Prokaryotic ultramicroforms in a Sphagnum peat bog of upper Volga catchment

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• 作者：S. E. Belova (1)
  A. V. Fedotova (1)
  S. N. Dedysh (1) dedysh@mail.ru
• 关键词：filterable microbial forms – Sphagnum peat bog – 16S rRNA gene clone libraries
• 刊名：Microbiology
• 出版年：2012
• 出版时间：September 2012
• 年：2012
• 卷：81
• 期：5
• 页码：614-620
• 全文大小：204.6 KB
• 参考文献：1. Fedotova, A.V., Belova, S.E., Kulichevskaya, I.S., and Dedysh, S.N., Molecular Identification of Filterable Bacteria and Archaea in the Water of Acidic Lakes of Northern Russia, Microbiology, 2012, vol. 81, no. 3, pp. 281–287.
  2. Zavarzin, G.A. and Dedysh, S.N., Microbial Processes in Wetland Ecosystems and Changes in Natural Waters Caused by Microbial Activity, Environmental and Climatic Changes and the Associated Technogenic Catastrophes, vol. 4: Biospheric Processes: Changes in Soils, Vegetation, and Territorial Waters of the Russian Federation and Element Cycles Caused by Global Climatic Changes and Catastrophic Processes, Zavarzin, G.A. and Kudeyarov, V.N., Eds., Pushchino, Moscow: IFKh i BPP RAN, IFZ RAN, 2008, pp. 80–96.
  3. Glissman, K., Chin, K.-J., Casper, P., and Conrad, R., Methanogenic Pathway and Archaeal Community Structure in the Sediment of Eutrophic Lake Dagow: Effect of Temperature, FEMS Microbial Ecol., 2004, vol. 48, pp. 389–399.
  4. Barberán, A., Fernández-Guerra, A., Auguet, J.-C., Galand, P., and Casamayor, E.O., Phylogenetic Ecology of Widespread Uncultured Clades of the Kingdom Euryarchaeota, Molecular Ecol., 2011, vol. 20, pp. 1988–1996.
  5. Dedysh, S.N., Pankratov, T.A., Belova, S.E., Kulichevskaya, I.S., and Liesack, W., Phylogenetic Analysis and In Situ Identification of Bacteria Community Composition in an Acidic Sphagnum Peat Bog, Appl. Environ. Microbiol., 2006, vol. 72, pp. 2110–2117.
  6. Lysak, L.V., Lapygina, E.V., Konova, I.A., and Zvyagintsev, D.G., Quantity and Taxonomic Composition of Ultramicrobacteria in Soils, Microbiology, 2010, vol. 79, no. 3, p. 408.
  7. Kulichevskaya, I.S., Belova, S.E., Komov, V.T., Dedysh, S.N., and Zavarzin, G.A., Phylogenetic Composition of Bacterial Communities in Small Boreal Lakes and Ombrotrophic Bogs of the Upper Volga Basin, Microbiology, 2011, vol. 80, no. 4, pp. 549–558.
  8. Panikov, N.S., Contribution of Nanosized Bacteria to the Total Biomass and Activity of a Soil Microbial Community, Adv. Appl Microbiol., 2005, vol. 57, pp. 243–296.
  9. Weisburg, W.G., Barns, S.M., Pelletier, D.A., and Lane, D.J., 16S Ribosomal DNA Amplification for Phylogenetic Study, J. Bacteriol., 1991, vol. 173, pp. 697–703.
  10. Gro?kopf, R., Janssen, P.H., and Liesack, W., Diversity and Structure of the Methanogenic Community in Anoxic Rice Paddy Soil Microcosms as Examined by Cultivation and Direct 16S rRNA Gene Sequence Retrieval, Appl. Environ. Microbiol., 1998, vol. 64, pp. 960–969.
  11. Shivaji, S., Kumari, K., Kishore, K.H., Pindi, P.K., Rao, P.S., Srinivas, T.N.R., Asthana, R., and Ravindra, R., Vertical Distribution of Bacteria in a Lake Sediment from Antarctica by Culture-Independent and Culture-Dependent Approaches, Res. Microbiol., 2011, vol. 162, pp. 191–203.
