Metabolic relationships between marine red algae and algae-associated bacteria

Abstract

Mutualistic interactions between marine phototrophs and associated bacteria are an important strategy for their successful survival in the ocean, but little is known about their metabolic relationships. Here, bacterial communities in the algal sphere (AS) and bulk solution (BS) of nine marine red algal cultures were analyzed, and Roseibium and Phycisphaera were identified significantly more abundantly in AS than in BS. The metabolic features of Roseibium RMAR6-6 (isolated and genome-sequenced), Phycisphaera MAG 12 (obtained by metagenomic sequencing), and a marine red alga, Porphyridium purpureum CCMP1328 (from GenBank), were analyzed bioinformatically. RMAR6-6 has the genetic capability to fix nitrogen and produce B vitamins (B1, B2, B5, B6, B9, and B12), bacterioferritin, dimethylsulfoniopropionate (DMSP), and phenylacetate that may enhance algal growth, whereas MAG 12 may have a limited metabolic capability, not producing vitamins B9 and B12, DMSP, phenylacetate, and siderophores, but with the ability to produce bacitracin, possibly modulating algal microbiome. P. purpureum CCMP1328 lacks the genetic capability to fix nitrogen and produce vitamin B12, DMSP, phenylacetate, and siderophore. It was shown that the nitrogen-fixing ability of RMAR6-6 promoted the growth of P. purpureum, and DMSP reduced the oxidative stress of P. purpureum. The metabolic interactions between strain RMAR6-6 and P. purpureum CCMP1328 were also investigated by the transcriptomic analyses of their monoculture and co-culture. Taken together, potential metabolic relationships between Roseibium and P. purpureum were proposed. This study provides a better understanding of the metabolic relationships between marine algae and algae-associated bacteria for successful growth.

Keywords

Metabolic relationship / Marine red algae / Symbiotic bacteria / Roseibium / Phycisphaera / Porphyridium

References

[1] Ainsworth TD, Krause L, Bridge T, Torda G, Raina JB, Zakrzewski M, Gates RD, Padilla-Gamiño JL, Spalding HL, Smith C, Woolsey ES, Bourne DG, Bongaerts P, Hoegh-Guldberg O, Leggat W. The coral core microbiome identifies rare bacterial taxa as ubiquitous endosymbionts. ISME J, 2015, 9: 2261-2274,

[2] Amin SA, Hmelo LR, van Tol HM, Durham BP, Carlson LT, Heal KR, Morales RL, Berthiaume CT, Parker MS, Djunaedi B, Ingalls AE, Parsek MR, Moran MA, Armbrust EV. Interaction and signaling between a cosmopolitan phytoplankton and associated bacteria. Nature, 2015, 522: 98-101,

[3] Astudillo-García C, Bell JJ, Webster NS, Glasl B, Jompa J, Montoya JM, Taylor MW. Evaluating the core microbiota in complex communities: a systematic investigation. Environ Microbiol, 2017, 19: 1450-1462,

[4] Baek JH, Kim KH, Moon JY, Yeo SH, Jeon CO. Acetobacter oryzoeni sp. nov., isolated from Korean rice wine vinegar. Int J Syst Evol Microbiol, 2020, 70: 2026-2033,

[5] Baek JH, Kim KH, Lee Y, Jeong SE, Jin HM, Jia B, Jeon CO. Elucidating the biodegradation pathway and catabolic genes of benzophenone-3 in Rhodococcus sp. S2–17. Environ Pollut, 2022, 299: 118890,

[6] Barros de Medeiros VP, da Costa WKA, da Silva RT, Pimentel TC, Magnani M. Microalgae as source of functional ingredients in new-generation foods: challenges, technological effects, biological activity, and regulatory issues. Crit Rev Food Sci Nutr, 2022, 62: 4929-4950,

[7] Bhattacharya D, Price DC, Chan CX, Qiu H, Rose N, Ball S, Weber AP, Arias MC, Henrissat B, Coutinho PM, Krishnan A, Zäuner S, Morath S, Hilliou F, Egizi A, Perrineau MM, Yoon HS. Genome of the red alga Porphyridium purpureum. Nat Commun, 2013, 4: 1941,

[8] Bondoso J, Godoy-Vitorino F, Balagué V, Gasol JM, Harder J, Lage OM. Epiphytic Planctomycetes communities associated with three main groups of macroalgae. FEMS Microbiol Ecol, 2017, 93: fiw255,

