Erratum: Evidence of a putative deep sea specific microbiome in marine sponges (PLoS ONE (2014) 9, 3 (e91092) DOI:10.1371/journal.pone.0091092);Evidence of a putative deep sea specific microbiome in marine sponges

PLoS ONE

Volumn 9, Issue 3, 2014, Pages

  Kennedy, Jonathan ^a   Flemer, Burkhardt ^a   Jackson, Stephen A ^a   Morrissey, John P ^a   O'Gara, Ferghal ^a,b   Dobson, Alan D W ^a  

^a UNIVERSITY COLLEGE CORK   (Ireland)

^b CURTIN UNIVERSITY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S; SEA WATER;

16S RRNA GENE; ARCHAEON; ARTICLE; CHROMATIALES; DEEP SEA SPECIES; INFLATELLA PELLICULA; LISSODENDORYX DIVERSICHELA; MARINE BACTERIUM; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; MICROBIOME; NONHUMAN; NUCLEOTIDE SEQUENCE; POECILLASTRA COMPRESSA; PYROSEQUENCING; SPONGE (PORIFERA); STELLETTA NORMANI; THAUMARCHAEOTA; ANIMAL; AQUATIC SPECIES; BACTERIUM; BIODIVERSITY; CLASSIFICATION; CLUSTER ANALYSIS; DNA SEQUENCE; GENETICS; MICROBIOLOGY; MICROFLORA; MOLECULAR GENETICS; PHYLOGENY;

ANIMALS; AQUATIC ORGANISMS; ARCHAEA; BACTERIA; BIODIVERSITY; CLUSTER ANALYSIS; MICROBIOTA; MOLECULAR SEQUENCE DATA; PHYLOGENY; PORIFERA; RNA, RIBOSOMAL, 16S; SEAWATER; SEQUENCE ANALYSIS, DNA;

EID: 84899953755     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0103400     Document Type: Erratum

References (54)

