Abstract
Using methods of molecular biology (PCR and cloning), we studied the diversity of microorganisms in the surface layers of bottom sediments from the bays of Gydan and Yenisei of the Kara Sea, which have different component composition of the pore water and mineralization level. Representatives of the domains Bacteria and Archaea were identified based on the analysis of the 16S rRNA gene fragment nucleotide sequences. The composition of the community of microorganisms in the bottom sediments changed with the changing salinity gradient of the pore waters. The phylogenetic analysis of the nucleotide sequences showed that the composition of the microbial communities in the southern parts of these bays was affected by fresh-water flows from rivers and streams from the lakes within the catchment area, whereas that in the northern parts was influenced by sea waters. The results indicate the presence of bacteria in the bottom sediments that are capable of using a wide range of substrates as a carbon source including hydrocarbons and organochlorine and aromatic compounds. These data can also indicate the presence of different pollutants in the sediments of these areas and the potential ability of bacteria to degrade chemical compounds that enter the waters and bottom sediments of the Kara Sea.
Similar content being viewed by others
References
Atlas of Arctic (Glav. Uprav. Geodez. Kartogr., Moscow, 1985) [in Russian].
V. A. Baitaz and O. N. Baitaz, “Microbiological studies: general bacterioplankton and bacteriobenthos,” in Hydrobiological Study of Baidaratskaya Inlet of the Kara Sea in 1990–1991 (Murm. Morsk. Biol. Inst., Kol’sk. Nauchn. Tsentr, Ross. Akad. Nauk, Apatity, 1993), pp. 6–13.
V. S. Butkevich, “Bacterial population of Arctic seas and its distribution in water and ground,” in Selected Works (Akad. Nauk SSSR, Moscow, 1958), No. 2, pp. 77–134.
V. V. Vedernikov, A. B. Demidov, and A. I. Sud’bin, “Primary production and chlorophyll in the Kara Sea in September of 1993,” Okeanologiya (Moscow) 34(5), 693–703 (1994).
M. E. Vinogradov and E. A. Shushkina, Activity of Planktonic Communities of Ocean Epipelagial (Nauka, Moscow, 1987) [in Russian].
B. L. Isachenko, “Microbiological characteristic of the grounds and water of the Kara Sea,” in Selected Works (Akad. Nauk SSSR, Moscow, 1951), pp. 334–363.
T. V. Koronelli, S. G. Dermicheva, and V. V. Il’inskii, “Species structure of carbon-oxidizing bacterial cenosises in ecosystems of different climatic zones,” Mikrobiologiya 63(5), 917–923 (1994).
A. E. Kriss, Marine Microbiology (Akad. Nauk SSSR, Moscow, 1959) [in Russian].
A. E. Kriss, Microbiological Oceanography (Nauka, Moscow, 1976) [in Russian].
A. Yu. Lein, I. I. Rusanov, A. S. Savvichev, et al., “Biogeochemical processes of the sulfur and carbon cycles in the Kara Sea,” Geochem. Int. 34(11), 925–941 (1996).
A. P. Lisitzyn, “Marginal oceanic filter,” Okeanologiya (Moscow) 34(5), 735–747 (1994).
A. P. Lisitzyn and M. E. Vinogradov, “International high-altitude expedition in the Kara Sea (49th cruise of R/V Dmitriy Mendeleev),” Okeanologiya (Moscow) 34(5), 643–651 (1994).
A. P. Lisitzyn, V. P. Shevchenko, and M. E. Vinogradov, “Flows of sedimentary particles in the Kara Sea and estuaries of Ob and Yenisei rivers,” Okeanologiya (Moscow) 34(5), 748–758 (1994).
I. N. Mitskevich and B. B. Namsaraev, “Population number and distribution of bacterioplankton in the Kara Sea in September of 1993,” Okeanologiya (Moscow) 34(5), 704–708 (1994).
S. A. Mosharov and I. V. Mosharova, “Comparative analysis of production and microbiological characteristics of the Kara and Chukchi seas,” in Physical, Geological, and Biological Studies of the Oceans and Seas (Nauchnyi Mir, Moscow, 2010), pp. 495–505.
B. B. Namsaraev, I. I. Rusanov, I. N. Mitskevich, et al., “Bacterial oxidation of methane in estuary of Yenisei River and the Kara Sea,” Okeanologiya (Moscow) 35(1), 88–93 (1995).
