Cyanobacteria and Diatoms in Biofilms of Two Karstic Streams in Germany and Changes of Their Communities Along Calcite Saturation Gradients

References

• Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. Journal of Molecular Biology 215:403–410.
   PubMed Web of Science ®Google Scholar
• Arp G, Bissett A, Brinkmann N, Cousin S, De Beer D, Friedl T, Mohr KI, Neu TR, Reimer A, Shiraishi F, Stackebrandt E and Zippel B. 2010. Tufa-forming biofilms of German karstwater streams: Microorganisms, exopolymers, hydrochemistry and calcification. In: Rogerson M, Pedley MM, editors. Geological Society Special Publication 336 (Tufas and Speleothems: Unraveling the Microbial and Physical Controls). London: Geological Society Of London. p83–118.
   Google Scholar
• Arp G, Wedemeyer N, Reitner J. 2001. Fluvial tufa formation in a hard-water creek (Deinschwanger Bach, Franconian Alb, Germany). Facies 44:1–22.
   Web of Science ®Google Scholar
• Beraldi-Campesi H, Arenas-Abad C, Garcia-Pichel F, Arellano-Aguilar O, Auqué L, Vázquez-Urbez M, Sancho C, Osácar C, Ruiz-Velasco S. 2012. Benthic bacterial diversity from freshwater tufas of the Iberian Range (Spain). FEMS Microbiol Ecol 80:363–379.
   PubMed Web of Science ®Google Scholar
• Bissett A, De Beer D, Schoon R, Shiraishi F, Reimer A, Arp G. 2008a. Microbial mediation of stromatolite formation in karst-water creeks. Limnol Oceanogr 53:1159–1168.
   Web of Science ®Google Scholar
• Bissett A, Reimer A, DeBeer D, Shiraishi F, Arp G. 2008b. Metabolic microenvironmental control by photosynthetic biofilms under changing macroenvironmental temperature and pH conditions. Appl Environ Microbiol 74:6306–6312.
   PubMed Web of Science ®Google Scholar
• Brinkmann N, Behnke A, Bruns S, Mohr K, Jahn R, Friedl T. 2007a. Assessing the diversity of diatoms in calcifying biofilms of hard-water creeks. In: Kusber W.-H, Jahn R, editors. Proceedings of the 1^st Central-European Diatom Meeting 2007, Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, ISBN 978-3-921800-63-8, © BGBM, Berlin 2007, p.11–14.
   Google Scholar
• Brinkmann N, Behnke A, Jahn R, Arp G, Friedl T. 2007b. Diversity of diatoms dominating biofilms on tufa stromatolites of hard-water creeks. In: Stackebrandt, E.; Wozniczka, M.; Weihs V, Sikorski, J, editors. Proceedings of the 11th International Conference on Culture Collections 2007 (ICCC 11). DSMZ, Braunschweig, p 41–44.
   Google Scholar
• Bruder K. 2006. Taxonomic Revision of Diatoms belonging to the family Naviculaceae based on morphological and molecular data. PhD Thesis, Universität Bremen, Germany.
   Google Scholar
• Bruder K, Medlin LK. 2008. Morphological and molecular investigations of naviculoid diatoms. II Selected genera and families. Diatom Res 23:283–329.
   Web of Science ®Google Scholar
• Castresana J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17:540–552.
   PubMed Web of Science ®Google Scholar
• Chafetz HS, Folk RL. 1984. Travertine: depositional morphology and the bacterially constructed constituents. J Sediment Petrol 54:289–316.
   Google Scholar
• Chatháin BN, Harrington TJ. 2008. Benthic diatoms of the river deel: diversity and community structure. Biol Environ Proc Roy Irish Acad, 108B, 1:29–42.
   Web of Science ®Google Scholar
• Couradeau E, Benzerara K, Gérard E, Estève I, Moreira D, Tavera R, López-Garcıa P. 2013. Cyanobacteria calcification in modern microbialites at the submicrometer-scale. Biogeosci Disc 10:3311–3339.
   Google Scholar
• Cousin S. 2009. Flavobacterial community structure in a hard-water rivulet and adjacent forest soil, Harz Mountain, Germany. Curr Microbiol 58:409–415.
   PubMed Web of Science ®Google Scholar
• Cousin S, Pauker O, Stackebrandt E. 2007. Flavobacterium aquidurense sp. nov. and Flavobacterium hercynium sp. nov., from a hard-water creek. Inter J System Evolution Microbiol 57:243–249.
   PubMed Web of Science ®Google Scholar
• Cousin S, Stackebrandt E. 2010. Spatial Bacterial Diversity in a Recent Freshwater Tufa Deposit. Geomicrobiol J 27: 275–291.
