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Global distribution of a chlorophyll f cyanobacterial marker

  • 1.

    Ting CS, Rocap G, King J, Chisholm SW. Cyanobacterial photosynthesis in the oceans: the origins and significance of divergent light-harvesting strategies. Trends Microbiol. 2002;10:134–42.

  • 2.

    Chen M, Schliep M, Willows RD, Cai ZL, Neilan BA, Scheer H. A red-shifted chlorophyll. Science. 2010;329:1318–9.

  • 3.

    Gan F, Zhang S, Rockwell NC, Martin SS, Lagarias JC, Bryant DA. Extensive remodeling of a cyanobacterial photosynthetic apparatus in far-red light. Science. 2014;345:1312–7.

  • 4.

    Nürnberg DJ, Morton J, Santabarbara S, Telfer A, Joliot P, Antonaru LA, et al. Photochemistry beyond the red limit in chlorophyll f–containing photosystems. Science. 2018;360:1210–3.

    • PubMed
    • Google Scholar
  • 5.

    Gan F, Bryant DA. Adaptive and acclimative responses of cyanobacteria to far‐red light. Environ Microbiol. 2015;17:3450–65.

  • 6.

    Chen M, Blankenship RE. Expanding the solar spectrum used by photosynthesis. Trends Plant Sci. 2011;16:427–31.

  • 7.

    Gan F, Shen G, Bryant DA. Occurrence of far-red light photoacclimation (FaRLiP) in diverse cyanobacteria. Life. 2015;5:4–24.

    • CAS
    • Google Scholar
  • 8.

    Averina S, Velichko N, Senatskaya E, Pinevich A. Far-red light photoadaptations in aquatic cyanobacteria. Hydrobiologia. 2018;813:1–17.

    • CAS
    • Google Scholar
  • 9.

    Zhang Z, Li Z, Yin Y, Li Y, Jia Y, Chen M, et al. Widespread occurrence and unexpected diversity of red‐shifted chlorophyll producing cyanobacteria in humid subtropical forest ecosystems. Environ Microbiol. 2019;21:1497–510.

  • 10.

    Chen M, Li Y, Birch D, Willows RD. A cyanobacterium that contains chlorophyll f–a red‐absorbing photopigment. FEBS Lett. 2012;586:3249–54.

  • 11.

    Behrendt L, Brejnrod A, Schliep M, Sørensen SJ, Larkum AW, Kühl M. Chlorophyll f-driven photosynthesis in a cavernous cyanobacterium. ISME J. 2015;9:2108–11.

  • 12.

    Akutsu S, Fujinuma D, Furukawa H, Watanabe T, Ohnishi-Kameyama M, Ono H, et al. Pigment analysis of a chlorophyll f-containing cyanobacterium strain KC1 isolated from Lake Biwa. Photochem Photobiol. 2011;33:35–40.

    • CAS
    • Google Scholar
  • 13.

    Miyashita H, Ohkubo S, Komatsu H, Sorimachi Y, Fukayama D, Fujinuma D, et al. Discovery of chlorophyll d in Acaryochloris marina and chlorophyll f in a unicellular cyanobacterium, strain KC1, isolated from Lake Biwa. J Phys Chem Biophys. 2014;4:149.

    • Google Scholar
  • 14.

    Gómez-Lojero C, Leyva-Castillo L, Herrera-Salgado P, Barrera-Rojas J, Ríos-Castro E, Gutiérrez-Cirlos E. Leptolyngbya CCM 4, a cyanobacterium with far-red photoacclimation from Cuatro Ciénegas Basin, México. Photosynthetica. 2018;56:342–53.

    • Google Scholar
  • 15.

    Ohkubo S, Miyashita H. A niche for cyanobacteria producing chlorophyll f within a microbial mat. ISME J. 2017;11:2368–78.

  • 16.

    Trampe E, Kühl M. Chlorophyll f distribution and dynamics in cyanobacterial beachrock biofilms. J Phycol. 2016;52:990–6.

  • 17.

    Roush D, Couradeau E, Guida B, Neuer S, Garcia-Pichel F. A new niche for anoxygenic phototrophs as endoliths. Appl Environ Microbiol. 2018;84:e02055–17.

  • 18.

    Solden L, Lloyd K, Wrighton K. The bright side of microbial dark matter: lessons learned from the uncultivated majority. Curr Opin Microbiol. 2016;31:217–26.

    • PubMed
    • Google Scholar
  • 19.

    Miyashita H, Ikemoto H, Kurano N, Miyachi S, Chihara M. Acaryochloris marina gen. et sp. Nov.(cyanobacteria), an oxygenic photosynthetic prokaryote containing Chl d as a major pigment. J Phycol. 2003;39:1247–53.