  12. Reddy, P.V.V., Rao, S.S.S.N., Pratibha, M.S., Sailaja, B., Kavya, B., Manorama, R.R., Singh, S.M., Srinivas, T.N.R., and Shivaji, S., Bacterial Diversity and Bioprospecting for Cold-Active Enzymes from Culturable Bacteria Associated with Sediment from a Melt Water Stream of Midtre Lovenbreen Glacier, an Arctic Glacier, Res. Microbiol., 2009, vol. 160, pp. 538–546.
  13. Hahn, M.W., Luensdorf, H., Wu, Q., Schauer, M., Hoefle, M.G., Boenigk, J., and Stadler, P., Isolation of Novel Ultramicrobacteria Classified as Actinobacteria from Five Freshwater Habitats in Europe and Asia, Appl. Environ. Microbiol., 2003, vol. 69, pp. 1442–1451.
  14. Hahn, M.W., Description of Seven Candidate Species Affiliated with the Phylum Actinobacteria, Representing Planktonic Freshwater Bacteria, Int. J. Syst. Evol. Microbiol., 2009, vol. 59, pp. 112–117.
  15. Silbaq, F.S., Viable Ultramicrocells in Drinking Water, J. Appl. Microbiol., 2009, vol. 106, pp. 106–117.
  16. MacDonell, M.T. and Hood, M.A., Isolation and Characterization of Ultramicrobacteria from a Gulf Coast Estuary, Appl. Environ. Microbiol., 1982, vol. 43, pp. 566–571.
  17. Haller, C.M., R?lleke, S., Vybiral, D., Witte, A., and Velimirov, B., Investigation of 0.2 μm Filterable Bacteria from the Western Mediterranean Sea Using a Molecular Approach: Dominance of Potential Starvation Forms, FEMS Microbiol. Ecol., 1999, vol. 31, pp. 153–161.
  18. Naganuma, T., Miyoshi, T., and Kimura, H., Phylotype Diversity of Deep-Sea Hydrothermal Vent Prokaryotes Trapped by 0.2- and 0.1 μm-Pore-Size Filters, Extremophiles, 2007, vol. 11, pp. 637–646.
  19. Loveland-Kurtze, J., Miteva, V., and Brencheley, J., Novel Ultramicrobacterial Isolates from a Deep Greenland Ice Core Represent a Proposed New Species, Cryseobacterium greenlandense sp. nov., Extremophiles, 2010, vol. 14, pp. 61–69.
  20. Suzina, N.E., Duda, V.I., Esikova, T.Z., Shorokhova, A.P., Gafarov, A.B., Oleinikov, R.R., Akimov, V.N., Abashina, T.N., Polivtseva, V.N., and Boronin, A.M., Novel Ultramicrobacteria, Strains NF4 and NF5, of the Genus Chryseobacterium: Facultative Epibionts of Bacillus subtilis, Microbiology, 2011, vol. 80, no. 4, pp. 535–548.
  21. Br?uer, S.L., Cadillo-Quiroz, H., Yashiro, E., Yavitt, J.B., and Zinder, S., Isolation of a Novel Acidiphilic Methanogen from an Acidic Peat Bog, Nature, 2006, vol. 442, pp. 192–194.
  22. Br?uer, S.L., Cadillo-Quiroz, H., Ward, R.J., Yavitt, J.B., and Zinder, S., Methanoregula boonei gen. nov., sp. nov., an Acidiphilic Methanogen Isolated from an Acidic Peat Bog, Int. J. Syst. Evol. Microbiol., 2011, vol. 61, pp. 45–52.
  23. Kotelnikova, S., Macario, A.J.L., and Pedersen, K., Methanobacterium subterraneum sp. nov., a New Alkaliphilic, Eurythermic and Halotolerant Methanogen Isolated from Deep Granitic Groundwater, Int. J. Syst. Evol. Microbiol., 1998, vol. 48, pp. 357–367.
  24. Grosskopf, R., Stubner, S., and Liesack, W., Novel Euryarchaeotal Lineages Detected on Rice Roots and in the Anoxic Bulk Soil of Flooded Rice Microcosms, Appl. Environ. Microbiol., 1998, vol. 64, no. 12, pp. 4983–4989.
  25. Galand, P.E., Lovejoy, C., Pouliot, J., and Vincent, W.F., Heterogeneous Archaeal Communities in the Particle-Rich Environment of an Arctic Shelf Ecosystem, J. Mar. Syst., 2008, vol. 74, pp. 774–782.
