Modern Rivularia Freshwater Stromatolites as Models for Formation of Laminated Stromatolitic Crusts

References

• Alsenani F, Tupally KR, Chua ET, Eltanahy E, Alsufyani H, Parekh HS, Schenk PM. 2020. Evaluation of microalgae and cyanobacteria as potential sources of antimicrobial compounds. Saudi Pharm J 28(12):1834–1841.
   PubMed Web of Science ®Google Scholar
• Andrews S, Lindenbaum P, Howard B, Ewels P. 2015. FastQC [ComputerSoftware]. Available at https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
   Google Scholar
• Arp G, Bissett A, Brinkmann N, Cousin S, de Beer D, Friedl T, Mohr KI, Neu TR, Reimer A, Shiraishi F, et al. 2010. Tufa-forming biofilms of German karstwater streams: microorganisms, exopolymers, hydrochemistry and calcification. Geol Soc Spec Publ 336(1):83–118.
   Google Scholar
• Arp G, Helms G, Karlinska K, Schumann G, Reimer A, Reitner J, Trichet J. 2012. Photosynthesis versus exopolymer degradation in the formation of microbialites on the atoll of Kiritimati, Republic of Kiribati, Central Pacific. Geomicrobiol J 29(1):29–65.
   Web of Science ®Google Scholar
• Arp G, Reimer A, Reitner J. 2002. Calcification of cyanobacterial filaments: Girvanella and the origin of lower Paleozoic lime mud [comment]. Geology 30(6):579–580.
   Web of Science ®Google Scholar
• Arp G, Reimer A, Reitner J. 2003. Microbialite formation in seawater of increased alkalinity, Satonda Crater Lake, Indonesia. J Sediment Res 73(1):105–127.
   Web of Science ®Google Scholar
• Arp G, Reimer A, Reitner J. 2001. Photosynthesis-induced biofilm calcification and calcium concentrations in Phanerozoic oceans. Science 292(5522):1701–1704.
   PubMed Web of Science ®Google Scholar
• Arp G, Thiel V, Reimer A, Michaelis W, Reitner J. 1999. Biofilm exopolymers control microbialite formation at thermal springs discharging into the alkaline Pyramid Lake, Nevada, USA. Sediment Geol 126(1–4):159–176.
   Web of Science ®Google Scholar
• Bauer A, Forchhammer K. 2021. Bacterial predation on Cyanobacteria. Microb Physiol 31(2):99–108.
   PubMedGoogle Scholar
• Berg KA, Lyra C, Sivonen K, Paulin L, Suomalainen S, Tuomi P, Rapala J. 2009. High diversity of cultivable heterotrophic bacteria in association with cyanobacterial water blooms. ISME J 3(3):314–325.
   PubMed Web of Science ®Google Scholar
• Brinkmann N, Hodač L, Mohr KI, Hodačová A, Jahn R, Ramm J, Hallmann C, Arp G, Friedl T. 2015. Cyanobacteria and diatoms in biofilms of two karstic streams in Germany and changes of their communities along calcite saturation gradients. Geomicrobiol J 32(3–4):255–274.
   Web of Science ®Google Scholar
• Cannon GC, Bradburne CE, Aldrich HC, Baker SH, Heinhorst S, Shively JM. 2001. Microcompartments in prokaryotes: carboxysomes and related polyhedra. Appl Environ Microbiol 67(12):5351–5361.
   PubMed Web of Science ®Google Scholar
• Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, et al. 2010. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7(5):335–336.
   PubMed Web of Science ®Google Scholar
• Caudwell C, Delcourt A, Lang J, Pascal A. 1997. Biocoenosis and induration of freshwater Rivularia stromatolites in a temperate climate. Geomicrobiol J 14(4):285–298.
   Web of Science ®Google Scholar
• Caudwell C, Lang J, Pascal A. 2001. Lamination of swampy-rivulets Rivularia haematites stromatolites in a temperate climate. Sediment Geol 143(1–2):125–147.
   Web of Science ®Google Scholar
• Copeland A, Zhang X, Misra M, Lapidus A, Nolan M, Lucas S, Deshpande S, Cheng JF, Tapia R, Goodwin LA, et al. 2012. Complete genome sequence of the aquatic bacterium Runella slithyformis type strain (LSU 4(T)). Stand Genomic Sci 6(2):145–154.
   PubMed Web of Science ®Google Scholar
• Decho AW. 2010. Overview of biopolymer-induced mineralization: what goes on in biofilms? Ecol Eng 36(2):137–144.
