
Cooper MB, Smith AG. Exploring mutualistic interactions between microalgae and bacteria in the omics age. Curr Opin Plant Biol. 2015;26:147–53.
Not F, Probert I, Ribeiro CG, Crenn K, Guillou L, Jeanthon C, et al. Photosymbiosis in marine pelagic environments. In: Stahl L, Cretoiu M (eds). The Marine Microbiome. Springer: Cham, Switzerland, 2016. p. 305–32.
Zhou J, Lyu Y, Richlen ML, Anderson DM, Cai Z. Quorum sensing is a language of chemical signals and plays an ecological role in algal-bacterial interactions. Crit Rev Plant Sci. 2016;35:81–105.
Krohn-Molt I, Wemheuer B, Alawi M, Poehlein A, Güllert S, Schmeisser C, et al. Metagenome survey of a multispecies and alga-associated biofilm revealed key elements of bacterial-algal interactions in photobioreactors. Appl Environ Microbiol. 2013;79:6196–206.
Hays SG, Patrick WG, Ziesack M, Oxman N, Silver PA. Better together: engineering and application of microbial symbioses. Curr Opin Biotechnol. 2015;36:40–49.
Flemming H-C, Wingender J, Szewzyk U, Steinberg P, Rice SA, Kjelleberg S. Biofilms: an emergent form of bacterial life. Nat Rev Microbiol. 2016;14:563.
Riding R. Microbial carbonates: the geological record of calcified bacterial–algal mats and biofilms. Sedimentology. 2000;47:179–214.
Arp G, Reimer A, Reitner J. Photosynthesis-induced biofilm calcification and calcium concentrations in Phanerozoic oceans. Science. 2001;292:1701–4.
Riding R. Cyanobacterial calcification, carbon dioxide concentrating mechanisms, and Proterozoic–Cambrian changes in atmospheric composition. Geobiology. 2006;4:299–316.
Dupraz C, Reid RP, Braissant O, Decho AW, Norman RS, Visscher PT. Processes of carbonate precipitation in modern microbial mats. Earth-Sci Rev. 2009;96:141–62.
Visscher PT, Stolz JF. Microbial mats as bioreactors: populations, processes, and products. Palaeogeogr Palaeocl. 2005;219:87–100.
Braissant O, Decho AW, Dupraz C, Glunk C, Przekop KM, Visscher PT. Exopolymeric substances of sulfate-reducing bacteria: interactions with calcium at alkaline pH and implication for formation of carbonate minerals. Geobiology. 2007;5:401–11.
Decho AW. Overview of biopolymer-induced mineralization: what goes on in biofilms? Ecol Eng. 2010;36:137–44.
Shiraishi F. Chemical conditions favoring photosynthesis-induced CaCO3 precipitation and implications for microbial carbonate formation in the ancient ocean. Geochim Cosmochim Acta. 2012;77:157–74.
Werner U, Blazejak A, Bird P, Eickert G, Schoon R, Abed RMM, et al. Microbial photosynthesis in coral reef sediments (Heron Reef, Australia). Estuar Coast Shelf Sci. 2008;76:876–88.
Heil CA, Chaston K, Jones A, Bird P, Longstaff B, Costanzo S, et al. Benthic microalgae in coral reef sediments of the southern Great Barrier Reef, Australia. Coral Reefs. 2004;23:336–43.
Yamashita H, Koike K. Genetic identity of free-living Symbiodinium obtained over a broad latitudinal range in the Japanese coast. Phycol Res. 2013;61:68–80.
Trench R. Microalgal–invertebrate symbioses-a review. Endocytobiosis Cell Res. 1993;9:135–75.
Coffroth MA, Lewis CF, Santos SR, Weaver JL. Environmental populations of symbiotic dinoflagellates in the genus Symbiodinium can initiate symbioses with reef cnidarians. Curr Biol. 2006;16:R985–R987.
Frommlet JC, Sousa ML, Alves A, Vieira SI, Suggett DJ, Serôdio J. Coral symbiotic algae calcify ex hospite in partnership with bacteria. Proc Natl Acad Sci USA. 2015;112:6158–63.
Marlow J, Peckmann J, Orphan V. Autoendoliths: a distinct type of rock-hosted microbial life. Geobiology. 2015;13:303–7.