[9] Böttger LH, Miller EP, Andresen C, Matzanke BF, Küpper FC, Carrano CJ. Atypical iron storage in marine brown algae: a multidisciplinary study of iron transport and storage in Ectocarpus siliculosus. J Exp Bot, 2012, 63: 5763-5772,

[10] Buchan A, LeCleir GR, Gulvik CA, González JM. Master recyclers: features and functions of bacteria associated with phytoplankton blooms. Nat Rev Microbiol, 2014, 12: 686-698,

[11] Camp EF, Kahlke T, Nitschke MR, Varkey D, Fisher NL, Fujise L, Goyen S, Hughes DJ, Lawson CA, Ros M, Woodcock S, Xiao K, Leggat W, Suggett DJ. Revealing changes in the microbiome of Symbiodiniaceae under thermal stress. Environ Microbiol, 2020, 22: 1294-1309,

[12] Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics, 2020, 36: 1925-1927,

[13] Christie-Oleza JA, Sousoni D, Lloyd M, Armengaud J, Scanlan DJ. Nutrient recycling facilitates long-term stability of marine microbial phototroph–heterotroph interactions. Nat Microbiol, 2017, 2: 17100,

[14] Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, da Costa MS, Rooney AP, Yi H, Xu XW, De Meyer S, Trujillo ME. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Sys Evol Microbiol, 2018, 68: 461-466,

[15] Cirri E, Pohnert G. Algae−bacteria interactions that balance the planktonic microbiome. New Phytol, 2019, 223: 100-106,

[16] Cooper MB, Kazamia E, Helliwell KE, Kudahl UJ, Sayer A, Wheeler GL, Smith AG. Crossexchange of B-vitamins underpins a mutualistic interaction between Ostreococcus tauri and Dinoroseobacter shibae. ISME J, 2019, 13: 334-345,

[17] Croft MT, Lawrence AD, Raux-Deery E, Warren MJ, Smith AG. Algae acquire vitamin B12 through a symbiotic relationship with bacteria. Nature, 2005, 438: 90-93,

[18] Curson AR, Liu J, Bermejo Martínez A, Green RT, Chan Y, Carrión O, Williams BT, Zhang SH, Yang GP, Bulman Page PC, Zhang XH, Todd JD. Dimethylsulfoniopropionate biosynthesis in marine bacteria and identification of the key gene in this process. Nat Microbiol, 2017, 2: 17009,

[19] Curson ARJ, Williams BT, Pinchbeck BJ, Sims LP, Martínez AB, Rivera PPL, Kumaresan D, Mercadé E, Spurgin LG, Carrión O, Moxon S, Cattolico RA, Kuzhiumparambil U, Guagliardo P, Clode PL, Raina JB, Todd JD. DSYB catalyses the key step of dimethylsulfoniopropionate biosynthesis in many phytoplankton. Nat Microbiol, 2018, 3: 430-439,

[20] Dawczynski C, Schäfer U, Leiterer M, Jahreis G. Nutritional and toxicological importance of macro, trace, and ultra-trace elements in algae food products. J Agric Food Chem, 2007, 55: 10470-10475,

[21] Delgado MJ, Bedmar EJ, Downie JA. Genes involved in the formation and assembly of rhizobial cytochromes and their role in symbiotic nitrogen fixation. Adv Microb Physiol, 1998, 40: 191-231,

[22] Dungan AM, Bulach D, Lin H, van Oppen MJH, Blackall LL. Development of a free radical scavenging bacterial consortium to mitigate oxidative stress in cnidarians. Microb Biotechnol, 2021, 14: 2025-2040,

[23] Egan S, Harder T, Burke C, Steinberg P, Kjelleberg S, Thomas T. The seaweed holobiont: understanding seaweed–bacteria interactions. FEMS Microbiol Rev, 2013, 37: 462-476,

[24] Fries L. Growth regulating effects of phenylacetic acid and p-hydroxyphenylacetic acid on Fucus spiralis L. (Phaeophyceae, Fucales) in axenic culture. Phycologia, 1977, 16: 451-455,

[25] Ghaderiardakani F, Quartino ML, Wichard T. Microbiome-dependent adaptation of seaweeds under environmental stresses: a perspective. Front Mar Sci, 2020, 7,

[26] Guillard RRL, Hargraves PE. Stichochrysis immobilis is a diatom, not a chrysophyte. Phycologia, 1993, 32: 234-236,

[27] Guillén-Navarro K, Araíza G, García-de los Santos A, Mora Y, Dunn MF. The Rhizobium etli bioMNY operon is involved in biotin transport. FEMS Microbiol Lett, 2005, 250: 209-219,

