Bergquist PR. Sponges. London, United Kingdom: Hutchinson and Co. Ltd; 1978.
Brain CKB, Prave AR, Hoffmann KH, Fallick AE, Botha A, Herd DA, et al. The first animals: Ca. 760-million-year-old sponge-like fossils from Namibia. S Afr J Sci. 2012;108:1–8.
Hooper JNA, van Soest RWM. Systema Porifera: a guide to the classification of sponges. New York: Kluwer Academic/Plenum Publishers; 2002.
Webster NS. Sponge disease: a global threat? Environ Microbiol. 2007;9:1363–75.
Bell JJ. The functional roles of marine sponges. Estuar Coast Shelf Sci. 2008;79:341–53.
de Goeij JM, van Oevelen D, Vermeij MJA, Middelburg JJ, Osinga R, de Goeij AFPM, et al. Surviving in a Marine Desert: the sponge loop retains resources within coral reefs. Science. 2013;342:108–10.
Taylor MW, Radax R, Steger D, Wagner M. Sponge-associated microorganisms: evolution, ecology, and biotechnological potential. Microbiol Mol Biol Rev. 2007;71:295–347.
Wehrl M, Steinert M, Hentschel U. Bacterial uptake by the marine sponge Aplysina aerophoba. Microb Ecol. 2007;53:355–65.
Thomas T, Rusch D, DeMaere MZ, Yung PY, Lewis M, Halpern A, et al. Functional genomic signatures of sponge bacteria reveal unique and shared features of symbiosis. ISME J. 2010;4:1557–67.
Nguyen MTHD, Liu M, Thomas T. Ankyrin-repeat proteins from sponge symbionts modulate amoebal phagocytosis. Mol Ecol. 2013;23:1635–45.
Reynolds D, Thomas T. Evolution and function of eukaryotic-like proteins from sponge symbionts. Mol Ecol. 2016;25:5242–53.
Jahn MT, Arkhipova K, Markert SM, Stigloher C, Lachnit T, Pita L, et al. A phage protein aids bacterial symbionts in eukaryote immune evasion. Cell Host Microbe. 2019;26:542–50.e5.
Degnan SM. The surprisingly complex immune gene repertoire of a simple sponge, exemplified by the NLR genes: a capacity for specificity? Dev Comp Immunol. 2015;48:269–74.
Hentschel U, Usher KM, Taylor MW. Marine sponges as microbial fermenters. FEMS Microbiol Ecol. 2006;55:167–77.
Moitinho-Silva L, Steinert G, Nielsen S, Hardoim CCP, Wu YC, McCormack GP, et al. Predicting the HMA-LMA status in marine sponges by machine learning. Front Microbiol. 2017;8:1–14.
Moitinho-Silva L, Nielsen S, Amir A, Gonzalez A, Ackermann GL, Cerrano C, et al. The sponge microbiome project. Gigascience. 2017;6:1–7.
Hentschel U, Hopke J, Horn M, Friedrich AB, Wagner M, Hacker J, et al. Molecular evidence for a uniform microbial community in sponges from different oceans. Appl Environ Microbiol. 2002;68:4431–40.
Simister RL, Deines P, Botté ES, Webster NS, Taylor MW. Sponge-specific clusters revisited: a comprehensive phylogeny of sponge-associated microorganisms. Environ Microbiol. 2012;14:517–24.
Taylor MW, Tsai P, Simister RL, Deines P, Botte E, Ericson G, et al. “Sponge-specific” bacteria are widespread (but rare) in diverse marine environments. ISME J. 2013;7:438–43.
Croué J, West NJ, Escande M-L, Intertaglia L, Lebaron P, Suzuki MT. A single betaproteobacterium dominates the microbial community of the crambescidine-containing sponge Crambe crambe. Sci Rep. 2013;3:2583.
