Martin WF, Bryant DA, Beatty JT. A physiological perspective on the origin and evolution of photosynthesis. FEMS Microbiol Rev. 2018;42:205–31.
Google Scholar
Partensky F, Blanchot J, Vaulot D. Differential distribution and ecology of Prochlorococcus and Synechococcus in oceanic waters: a review. Bull Oceanogr Monaco, no Spec. 1999;19:457–76.
Zwirglmaier K, Jardillier L, Ostrowski M, Mazard S, Garczarek L, Vaulot D, et al. Global phylogeography of marine Synechococcus and Prochlorococcus reveals a distinct partitioning of lineages among oceanic biomes. Environ Microbiol. 2008;10:147–61.
Google Scholar
Callieri C. Picophytoplankton in freshwater ecosystems: the importance of small-sized phototrophs. Freshw Rev. 2008;1:1–28.
Google Scholar
Stal LJ. Physiological ecology of cyanobacteria in microbial mats and other communities. New Phytol. 1995;131:1–32.
Google Scholar
Rikkinen J. Cyanobacteria in terrestrial symbiotic systems. In: Hallenbeck PC editor. Modern topics in the phototrophic prokaryotes. Switzerland: Springer; 2017. p. 243–94.
Badger MR, Price GD, Long BM, Woodger FJ. The environmental plasticity and ecological genomics of the cyanobacterial CO2 concentrating mechanism. J Exp Bot. 2006;57:249–65.
Google Scholar
Rae BD, Long BM, Badger MR, Price GD. Functions, compositions, and evolution of the two types of carboxysomes: polyhedral microcompartments that facilitate CO2 fixation in cyanobacteria and some proteobacteria. Microbiol Mol Biol Rev. 2013;77:357–79.
Google Scholar
Bar-On YM, Phillips R, Milo R. The biomass distribution on Earth. Proc Natl Acad Sci USA. 2018;115:6506–11.
Google Scholar
Buitenhuis ET, Li WKW, Vaulot D, Lomas MW, Landry MR, Partensky F, et al. Picophytoplankton biomass distribution in the global ocean. Earth Syst Sci Data. 2012;4:37–46.
Google Scholar
Flombaum P, Gallegos JL, Gordillo RA, Rincón J, Zabala LL, Jiao N, et al. Present and future global distributions of the marine Cyanobacteria Prochlorococcus and Synechococcus. Proc Natl Acad Sci USA. 2013;110:9824–9.
Google Scholar
Field CB, Behrenfeld MJ, Randerson JT, Falkowski P. Primary production of the biosphere: integrating terrestrial and oceanic components. Science. 1998;281:237–40.
Google Scholar
Garcia-Pichel F, Belnap J, Neuer S, Schanz F. Estimates of global cyanobacterial biomass and its distribution. Arch Hydrobiol Suppl Algol Stud. 2003;109:213.
Scanlan DJ, Ostrowski M, Mazard S, Dufresne A, Garczarek L, Hess WR, et al. Ecological genomics of marine picocyanobacteria. Microbiol Mol Biol Rev. 2009;73:249–99.
Google Scholar
Doré H, Farrant GK, Guyet U, Haguait J, Humily F, Ratin M, et al. Evolutionary mechanisms of long-term genome diversification associated with niche partitioning in marine picocyanobacteria. Front Microbiol. 2020;11:2129.
Google Scholar
Dufresne A, Ostrowski M, Scanlan DJ, Garczarek L, Mazard S, Palenik BP, et al. Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria. Genome Biol. 2008;9:R90.
Google Scholar
Badger MR, Hanson D, Price GD. Evolution and diversity of CO2 concentrating mechanisms in cyanobacteria. Funct Plant Biol. 2002;29:161–73.
Google Scholar
Whitehead L, Long BM, Price GD, Badger MR. Comparing the in vivo function of α-carboxysomes and β-carboxysomes in two model cyanobacteria. Plant Physiol. 2014;165:398–411.