   Web of Science ®Google Scholar
• Darriba D, Taboada GL, Doallo R, Posada D. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nat Meth 9:772–772.
   PubMed Web of Science ®Google Scholar
• Dittrich M, Sibler S. 2010. Calcium carbonate precipitation by cyanobacteria polysaccharides. In: Pedley HM, Rogerson M, editors. Tufas and Speleotherms: Unraveling the Microbial and Physical Controls). Geological Society Special Publications. London: Geological Society of London, 336:51–63.
   Google Scholar
• Elwood HJ, O1sen GJ, Sogin ML. 1985. The small subunit ribosomal RNA Gene sequences from the hypotrichous ciliates Oxytricha nova and Stylonychia pustulata. Molecular Biology and Evolution 2:399–410.
   PubMed Web of Science ®Google Scholar
• Emeis KC, Richnow HH, Kempe S. 1987. Travertine formation in Plitvice National Park, Yugoslavia: chemical versus biological control. Sedimentology 34:595–609.
   Web of Science ®Google Scholar
• Evans KM, Wortley AH, Mann DG. 2007. An assessment of potential diatom ‘barcode’ genes (coxI, rbcL, 18S and ITS rDNA) and their effectiveness in determining relationships in Sellaphora (Bacillariophyta). Protist 158:349–364.
   PubMed Web of Science ®Google Scholar
• Ferrari SG, Italiano MC, Silva JS. 2002. Effect of a cyanobacteria community on calcium carbonate precipitation in Puente del Inca (Mendoza, Argentina). Acta Botanica Croatica 6:1–9.
   Google Scholar
• Freytet P, Verrecchia EP. 1998. Freshwater organisms that build stromatolites: a synopsis of biocrystallization by prokaryotic and eukaryotic algae. Sedimentology 45:535–563.
   Web of Science ®Google Scholar
• Friedl T, Lorenz M. 2012. The Culture Collection of Algae at Göttingen University (SAG): A biological resource for biotechnological and biodiversity research. Proced Environ Sci 15:110–117.
   Google Scholar
• Golubić S. 1976. Organisms that build stromatolites. In: Walter MR, editor. Stromatolites; Developments in Sedimentology, vol. 20. Amsterdam: Elsevier, p113–126.
   Google Scholar
• Golubić S, Violante C, Plenković-Moraj A, Grgasović T. 2008. Travertines and calcareous tufa deposits: an insight into diagenesis. Geol Croat 61:363–378.
   Google Scholar
• Grüninger W. 1965. Rezente Kalktuffbildung im Bereich der Uracher Wasserfälle. Abhandlungen zur Karst und Höhlenkunde, Reihe E, 2.
   Google Scholar
• Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. System Biol 52:696–704.
   PubMed Web of Science ®Google Scholar
• Hall TA. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41:95–98.
   Google Scholar
• Hallmann C, Stannek L, Fritzlar D, Hause-Reitner D, Friedl T, Hoppert M. 2013. Molecular diversity of phototrophic biofilms on building stone. FEMS Microbiol Ecol 84:355–372.
   PubMed Web of Science ®Google Scholar
• Hammer Ø, Harper DAT, Ryan PD. 2001. PAST: Palaeolontological Statistics software package for education and data analysis. Palaeolontologia Electronica 4: 9pp.
   Google Scholar
• Hepperle D. 2004. SeqAssem. A sequence analysis tool contig assembler and trace data visualization tool for molecular sequences. Win32-Version. Distributed by the author via: http://science.do-mix.de.
   Google Scholar
• Herman JS, Lorah MM. 1987. CO2 outgassing and calcite precipitation in Falling Spring Creek, Virginia, USA. Chem Geol 62:251–262.
   Web of Science ®Google Scholar
• Hill MO. 1979. Decorana – a fortran program for Detrended correspondence analysis and reciprocal averaging. Section of Ecology and Systematics, Cornell University, Ithaca.
   Google Scholar
• Hope ACA. 1968. A simplified Monte Carlo significance test procedure. J Roy Stat Soc Ser B 30:582–598.
   Google Scholar
• Huber T, Faulkner G, Hugenholtz P. 2004. BELLEROPHON: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20:2317–2319.
   PubMed Web of Science ®Google Scholar
• Huelsenbeck JP, Ronquist F. 2001. MRBAYES: Bayesian inference of phylogeny. Bioinformatics 17:754–755.
   PubMed Web of Science ®Google Scholar
• Janssen A, Swennen R, Podoorb N, Keppens E. 1999. Biological and diagenetic influence in recent and fossil tufa deposits from Belgium. Sedimen Geol 126:75–95.