Fan L, Reynolds D, Liu M, Stark M, Kjelleberg S, Webster NS, et al. Functional equivalence and evolutionary convergence in complex communities of microbial sponge symbionts. PNAS. 2012;109:E1878–87.
Simister RL, Taylor MW, Rogers KM, Schupp PJ, Deines P. Temporal molecular and isotopic analysis of active bacterial communities in two New Zealand sponges. FEMS Microbiol Ecol. 2013;85:195–205.
Gantt SE, López-Legentil S, Erwin PM. Stable microbial communities in the sponge Crambe crambe from inside and outside a polluted Mediterranean harbor. FEMS Microbiol Lett. 2017;364:1–7.
Bin JeongJ, Kim KH, Park JS. Sponge-specific unknown bacterial groups detected in marine sponges collected from Korea through barcoded pyrosequencing. J Microbiol Biotechnol. 2015;25:1–10.
Thiel V, Neulinger SC, Staufenberger T, Schmaljohann R, Imhoff JF. Spatial distribution of sponge-associated bacteria in the Mediterranean sponge Tethya aurantium. FEMS Microbiol Ecol. 2006;59:47–63.
Fieth RA, Gauthier M-EA, Bayes J, Green KM, Degnan SM. Ontogenetic changes in the bacterial symbiont community of the tropical demosponge Amphimedon queenslandica: metamorphosis is a new beginning. Front Mar Sci. 2016;3:1–20.
Batani G. Fluorescence in situ hybridisation for the localisation and culturing of marine bacteria: co-localisation of symbionts in sponges (Unpublished PhD thesis chapter). UNSW Sydney. 2018.
Waterworth SC, Jiwaji M, Kalinski JCJ, Parker-Nance S, Dorrington RA. A place to call home: an analysis of the bacterial communities in two Tethya rubra Samaai and Gibbons 2005 populations in algoa bay, South Africa. Mar Drugs. 2017;15:95.
Wu S, Ou H, Liu T, Wang D, Zhao J. Structure and dynamics of microbiomes associated with the marine sponge Tedania sp. during its life cycle. FEMS Microbiol Ecol. 2018;94:1–9.
Matcher GF, Waterworth SC, Walmsley TA, Matsatsa T, Parker-Nance S, Davies-Coleman MT, et al. Keeping it in the family: coevolution of latrunculid sponges and their dominant bacterial symbionts. Microbiologyopen. 2017;6:1–13.
Jackson SA, Flemer B, McCann A, Kennedy J, Morrissey JP, O’Gara F, et al. Archaea appear to dominate the microbiome of Inflatella pellicula deep sea sponges. PLoS ONE. 2013;8:1–8.
Steinert G, Taylor MW, Deines P, Simister RL, de Voogd NJ, Hoggard M, et al. In four shallow and mesophotic tropical reef sponges from Guam the microbial community largely depends on host identity. PeerJ. 2016;4:e1936.
Gauthier M-EA, Watson JR, Degnan SM. Draft genomes shed light on the dual bacterial symbiosis that dominates the microbiome of the coral reef sponge Amphimedon queenslandica. Front Mar Sci. 2016;3:1–18.
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Cold Spring Harb Lab Press. 2014;25:1043–55.
Mukherjee S, Stamatis D, Bertsch J, Ovchinnikova G, Verezemska O, Isbandi M, et al. Genomes OnLine database (GOLD) v.6: data updates and feature enhancements. Nucleic Acids Res. 2017;45:D446–56.
Huntemann M, Ivanova NN, Mavromatis K, James Tripp H, Paez-Espino D, Palaniappan K, et al. The standard operating procedure of the DOE-JGI microbial genome annotation pipeline (MGAP v.4). Stand Genom Sci. 2015;10:4–9.
Eddy S. Profile hidden Markov models. Bioinformatics. 1998;14:755–63.
Pruesse E, Peplies J, Glöckner FO. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics. 2012;28:1823–9.
Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar, et al. ARB: a software environment for sequence data. Nucleic Acids Res. 2004;32:1363–71.