Frommlet JC, Wangpraseurt D, Sousa ML, Guimarães B, Medeiros da Silva M, Kühl M, et al. Symbiodinium-induced formation of microbialites: mechanistic insights from in vitro experiments and the prospect of its occurrence in nature. Front Microbiol. 2018;9:998.
Nitschke MR, Davy SK, Ward S. Horizontal transmission of Symbiodinium cells between adult and juvenile corals is aided by benthic sediment. Coral Reefs. 2016;35:335–44.
Kawaguchi T, Decho AW. A laboratory investigation of cyanobacterial extracellular polymeric secretions (EPS) in influencing CaCO3 polymorphism. J Cryst Growth. 2002;240:230–5.
Arp G, Helms G, Karlinska K, Schumann G, Reimer A, Reitner J, et al. Photosynthesis versus exopolymer degradation in the formation of microbialites on the atoll of Kiritimati, Republic of Kiribati, Central Pacific. Geomicrobiol J. 2012;29:29–65.
More T, Yadav J, Yan S, Tyagi R, Surampalli R. Extracellular polymeric substances of bacteria and their potential environmental applications. J Environ Manag. 2014;144:1–25.
Shiraishi F, Bissett A, de Beer D, Reimer A, Arp G. Photosynthesis, respiration and exopolymer calcium-binding in biofilm calcification (Westerhöfer and Deinschwanger Creek, Germany). Geomicrobiol J. 2008;25:83–94.
Guillard RR. Culture of phytoplankton for feeding marine invertebrates. In: Smith WL, Chanley MH (eds). Culture of marine invertebrate animals. Springer: Boston, MA, 1975. p. 29–60.
Bulgarelli D, Rott M, Schlaeppi K, van Themaat EVL, Ahmadinejad N, Assenza F, et al. Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature. 2012;488:91.
Bodenhausen N, Horton MW, Bergelson J. Bacterial communities associated with the leaves and the roots of Arabidopsis thaliana. PLoS ONE. 2013;8:e56329.
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high–throughput community sequencing data. Nat Methods. 2010;7:335–6.
Rognes T, Flouri T, Nichols B, Quince C, Mahé F. VSEARCH: a versatile open source tool for metagenomics. PeerJ. 2016;4:e2584.
Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics. 2011;27:2194–2200.
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. 2012;41:D590–D596.
R Core Team. R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing; 2019. https://www.Rproject.org/.
Aßhauer KP, Wemheuer B, Daniel R, Meinicke P. Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data. Bioinformatics. 2015;31:2882–4.
Iwai S, Weinmaier T, Schmidt BL, Albertson DG, Poloso NJ, Dabbagh K, et al. Piphillin: improved prediction of metagenomic content by direct inference from human microbiomes. PLoS ONE. 2016;11:e0166104.
Roesler CS, Barnard AH. Optical proxy for phytoplankton biomass in the absence of photophysiology: Rethinking the absorption line height. Methods Oceanogr. 2013;7:79–94.
Jain R, Raghukumar S, Tharanathan R, Bhosle N. Extracellular polysaccharide production by thraustochytrid protists. Mar Biotechnol. 2005;7:184–92.
Claquin P, Probert I, Lefebvre S, Veron B. Effects of temperature on photosynthetic parameters and TEP production in eight species of marine microalgae. Aquat Microb Ecol. 2008;51:1–11.
Merritt JH, Kadouri DE, O’Toole GA. Growing and analyzing static biofilms. Curr Protoc Microbiol. 2011;22:1B. 1.1–1B. 1.18.
McMurdie PJ, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE. 2013;8:e61217.
Oksanen J, Kindt R, Legendre P, O’Hara B, Stevens MHH, Oksanen MJ, et al. The vegan package. Community Ecol Package. 2007;10:631–7.
McMurdie PJ, Holmes S. Waste not, want not: why rarefying microbiome data is inadmissible. PLoS Comput Biol. 2014;10:e1003531.
Lawson CA, Raina JB, Kahlke T, Seymour JR, Suggett DJ. Defining the core microbiome of the symbiotic dinoflagellate, Symbiodinium. Environ Microbiol Rep. 2018;10:7–11.