   Web of Science ®Google Scholar
• Jaarsma NG, Bergman M, Schulze FH, Vaate AB. 2007. Macro-invertebrates in a dynamic river environment: analysis of time series from artificial substrates, using a ‘white box’ neural network modeling method. Aquat Ecol 41:413–425.
   Web of Science ®Google Scholar
• Kamennaya NA, Ajo-Franklin CM, Northen T, Jansson C. 2012. Cyanobacteria as biocatalysts for carbonate mineralization. Minerals 2:338–364.
   Web of Science ®Google Scholar
• Katoh K, Misawa K, Kuma K, Miyata T. 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucl Acids Res 30:3059–3066.
   PubMed Web of Science ®Google Scholar
• Komárek J, Anagnostidis K. 2005. Cyanoprokaryota, part 2. Oscillatoriales. In: Büdel, B., Gärtner, G., Krienitz, L. & Schagerl, M. (eds) Süßwasserflora von Mitteleuropa Band 19/2. Gustav Fischer, Jena, 1–759.
   Google Scholar
• Komárek J. 2011. Recent changes (2008) in cyanobacteria taxonomy based on a combination of molecular background with phenotype and ecological consequences (genus and species concept). Hydrobiologia 639:245–259.
   Web of Science ®Google Scholar
• Komárek J, Kaštovský J, Jezberová, J. 2011. Phylogenetic and taxonomic delimitation of the cyanobacterial genera Aphanothece Nägeli and Anathece (Komárek et Anagnostidis) comb. nova. European Journal of Phycology 46:315–326.
   Google Scholar
• Korelusová J, Kaštovský J, Komárek, J. 2009. Heterogeneity of the cyanobacteria genus Synechocystis and description of a new genus, Geminocystis. Journal of Phycology 45:928–937.
   Web of Science ®Google Scholar
• Krammer K, Lange-Bertalot H. 1986. Bacillariophyceae. 1. Teil: Naviculaceae in Ettl H, Gerloff J, Heynig H and Mollenhauer D (eds) Süsswasserflora von Mitteleuropa, Band 2/1. Stuttgart/NewYork: Gustav Fischer Verlag.
   Google Scholar
• Lamprinou V, Danielidis DB, Economou-Amilli A, Pantazidou A. 2012. Distribution survey of Cyanobacteria in three Greek caves of Peloponnese. Inter J Speleol 41:267–272.
   Web of Science ®Google Scholar
• Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar, Buchner A, Lai T, Steppi S, Jobb G, Förster W, Brettske I, Gerber S, Ginhart AW, Gross O, Grumann S, Hermann S, Jost R, König A, Liss T, Lüßmann R, May M, Nonhoff B, Reichel, Strehlow R, Stamatakis A, Stuckmann N, Vilbig A, Lenke M, Ludwig T, Bode A, Schleifer KH. 2004. ARB: a software environment for sequence data. Nucl Acids Res 32:1363–1371.
   PubMed Web of Science ®Google Scholar
• Maidak BL, Cole JR, Parker CT Jr, Garrity GM, Larsen N, Li B, Lilburn TG, McCaughey MJ, Olsen GJ, Overbeek R, Pramanik S, Schmidt TM, Tiedje JM, Woese CR. 1999. A new version of the RDP (Ribosomal Database Project). Nucl Acids Res 27:171–173.
   PubMed Web of Science ®Google Scholar
• Marande W, Lopez-Garcia P, Moreira D. 2009. Eukaryotic diversity and phylogeny using small- and large-subunit ribosomal RNA genes from environmental samples. Environ Microbiol 11: 3179–3188.
   Google Scholar
• Margheri MC, Piccardi R, Ventura S, Viti C, Giovannetti L 2003. Genotypic diversity of oscillatoriacean strains belonging to the genera Geitlerinema and Spirulina determined by 16S rDNA restriction analysis. Current Microbiology, 46:359–364.
   Google Scholar
• Medlin LK, Kaczmarska I. 2004. Evolution of the diatoms: V. Morphological and cytological support for the major clades and a taxonomic revision. Phycologia 43:245–270.
   Web of Science ®Google Scholar
• Merz M. 1992. The biology of carbonate precipitation by cyanobacteria. Facies 26:81–102.
   Google Scholar
• Merz-Preiß M, Riding R. 1999. Cyanobacteria tufa calcification in two fresh-water streams: ambient environment, chemical thresholds and biological processes. Sedimentary Geology 126:103–124.