Google Scholar
Castenholz RW, Wilmotte A, Herdman M, Rippka R, Waterbury JB, Iteman I, et al. Phylum BX. cyanobacteria. In: Boone DR, Castenholz RW, Garrity GM editors. Bergey’s manual of systematic bacteriology. New York, NY: Springer; 2001. p. 473–599.
Cabello‐Yeves PJ, Picazo A, Camacho A, Callieri C, Rosselli R, Roda-Garcia JJ, et al. Ecological and genomic features of two widespread freshwater picocyanobacteria. Environ Microbiol. 2018;20:3757–71.
Google Scholar
Di Cesare A, Cabello-Yeves PJ, Chrismas NAM, Sánchez-Baracaldo P, Salcher MM, Callieri C, et al. Genome analysis of the freshwater planktonic Vulcanococcus limneticus sp. nov. reveals horizontal transfer of nitrogenase operon and alternative pathways of nitrogen utilization. BMC Genomics. 2018;19:259.
Google Scholar
Sánchez-Baracaldo P, Bianchini G, Di Cesare A, Callieri C, Chrismas NAM. Insights into the evolution of picocyanobacteria and phycoerythrin genes (mpeBA and cpeBA). Front Microbiol. 2019;10:a45.
Google Scholar
Callieri C, Mandolini E, Bertoni R, Lauceri R, Picazo A, Camacho A, et al. Atlas of picocyanobacteria monoclonal strains from the collection of CNR-IRSA, Italy. J Limnol. 2021;80:2002.
Google Scholar
Herdman M, Castenholz RW, Iteman I, Waterbury JB, Rippka R. Subsection I (Formerly Chroococcales Wettstein 1924, emend. Rippka, Deruelles, Waterbury, Herdman and Stanier 1979). In: Boone DR, Castenholz RW, Garrity GM, editors. Bergey’s manual of systematic bacteriology, Vol 1, 2nd ed., The archaea and the deeply branching and phototrophic bacteria. New York: Springer; 2001. p. 493–514.
Cabello-Yeves PJ, Haro-Moreno JM, Martin-Cuadrado A, Ghai R, Picazo A, Camacho A, et al. Novel Synechococcus genomes reconstructed from freshwater reservoirs. Front Microbiol. 2017;8:1151.
Google Scholar
Badger MR, Price GD. CO2 concentrating mechanisms in cyanobacteria: molecular components, their diversity and evolution. J Exp Bot. 2003;54:609–22.
Google Scholar
Wheatley NM, Sundberg CD, Gidaniyan SD, Cascio D, Yeates TO. Structure and identification of a pterin dehydratase-like protein as a ribulose-bisphosphate carboxylase/oxygenase (RuBisCO) assembly factor in the α-carboxysome. J Biol Chem. 2014;289:7973–81.
Google Scholar
Huang F, Kong WW, Sun Y, Chen T, Dykes GF, Jiang Y, et al. Rubisco accumulation factor 1 (Raf1) plays essential roles in mediating Rubisco assembly and carboxysome biogenesis. Proc Natl Acad Sci USA. 2020;117:17418–28.
Google Scholar
Kerfeld CA, Melnicki MR. Assembly, function and evolution of cyanobacterial carboxysomes. Curr Opin Plant Biol. 2016;31:66–75.
Google Scholar
Kupriyanova E, Pronina N, Los D. Carbonic anhydrase—a universal enzyme of the carbon-based life. Photosynthetica. 2017;55:3–19.
Google Scholar
DiMario RJ, Machingura MC, Waldrop GL, Moroney JV. The many types of carbonic anhydrases in photosynthetic organisms. Plant Sci. 2018;268:11–17.
Heinhorst S, Cannon GC. A novel evolutionary lineage of carbonic anhydrase (epsilon class) is a component of the carboxysome shell. J Bacteriol. 2004;186:623–30.
Google Scholar
Sawaya MR, Cannon GC, Heinhorst S, Tanaka S, Williams EB, Yeates TO, et al. The structure of beta-carbonic anhydrase from the carboxysomal shell reveals a distinct subclass with one active site for the price of two. J Biol Chem. 2006;281:7546–55.