1. Weisz JB, Lindquist N, Martens CS (2008) Do associated microbial abundances impact marine demosponge pumping rates and tissue densities. Oecologia 155: 367-376. doi:10.1007/s00442-007-0910-0
2. Taylor MW, Radax R, Steger D, Wagner M (2007) Sponge-associated microorganisms: evolution, ecology, and biotechnological potential. Microbiol Mol Biol Rev 71: 295-347. doi:10.1128/MMBR.00040-06 (Pubitemid 46954308)
3. Webster NS, Taylor MW, Behnam F, Lücker S, Rattei T, et al. (2010) Deep sequencing reveals exceptional diversity and modes of transmission for bacterial sponge symbionts. Environ Microbiol 12: 2070-2082. doi:10.1111/j.1462-2920.2009.02065.x
4. Hentschel U, Fieseler L, Wehrl M, Gernert C, Steinert M, et al. (2003) Microbial diversity of marine sponges. In: Mueller W, editor. Marine Molecular Biotechnology. Berlin: Springer. pp. 59-88.
5. Hentschel U, Schmid M, Wagner M, Fieseler L, Gernert C, et al. (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. (Pubitemid 32320007)
6. Webster NS, Hill RT (2001) The culturable microbial community of the Great Barrier Reef sponge Rhopaloeides odorabile is dominated by an a-Proteobacterium. Marine Biology 138: 843-851. doi:10.1007/s002270000503 (Pubitemid 32406429)
7. Kennedy J, Baker P, Piper C, Cotter PD, Walsh M, et al. (2009) Isolation and analysis of bacteria with antimicrobial activities from the marine sponge Haliclona simulans collected from Irish waters. Mar Biotechnol (NY) 11: 384-396. doi:10.1007/s10126-008-9154-1
8. Flemer B, Kennedy J, Margassery LM, Morrissey JP, O'Gara F, et al. (2012) Diversity and antimicrobial activities of microbes from two Irish marine sponges, Suberites carnosus and Leucosolenia sp. J Appl Microbiol 112: 289-301. doi:10.1111/j.1365-2672.2011.05211.x
9. Webster NS, Watts JE, Hill RT (2001) Detection and phylogenetic analysis of novel crenarchaeote and euryarchaeote 16S ribosomal RNA gene sequences from a Great Barrier Reef sponge. Mar Biotechnol (NY) 3: 600-608. doi:10.1007/s10126- 001-0065-7. (Pubitemid 34115376)
10. 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. doi:10.1111/j.1574-6941.2006. 00217.x (Pubitemid 44952408)
11. Kennedy J, Codling CE, Jones B V, 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. doi:10.1111/ j.1462-2920.2008.01614.x
12. Sogin ML, Morrison HG, Huber JA, Mark Welch D, Huse SM, et al. (2006) Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc Natl Acad Sci U S A 103: 12115-12120. doi:10.1073/pnas. 0605127103 (Pubitemid 44215820)
13. Lee OO, Wang Y, Yang J, Lafi FF, Al-Suwailem A, et al. (2011) Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea. ISME J 5: 650-664. doi:10.1038/ismej.2010.165
14. Schmitt S, Hentschel U, Taylor MW (2011) Deep sequencing reveals diversity and community structure of complex microbiota in five Mediterranean sponges. Hydrobiologia 687: 341-351. doi:10.1007/s10750-011-0799-9
15. Jackson SA, Kennedy J, Morrissey JP, O'Gara F, Dobson ADW (2012) Pyrosequencing reveals diverse and distinct sponge-specific microbial communities in sponges from a single geographical location in Irish waters. Microb Ecol 64: 105-116. doi:10.1007/s00248-011-0002-x
16. Radax R, Rattei T, Lanzen A, Bayer C, Rapp HT, et al. (2012) Metatranscriptomics of the marine sponge Geodia barretti: tackling phylogeny and function of its microbial community. Environ Microbiol 14: 1308-1324. doi:10.1111/j.1462-2920.2012.02714.x
17. White JR, Patel J, Ottesen A, Arce G, Blackwelder P, et al. (2012) Pyrosequencing of bacterial symbionts within Axinella corrugata sponges: diversity and seasonal variability. PLoS One 7: e38204. doi:10.1371/journal. pone.0038204
18. Trindade-Silva AE, Rua C, Silva GGZ, Dutilh BE, Moreira APB, et al. (2012) Taxonomic and functional microbial signatures of the endemic marine sponge Arenosclera brasiliensis. PLoS One 7: e39905. doi:10.1371/journal.pone. 0039905
19. Schmitt S, Tsai P, Bell J, Fromont J, Ilan M, et al. (2012) Assessing the complex sponge microbiota: core, variable and species-specific bacterial communities in marine sponges. ISME J 6: 564-576. doi:10.1038/ismej.2011.116
20. Simister RL, Deines P, Botté ES, Webster NS, Taylor MW (2012) Sponge-specific clusters revisited: a comprehensive phylogeny of sponge-associated microorganisms. Environ Microbiol 14: 517-524. doi:10.1111/j.1462-2920.2011.02664.x
21. Romanenko LA, Uchino M, Tanaka N, Frolova GM, Mikhailov V V (2008) Lysobacter spongiicola sp. nov., isolated from a deep-sea sponge. Int J Syst Evol Microbiol 58: 370-374. doi:10.1099/ijs.0.65391-0 (Pubitemid 351298408)
22. Romanenko LA, Uchino M, Falsen E, Frolova GM, Zhukova N V, et al. (2005) Pseudomonas pachastrellae sp. nov., isolated from a marine sponge. Int J Syst Evol Microbiol 55: 919-924. doi:10.1099/ijs.0.63176-0 (Pubitemid 40485091)
23. Brück WM, Sennett SH, Pomponi SA, Willenz P, McCarthy PJ (2008) Identification of the bacterial symbiont Entotheonella sp. in the mesohyl of the marine sponge Discodermia sp. ISME J 2: 335-339. doi:10.1038/ismej.2007.91 (Pubitemid 351334281)
24. Brück WM, Brück TB, Self WT, Reed JK, Nitecki SS, et al. (2010) Comparison of the anaerobic microbiota of deep-water Geodia spp. and sandy sediments in the Straits of Florida. ISME J 4: 686-699. doi:10.1038/ismej.2009. 149
25. 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. doi:10.1007/s00248-007-9348-5
26. Thiel V, Leininger S, Schmaljohann R, Brümmer F, Imhoff JF (2007) Spongespecific bacterial associations of the Mediterranean sponge Chondrilla nucula (Demospongiae, Tetractinomorpha). Microb Ecol 54: 101-111. doi:10.1007/s00248-006-9177-y (Pubitemid 47036686)