   Web of Science ®Google Scholar
• Della Porta G, Hoppert M, Hallmann C, Schneider D, Reitner J. 2022. The influence of microbial mats on travertine precipitation in active hydrothermal systems (Central Italy). Depos Rec 8(1):165–209.
   Web of Science ®Google Scholar
• Dziallas C, Grossart H-P. 2011. Temperature and biotic factors influence bacterial communities associated with the cyanobacterium Microcystis sp. Environ Microbiol 13(6):1632–1641.
   PubMed Web of Science ®Google Scholar
• Edgar RC. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26(19):2460–2461.
   PubMed Web of Science ®Google Scholar
• Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27(16):2194–2200.
   PubMed Web of Science ®Google Scholar
• Egelkamp R, Schneider D, Hertel R, Daniel R. 2017. Nitrile-degrading bacteria isolated from compost. Front Environ Sci 5:58.
   Web of Science ®Google Scholar
• Flügel E. 2009. Microfacies of Carbonate Rocks. 2nd ed. Berlin: Springer.
   Google Scholar
• Foster JS, Green SJ. 2011. Microbial diversity in modern stromatolites. In: Tewari V, Seckbach J, editors. Stromatolites: Interaction of Microbes with Sediments. Cellular Origin, Life in Extreme Habitats and Astrobiology, Vol. 18. Dordrecht: Springer, p383–405.
   Google Scholar
• Gautret P, Camoin G, Golubic S, Sprachta S. 2004. Biochemical control of calcium carbonate precipitation in modern lagoonal microbialites, Tikehau Atoll, French Polynesia. J Sediment Res 74(4):462–478.
   Web of Science ®Google Scholar
• Gerphagnon M, Macarthur DJ, Latour D, Gachon CM, Van Ogtrop F, Gleason FH, Sime-Ngando T. 2015. Microbial players involved in the decline of filamentous and colonial cyanobacterial blooms with a focus on fungal parasitism. Environ Microbiol 17(8):2573–2587.
   PubMed Web of Science ®Google Scholar
• Grasshoff K, Kremling K, Ehrhardt M. 2009. Methods of seawater analysis. Hoboken, NJ: John Wiley & Sons.
   Google Scholar
• Hodač L, Brinkmann N, Mohr K, Arp G, Hallmann C, Ramm J, Spitzer K, Friedl T. 2015. Diversity of microscopic green algae (Chlorophyta) in calcifying biofilms of two karstic streams in Germany. Geomicrobiol J 32(3–4):275–290.
   Web of Science ®Google Scholar
• Hoefs J. 2015. Stable Isotope Geochemistry. 7th ed. Heidelberg: Springer.
   Google Scholar
• Hoffmann F, Janussen D, Dröse W, Arp G, Reitner J. 2003. Histological investigation of organisms with hard skeletons: a case study of siliceous sponges. Biotech Histochem 78(3–4):191–199.
   PubMed Web of Science ®Google Scholar
• Johnson DB, Beddows PA, Flynn TM, Osburn MR. 2018. Microbial diversity and biomarker analysis of modern freshwater microbialites from Laguna Bacalar, Mexico. Geobiology 16(3):319–337.
   PubMed Web of Science ®Google Scholar
• Kadnikov VV, Mardanov AV, Beletsky AV, Rakitin AL, Frank YA, Karnachuk OV, Ravin NV. 2019. Phylogeny and physiology of candidate phylum BRC1 inferred from the first complete metagenome-assembled genome obtained from deep subsurface aquifer. Syst Appl Microbiol 42(1):67–76.
   PubMed Web of Science ®Google Scholar
• Kamran A, Sauter A, Reimer A, Wacker T, Reitner J, Hoppert M. 2020. Cyanobacterial mats in calcite-precipitating serpentinite-hosted alkaline springs of the Voltri Massif, Italy. Microorganisms 9(1):62.
   PubMed Web of Science ®Google Scholar
• Karl H-V, Arp G, Siedersbeck E, Reitner J. 2014. A large ichthyosaur vertebra from the lower Kössen Formation (Upper Norian) of the Lahnewiesgraben near Garmisch-Partenkirchen, Germany. In: Wiese F, Reich M, Arp G, editors. Spongy, Slimy, Cosy & More… Commemorative Volume in Celebration of the 60th Birthday of Joachim Reitner. Göttingen Contributions to Geosciences, Vol. 77. Göttingen: Universitätsverlag, p191–197.