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Res. 2013;41:590–6.
Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30:1312–3.
Letunic I, Bork P. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res. 2016;44:W242–5.
Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics. 2020;36:1925–7.
Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A, Chaumeil PA, et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol. 2018;36:996–1004.
Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol. 2005;187:6258–64.
Rodriguez-R LM, Konstantinidis KT. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. Peer J Prepr. 2016;4:e1900v1.
Thomas T, Moitinho-Silva L, Lurgi M, Björk JR, Easson C, Astudillo-García C, et al. Diversity, structure and convergent evolution of the global sponge microbiome. Nat Commun. 2016;7:11870.
Díez-Vives C, Moitinho-Silva L, Nielsen S, Reynolds D, Thomas T. Expression of eukaryotic-like protein in the microbiome of sponges. Mol Ecol. 2017;26:1432–51.
Öztürk B, De Jaeger L, Smidt H, Sipkema D. Culture-dependent and independent approaches for identifying novel halogenases encoded by Crambe crambe (marine sponge) microbiota. Sci Rep. 2013;3:1–9.
Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics. 2011;12:1–16.
Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10:R25.
Li B, Ruotti V, Stewart RM, Thomson JA, Dewey CN. RNA-Seq gene expression estimation with read mapping uncertainty. Bioinformatics. 2010;26:493–500.
Wagner GP, Kin K, Lynch VJ. Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples. Theory Biosci. 2012;131:281–5.
Webster NS, Hill RT. The culturable microbial community of the great barrier reef sponge Rhopaloeides odorabile is dominated by an α-Proteobacterium. Mar Biol. 2001;138:843–51.
Engelberts JP, Robbins SJ, de Goeij JM, Aranda M, Bell SC, Webster NS. Characterization of a sponge microbiome using an integrative genome-centric approach. ISME J. 2020;14:1100–10.
Moitinho-Silva L, Díez-Vives C, Batani G, Esteves AIS, Jahn MT, Thomas T. Integrated metabolism in sponge-microbe symbiosis revealed by genome-centered metatranscriptomics. ISME J. 2017;11:1651–66.
Lobb B, Tremblay BJM, Moreno-Hagelsieb G, Doxey AC. An assessment of genome annotation coverage across the bacterial tree of life. Microb Genom. 2020;6:e000341.
Lopez JV, Ranzer LK, Ledger A, Schoch B, Duckworth A, Mccarthy PJ, et al. Comparison of bacterial diversity within the coral reef sponge, axinella corrugata, the encrusting coral erythropodium caribaeorum. Proc. 11 Int. Coral Reef Symp. 2008;2:1362–6.
Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W, Schleifer KH, et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol. 2014;12:635–45.
Konstantinidis KT, Rosselló-Móra R, Amann R. Uncultivated microbes in need of their own taxonomy. ISME J. 2017;11:2399–406.
Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-smith M, Doud D, Jarett J, et al. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol. 2017;35:725–31.
Chuvochina M, Rinke C, Parks DH, Rappé MS, Tyson GW, Yilmaz P, et al. The importance of designating type material for uncultured taxa. Syst Appl Microbiol. 2019;42:15–21.
Tripp E. Crowell’s handbook of classical mythology. New York: Thomas Y. Crowell Company; 1970.
Athanassakis AN. Hesiod: Theogony, Works and Days, Shield. 2nd ed. Baltimore and London: The John Hopkins University Press; 2005.
Webster NS, Negri AP, Munro MMHG, Battershill CN. Diverse microbial communities inhabit Antarctic sponges. Environ Microbiol. 2004;6:288–300.
Coelho FJRC, Cleary DFR, Gomes NCM, Pólonia ARM, Huang YM, Liu LL, et al. Sponge prokaryote communities in Taiwanese coral reef and shallow hydrothermal vent ecosystems. Microb Ecol. 2018;75:239–54.