    • CAS
    • Google Scholar
  • 20.

    Kashiyama Y, Miyashita H, Ohkubo S, Ogawa NO, Chikaraishi Y, Takano Y, et al. Evidence of global chlorophyll d. Science. 2008;321:658.

  • 21.

    Murakami A, Miyashita H, Iseki M, Adachi K, Mimuro M. Chlorophyll d in an epiphytic cyanobacterium of red algae. Science. 2004;303:1633.

  • 22.

    Behrendt L, Nielsen JL, Sorensen SJ, Larkum AW, Winther JR, Kuhl M. Rapid TaqMan-based quantification of chlorophyll d-containing cyanobacteria in the genus Acaryochloris. Appl Environ Microbiol. 2014;80:3244–9.

  • 23.

    Warden JG, Casaburi G, Omelon CR, Bennett PC, Breecker DO, Foster JS. Characterization of microbial mat microbiomes in the modern thrombolite ecosystem of Lake Clifton, Western Australia using shotgun metagenomics. Front Microbiol. 2016;7:1064.

  • 24.

    Moore LS, Burne R. The modern thrombolites of Lake Clifton, western Australia. In: Monty C, Bertrand-Sarfati J, editors. Phanerozoic stromatolites II: Springer; 1994. pp. 3–29.

  • 25.

    Rippka R, Deruelles J, Waterbury JB, Herdman M, Stanier RY. Generic assignments, strain histories and properties of pure cultures of cyanobacteria. Microbiology. 1979;111:1–61.

    • Google Scholar
  • 26.

    Guillard RR, Ryther JH. Studies of marine planktonic diatoms: I. Cyclotella nana Hustedt, and Detonula confervacea (Cleve) Gran. Can J Microbiol. 1962;8:229–39.

  • 27.

    NIES. CB medium. 2019. http://mcc.nies.go.jp/medium/en/cb.pdf.

  • 28.

    Miyashita H, Kurano N, Miyachi S. Composition and nature of extracellular polysaccharide produced by newly isolated coccoid prasimophyte, Prasinococcus capsulatus. J Mar Biotechnol. 1995;3:136–9.

    • CAS
    • Google Scholar
  • 29.

    Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol. 2011;7:539.

  • 30.

    Galtier N, Gouy M, Gautier C. SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. Bioinformatics. 1996;12:543–8.

    • CAS
    • Google Scholar
  • 31.

    Waterhouse AM, Procter JB, Martin DM, Clamp M, Barton GJ. Jalview Version 2—a multiple sequence alignment editor and analysis workbench. Bioinformatics. 2009;25:1189–91.

  • 32.

    Wang J, Xia F, Zeleke J, Zou B, Rhee S, Quan Z. An improved protocol with a highly degenerate primer targeting copper-containing membrane-bound monooxygenase genes for community analysis of methane-and ammonia-oxidizing bacteria. FEMS Microbiol Ecol. 2017;93:fiw244.

    • PubMed
    • Google Scholar
  • 33.

    Rose TM. CODEHOP-mediated PCR–a powerful technique for the identification and characterization of viral genomes. Virol J. 2005;2:20.

  • 34.

    Okonechnikov K, Golosova O, Fursov M. UGENE team. Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics. 2012;28:1166–7.

  • 35.

    Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, et al. Fiji: an open-source platform for biological-image analysis. Nat Methods. 2012;9:676–82.

    • CAS
    • Google Scholar
  • 36.

    Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Ostell J, Pruitt KD, et al. GenBank. Nucleic Acids Res. 2017;46:D41–7.

    • PubMed Central
    • Google Scholar
  • 37.

    Markowitz VM, Chen IA, Palaniappan K, Chu K, Szeto E, Grechkin Y, et al. IMG: the integrated microbial genomes database and comparative analysis system. Nucleic Acids Res. 2011;40:D115–22.

    • PubMed Central
    • Google Scholar
  • 38.

    Levi K, Rynge M, Abeysinghe E, Edwards RA. Searching the sequence read archive using Jetstream and Wrangler. In: PEARC 18: Proceedings of the Practice and Experience on Advanced Research Computing. Pittsburgh, PA, USA, ACM; 2018. https://doi.org/10.1145/3219104.3229278.

  • 39.

    Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel RD, Bairoch A. ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res. 2003;31:3784–8.

  • 40.

    Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 2003;52:696–704.

    • PubMed
    • Google Scholar
  • 41.

