.x. PMID 19146522
Stein JL, Marsh TL, Wu KY, Shizuya H, DeLong EF (1996) Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon. J Bacteriol 178(3):591–599. https://doi.org/10.1128/jb.178.3.591-599.1996. PMID 8550487
Stierle AC, Cardellina JH, Singleton FL (1988) A marine micrococcus produces metabolites ascribed to the sponge Tedania ignis. Experientia 44(11–12):1021. https://doi.org/10.1007/BF01939910. PMID 3197807
Taylor MW, Radax R, Steger D, Wagner M (2007) Sponge-associated microorganisms: evolution, ecology, and biotechnological potential. Microbiol Mol Biol Rev 71(2):295–347. https://doi.org/10.1128/MMBR.00040-06. PMID 17554047
Thomas T, Rusch D, DeMaere MZ, Yung PY, Lewis M, Halpern A, Heidelberg KB, Egan S, Steinberg PD, Kjelleberg S (2010) Functional genomic signatures of sponge bacteria reveal unique and shared features of symbiosis. ISME J 4(12):1557–1567. https://doi.org/10.1038/ismej.2010.74. PMID 20520651
Thomas T, Moitinho-Silva L, Lurgi M, Björk JR, Easson C, Astudillo-García C, Olson JB, Erwin PM, López-Legentil S, Luter H, Chaves-Fonnegra A, Costa R, Schupp PJ, Steindler L, Erpenbeck D, Gilbert J, Knight R, Ackermann G, Victor Lopez J, Taylor MW, Thacker RW, Montoya JM, Hentschel U, Webster NS (2016) Diversity, structure and convergent evolution of the global sponge microbiome. Nat Commun 7:11870. https://doi.org/10.1038/ncomms11870. PMID 27306690
Trindade M, van Zyl LJ, Navarro-Fernández J, Abd Elrazak A (2015) Targeted metagenomics as a tool to tap into marine natural product diversity for the discovery and production of drug candidates. Front Microbiol 6:890. https://doi.org/10.3389/fmicb.2015.00890. PMID 26379658
Ueoka R, Uria AR, Reiter S, Mori T, Karbaum P, Peters EE, Helfrich EJN, Morinaka BI, Gugger M, Takeyama H, Matsunaga S, Piel J (2015) Metabolic and evolutionary origin of actin-biding polyketides from diverse organisms. Nat Chem Biol 11:705.e12
Unson MD, Faulkner DJ (1993) Cyanobacterial symbiont biosynthesis of chlorinated metabolites from Dysidea herbacea (Porifera). Experientia 49(4):349–353. https://doi.org/10.1007/BF01923420
Uria AR, Fawzya YN, Chasanah E (2005) Novel molecular methods for discovery and engineering of biocatalysts from uncultured marine microorganisms. J Coast Dev 8(2):53–71
Uriz MJ, Turon X, Becerro MA, Galera J (1996) Feeding deterrence in sponges. The role of toxicity, physical defenses, energetic contents, and life-history stage. J Exp Mar Biol Ecol 205(1–2):187–204. https://doi.org/10.1016/S0022-0981(96)02609-3
van Soest RWM, Boury-Esnault N, Vacelet J, Dohrmann M, Erpenbeck D, De Voogd NJ et al (2012) Global diversity of sponges (Porifera). PLoS One 7(4):e35105. https://doi.org/10.1371/journal.pone.0035105. PMID 22558119
Vogel S (1977) Current-induced flow through living sponges in nature. Proc Natl Acad Sci U S A 74(5):2069–2071. https://doi.org/10.1073/pnas.74.5.2069. PMID 266728
Webster NS, Hill RT (2001) The culturable community of the Great Barrier Reef sponge Rhopaloeidesodorabile is dominated by an proteobacterium. Mar Biol 138(4):843–851. https://doi.org/10.1007/s002270000503
Webster NS, Thomas T (2016) The sponge hologenome. mBio 7(2):e00135-16. https://doi.org/10.1128/mBio.00135-16. PMID 27103626
Webster NS, Wilson KJ, Blackall LL, Hill RT (2001) Phylogenetic diversity of bacteria associated with the marine sponge Rhopaloeidesodorabile. Appl Environ Microbiol 67(1):434–444. https://doi.org/10.1128/AEM.67.1.434-444.2001. PMID 11133476
Weiland N, Löscher C, Metzger R, Schmitz R (2010) Construction and screening of marine metagenomic libraries. Methods Mol Biol 668:51–65
Wilson MC, Piel J (2013) Metagenomic approaches for exploiting uncultivated bacteria as a resource for novel biosynthetic enzymology. Chem Biol 20(5):636–647. https://doi.org/10.1016/j.chembiol.2013.04.011. PMID 23706630
Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, Hooper SD, Pati A, Lykidis A, Spring S, Anderson IJ, D’haeseleer P, Zemla A, Singer M, Lapidus A, Nolan M, Copeland A, Han C, Chen F, Cheng JF, Lucas S, Kerfeld C, Lang E, Gronow S, Chain P, Bruce D, Rubin EM, Kyrpides NC, Klenk HP, Eisen JA (2009) A phylogeny-driven genomic encyclopaedia of bacteria and archaea. Nature 462(7276):1056–1060. https://doi.org/10.1038/nature08656. PMID 20033048
Yun J, Ryu S (2005) Screening for novel enzymes from metagenome and SIGEX, as a way to improve it. Microb Cell Factories 4(1):8. https://doi.org/10.1186/1475-2859-4-8. PMID 15790425
Zhang W, Zhang X, Cao X, Xu J, Zhao Q, Yu X, ** M, Deng M (2003) Optimizing the formation of in vitro sponge primmorphs from the Chinese sponge Stylotella agminata (Ridley). J Biotechnol 100(2):161–168. https://doi.org/10.1016/s0168-1656(02)00255-9. PMID 12423910
Zhang L, An R, Wang J, Sun N, Zhang S, Hu J, Kuai J (2005) Exploring novel bioactive compounds from marine microbes. Curr Opin Microbiol 8(3):276–281. https://doi.org/10.1016/j.mib.2005.04.008. PMID 15939350
Zhang F, Blasiak LC, Karolin JO, Powell RJ, Geddes CD, Hill RT (2015) Phosphorus sequestration in the form of polyphosphate by microbial symbionts in marine sponges. Proc Natl Acad Sci U S A 112(14):4381–4386. https://doi.org/10.1073/pnas.1423768112. PMID 25713351
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Berde, C.V., Berde, V.B., Reddy, P.N., Veera Bramhachari, P. (2023). Bioprospection of Marine Sponge Microbiome for Bioactive Metabolites Employing Advanced Metagenomics Tools. In: Veera Bramhachari, P., Berde, C.V. (eds) Marine Bioactive Molecules for Biomedical and Pharmacotherapeutic Applications. Springer, Singapore. https://doi.org/10.1007/978-981-99-6770-4_2
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