Sipkema D, de Caralt S, Morillo JA, Al-Soud WAB, Sørensen SJ, Smidt H, et al. Similar sponge-associated bacteria can be acquired via both vertical and horizontal transmission. Environ Microbiol. 2015;17:3807–21.
Bjork JR, Diez-Vives C, Astudillo-Garcia C, Archie E, Montoya JM. Vertical transmission of sponge microbiota is inconsistent and unfaithful. Nat Ecol Evol. 2019;3:1172–83.
Gonzalez-Zapata FL, Bongaerts P, Ramírez-Portilla C, Adu-Oppong B, Walljasper G, Reyes A, et al. Holobiont diversity in a reef-building coral over its entire depth range in the mesophotic zone. Front Mar Sci. 2018;5:1–13.
Yang S, Sun W, Zhang F, Li Z. Phylogenetically diverse denitrifying and ammonia-oxidizing bacteria in corals Alcyonium gracillimum and Tubastraea coccinea. Mar Biotechnol. 2013;15:540–51.
Høj L, Levy N, Baillie BK, Clode PL, Strohmaier RC, Siboni N, et al. Crown-of-thorns sea star Acanthaster cf. solaris has tissue—characteristic microbiomes with potential roles in health and reproduction. Appl Environ Microbiol. 2018;84:1–18.
Schmitt S, Deines P, Behnam F, Wagner M, Taylor MW. Chloroflexi bacteria are more diverse, abundant, and similar in high than in low microbial abundance sponges. FEMS Microbiol Ecol. 2011;78:497–510.
Bergquist PR, Kelly-Borges M. An evaluation of the genus Tethya (Porifera: Demospongiae: Hadromerjda) with descriptions of new species from the southwest Pacific. Beagle Rec Mus Art Galleries North Territ. 1991;8:37–72.
Hoshino T, Yilmaz LS, Noguera DR, Daims H, Wagner M. Quantification of target molecules needed to detect microorganisms by fluorescence in situ hybridization (FISH) and catalyzed reporter deposition-FISH. Appl Environ Microbiol. 2008;74:5068–77.
Moran NA, Wernegreen JJ. Lifestyle evolution in symbiotic bacteria: insights from genomics. Trends Ecol Evol. 2000;15:321–6.
Vacelet J, Donadey C. Electron microscope study of the association between some sponges and bacteria. J Exp Mar Bio Ecol. 1977;30:301–14.
Maldonado M. Intergenerational transmission of symbiotic bacteria in oviparous and viviparous demosponges, with emphasis on intracytoplasmically-compartmented bacterial types. J Mar Biol Assoc UK. 2007;87:1701–13.
Ilan M, Abelson A. The life of a sponge in a sandy lagoon. Biol Bull. 1995;189:363–9.
Borisov VB, Gennis RB, Hemp J, Verkhovsky MI. The cytochrome bd respiratory oxygen reductases. Biochim Biophys Acta Bioenerg. 2011;1807:1398–413.
Lavy A, Keren R, Yahel G, Ilan M. Intermittent hypoxia and prolonged suboxia measured in situ in a marine sponge. Front Mar Sci. 2016;3:1–11.
Hoffmann F, Larsen O, Thiel V, Rapp HT, Pape T, Michaelis W, et al. An anaerobic world in sponges. Geomicrobiol J. 2005;22:1–10.
Moreno-Vivian C, Cabello C, Martinez-Luque M, Blasco R, Castillo F. Prokaryotic nitrate reduction: molecular properties and functional distinction among bacterial nitrate reductases. J Bacteriol. 1999;181:6573–84.
Toffanin A, Wu Q, Maskus M, Casella S, Abruña HD, Shapleigh JP. Characterization of the gene encoding nitrite reductase and the physiological consequences of its expression in the nondenitrifying Rhizobium “hedysari” strain HCNT1. Appl Environ Microbiol. 1996;62:4019–25.