Google Scholar
Heinhorst S, Williams EB, Cai F, Murin CD, Shively JM, Cannon GC. Characterization of the carboxysomal carbonic anhydrase CsoSCA from Halothiobacillus neapolitanus. J Bacteriol. 2006;188:8087–94.
Google Scholar
Omata T, Takahashi Y, Yamaguchi O, Nishimura T. Structure, function and regulation of the cyanobacterial high-affinity bicarbonate transporter, BCT1. Funct Plant Biol. 2002;29:151–9.
Google Scholar
Omata T, Price GD, Badger MR, Okamura M, Gohta S, Ogawa T. Identification of an ATP-binding cassette transporter involved in bicarbonate uptake in the cyanobacterium Synechococcus sp. strain PCC 7942. Proc Natl Acad Sci USA. 1999;96:13571–6.
Google Scholar
Shelden MC, Howitt SM, Price GD. Membrane topology of the cyanobacterial bicarbonate transporter, BicA, a member of the SulP (SLC26A) family. Mol Membr Biol. 2010;27:12–22.
Google Scholar
Price GD, Howitt SM. The cyanobacterial bicarbonate transporter BicA: its physiological role and the implications of structural similarities with human SLC26 transporters. Biochem Cell Biol. 2011;89:178–88.
Google Scholar
Price GD, Woodger FJ, Badger MR, Howitt SM, Tucker L. Identification of a SulP-type bicarbonate transporter in marine cyanobacteria. Proc Natl Acad Sci USA. 2004;101:18228–33.
Google Scholar
Bonfil DJ, Ronen-Tarazia M, Sültemeyer D, Lieman-Hurwitza J, Schatz D, Kaplan A. A putative HCO−3 transporter in the cyanobacterium Synechococcus sp. strain PCC 7942. FEBS Lett. 1998;430:236–40.
Google Scholar
Price GD, Shelden MC, Howitt SM. Membrane topology of the cyanobacterial bicarbonate transporter, SbtA, and identification of potential regulatory loops. Mol Membr Biol. 2011;28:265–75.
Google Scholar
Shibata M, Katoh H, Sonoda M, Ohkawa H, Shimoyama M, Fukuzawa H. Genes essential to sodium-dependent bicarbonate transport in cyanobacteria: function and phylogenetic analysis. J Biol Chem. 2002;277:18658–64.
Google Scholar
Zhang P, Battchikova N, Jansen T, Appel J, Ogawa T, Aro EM. Expression and functional roles of the two distinct NDH-1 complexes and the carbon acquisition complex NdhD3/NdhF3/CupA/Sll1735 in Synechocystis sp PCC 6803. Plant Cell. 2004;16:3326–40.
Google Scholar
Price GD, Badger MR, Woodger FJ, Long BM. Advances in understanding the cyanobacterial CO2-concentrating-mechanism (CCM): functional components, Ci transporters, diversity, genetic regulation and prospects for engineering into plants. J Exp Bot. 2008;59:1441–61.
Google Scholar
Battchikova N, Eisenhut M, Aro E-M. Cyanobacterial NDH-1 complexes: novel insights and remaining puzzles. Biochim Biophys Acta Bioenerg. 2011;1807:935–44.
Google Scholar
Koester RP, Pignon CP, Kesler DC, Willison RS, Kang M, Shen Y. Transgenic insertion of the cyanobacterial membrane protein ictB increases grain yield in Zea mays through increased photosynthesis and carbohydrate production. PLoS ONE. 2021;16:e0246359.
Johnson ZI, Zinser ER, Coe A, McNulty NP, Woodward EMS, Chisholm SW. Niche partitioning among Prochlorococcus ecotypes along ocean-scale environmental gradients. Science. 2006;311:1737–40.
Google Scholar
Callieri C, Coci M, Corno G, Macek M, Modenutti B, Balseiro E. Phylogenetic diversity of nonmarine picocyanobacteria. FEMS Microbiol Ecol. 2013;85:293–301.
Google Scholar
Schallenberg LA, Pearman JK, Burns CW, Wood SA. Spatial abundance and distribution of picocyanobacterial communities in two contrasting lakes revealed using environmental DNA metabarcoding. FEMS Microbiol Ecol. 2021;97:fiab075.