27. Gunasekera SP, Zuleta IA, Longley RE, Wright AE, Pomponi SA (2003) Discorhabdins S, T, and U, new cytotoxic pyrroloiminoquinones from a deepwater Caribbean sponge of the genus Batzella. J Nat Prod 66: 1615-1617. doi:10.1021/np030292s (Pubitemid 38036718)
28. Hickford SJH, Blunt JW, Munro MHG (2009) Antitumour polyether macrolides: four new halichondrins from the New Zealand deep-water marine sponge Lissodendoryx sp. Bioorg Med Chem 17: 2199-2203. doi:10.1016/j.bmc.2008.10.093
29. Radax R, Hoffmann F, Rapp HT, Leininger S, Schleper C (2012) Ammonia-oxidizing archaea as main drivers of nitrification in cold-water sponges. Environ Microbiol 14: 909-923. doi:10.1111/j.1462-2920.2011.02661.x
30. Pape T, Hoffmann F, Quéric N-V, Juterzenka K, Reitner J, et al. (2006) Dense populations of Archaea associated with the demosponge Tentorium semisuberites Schmidt, 1870 from Arctic deep-waters. Polar Biology 29: 662-667. doi:10.1007/s00300-005-0103-4 (Pubitemid 43999272)
31. Bragg L, Stone G, Imelfort M, Hugenholtz P, Tyson GW (2012) Fast, accurate error-correction of amplicon pyrosequences using Acacia. Nat Methods 9: 425-426. doi:10.1038/nmeth.1990
32. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, et al. (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7: 335-336. doi:10.1038/nmeth.f.303
33. 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: 6241-6246. (Pubitemid 26230289)
34. Hallam SJ, Konstantinidis KT, Putnam N, Schleper C, Watanabe Y, et al. (2006) Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum. Proc Natl Acad Sci U S A 103: 18296-18301. doi:10.1073/pnas. 0608549103 (Pubitemid 44871652)
35. Walker CB, de la Torre JR, Klotz MG, Urakawa H, Pinel N, et al. (2010) Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea. Proc Natl Acad Sci U S A 107: 8818-8823. doi:10.1073/pnas.0913533107
36. Kubota N, Kanemori M, Sasayama Y, Masato A, Fukumori Y (2007) Identification of Endosymbionts in Oligobrachia mashikoi (Siboglinidae, Annelida). Microbes and Environments 22: 136-144.
37. Nishijima M, Lindsay DJ, Hata J, Nakamura A, Kasai H, et al. (2010) Association of thioautotrophic bacteria with deep-sea sponges. Mar Biotechnol (NY) 12: 253-260. doi:10.1007/s10126-009-9253-7
38. Arellano SM, Lee OO, Lafi FF, Yang J, Wang Y, et al. (2013) Deep sequencing of Myxilla (Ectyomyxilla) methanophila, an epibiotic sponge on cold-seep tubeworms, reveals methylotrophic, thiotrophic, and putative hydrocarbon-degrading microbial associations. Microb Ecol 65: 450-461. doi:10.1007/s00248-012-0130-y
39. 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: 497-510. doi:10.1111/j.1574-6941. 2011.01179.x
40. Giles EC, Kamke J, Moitinho-Silva L, Taylor MW, Hentschel U, et al. (2013) Bacterial community profiles in low microbial abundance sponges. FEMS Microbiol Ecol 83: 232-241. doi:10.1111/j.1574-6941.2012.01467.x
41. Moitinho-Silva L, Bayer K, Cannistraci C V, Giles EC, Ryu T, et al. (2013) Specificity and transcriptional activity of microbiota associated with low and high microbial abundance sponges from the Red Sea. Mol Ecol. doi:10.1111/mec.12365
42. Schläppy M-L, Schöttner SI, Lavik G, Kuypers MMM, Beer D, et al. (2009) Evidence of nitrification and denitrification in high and low microbial abundance sponges. Marine Biology 157: 593-602. doi:10.1007/s00227- 009-1344-5
43. Raggi L, Schubotz F, Hinrichs K-U, Dubilier N, Petersen JM (2013) Bacterial symbionts of Bathymodiolus mussels and Escarpia tubeworms from Chapopote, an asphalt seep in the southern Gulf of Mexico. Environ Microbiol 15: 1969-1987. doi:10.1111/1462-2920.12051
44. Muller F, Brissac T, Le Bris N, Felbeck H, Gros O (2010) First description of giant Archaea (Thaumarchaeota) associated with putative bacterial ectosymbionts in a sulfidic marine habitat. Environ Microbiol 12: 2371-2383. doi:10.1111/j.1462-2920.2010.02309.x
45. Brady SF (2007) Construction of soil environmental DNA cosmid libraries and screening for clones that produce biologically active small molecules. Nat Protoc 2: 1297-1305. doi:10.1038/nprot.2007.195
46. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, et al. (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72: 5069-5072. doi:10.1128/ AEM.03006-05
47. Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, et al. (2010) PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 26: 266-267. doi:10.1093/bioinformatics/btp636
48. Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward D V, et al. (2011) Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res 21: 494-504. doi:10.1101/gr.112730. 110
49. Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, et al. (2008) The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9: 386. doi:10.1186/1471-2105-9-386
50. Lane D (1991) 16S/23S rRNA Sequencing. In: Stackebrandt E, Goodfellow M, editors. Nucleic Acids Techniques in Bacterial Systematics. Chichester: John Wiley & Sons. pp. 115-138.
51. DeLong EF (1992) Archaea in Coastal Marine Environments. Proc Natl Acad Sci U S A 89: 5685-5689. doi:10.1073/pnas.89.12.5685
52. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739. doi:10.1093/molbev/msr121
53. Tamura K, Nei M, Kumar S (2004) Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci U S A 101: 11030-11035. doi:10.1073/pnas.0404206101 (Pubitemid 38989579)
54. Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10: 512-526. (Pubitemid 23157236)