    Miller MA, Pfeiffer W, Schwartz T. Creating the CIPRES science gateway for inference of large phylogenetic trees. Gateway Computing Environments Workshop (GCE). New Orleans, LA, USA: Ieee; 2010.

  • 42.

    Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30:1312–3.

  • 43.

    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.

  • 44.

    Li Y, Lin Y, Garvey CJ, Birch D, Corkery RW, Loughlin PC, et al. Characterization of red-shifted phycobilisomes isolated from the chlorophyll f-containing cyanobacterium Halomicronema hongdechloris. Biochim Biophys Acta. 2016;1857:107–14.

  • 45.

    Sidler WA. Phycobilisome and phycobiliprotein structures. In: Bryant DA, editor. The molecular biology of cyanobacteria. Springer; 1994. pp. 139–216.

  • 46.

    Chen M, Hernandez-Prieto MA, Loughlin PC, Li Y, Willows RD. Genome and proteome of the chlorophyll f-producing cyanobacterium Halomicronema hongdechloris: adaptative proteomic shifts under different light conditions. BMC Genom. 2019;20:207.

    • Google Scholar
  • 47.

    Bryant DA, Shen G, Turner GM, Soulier N, Laremore TN, Ho M. Far-red light allophycocyanin subunits play a role in chlorophyll d accumulation in far-red light. Photosynth Res. 2020;143:81–95.

  • 48.

    Ho M, Gan F, Shen G, Bryant DA. Far-red light photoacclimation (FaRLiP) in Synechococcus sp. PCC 7335. II. Characterization of phycobiliproteins produced during acclimation to far-red light. Photosynth Res. 2017;131:187–202.

  • 49.

    Miao D, Ding W, Zhao B, Lu L, Xu Q, Scheer H, et al. Adapting photosynthesis to the near-infrared: non-covalent binding of phycocyanobilin provides an extreme spectral red-shift to phycobilisome core-membrane linker from Synechococcus sp. PCC7335. Biochim Biophys Acta. 2016;1857:688–94.

  • 50.

    Airs R, Temperton B, Sambles C, Farnham G, Skill S, Llewellyn C. Chlorophyll f and chlorophyll d are produced in the cyanobacterium Chlorogloeopsis fritschii when cultured under natural light and near-infrared radiation. FEBS Lett. 2014;588:3770–7.

  • 51.

    Nürnberg DJ, Mariscal V, Parker J, Mastroianni G, Flores E, Mullineaux CW. Branching and intercellular communication in the Section V cyanobacterium Mastigocladus laminosus, a complex multicellular prokaryote. Mol Microbiol. 2014;91:935–49.

    • PubMed
    • Google Scholar
  • 52.

    Fewer David. Molecular evidence for the antiquity of group I introns interrupting transfer RNA genes in cyanobacteria. Göttingen: University of Göttingen; 2002.

    • Google Scholar
  • 53.

    Ramos V, Morais J, Vasconcelos VM. A curated database of cyanobacterial strains relevant for modern taxonomy and phylogenetic studies. Sci Data. 2017;4:170054.

  • 54.

    Schirrmeister BE, Antonelli A, Bagheri HC. The origin of multicellularity in cyanobacteria. BCM Evol Biol. 2011;11:45.

    • Google Scholar
  • 55.

    Shih PM, Wu D, Latifi A, Axen SD, Fewer DP, Talla E, et al. Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing. Proc Natl Acad Sci USA. 2013;110:1053–8.

  • 56.

    Diez B, Bauer K, Bergman B. Epilithic cyanobacterial communities of a marine tropical beach rock (Heron Island, Great Barrier Reef): diversity and diazotrophy. Appl Environ Microbiol. 2007;73:3656–68.

  • 57.

    Petrou K, Trimborn S, Kühl M, Ralph PJ. Desiccation stress in two intertidal beachrock biofilms. Mar Biol. 2014;161:1765–73.

    • CAS
    • Google Scholar
  • 58.

    Wacey D, Gleeson D, Kilburn M. Microbialite taphonomy and biogenicity: new insights from NanoSIMS. Geobiology. 2010;8:403–16.

  • 59.

    Zhang H, Ning K. The Tara Oceans project: new opportunities and greater challenges ahead. Genom Proteom Bioinform. 2015;13:275–7.

    • Google Scholar
  • 60.

    Babilonia J, Foster JS, Conesa A, Casaburi G, Pereira C, Louyakis A, et al. Comparative metagenomics provides insight into the ecosystem functioning of the Shark Bay stromatolites, Western Australia. Front Microbiol. 2018;9:1359.

  • 61.

    Nayfach S, Pollard KS. Toward accurate and quantitative comparative metagenomics. Cell. 2016;166:1103–16.