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550.
Pollard KS, Dudoit S, van der Laan MJ. Multiple testing procedures: the multtest package and applications to genomics. In: Gentleman R, Carey VJ, Huber W, Irizarry RA, Dudoit S (eds). Bioinformatics and computational biology solutions using R and bioconductor. Springer: New York, NY, 2005, p. 249–71.
DeLong EF, Franks DG, Alldredge AL. Phylogenetic diversity of aggregate-attached vs. free-living marine bacterial assemblages. Limnol Oceanogr. 1993;38:924–34.
Yilmaz P, Yarza P, Rapp JZ, Glöckner FO. Expanding the world of marine bacterial and archaeal clades. Front Microbiol. 2016;6:1524.
Malanoski AP, Lin B, Eddie BJ, Wang Z, Hervey WJ IV, Glaven SM. Relative abundance of ‘Candidatus Tenderia electrophaga’ is linked to cathodic current in an aerobic biocathode community. Microb Biotechnol. 2018;11:98–111.
Wegner C-E, Richter-Heitmann T, Klindworth A, Klockow C, Richter M, Achstetter T, et al. Expression of sulfatases in Rhodopirellula baltica and the diversity of sulfatases in the genus Rhodopirellula. Mar Genom. 2013;9:51–61.
Cai H-Y, Yan Z-S, Wang A-J, Krumholz LR, Jiang H-L. Analysis of the attached microbial community on mucilaginous cyanobacterial aggregates in the eutrophic Lake Taihu reveals the importance of Planctomycetes. Microb Ecol. 2013;66:73–83.
Pizzetti I, Fuchs BM, Gerdts G, Wichels A, Wiltshire KH, Amann R. Temporal variability of coastal Planctomycetes clades at station Kabeltonne, North Sea. Appl Environ Microbiol. 2011;77:5009–17.
Havemann SA, Foster JS. Comparative characterization of the microbial diversities of an artificial microbialite model and a natural stromatolite. Appl Environ Microbiol. 2008;74:7410–21.
Proemse BC, Eberhard RS, Sharples C, Bowman JP, Richards K, Comfort M, et al. Stromatolites on the rise in peat-bound karstic wetlands. Sci Rep. 2017;7:15384.
Diaz MR, Piggot AM, Eberli GP, Klaus JS. Bacterial community of oolitic carbonate sediments of the Bahamas Archipelago. Mar Ecol Prog Ser. 2013;485:9–24.
Saghaï A, Zivanovic Y, Zeyen N, Moreira D, Benzerara K, Deschamps P, et al. Metagenome-based diversity analyses suggest a significant contribution of non-cyanobacterial lineages to carbonate precipitation in modern microbialites. Front Microbiol. 2015;6:797.
Probandt D, Knittel K, Tegetmeyer H, Ahmerkamp S, Holtappels M, Amann R. Permeability shapes bacterial communities in sublittoral surface sediments. Environ Microbiol. 2017;19:1584–99.
Probandt D, Eickhorst T, Ellrott A, Amann R, Knittel K. Microbial life on a sand grain: from bulk sediment to single grains. ISME J. 2018;12:623.
Rasheed M, Wild C, Franke U, Huettel M. Benthic photosynthesis and oxygen consumption in permeable carbonate sediments at Heron Island, Great Barrier Reef, Australia. Estuar Coast Shelf Sci. 2004;59:139–50.
Takabayashi M, Adams LM, Pochon X, Gates RD. Genetic diversity of free-living Symbiodinium in surface water and sediment of Hawai’i and Florida. Coral Reefs. 2012;31:157–67.
Rosenberg E. The family Chitinophagaceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds). The Prokaryotes. Springer: Berlin, Heidelberg, 2014. p. 493–5.
Levin RA, Suggett DJ, Nitschke MR, Oppen MJ, Steinberg PD. Expanding the Symbiodinium (Dinophyceae, Suessiales) toolkit through protoplast technology. J Eukaryot Microbiol. 2017;64:588–97.
Yan S, Fuchs BM, Lenk S, Harder J, Wulf J, Jiao N-Z, et al. Biogeography and phylogeny of the NOR5/OM60 clade of Gammaproteobacteria. Syst Appl Microbiol. 2009;32:124–39.
