790
Views
18
CrossRef citations to date
0
Altmetric
Original Articles

Metagenomic and Metatranscriptomic Analyses of Bacterial Communities Derived From a Calcifying Karst Water Creek Biofilm and Tufa

, , , &
Pages 316-331 | Received 01 Sep 2013, Accepted 01 Mar 2014, Published online: 03 Apr 2015

References

  • Ali Z, Cousin S, Fruhling A, Brambilla E, Schumann P, Yang Y, Stackebrandt E. 2009. Flavobacterium rivuli sp. nov., Flavobacterium subsaxonicum sp. nov., Flavobacterium swingsii sp. nov. and Flavobacterium reichenbachii sp. nov., isolated from a hard water rivulet. Inter J Syst Evolut Microbiol 59:2610–2617.
  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 215:403–410.
  • Anagnostidis K, Komárek J. 1988. Modern approach to the classification system of cyanophytes. 3 - Oscillatoriales. Algological Studies/Archiv für Hydrobiologie 50-53:32–472.
  • Arp G, Bissett A, Brinkmann N, Cousin S, de Beer D, Friedl T, Mohr K, Neu TR, Reimer A, Shiraishi F, Stackebrandt E, Zippel B. 2010. Tufa-forming biofilms of German karstwater streams: microorganisms, exopolymers, hydrochemistry and calcification. Geol Soc Lond 336:83–118.
  • Baldrian P, Kolarik M, Stursova M, Kopecky J, Valaskova V, Vetrovsky T, Zifcakova L, Snajdr J, Ridl J, Vlcek C, Voriskova J. 2012. Active and total microbial communities in forest soil are largely different and highly stratified during decomposition. ISME J 6:248–258.
  • Bayles KW. 2007. The biological role of death and lysis in biofilm development. Nat Rev Microbiol 5:721–726.
  • Bengtsson MM, Ovreas L. 2010. Planctomycetes dominate biofilms on surfaces of the kelp Laminaria hyperborea. BMC Microbiol 10:261.
  • Beraldi-Campesi H, Arenas-Abad C, Garcia-Pichel F, Arellano-Aguilar O, Auque L, Vazquez-Urbez M, Sancho C, Osacar C, Ruiz-Velasco S. 2012. Benthic bacterial diversity from freshwater tufas of the Iberian Range (Spain). FEMS Microbiol Ecol 80:363–379.
  • Bissett A, Reimer A, de Beer D, Shiraishi F, Arp G. 2008. Metabolic microenvironmental control by photosynthetic biofilms under changing macroenvironmental temperature and pH conditions. Appl Environ Microbiol 74:6306–6312.
  • Brinkmann N, Hodač L, Mohr KI, Hodačová A, Jahn R, Ramm J Hallmann C, Arp G, Friedl T. 2014, this issue. Cyanobacteria and diatoms in biofilms of two karstic streams in Germany and changes of their communities along calcite saturation gradients. Geomicrobiol J, this issue.
  • Burger O. 1911. Über schwäbische Kalktuffe insbesondere des Echaztales, Universität Tübingen, Tübingen.
  • Cadel-Six S, Peyraud-Thomas C, Brient L, de Marsac NT, Rippka R, Mejean A. 2007. Different genotypes of anatoxin-producing cyanobacteria coexist in the Tarn River, France. Appl Environ Microbiol 73:7605–7614.
  • Campbell SE. 1980. Palaeoconchocelis starmachii, a carbonate boring microfossil from the Upper Silurian of Poland (425 million years old): implications for the evolution of the Bangiaceae (Rhodophyta). Phycologia 19:25–36.
  • Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R. 2010. QIIME allows analysis of high-throughput community sequencing data. Nat Meth 7:335–336.
  • Casamatta DA, Johansen JR, Vis ML, Broadwater ST. 2005. Molecular and morphological characterization of ten polar and near-polar strains within the Oscillatoriales (Cyanobacteria). J Phycol 41:421–438.
  • Cousin S. 2009. Flavobacterial community structure in a hardwater rivulet and adjacent forest soil, Harz Mountain, Germany. Curr Microbiol 58:409–415.
  • Cousin S, Pauker O, Stackebrandt E. 2007. Flavobacterium aquidurense sp. nov. and Flavobacterium hercynium sp. nov., from a hard-water creek. Inter J Syst Evolution Microbiol 57:243–249.
  • Cousin S, Stackebrandt E. 2010. Spatial Bacterial Diversity in a Recent Freshwater Tufa Deposit. Geomicrobiol J 27:275–291.
  • DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL. 2006. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72:5069–5072.
  • Dürr S, Thomason J. 2010. Biofouling, 1st ed. Chichester, West Sussex England; Ames, Iowa: Wiley-Blackwell.
  • Edgar RC. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460–2461.
  • Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27:2194–2200.
  • Garrity GM, Brenner DJ, Krieg NR, Staley JT. 2005a. Part C The Alpha-, Beta-, Delta-, and Epsilonproteobacteria, vol. 2. New York: Springer.
  • Garrity GM, Brenner DJ, Krieg NR, Staley JT. 2005b. Part B The Gammaproteobacteria, vol. 2. New York: Springer:
  • Gonzalez-Munoz MT, Rodriguez-Navarro C, Martinez-Ruiz F, Arias JM, Merroun ML, Rodriguez-Gallego M. 2010. Bacterial biomineralization: New insights from Myxococcus-induced mineral precipitation. Geol Soc (Lond) 336:31–50.
  • Heath MW, Wood SA, Ryan KG. 2010. Polyphasic assessment of fresh-water benthic mat-forming cyanobacteria isolated from New Zealand. FEMS Microbiol Ecol 73:95–109.
  • Hodač L, Brinkmann N, Mohr KI, Arp G, Hallmann C, Ramm J, Spitzer K, Friedl T. 2014, accepted. Diversity of microscopic green algae (Chlorophyta) in calcifying biofilms of two karstic streams in Germany. Geomicrobiol J..
  • Jroundi F, Fernandez-Vivas A, Rodriguez-Navarro C, Bedmar EJ, Gonzalez-Munoz MT. 2010. Bioconservation of deteriorated monumental calcarenite stone and identification of bacteria with carbonatogenic activity. Microb Ecol 60:39—54.
  • Kempe S, Kazmierczak J. 1994. The role of alkalinity in the evolution of ocean chemistry, organization of living systems, and biocalcification processes. Bull. Inst. Oceanogr.: Monaco, p61–117.
  • Khattar JI, Singh DP, Jindal N, Kaur N, Singh Y, Rahi P, Gulati A. 2010. Isolation and characterization of exopolysaccharides produced by the cyanobacterium Limnothrix redekei PUPCCC 116. Appl Biochem Biotechnol 162:1327–1338.
  • Klähn H. 1923. Die Petrogenese der Kalktuffe nebst einigen sich daraus ergebenden geologischen Problemen. Geologisches Archiv. pp 298–316.
  • Kleinteich J, Wood SA, Küpper FC, Camacho A, Quesada A, Frickey T, Dietrich DR. 2012. Temperature related changes in polar cyanobacterial mat diversity and toxin production. Nat Clim Change 2:356–360.
  • La Touche THD. 1913. Geology of the Northern Shan States, vol. 39. Memoirs of the Geological Survey of India. Calcutta: Office of the Geological Survey. London: K. Paul, Trench, Trübner & co., 1913.
  • Lee ZM, Bussema C, 3rd, Schmidt TM. 2009. rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea. Nucleic acids research 37:D489–493.
  • Lennon JT, Jones SE. 2011. Microbial seed banks: the ecological and evolutionary implications of dormancy. Nat Rev Microbiol 9:119–130.
  • Martin M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J 17:10–12.
  • Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, Wilkening J, Edwards RA. 2008. The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinform 9:386.
  • Muurholm S, Cousin S, Pauker O, Brambilla E, Stackebrandt E. 2007. Pedobacter duraquae sp. nov., Pedobacter westerhofensis sp. nov., Pedobacter metabolipauper sp. nov., Pedobacter hartonius sp. nov. and Pedobacter steynii sp. nov., isolated from a hard-water rivulet. Inter J System Evolution Microbiol 57:2221–2227.
  • Nacke H, Thurmer A, Wollherr A, Will C, Hodač L, Herold N, Schöning I, Schrumpf M, Daniel R. 2011. Pyrosequencing-based assessment of bacterial community structure along different management types in German forest and grassland soils. PLoS One 6:e17000.
  • Ng CC, Huang WC, Chang CC, Tzeng WS, Chen TW, Liu YS, Shyu YT. 2006. Tufa microbial diversity revealed by 16S rRNA cloning in Taroko National Park, Taiwan. Soil Biol Biochem 38:342–348.
  • Pedley M. 2013. The morphology and function of thrombolitic calcite precipitating biofilms: A universal model derived from freshwater mesocosm experiments. Sedimentology, accepted.
  • Pentecost A, Bauld J. 1988. Nucleation of calcite on the sheaths of cyanobacteria using a simple diffusion cell. Geomicrobiol J 6:129–135.