   Web of Science ®Google Scholar
• Moniz MBJ, Kaczmarska I. 2010. Barcoding of Diatoms: Nuclear Encoded ITS Revisited. Protist 161:7–34.
   PubMed Web of Science ®Google Scholar
• Mudimu O, Rybalka N, Bauersachs T, Friedl T, Schulz R. 2014. Influence of different CO2 concentrations on microalgae growth rate, α-tocopherol content and fatty acid composition. Geomicrobiol J, submitted.
   Google Scholar
• Pawlowski J, Audic S, Adl S, Bass D, Belbahri L, Berney C, Bowser SS, Cepicka I, Decelle J, Dunthorn M, Fiore-Donno AM, Gile GH, Holzmann M, Jahn R, Jirků M, Keeling PJ, Kostka M, Kudryavtsev A, Lara E, Lukeš J, Mann DG, Mitchell EAD, Nitsche F, Romeralo M, Saunders GW, Simpson AGB, Smirnov AV, Spouge JL, Stern RF, Stoeck T, Zimmermann J, Schindel D, de Vargas C. 2012. CBOL Protist Working Group: Barcoding eukaryotic richness beyond the animal, plant, and fungal kingdoms. PLOS Biol 10:e1001419.
   PubMed Web of Science ®Google Scholar
• Pentecost A. 2005. Travertine. Heidelberg: Springer.
   Google Scholar
• Pentecost A, Riding R. 1986. Calcification of cyanobacteria. In: Leadbeater BSC, Riding R. editors. Biomineralization in lower plants and animals. System Asso 30:73–90.
   Google Scholar
• Pentecost A, Bayari S, Yesertener C. 1997. Phototrophic microorganisms of the Pamukkale travertine, Turkey: Their distribution and influence on travertine deposition. Geomicrobiol J 14:269–283.
   Web of Science ®Google Scholar
• Pepe-Ranney C, Berelson WM, Corsetti F A, Treants M, Spear JR. 2012. Cyanobacteria construction of hot spring siliceous stromatolites in Yellowstone National Park. Environ Microbiol 14:1182–1197.
   PubMed Web of Science ®Google Scholar
• Pfender WF, Wootke SL, Hall T. 1988. Microbial communities of Pyrenophora-infested wheat straw as examined by multivariate analysis. Microb Ecol 15:95–113.
   PubMed Web of Science ®Google Scholar
• Pia J. 1934. Die Kalkbildung durch Pflanzen. Beihefte zum botanischen Zentralblatt Kassel. A, 52:1–72.
   Google Scholar
• Plenković-Moraj A, Horvatincic N, Primc-Habdija B. 2002. Periphyton and its role in tufa deposition in karstic waters (Plitvice Lakes, Croatia). Biologia 57:423–431.
   Web of Science ®Google Scholar
• Pniewski F, Friedl T, Latała A. 2010. Identification of diatom isolates from the Gulf of Gdańsk: testing of species identifications using morphology, 18S rDNA sequencing and DNA barcodes of strains from the Culture Collection of Baltic Algae (CCBA). Oceanol Hydrobiol Studies, 39:3–20.
   Web of Science ®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. Nucl Acids Res 41:D590–D596.
   PubMed Web of Science ®Google Scholar
• Reichardt E. 1995. Die Kieselalgenflora (Bacillariophyceae) des Wachsenden Steins von Usterling. Berichte der Bayerischen Botanischen Gesellschaft 65:87–92.
   Google Scholar
• Reichelt H. 1899. Über fossile Diatomeen aus Nordböhmen. Berichte der Naturforschenden Gesellschaft zu Leipzig 1899–1900:27–35.
   Google Scholar
• Riding R 1991. Classification of microbial carbonates. In: Riding R (ed) Calcareous Algae and Stromatolites. Berlin: Springer-Verlag, p21–51.
   Google Scholar
• Romari K, Vaulot D. 2004. Composition and temporal variability of picoeukaryote communities at a coastal site of the English Channel from 18S rDNA sequences. Limnol Oceanogr 49: 784–798.
   Web of Science ®Google Scholar
• Rott E. 1994. Der Algenaufwuchs in der Oberen Alz (Oberbayern). Berichte des Naturwissenschaftlich-Medizinischen Vereins in Innsbruck 81:229–253.
   Google Scholar
• Sabater S. 1990. Composition and dynamics of a highly diverse diatom assemblage in a limestone stream. Hydrobiologia 190:43–53.
   Web of Science ®Google Scholar
• Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ. 2009. Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541.
   PubMed Web of Science ®Google Scholar
• Schneider D, Reimer A, Hahlbrock A, Arp G, Reitner J, Daniel R. 2014. Metagenomic and metatranscriptomic analyses of bacterial communities derived from a calcifying karst water creek biofilm and tufa. Geomicrobiol J, submitted.