   Google Scholar
• Kleinteich J, Golubic S, Pessi IS, Velázquez D, Storme JY, Darchambeau F, Borges AV, Compère P, Radtke G, Lee SJ, et al. 2017. Cyanobacterial contribution to travertine deposition in the Hoyoux River system, Belgium. Microb Ecol 74(1):33–53.
   PubMed Web of Science ®Google Scholar
• Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, Glöckner FO. 2013. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res 41(1):e1.
   PubMed Web of Science ®Google Scholar
• Kuczynski J, Stombaugh J, Walters WA, González A, Caporaso JG, Knight R. 2011. Using QIIME to analyze 16S rRNA gene sequences from microbial communities. Curr Protoc Bioinform 36:10.7.1–10.7.20.
   Google Scholar
• Kuhnert C. 1967. Erläuterungen zur geologischen Karte von Bayern; Blatt Nr. 8432 Oberammergau. München: Bayerisches Geologisches Landesamt.
   Google Scholar
• Liu L, Wu Y, Hongxia J, Riding R. 2016. Calcified rivulariaceans from the Ordovician of the Tarim Basin, Northwest China, Phanerozoic lagoonal examples, and possible controlling factors. Palaeogeogr Palaeoclimatol Palaeoecol 448:371–381.
   Web of Science ®Google Scholar
• Logan BW, Rezak R, Ginsburg RN. 1964. Classification and environmental significance of algal stromatolites. J Geol 72(1):68–83.
   Web of Science ®Google Scholar
• Martin M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J 17(1):10–12.
   Google Scholar
• Masella AP, Bartram AK, Truszkowski JM, Brown DG, Neufeld JD. 2012. PANDAseq: Paired-end assembler for illumina sequences. BMC Bioinform 13:31.
   Google Scholar
• Mlewski EC, Pisapia C, Gomez F, Lecourt L, Soto Rueda E, Benzerara K, Ménez B, Borensztajn S, Jamme F, Réfrégiers M, et al. 2018. Characterization of pustular mats and related Rivularia-rich laminations in oncoids from the Laguna Negra Lake (Argentina). Front Microbiol 22:996.
   Google Scholar
• Momma K, Hashimoto W, Miyake O, Yoon H-J, Kawai S, Mishima Y, Mikami B, Murata K. 1999. Special cell surface structure, and novel macromolecule transport/depolymerization system of Sphingomonas sp. J Ind Microbiol Biotechnol 23(4–5):425–435.
   PubMed Web of Science ®Google Scholar
• Monty C. 1981. Phanerozoic Stromatolites. Berlin: Springer.
   Google Scholar
• Mulisch M, Welsch U. 2015. Romeis – Mikroskopische Technik. 19th ed. Heidelberg: Springer.
   Google Scholar
• Muñoz-Martín MA, Berrendero Gómez E, Perona E, Mateo P. 2020. Analysis of molecular diversity within single cyanobacterial colonies from environmental samples. Sci Rep 10(1):18453.
   PubMed Web of Science ®Google Scholar
• Obenlüneschloss J. 1991. Biologie und Ökologie von drei rezenten Süßwasser-Rivularien (Cyanobakterien) – Übertragbarkeit artspezifischer Verkalkungsstrukturen auf fossile Formen. Göttinger Arbeiten Geol Paläontol 50:1–86.
   Google Scholar
• Parkhurst DL, Appelo CAJ. 2013. Description of input and examples for PHREEQC version 3—A computer program for speciation, batch-reaction, one-dimensional transport, and inverse geochemical calculations: U.S. Geological survey techniques and methods, book 6, chap. A43, http://pubs.usgs.gov/tm/06/a4. Denver, CO: U.S. Geological Survey.
   Google Scholar
• Pentecost A, Franke U. 2010. Photosynthesis and calcification of the stromatolitic freshwater cyanobacterium Rivularia. Eur J Phycol 45(4):345–353.
   Web of Science ®Google Scholar
• Pentecost A. 1987. Growth and Calcification of the freshwater cyanobacterium Rivularia haematites. Proc R Soc Lond Ser B Biol Sci 232:125–136.
   Web of Science ®Google Scholar
• Perissinotto R, Bornman TG, Steyn P-P, Miranda NA, Dorrington RA, Matcher GF, Strydom N, Peer N. 2014. Tufa stromatolite ecosystems on the South African south coast. S Afr J Sci 110(9/10):8–96.
   Web of Science ®Google Scholar
• Peryt TM. 1983. Coated Grains. Berlin: Springer.
   Google Scholar
• Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO. 2013. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41(Database issue):D590–D596.