  • Perri E, Manzo E, Tucker ME. 2012. Multi-scale study of the role of the biofilm in the formation of minerals and fabrics in calcareous tufa. Sediment Geol 263–264:16–29.
  • Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glöckner FO. 2007. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucl Acids Res 35:7188–7196.
  • Rappé MS, Kemp PF, Giovannoni SJ. 1997. Phylogenetic Diversity of Marine Coastal Picoplankton 16S rRNA Genes Cloned from the Continental Shelf Off Cape Hatteras, North Carolina. Limnol Oceanogr 42:811–826.
  • Rastogi R, Wu M, Dasgupta I, Fox GE. 2009. Visualization of ribosomal RNA operon copy number distribution. BMC Microbiol 9:208.
  • Reeder J, Knight R. 2010. Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions. Nat Meth 7:668–669.
  • Rusznyak A, Akob DM, Nietzsche S, Eusterhues K, Totsche KU, Neu TR, Frosch T, Popp J, Keiner R, Geletneky J, Katzschmann L, Schulze ED, Küsel K. 2012. Calcite biomineralization by bacterial isolates from the recently discovered pristine karstic herrenberg cave. Appl Environ Microbiol 78:1157–1167.
  • Schmalenberger A, Schwieger F, Tebbe CC. 2001. Effect of primers hybridizing to different evolutionarily conserved regions of the small-subunit rRNA gene in PCR-based microbial community analyses and genetic profiling. Appl Environ Microbiol 67:3557–3563.
  • 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:e66662.
  • Schürmann E. 1918. Die chemisch-geologischen Vorgänge bei der Bildung des Uracher Wasserfalls. In: Württemberg JdVfvNi (ed): Württemberg, p58–68.
  • 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.
  • Shiraishi F, Reimer A, Bissett A, de Beer D, Arp G. 2008b. Microbial effects on biofilm calcification, ambient water chemistry and stable isotope records in a highly supersaturated setting (Westerhöfer Bach, Germany). Palaeogeogr Palaeoclimatol Palaeoecol 262:91–106.
  • Shiraishi F, Okumura T, Takahashi Y, Kano A. 2010. Influence of microbial photosynthesis on tufa stromatolite formation and ambient water chemistry, SW Japan. Geochim Cosmochim Acta 74:5289–5304.
  • Stewart FJ, Ottesen EA, DeLong EF. 2010. Development and quantitative analyses of a universal rRNA-subtraction protocol for microbial metatranscriptomics. ISME J 4:896–907.
  • Tripp HJ, Hewson I, Boyarsky S, Stuart JM, Zehr JP. 2011. Misannotations of rRNA can now generate 90% false positive protein matches in metatranscriptomic studies. Nucl Acids Res 39:8792–8802.
  • Unger F. Beiträge zur (Anatomie und) Physiologie der Pflanzen. VII. Über den anatomischen Bau des Moosstammes. VIII. Über die kalkausscheidenden Organe der Saxifraga enistala. Sitzungsberichte der Akademie der Wissenschaften Wien; Akademie der Wissenschaften Wien. 1861.
  • von Buch L. 1809. Geognostische Beobachtungen auf Reisen durch Deutschland und Italien, vol. Band II. Haude und Spener: Berlin.
  • Wood SA, Smith FM, Heath MW, Palfroy T, Gaw S, Young RG, Ryan KG. 2012. Within-mat variability in anatoxin-a and homoanatoxin-a production among benthic Phormidium (cyanobacteria) strains. Toxins (Basel) 4:900–912.
  • Yamada T, Sekiguchi Y, Hanada S, Imachi H, Ohashi A, Harada H, Kamagata Y. 2006. Anaerolinea thermolimosa sp. nov., Levilinea saccharolytica gen. nov., sp. nov. and Leptolinea tardivitalis gen. nov., sp. nov., novel filamentous anaerobes, and description of the new classes Anaerolineae classis nov. and Caldilineae classis nov. in the bacterial phylum Chloroflexi. Inter J System Evolution Microbiol 56:1331–1340.
  • Yoshida M, Ishii S, Fujii D, Otsuka S, Senoo K. 2012. Identification of active denitrifiers in rice paddy soil by DNA- and RNA-based analyses. Microb Environ 27:456–461.
  • Zippel B, Neu TR. 2011. Characterization of glycoconjugates of extracellular polymeric substances in tufa-associated biofilms by using fluorescence lectin-binding analysis. Appl Environ Microbiol 77:505–516.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.