  • 62.

    Muir P, Li S, Lou S, Wang D, Spakowicz DJ, Salichos L, et al. The real cost of sequencing: scaling computation to keep pace with data generation. Genome Biol. 2016;17:53.

  • 63.

    Lindemann SR, Moran JJ, Stegen JC, Renslow RS, Hutchison JR, Cole JK, et al. The epsomitic phototrophic microbial mat of Hot Lake, Washington: community structural responses to seasonal cycling. Front Microbiol. 2013;4:323.

  • 64.

    Royer CJ, Blouin NA, Brawley SH. More than meets the eye: regional specialisation and microbial cover of the blade of Porphyra umbilicalis (Bangiophyceae, Rhodophyta). Bot Mar. 2018;61:459–65.

    • CAS
    • Google Scholar
  • 65.

    Larkum AW, Chen M, Li Y, Schliep M, Trampe E, West J, et al. A novel epiphytic chlorophyll d‐containing cyanobacterium isolated from a mangrove‐associated ted alga. J Phycol. 2012;48:1320–7.

    • PubMed
    • Google Scholar
  • 66.

    Manning WM, Strain HH. Chlorophyll d, a green pigment of red algae. J Biol Chem. 1943;151:1–19.

    • CAS
    • Google Scholar
  • 67.

    Glazer AN. Structure and molecular organization of the photosynthetic accessory pigments of cyanobacteria and red algae. Mol Cell Biochem. 1977;18:125–40.

  • 68.

    Ritchie RJ, Larkum AW, Ribas I. Could photosynthesis function on Proxima Centauri b? Int J Astrobiol. 2018;17:147–76.

    • CAS
    • Google Scholar
  • 69.

    Bryant JA, Clemente TM, Viviani DA, Fong AA, Thomas KA, Kemp P, et al. Diversity and activity of communities inhabiting plastic debris in the North Pacific Gyre. mSystems. 2016;1:e00024–16.

  • 70.

    Zettler ER, Mincer TJ, Amaral-Zettler LA. Life in the “plastisphere”: microbial communities on plastic marine debris. Environ Sci Technol. 2013;47:7137–46.

  • 71.

    Ho MY, Shen G, Canniffe DP, Zhao C, Bryant DA. Light-dependent chlorophyll f synthase is a highly divergent paralog of PsbA of photosystem II. Science. 2016;26:353.

    • Google Scholar
  • 72.

    Cardona T, Murray JW, Rutherford AW. Origin and evolution of water oxidation before the last common ancestor of the cyanobacteria. Mol Biol Evol. 2015;32:1310–28.

  • 73.

    Cardona T, Sánchez-Baracaldo P, Rutherford AW, Larkum AW. Early Archean origin of Photosystem II. Geobiology. 2018;17:127–50.

  • 74.

    Rutherford A, Nitschke W. Photosystem II and the quinone-iron-containing reaction centers: comparisons and evolutionary perspectives. In: Baltscheffsky H, editor. Origin and evolution of biological energy conversion. New York: VCH Publishers; 1996. p. 143–74.

    • Google Scholar
  • 75.

    Murray JW. Sequence variation at the oxygen-evolving centre of photosystem II: a new class of ‘rogue’cyanobacterial D1 proteins. Photosynth Res. 2012;110:177–84.

  • 76.

    Robertson BR, Tezuka N, Watanabe MM. Phylogenetic analyses of Synechococcus strains (cyanobacteria) using sequences of 16S rDNA and part of the phycocyanin operon reveal multiple evolutionary lines and reflect phycobilin content. Int J Syst Evol Microbiol. 2001;51:861–71.

  • 77.

    Fewer D, Friedl T, Büdel B. Chroococcidiopsis and heterocyst-differentiating cyanobacteria are each other’s closest living relatives. Mol Phylogenet Evol. 2002;23:82–90.

  • 78.

    Sánchez-Baracaldo P. Origin of marine planktonic cyanobacteria. Sci Rep. 2015;5:17418.

  • 79.

    Awramik SM, Sprinkle J. Proterozoic stromatolites: the first marine evolutionary biota. Hist Biol. 1999;13:241–53.

    • Google Scholar
  • 80.

    Nübel U, Garcia-Pichel F, Muyzer G. PCR primers to amplify 16S rRNA genes from cyanobacteria. Appl Environ Microbiol. 1997;63:3327–32.

  • 81.

    Ferris MJ, Muyzer G, Ward DM. Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populations inhabiting a hot spring microbial mat community. Appl Environ Microbiol. 1996;62:340–6.


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