   PubMed Web of Science ®Google Scholar
• Reitner J, Hoffmann F, Dröse W. 2004. Workshop Geohistologie. In: Reitner J, Reich M, Schmidt G, editors. Geobiologie 2, 74. Jahrestagung der Paläontologischen Gesellschaft in Göttingen 02. bis 08. Oktober 2004, Exkursionen und Workshops. Göttingen: Universitätsverlag, p211–226.
   Google Scholar
• Reitner J, Paul J, Arp G, Hause-Reitner D. 1996. Lake Thetis domal microbialites – a complex framework of calcified biofilms and organomicrites (Cervantes, Western Australia). In: Reitner J, Neuweiler F, Gunkel F, editors. Globale und regionale Steuerungsfaktoren biogener Sedimentation: I. Reef Evolution. Research Reports. Göttinger Arbeiten Geol Paläontol Sb2. Göttingen: Geologisch-Paläontologische Institute der Georg-August-Universität Göttingen, p85–89.
   Google Scholar
• Reitner J, Wörheide G, Lange R, Schumann-Kindel G. 2001. Coralline demosponges – a geobiological portrait. In: Mori K, Ezaki Y, Sorauf J, editors. Proceedings of the 8th International Symposium on Fossil Cnidaria and Porifera, September 1999, Sendai. Bulletin of the Tohoku University Museum, Vol. 1, p219–235.
   Google Scholar
• Sambrook J, MacCallum PD, Russel D. 2000. Molecular Cloning: A Laboratory Manual. 3rd ed. Cold Spring Harbor, NY: CSH Laboratory Press.
   Google Scholar
• Schneider D, Arp G, Reimer A, Reitner J, Daniel R. 2013. Phylogenetic analysis of a microbialite-forming microbial mat from a hypersaline lake of the Kiritimati Atoll, Central Pacific. PLOS One 8(6):e66662.
   PubMed Web of Science ®Google Scholar
• Schneider D, Reimer A, Hahlbrock A, Arp G, Daniel R. 2015. Metagenomic and metatranscriptomic analyses of bacterial communities derived from a calcifying karst water creek biofilm and tufa. Geomicrobiol J 32(3–4):316–331.
   Web of Science ®Google Scholar
• Schneider J, Le Campion-Alsumard T. 1999. Construction and destruction of carbonates by marine and freshwater cyanobacteria. Eur J Phycol 34(4):417–426.
   Web of Science ®Google Scholar
• Secker NH, Chua JP, Laurie RE, McNoe L, Guy PL, Orlovich DA, Summerfield TC. 2016. Characterization of the cyanobacteria and associated bacterial community from an ephemeral wetland in New Zealand. J Phycol 52(5):761–773.
   PubMed Web of Science ®Google Scholar
• Sihvonen LM, Lyra C, Fewer DP, Rajaniemi-Wacklin P, Lehtimäki JM, Wahlsten M, Sivonen K. 2007. Strains of the cyanobacterial genera Calothrix and Rivularia isolated from the Baltic Sea display cryptic diversity and are distantly related to Gloeotrichia and Tolypothrix. FEMS Microbiol Ecol 61(1):74–84.
   PubMed Web of Science ®Google Scholar
• Strunecký O, Komárek J, Johansen J, Lukešová A, Elster J. 2013. Molecular and morphological criteria for revision of the genus Microcoleus (Oscillatoriales, Cyanobacteria). J Phycol 49(6):1167–1180.
   PubMed Web of Science ®Google Scholar
• Whitton BA, Matteo P, Whitton BA. 2012. Rivulariaceae. In: Ecology of Cyanobacteria II: Their Diversity in Space and Time. Dordrecht: Springer, p561–591.
   Google Scholar
• Wong HL, Smith DL, Visscher PT, Burns BP. 2015. Niche differentiation of bacterial communities at a millimeter scale in Shark Bay microbial mats. Sci Rep 5(1):15607.
   PubMedGoogle Scholar
• Zhang R, Wu Q, Piceno YM, Desantis TZ, Saunders FM, Andersen GL, Liu WT. 2013. Diversity of bacterioplankton in contrasting Tibetan lakes revealed by high-density microarray and clone library analysis. FEMS Microbiol Ecol 86(2):277–287.
   PubMed Web of Science ®Google Scholar
• Ziegler K, Stephan DP, Pistorius E, Ruppel HG, Lockau W. 2001. A mutant of the cyanobacterium Anabaena variabilis ATCC 29413 lacking cyanophycin synthetase: growth properties and ultrastructural aspects. FEMS Microbiol Lett 196(1):13–18.
   PubMed Web of Science ®Google Scholar