Google Scholar
Mózes A, Présing M, Vörös L. Seasonal dynamics of picocyanobacteria and picoeukaryotes in a large shallow lake (Lake Balaton, Hungary). Int Rev Hydrobiol. 2006;91:38–50.
Google Scholar
Vörös L, Callieri C, Balogh KV, Bertoni R. Freshwater picocyanobacteria along a trophic gradient and light quality range. Hydrobiologia. 1998;369/370:117–25.
Watanabe MF, Harada K, Carmichael WW, Fujiki H. Toxic microcystis. Boca Raton, FL: CRC Press; 1995.
Stockner J, Callieri C, Cronberg G. Picoplankton and other non-bloom-forming cyanobacteria in lakes. In: Whitton BA, Potts M editors. The ecology of cyanobacteria. The Netherlands: Springer; 2000. p. 195–231.
Flamholz AI, Prywes N, Moran U, Davidi D, Bar-On YM, Oltrogge LM. Revisiting trade-offs between Rubisco kinetic parameters. Biochemistry. 2019;58:3365–76.
Google Scholar
Filazzola A, Mahdiyan O, Shuvo A, Ewins C, Moslenko L, Sadid T. A database of chlorophyll and water chemistry in freshwater lakes. Sci Data. 2020;7:1–10.
Google Scholar
Cabello‐Yeves PJ, Zemskaya TI, Zakharenko AS, Sakirko MV, Ivanov VG, Ghai R, et al. Microbiome of the deep Lake Baikal, a unique oxic bathypelagic habitat. Limnol Oceanogr. 2019.
Rodrigo MA, Miracle MR, Vicente E. The meromictic Lake La Cruz (Central Spain). Patterns of stratification. Aquat Sci. 2001;63:406–16.
Google Scholar
Camacho A, Picazo A, Miracle MR, Vicente E. Spatial distribution and temporal dynamics of picocyanobacteria in a meromictic karstic lake. Arch Hydrobiol Suppl Algol Stud. 2003;109:171–84.
Vicente E, Camacho A, Rodrigo MA. Morphometry and physico-chemistry of the crenogenic meromictic Lake El Tobar (Spain). Int Ver für Theor und Angew Limnol Verhandlungen. 1993;25:698–704.
Google Scholar
Camacho A, Miracle MR, Vicente E. Which factors determine the abundance and distribution of picocyanobacteria in inland waters? A comparison among different types of lakes and ponds. Arch für Hydrobiol. 2003;157:321–38.
Google Scholar
Kaźmierczak J, Kempe S, Kremer B, López-García P, Moreira D, Tavera R. Hydrochemistry and microbialites of the alkaline crater lake Alchichica, Mexico. Facies. 2011;57:543–70.
Google Scholar
Ghai R, Mizuno CM, Picazo A, Camacho A, Rodriguez‐Valera F. Key roles for freshwater Actinobacteria revealed by deep metagenomic sequencing. Mol Ecol. 2014;23:6073–90.
Google Scholar
Cabello-Yeves PJ, Ghai R, Mehrshad M, Picazo A, Camacho A, Rodriguez-Valera F. Reconstruction of diverse Verrucomicrobial genomes from metagenome datasets of freshwater reservoirs. Front Microbiol. 2017;8:2131.
Google Scholar
de Hoyos C, Negro AI, Aldasoro JJ. Cyanobacteria distribution and abundance in the Spanish water reservoirs during thermal stratification. Limnetica. 2004;23:119–32.
Google Scholar
Raven J, Caldeira K, Eldefield H, Hoegh-Guldberg O, Liss P, Riebesell U, et al. Ocean acidification due to increasing atmospheric carbon dioxide. London: The Royal Society; 2005.
Mangan NM, Flamholz A, Hood RD, Milo R, Savage DF. pH determines the energetic efficiency of the cyanobacterial CO2 concentrating mechanism. Proc Natl Acad Sci USA. 2016;113:E5354–62.
Google Scholar
Tadesse I, Green FB, Puhakka JA. Seasonal and diurnal variations of temperature, pH and dissolved oxygen in advanced integrated wastewater pond system® treating tannery effluent. Water Res. 2004;38:645–54.