[28] Huerta-Cepas J, Forslund K, Coelho LP, Szklarczyk D, Jensen LJ, von Mering C, Bork P. Fast genome-wide functional annotation through orthology assignment by eggnog-Mapper. Mol Biol Evol, 2017, 34: 2115-2122,

[29] Ismail A, Ktari L, Ahmed M, Bolhuis H, Boudabbous A, Stal LJ, Cretoiu MS, El Bour M. Antimicrobial activities of bacteria associated with the brown alga Padina pavonica. Front Microbiol, 2016, 7: 1072,

[30] Jeong SE, Kim KH, Baek K, Jeon CO. Parasphingopyxis algicola sp nov, isolated from a marine red alga Asparagopsis taxiformis and emended description of the genus Parasphingopyxis Uchida et al. 2012. Int J Sys Evol Microbiol, 2017, 67: 3877-3881,

[31] Kazamia E, Czesnick H, Nguyen TT, Croft MT, Sherwood E, Sasso S, Hodson SJ, Warren MJ, Smith AG. Mutualistic interactions between vitamin B12-dependent algae and heterotrophic bacteria exhibit regulation. Environ Microbiol, 2012, 14: 1466-1476,

[32] Kramer J, Özkaya Ö, Kümmerli R. Bacterial siderophores in community and host interactions. Nat Rev Microbiol, 2020, 18: 152-163,

[33] Kumar S, Stecher G, Tamura K. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol, 2016, 33: 1870-1874,

[34] Lage OM, Bondoso J. Planctomycetes and macroalgae, a striking association. Front Microbiol, 2014, 5: 267,

[35] 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,

[36] Lee I, Kim YO, Park SC, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Sys Evol Microbiol, 2016, 66: 1100-1103,

[37] Lee HJ, Jeong SE, Lee S, Kim S, Han H, Jeon CO. Effects of cosmetics on the skin microbiome of facial cheeks with different hydration levels. MicrobiologyOpen, 2018, 7,

[38] Lee J, Kim D, Bhattacharya D, Yoon HS. Expansion of phycobilisome linker gene families in mesophilic red algae. Nat Commun, 2019, 10: 4823,

[39] Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 2009, 25: 1754-1760,

[40] Li J, Majzoub ME, Marzinelli EM, Dai Z, Thomas T, Egan S. Bacterial controlled mitigation of dysbiosis in a seaweed disease. ISME J, 2022, 16: 378-387,

[41] Lin HY, Lin HJ. Polyamines in microalgae: something borrowed, something new. Mar Drugs, 2018, 17: 1,

[42] Maire J, Girvan SK, Barkla SE, Perez-Gonzalez A, Suggett DJ, Blackall LL, van Oppen MJH. Intracellular bacteria are common and taxonomically diverse in cultured and in hospite algal endosymbionts of coral reefs. ISME J, 2021, 15: 2028-2042,

[43] Matthews JL, Raina JB, Kahlke T, Seymour JR, van Oppen MJH, Suggett DJ. Symbiodiniaceae-bacteria interactions: rethinking metabolite exchange in reef-building corals as multi-partner metabolic networks. Environ Microbiol, 2020, 22: 1675-1687,

[44] Miran W, Jang J, Nawaz M, Shahzad A, Jeong SE, Jeon CO, Lee DS. Mixed sulfatereducing bacteria-enriched microbial fuel cells for the treatment of wastewater containing copper. Chemosphere, 2017, 189: 134-142,

[45] Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res, 2007, 35: W182-W185,

[46] Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. metaSPAdes: a new versatile metagenomic assembler. Genome Res, 2017, 27: 824-834,

[47] Pacheco D, Araújo GS, Cotas J, Gaspar R, Neto JM, Pereira L. Invasive seaweeds in the Iberian Peninsula: a contribution for food supply. Mar Drugs, 2020, 18: 560,

[48] Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res, 2015, 25: 1043-1055,

[49] Rambo IM, Dombrowski N, Constant L, Erdner D, Baker BJ. Metabolic relationships of uncultured bacteria associated with the microalgae Gambierdiscus. Environ Microbiol, 2020, 22: 1764-1783,

[50] Rooney-Varga JN, Giewat MW, Savin MC, Sood S, LeGresley M, Martin JL. Links between phytoplankton and bacterial community dynamics in a coastal marine environment. Microb Ecol, 2005, 49: 163-175,

[51] Samo TJ, Kimbrel JA, Nilson DJ, Pett-Ridge J, Weber PK, Mayali X. Attachment between heterotrophic bacteria and microalgae influences symbiotic microscale interactions. Environ Microbiol, 2018, 20: 4385-4400,