Spring S, Scheuner C, Goeker M, Klenk H-P. A taxonomic framework for emerging groups of ecologically important marine gammaproteobacteria based on the reconstruction of evolutionary relationships using genome-scale data. Front Microbiol. 2015;6:281.
Biebl H, Pukall R, Lünsdorf H, Schulz S, Allgaier M, Tindall BJ, et al. Description of Labrenzia alexandrii gen. nov., sp. nov., a novel alphaproteobacterium containing bacteriochlorophyll a, and a proposal for reclassification of Stappia aggregata as Labrenzia aggregata comb. nov., of Stappia marina as Labrenzia marina comb. nov. and of Stappia alba as Labrenzia alba comb. nov., and emended descriptions of the genera Pannonibacter, Stappia and Roseibium, and of the species Roseibium denhamense and Roseibium hamelinense. Int J Syst Evol Microbiol. 2007;57:1095–107.
Klein B, Grossi V, Bouriat P, Goulas P, Grimaud R. Cytoplasmic wax ester accumulation during biofilm-driven substrate assimilation at the alkane–water interface by Marinobacter hydrocarbonoclasticus SP17. Res Microbiol. 2008;159:137–44.
Grossart HP, Levold F, Allgaier M, Simon M, Brinkhoff T. Marine diatom species harbour distinct bacterial communities. Environ Microbiol. 2005;7:860–73.
González JM, Fernández-Gómez B, Fernàndez-Guerra A, Gómez-Consarnau L, Sánchez O, Coll-Lladó M, et al. Genome analysis of the proteorhodopsin-containing marine bacterium Polaribacter sp. MED152 (Flavobacteria). Proc Natl Acad Sci USA. 2008;105:8724–9.
Park S, Akira Y, Kogure K. The family Rhodothermaceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds). The Prokaryotes. Springer: Berlin, Heidelberg, 2014. p. 849–56.
Bowman JP. The family Cryomorphaceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds). The Prokaryotes. Springer: Berlin, Heidelberg, 2014. p. 539–50.
Reichenbach H. Nannocystaceae fam. nov. In: Whitman WB, Rainey F, Kämpfer P, Trujillo M, Chun J, DeVos P, Hedlund B, and Dedysh S (eds). Bergey’s Manual of Systematics of Archaea and Bacteria. John Wiley & Sons: Hoboken, New Jersey, 2015. p. 1–2.
Flemming H-C, Wingender J. The biofilm matrix. Nat Rev Microbiol. 2010;8:623.
Dash S, Nogata Y, Zhou X, Zhang Y, Xu Y, Guo X, et al. Poly-ethers from Winogradskyella poriferorum: antifouling potential, time-course study of production and natural abundance. Bioresour Technol. 2011;102:7532–7.
Yellowlees D, Rees TAV, Leggat W. Metabolic interactions between algal symbionts and invertebrate hosts. Plant Cell Environ. 2008;31:679–94.
Neave MJ, Michell CT, Apprill A, Voolstra CR. Endozoicomonas genomes reveal functional adaptation and plasticity in bacterial strains symbiotically associated with diverse marine hosts. Sci Rep. 2017;7:40579.
Lux R, Jahreis K, Bettenbrock K, Parkinson JS, Lengeler JW. Coupling the phosphotransferase system and the methyl-accepting chemotaxis protein-dependent chemotaxis signaling pathways of Escherichia coli. Proc Natl Acad Sci USA. 1995;92:11583–7.
Ymele-Leki P, Houot L, Watnick PI. Mannitol and the mannitol-specific enzyme IIB subunit activate Vibrio cholerae biofilm formation. Appl Environ Microbiol. 2013;79:4675–83.
Willems A. The family Phyllobacteriaceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds). The Prokaryotes. Springer: Berlin, Heidelberg, 2014. p. 355–418.
Charles C, Rout SP, Patel K, Akbar S, Laws AP, Jackson B, et al. Floc formation reduces the pH stress experienced by microorganisms living in alkaline environments. Appl Environ Microbiol. 2017;83:e02985-16.
Edgcomb V, Bernhard J, Beaudoin D, Pruss S, Welander P, Schubotz F, et al. Molecular indicators of microbial diversity in oolitic sands of Highborne Cay, Bahamas. Geobiology. 2013;11:234–51.