Google Scholar
Gao Y, Zhang Z, Liu X, Yi N, Zhang L, Song W, et al. Seasonal and diurnal dynamics of physicochemical parameters and gas production in vertical water column of a eutrophic pond. Ecol Eng. 2016;87:313–23.
Google Scholar
Schindler DW. Recent advances in the understanding and management of eutrophication. Limnol Oceanogr. 2006;51:356–63.
Google Scholar
Bosak T, Bush JWM, Flynn MR, Liang B, Ono S, Petroff AP, et al. Formation and stability of oxygen‐rich bubbles that shape photosynthetic mats. Geobiology. 2010;8:45–55.
Google Scholar
Zeebe RE, Wolf-Gladrow D. CO2 in seawater: equilibrium, kinetics, isotopes. Amsterdam: Elsevier Science B.V.; 2001.
Rae BD, Förster B, Badger MR, Price GD. The CO2-concentrating mechanism of Synechococcus WH5701 is composed of native and horizontally-acquired components. Photosynth Res. 2011;109:59–72.
Google Scholar
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
Martín-Cuadrado A-B, López-García P, Alba J-C, Moreira D, Monticelli L, Strittmatter A, et al. Metagenomics of the deep Mediterranean, a warm bathypelagic habitat. PLoS ONE. 2007;2:e914.
Google Scholar
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–20.
Google Scholar
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19:455–77.
Google Scholar
Hyatt D, Chen G-L, LoCascio PF, Land ML, Larimer FW, Hauser LJ, et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinforma. 2010;11:1.
Google Scholar
Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2015;12:59–60.
Google Scholar
Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28:27–30.
Google Scholar
Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res. 2013;42:D206–14.
Google Scholar
Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS, et al. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 2001;29:22–8.
Google Scholar
Haft DH, Loftus BJ, Richardson DL, Yang F, Eisen JA, Paulsen IT, et al. TIGRFAMs: a protein family resource for the functional identification of proteins. Nucleic Acids Res. 2001;29:41–3.
Google Scholar
Kang D, Li F, Kirton E, Thomas A, Egan R, An H, et al. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ Prepr. 2019;7:e27522v1.
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;25:1043–55.
Google Scholar
Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A, Chaumeil P-A, et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol. 2018;36:996–1004.
Google Scholar
Asnicar F, Thomas AM, Beghini F, Mengoni C, Manara S, Manghi P, et al. Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0. Nat Commun. 2020;11:1–10.
Google Scholar
Garczarek L, Guyet U, Doré H, Farrant GK, Hoebeke M, Brillet-Guéguen L, et al. Cyanorak v2.1: a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes. Nucleic Acids Res. 2021;49:D667–76.
Google Scholar
Erwin PM, Thacker RW. Cryptic diversity of the symbiotic cyanobacterium Synechococcus spongiarum among sponge hosts. Mol Ecol. 2008;17:2937–47.
Google Scholar
Usher KM, Toze S, Fromont J, Ku J, Sutton DC. A new species of cyanobacterial symbiont from the marine sponge Chondrilla nucula. Symbiosis. 2004.
Holtman CK, Chen Y, Sandoval P, Gonzales A, Nalty MS, Thomas TL, et al. High-throughput functional analysis of the Synechococcus elongatus PCC 7942 genome. DNA Res. 2005;12:103–15.
Google Scholar
Chen M-Y, Teng W-K, Zhao L, Hu C-X, Zhou Y-K, Han B-P, et al. Comparative genomics reveals insights into cyanobacterial evolution and habitat adaptation. ISME J. 2021;15:211–27.
Google Scholar
Katoh K, Misawa K, Kuma K, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002;30:3059–66.
Google Scholar
Price MN, Dehal PS, Arkin AP. FastTree 2–approximately maximum-likelihood trees for large alignments. PLoS ONE. 2010;5:e9490.
Google Scholar
Rozen S, Skaletsky H. Primer3 on the WWW for general users and for biologist programmers. Methods Mol. Biol. 2000;132:365–86.
Google Scholar
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