  26. H?j, L., Olsen, R.A. and Torsvik, V.L., Effects of Temperature on the Diversity and Community Structure of Known Methanogenic Groups and Other Archaea in High Arctic Peat, ISME J., vol. 2, pp. 37–48.
  27. Pouliot, J., Galand, P.E., Lovejoy, C., and Vincent, W.F., Vertical Structure of Archaeal Communities and the Distribution of Ammonia Monooxygenase A Gene Variants in Two Meromictic High Arctic Lakes, Environ. Microbiol., 2009, vol. 11, pp. 687–699.
  28. Juottonen, H., Tuittila, E.-S., Juutinen, S., Fritze, H., and Yrj?l?, K., Seasonality of rDNA- and rRNA-Derived Archaeal Communities and Methanogenic Potential in a Boreal Mire, ISME J., 2008, vol. 2, pp. 1157–1168.
  29. Brochier-Armanet, C., Boussau, B., Gribaldo, S., and Forterre, P., Mesophilic Crenarchaeota: Proposal for a Third Archaeal Phylum, the Thaumarchaeota, Nat. Rev. Microbiol., 2008, vol. 6, pp. 245–252.
  30. Pester, M., Schleper, C., and Wagner, M., The Thaumarchaeota: An Emerging View of Their Phylogeny and Ecophysiology, Curr. Opin. Microbiol., 2011, vol. 14, no. 3, pp. 300–306.
  31. K?nneke, M., Bernhard, A.E., de la Torre, J.R., Walker, C.B., Waterbury, J.B., and Stahl, D.A., Isolation of an Autotrophic Ammonia-Oxidizing Marine Archaeon, Nature, 2005, vol. 437, pp. 543–546.
  32. Cadillo-Quiroz, H., Yavitt, J.B., Zinder, S.H., and Thies, J.E., Diversity and Community Structure of Archaea Inhabiting the Rhizoplane of Two Contrasting Plants from an Acidic Bog, Microb. Ecol., 2010, vol. 59, pp. 757–767.
  33. Narihiro, T., Hori, T., Nagata, O., Hoshino, T., Yumoto, I., and Kamagata, Y., The Impact of Aridification and Vegetation Type on Changes in the Community Structure of Methane-Cycling Microorganisms in Japanese Wetland Soils, Biosci. Biotechnol. Biochem., 2011, vol. 75, no. 9, pp. 1727–1737.
• 作者单位：1. Winogradsky Institute of Microbiology, Russian Academy of Sciences, pr. 60-letiya Oktyabrya 7, k. 2, Moscow, 117312 Russia
• ISSN：1608-3237

文摘

The waters of small lakes located in swampy catchment areas of upper Volga contain considerable amounts of ultrasmall microbial cells that pass through 0.22-μm-pore-size filters. As shown in our previous study [1], most of these cells represent the bacterial genera Herbaspirillum, Herminiimonas, Curvibacter, and Burkholderia of the class Betaproteobacteria, as well as euryarchaea of the uncharacterized clade LDS. The aim of the present study was to investigate the possible effect of the waters draining swampy areas on the composition of the filterable microbial fraction in lakes fed by swampy catchments. To address this question molecular identification was performed of prokaryotic ultramicroforms in the peat of the ombrotrophic Sphagnum bog Obukhovskoe, located, like the lakes studied previously [1], in the Mologa-Sheksna catchment area. The number of filterable microorganisms in 1 g wet peat was 3.8 × 106 cells, or 0.5% of total microbial cell number in the peat. From the DNA of the filterable cell fraction, 100 clones of bacterial and 77 clones of archaeal 16S rRNA genes were obtained. The bacterial clone library contained 16S rRNA gene sequences representing the classes Beta- and Gammaproteobacteria (the genera Janthinobacterium and Pseudomonas, respectively) and the phylum Bacteroidetes (the genera Chryseobacterium and Epilithonimonas) and differed significantly from the clone library of bacterial ultramicroforms of lake water. By contrast, the pools of filterable archaea in bogs and lakes were essentially similar. They were represented by the euryarchaeal clade LDS and methanogens of the orders Methanobacteriales and Methanosarcinales. Additionally, the pool of filterable archaea of the bog included methanogens of the order Methanomicrobiales and representatives of the uncharacterized euryarchaeal clade RC-V (Rice Cluster V) and of the phylum Thaumarchaeota.