   Google Scholar
• Sims PA, Mann DG, Medlin LK. 2006. Evolution of diatoms: insights from fossil, biological and molecular data. Phycologia 45:361–402.
   Web of Science ®Google Scholar
• Shiraishi F, Bissett A, De Beer D, Reimer A, Arp G. 2008a. Photosynthesis, Respiration and Exopolymer Calcium-Binding in Biofilm Calcification (Westerhöfer and Deinschwanger Creek, Germany). Geomicrobiol J 25:83–94.
   Web of Science ®Google Scholar
• Shiraishi F, Bissett A, De Beer D, Reimer A, Arp G. 2008b. Microbial effects on biofilm calcification, ambient water chemistry and stable isotope records (Westerhöfer Bach, Germany). Palaeogeogr Palaeoclimatol Palaeoecol 262:91–106.
   Web of Science ®Google Scholar
• Sorhannus U. 2007. A nuclear-encoded small-subunit ribosomal RNA timescale for diatom evolution. Marine Micropaleontology 65:1–12.
   Web of Science ®Google Scholar
• Spitzer S, Brinkmann N, Reimer A, Ionescu D, Friedl T, de Beer D, Arp G. 2014. Effect of variable PCO2 on Ca2+ removal and potential calcification of cyanobacteria biofilms—An experimental microsensor study. Geomicrobiol J, accepted.
   Google Scholar
• Stamatakis A. 2006. RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688–2690.
   PubMed Web of Science ®Google Scholar
• Stock A, Breiner HW, Pachiadaki M, Edgcomb V, Filker S, La Cono V, Yakimov MM, Stoeck T. 2012. Microbial eukaryote life in the new hypersaline deep-sea basin Thetis. Extremophiles 16:21–34.
   PubMed Web of Science ®Google Scholar
• Stoeck T, Hayward B, Taylor GT 2006. A multiple PCR-primer approach to access the microeukaryotic diversity in environmental samples. Protist 157:31–43.
   PubMed Web of Science ®Google Scholar
• Talavera G, Castresana J. 2007. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. System Biol 56:564–577.
   PubMed Web of Science ®Google Scholar
• Tavera R, Novelo E, López S. 2013. Cyanoprokaryota (Cyanobacteria) in karst environments in Yucatán, Mexico. Botan Sci 91:27–52.
   Web of Science ®Google Scholar
• Ter Braak CJF, Šmilauer P. 2002. CANOCO Reference Manual and CanoDraw for Windows User's Guide: Software for Canonical Community Ordination (version 4.5). Ithaca, NY: Microcomputer Power.
   Google Scholar
• Theriot EC, Cannone JJ, Gutell RR, Alverson AJ. 2009. The limits of nuclear-encoded SSU rDNA for resolving the diatom phylogeny. Euro J Phycol 44:277–290.
   PubMed Web of Science ®Google Scholar
• Thomazeau S, Houdan-Fourmont, A, Couté, A, Duval, C, Couloux, A, Rousseau, F, Bernard, C. 2010. The contribution of sub-Saharan african strains to the phylogeny of cyanobacteria: focusing on the Nostocaceae (Nostocales, Cyanobacteria). J Phycol 46:564–579.
   Web of Science ®Google Scholar
• Usdowski E, Hoefs J, Menschel G. 1979. Relationship between 13C and 18O fractionation and changes in major element composition in a recent calcite-depositing spring-a model of chemical variations with inorganic CaCO3 precipitation. Earth Planet Sci Lett 42:267–276.
   Web of Science ®Google Scholar
• Wilmotte A. 1994. Molecular evolution and taxonomy of cyanobacteria. In: The molecular biology of cyanobacteria. In: Bryant DA, editor. The Netherlands: Kluwer Academic Publishers, p1–25.
   Google Scholar
• Winsoborough BM, Golubić S. 2004. The role of diatoms in stromatolite growth: two examples from modern freshwater settings. J Phycol 23:195–201.
   Google Scholar
• Zimmermann J, Jahn R, Gemeinholzer B. 2011. Barcoding diatoms: evaluation of the V4 subregion on the 18S rRNA gene, including new primers and protocols. Organ Diver Evol 11:173–192.
   Web of Science ®Google Scholar
• Zippel B, Neu TR. 2010. Characterization of glycoconjugates of extracellular polymeric substances in tufa-associated biofilms by using fluorescence lectin-binding analysis. Appl Environ Microbiol 77:505–516.
   PubMed Web of Science ®Google Scholar