[52] Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C. Metagenomic biomarker discovery and explanation. Genome Biol, 2011, 12: R60,

[53] Segev E, Wyche TP, Kim KH, Petersen J, Ellebrandt C, Vlamakis H, Barteneva N, Paulson JN, Chai L, Clardy J, Kolter R. Dynamic metabolic exchange governs a marine algal-bacterial interaction. Elife, 2016, 5: e17473,

[54] Seyedsayamdost MR, Case RJ, Kolter R, Clardy J. The Jekyll-and-Hyde chemistry of Phaeobacter gallaeciensis. Nat Chem, 2011, 3: 331-335,

[55] Seymour JR, Amin SA, Raina JB, Stocker R. Zooming in on the phycosphere: the ecological interface for phytoplankton−bacteria relationships. Nat Microbiol, 2017, 2: 17065,

[56] Shaked Y, Lis H. Disassembling iron availability to phytoplankton. Front Microbiol, 2012, 3: 123,

[57] Shibl AA, Isaac A, Ochsenkühn MA, Cárdenas A, Fei C, Behringer G, Arnoux M, Drou N, Santos MP, Gunsalus KC, Voolstra CR, Amin SA. Diatom modulation of select bacteria through use of two unique secondary metabolites. Proc Nati Acad Sci USA, 2020, 117: 27445-27455,

[58] Sieber CMK, Probst AJ, Sharrar A, Thomas BC, Hess M, Tringe SG, Banfield JF. Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy. Nat Microbiol, 2018, 3: 836-843,

[59] Singh RP, Reddy CR. Seaweed–microbial interactions: key functions of seaweed associated bacteria. FEMS Microbiol Ecol, 2014, 88: 213-230,

[60] Sriswasdi S, Yang CC, Iwasaki W. Generalist species drive microbial dispersion and evolution. Nat Commun, 2017, 8: 1162,

[61] Stothard P, Wishart DS. Circular genome visualization and exploration using CGView. Bioinformatics, 2005, 21: 537-539,

[62] Strom S, Wolfe G, Slajer A, Lambert S, Clough J. Chemical defense in the microplankton II: Inhibition of protist feeding by β-dimethylsulfoniopropionate (DMSP). Limnol Oceanogr, 2003, 48: 230-237,

[63] Sunda W, Kieber DJ, Kiene RP, Huntsman S. An antioxidant function for DMSP and DMS in marine algae. Nature, 2002, 418: 317-320,

[64] Thume K, Gebser B, Chen L, Meyer N, Kieber DJ, Pohnert G. The metabolite dimethylsulfoxonium propionate extends the marine organosulfur cycle. Nature, 2018, 563: 412-415,

[65] Tortell PD, Maldonado MT, Granger J, Price NM. Marine bacteria and biogeochemical cycling of iron in the oceans. FEMS Microbiol Ecol, 1999, 29: 1-11,

[66] van Tol HM, Amin SA, Armbrust EV. Ubiquitous marine bacterium inhibits diatom cell division. ISME J, 2017, 11: 31-42,

[67] Vraspir JM, Butler A. Chemistry of marine ligands and siderophores. Ann Rev Mar Sci, 2009, 1: 43-63,

[68] Wienhausen G, Noriega-Ortega BE, Niggemann J, Dittmar T, Simon M. The exometabolome of two model strains of the Roseobacter group: a marketplace of microbial metabolites. Front Microbiol, 2017, 8: 1985,

[69] Xu B, Bo Y, Sun X, Wang H, Guo H, Zhou C, Ruan R, Yan X, Cheng P. Review of the effect of polyamines in microalgae when ingested by shellfish. Algal Res, 2021, 58,

[70] Yang EC, Boo SM, Bhattacharya D, Saunders GW, Knoll AH, Fredericq S, Graf L, Yoon HS. Divergence time estimates and the evolution of major lineages in the florideophyte red algae. Sci Rep, 2016, 6: 21361,

[71] Zehr JP, Capone DG. Changing perspectives in marine nitrogen fixation. Science, 2020, 368: eaay9514,

[72] Zehr JP, Shilova IN, Farnelid HM, Muñoz-Marín MD, Turk-Kubo KA. Unusual marine unicellular symbiosis with the nitrogen-fixing cyanobacterium UCYN-A. Nat Microbiol, 2016, 2: 16214,

[73] Zheng Q, Wang Y, Lu J, Lin W, Chen F, Jiao N. Metagenomic and metaproteomic insights into photoautotrophic and heterotrophic interactions in a Synechococcus culture. Mbio, 2020, 11: e03261-19,