O’Reilly S, Mariotti G, Winter A, Newman S, Matys E, McDermott F, et al. Molecular biosignatures reveal common benthic microbial sources of organic matter in ooids and grapestones from Pigeon Cay, The Bahamas. Geobiology. 2017;15:112–30.
Jeong HJ, Lee SY, Kang NS, Yoo YD, Lim AS, Lee MJ, et al. Genetics and morphology characterize the Dinoflagellate Symbiodinium voratum, n. sp., (Dinophyceae) as the sole representative of Symbiodinium Clade E. J Eukaryot Microbiol. 2014;61:75–94.
Keawtawee T, Fukami K, Songsangjinda P, Muangyao P. Isolation and characterization of Noctiluca-killing bacteria from a shrimp aquaculture pond in Thailand. Fish Sci. 2011;77:657–64.
Holmström C, Kjelleberg S. Marine Pseudoalteromonas species are associated with higher organisms and produce biologically active extracellular agents. FEMS Microbiol Ecol. 1999;30:285–93.
Uhlinger DJ, White DC. Relationship between physiological status and formation of extracellular polysaccharide glycocalyx in Pseudomonas atlantica. Appl Environ Microbiol. 1983;45:64–70.
Dupraz C, Visscher PT. Microbial lithification in marine stromatolites and hypersaline mats. Trends Microbiol. 2005;13:429–38.
Spadafora A, Perri E, McKenzie JA, Vasconcelos C. Microbial biomineralization processes forming modern Ca:Mg carbonate stromatolites. Sedimentology. 2010;57:27–40.
Beenken KE, Spencer H, Griffin LM, Smeltzer MS. Impact of extracellular nuclease production on the biofilm phenotype of Staphylococcus aureus under in vitro and in vivo conditions. Infect Immun. 2012;80:1634–8.
Tseng BS, Reichhardt C, Merrihew GE, Araujo-Hernandez SA, Harrison JJ, MacCoss MJ, et al. A biofilm matrix-associated protease inhibitor protects Pseudomonas aeruginosa from proteolytic attack. mBio. 2018;9:e00543–00518.
Aguilera A, Souza-Egipsy V, San Martín-Úriz P, Amils R. Extracellular matrix assembly in extreme acidic eukaryotic biofilms and their possible implications in heavy metal adsorption. Aquat Toxicol. 2008;88:257–66.
Fitt W, Trench R. The relation of diel patterns of cell division to diel patterns of motility in the symbiotic dinoflagellate Symbiodinium microadriaticum Freudenthal in culture. New Phytol. 1983;94:421–32.
Lee SY, Jeong HJ, Kang NS, Jang TY, Jang SH, Lajeunesse TC. Symbiodinium tridacnidorum sp. nov., a dinoflagellate common to Indo-Pacific giant clams, and a revised morphological description of Symbiodinium microadriaticum Freudenthal, emended Trench & Blank. Eur J Phycol. 2015;50:155–72.
Steinke M, Brading P, Kerrison P, Warner ME, Suggett DJ. Concentrations of dimethylsulfoniopropionate and dimethyl sulfide are strain-specific in symbiotic dinoflagellates (Symbiodinium sp., Dinophyceae). J Phycol. 2011;47:775–83.
LaJeunesse TC. Investigating the biodiversity, ecology, and phylogeny of endosymbiotic dinoflagellates in the genus Symbiodinium using the its region: In search of a “species” level marker. J Phycol. 2001;37:866–80.
Parkinson JE, Coffroth MA, LaJeunesse TC. New species of Clade B Symbiodinium (Dinophyceae) from the greater Caribbean belong to different functional guilds: S. aenigmaticum sp. nov., S. antillogorgium sp. nov., S. endomadracis sp. nov., and S. pseudominutum sp. nov. J Phycol. 2015;51:850–8.
LaJeunesse TC, Lambert G, Andersen RA, Coffroth MA, Galbraith DW. Symbiodinium (Pyrrhophyta) genome sizes (DNA content) are smallest among dinoflagellates. J Phycol. 2005;41:880–6.
Source: Ecology - nature.com