Jones PM, George AM. The ABC transporter structure and mechanism: perspectives on recent research. Cell Mol Life Sci. 2004;61:682–99.
Mulligan C, Fischer M, Thomas GH. Tripartite ATP-independent periplasmic (TRAP) transporters in bacteria and archaea. FEMS Microbiol Rev. 2011;35:68–86.
Vastermark A, Wollwage S, Houle ME, Rio R, Saier MH. Expansion of the APC superfamily of secondary carriers. Proteins Struct Funct Bioinform. 2014;82:2797–811.
Pao SS, Paulsen IT, Saier MH. Major facilitator superfamily. Microbiol Mol Biol Rev. 1998;62:1–34.
Ziegler C, Bremer E, Krämer R. The BCCT family of carriers: from physiology to crystal structure. Mol Microbiol. 2010;78:13–34.
Andrade SLA, Einsle O. The Amt/Mep/Rh family of ammonium transport proteins (Review). Mol Membr Biol. 2007;24:357–65.
Kamke J, Sczyrba A, Ivanova N, Schwientek P, Rinke C, Mavromatis K, et al. Single-cell genomics reveals complex carbohydrate degradation patterns in poribacterial symbionts of marine sponges. ISME J. 2013;7:2287–300.
Clifford EL, Hansell DA, Varela MM, Nieto-Cid M, Herndl GJ, Sintes E. Crustacean zooplankton release copious amounts of dissolved organic matter as taurine in the ocean. Limnol Oceanogr. 2017;62:2745–58.
Karimi E, Keller-Costa T, Slaby BM, Cox CJ, da Rocha UN, Hentschel U, et al. Genomic blueprints of sponge-prokaryote symbiosis are shared by low abundant and cultivatable Alphaproteobacteria. Sci Rep. 2019;9:1–15.
Dahl C, Franz B, Hensen D, Kesselheim A, Zigann R. Sulfite oxidation in the purple sulfur bacterium Allochromatium vinosum: Identification of SoeABC as a major player and relevance of SoxYZ in the process. Microbiology. 2013;159:2626–38.
Bardischewsky F, Quentmeier A, Friedrich CG. The flavoprotein SoxF functions in chemotrophic thiosulfate oxidation of Paracoccus pantotrophus in vivo and in vitro. FEMS Microbiol Lett. 2006;258:121–6.
Gregersen LH, Bryant DA, Frigaard NU. Mechanisms and evolution of oxidative sulfur metabolism in green sulfur bacteria. Front Microbiol. 2011;2:1–14.
Lavy A, Keren R, Yu K, Thomas BC, Alvarez-Cohen L, Banfield JF, et al. A novel Chromatiales bacterium is a potential sulfide oxidizer in multiple orders of marine sponges. Environ Microbiol. 2018;20:800–14.
Tian R-M, Wang Y, Bougouffa S, Gao ZM, Cai L, Bajic V, et al. Genomic analysis reveals versatile heterotrophic capacity of a potentially symbiotic sulfur-oxidizing bacterium in sponge. Environ Microbiol. 2014;16:3548–61.
Keller MD, Kiene RP, Matrai PA, Bellows WK. Production of glycine betaine and dimethylsulfoniopropionate in marine phytoplankton. II. N-limited chemostat cultures. Mar Biol. 1999;135:249–57.
Diaz MR, Visscher PT, Taylor BF. Metabolism of dimethylsulfoniopropionate and glycine betaine by a marine bacterium. FEMS Microbiol Lett. 1992;96:61–5.
Sun J, Steindler L, Thrash JC, Halsey KH, Smith DP, Carter AE, et al. One carbon metabolism in SAR11 pelagic marine bacteria. PLoS ONE. 2011;6:e23973.
Equar MY, Tani Y, Mihara H. Purification and properties of glycine oxidase from pseudomonas putida KT2440. J Nutr Sci Vitaminol. 2015;61:506–10.
Karimi E, Slaby BM, Soares AR, Blom J, Hentschel U, Costa R. Metagenomic binning reveals versatile nutrient cycling and distinct adaptive features in alphaproteobacterial symbionts of marine sponges. FEMS Microbiol Ecol. 2018;94:1–18.
Moreno-Pino M, Cristi A, Gillooly JF, Trefault N. Characterizing the microbiomes of Antarctic sponges: a functional metagenomic approach. Sci Rep. 2020;10:1–12.
Mayer J, Huhn T, Habeck M, Denger K, Hollemeyer K, Cook AM. 2,3-Dihydroxypropane-1-sulfonate degraded by Cupriavidus pinatubonensis JMP134: purification of dihydroxypropanesulfonate 3-dehydrogenase. Microbiology. 2010;156:1556–64.
Michael AJ. Polyamines in eukaryotes, bacteria, and archaea. J Biol Chem. 2016;291:14896–903.
Tsukamoto S, Kato H, Hirota H, Fusetani N. Pseudoceratidine: a new antifouling spermidine derivative from the marine sponge Pseudoceratina purpurea. Tetrahedron Lett. 1996;37:1439–40.
Igarashi K, Kashiwagi K. Polyamine transport in bacteria and yeast. Biochem J. 1999;344:633–42.
Shah P, Swiatlo E. A multifaceted role for polyamines in bacterial pathogens. Mol Microbiol. 2008;68:4–16.
Schneider BL, Reitzer L. Pathway and enzyme redundancy in putrescine catabolism in Escherichia coli. J Bacteriol. 2012;194:4080–8.
Mou X, Sun S, Rayapati P, Moran MA. Genes for transport and metabolism of spermidine in Ruegeria pomeroyi DSS-3 and other marine bacteria. Aquat Microb Ecol. 2010;58:311–21.
Dasu VV, Nakada Y, Ohnishi-Kameyama M, Kimura K, Itoh Y. Characterization and a role of Pseudomonas aeruginosa spermidine dehydrogenase in polyamine catabolism. Microbiology. 2006;152:2265–72.
Tofalo R, Cocchi S, Suzzi G. Polyamines and gut microbiota. Front Nutr. 2019;6:1–5.
Sharfstein ST, Keasling JD. Polyphosphate metabolism in Escherichia coli. Ann N Y Acad Sci. 1994;745:77–91.
Zhang F, Blasiak LC, Karolin JO, Powell RJ, Geddes CD, Hill RT. Phosphorus sequestration in the form of polyphosphate by microbial symbionts in marine sponges. Proc Natl Acad Sci USA. 2015;112:4381–6.
Wang L, Yan J, Wise MJ, Liu Q, Asenso J, Huang Y, et al. Distribution patterns of polyphosphate metabolism pathway and its relationships with bacterial durability and virulence. Front Microbiol. 2018;9:1–10.
Romano S, Schulz-Vogt HN, González JM, Bondarev V. Phosphate limitation induces drastic physiological changes, virulence-related gene expression, and secondary metabolite production in Pseudovibrio sp. strain FO-BEG1. Appl Environ Microbiol. 2015;81:3518–28.
Bergquist PR. In: eLS (ed) Porifera (Sponges). John Wiley & Sons, Ltd. 2001.
Kovacs-Simon A, Titball RW, Michell SL. Lipoproteins of bacterial pathogens. Infect Immun. 2011;79:548–61.
Aoki S, Ito M, Iwasaki W. From β- To α-proteobacteria: The origin and evolution of rhizobial nodulation genes nodij. Mol Biol Evol. 2013;30:2494–508.
Darby AC, Cho NH, Fuxelius HH, Westberg J, Andersson SGE. Intracellular pathogens go extreme: genome evolution in the Rickettsiales. Trends Genet. 2007;23:511–20.
Kuo CH, Ochman H. Inferring clocks when lacking rocks: the variable rates of molecular evolution in bacteria. Biol Direct. 2009;4:35.
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