T. V. Pogodaeva, I. N. Dolya, I. V. Tomberg, et al., “Pore water of bottom sediments in Yenisei Bay and Gydanskaya Inlet (the Kara Sea),” in Nature of Shelf and Archipelagos of European Arctic, No. 10, 253–256 (2010).
A. S. Savvichev, E. E. Zakharova, E. F. Veslopolova, et al., “Microbial processes of the carbon and sulfur cycles in the Kara Sea,” Oceanology (Engl. Transl.) 50(6), 942–957 (2010).
A. F. Sazhin, N. D. Romanova, and S. A. Mosharov, “Bacterial and primary production in the pelagic zone of the Kara Sea,” Oceanology (Engl. Transl.) 50(5), 759–765 (2010).
L. M. Sorokovikova, “Transformation of main ions and water mineralization in the Yenisei River in conditions of regulated drainage,” Vodn. Resur. 20(3), 320–325 (1993).
M. Yu. Suslova, V. V. Parfenova, O. N. Pavlova, et al., “Diversity and distribution of cultivated microbial community in the regions of Lower Yenisei River and the Kara Sea shelf,” Kriosfera Zemli 15(4), 106–109 (2011).
M. Yu. Suslova, I. A. Lipko, E. V. Mamaeva, et al., “Diversity of cultivable bacteria isolated from the water column and bottom sediments of the Kara Sea shelf,” Microbiology (Moscow) 81(4), 484–491 (2012).
N. G. Teplinskaya, “Bacterioplankton and bacteriobenthos of the Kara Sea,” in Ecology and Biological Resources of the Kara Sea (Kol’sk. Nauchn. Tsentr, Akad. Nauk SSSR, Apatity, 1989), pp. 29–37.
I. V. Tomberg, L. M. Sorokovikova, N. P. Sez’ko, et al., “Hydrochemical characteristic of the Gydanskaya Inlet,” in Nature of Shelves and Archipelagoes of European Arctic, No. 10, 292–295 (2010).
M. V. Flint, “Cruise 54th of the research vessel Akademik Mstislav Keldysh in the Kara Sea,” Oceanology (Engl. Transl.) 50(5), 637–642 (2010).
S. F. Altschul, T. L. Madden, A. A. Schaffer, et al., “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs,” Nucleic Acids Res. 5, 3389–3402 (1997).
A. J. Baldwin, J. A. Moss, J. D. Pakulski, et al., “Microbial diversity in a Pacific Ocean transect from the Arctic to Antarctic circles,” Aquat. Microbiol. Ecol. 102, 41–91 (2005).
N. Bano, S. Ruffin, B. Ransom, et al., “Phylogenetic composition of Arctic Ocean archaeal assemblages and comparison with Antarctic assemblages,” Appl. Environ. Microbiol. 70(2), 781–789 (2004).
J. P. Bowman, S. A. McCammon, J. A. E. Gibson, et al., “Prokaryotic metabolic activity and community structure in Antarctic continental shelf sediments,” Appl. Environ. Microbiol. 69, 2448–2462 (2003).
D. H. Buckley, V. Huangyutitham, S.-F. Hsu, et al., “Diversity of Planctomycetes in soil in relation to soil history,” Appl. Environ. Microbiol. 72(7), 4522–4531 (2006).
M. T. Cottrell and D. L. Kirchman, “Natural assemblages of marine proteobacteria and members of the Cytophaga-Flavobacter cluster consuming low- and high-molecular-weight dissolved organic matter,” Appl. Environ. Microbiol. 66(4), 1692–1697 (2000).
P. F. Dunfield, A. Yuryev, P. Senin, et al., “Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia,” Nature 6(450/7171), 879–882 (2007).
J. M. De Bruyn, L. T. Nixon, M. N. Fawaz, et al., “Global biogeography and quantitative seasonal dynamics of Gemmatimonadetes in soil,” Appl. Environ. Microbiol. 77(17), 6295–6300 (2011).
M. S. Elshahed, N. H. Youssef, Q. Luo, et al., “Phylogenetic and metabolic diversity of Planctomycetes from anaerobic, sulfide- and sulfur-rich Zodletone Spring, Oklahoma,” Appl. Environ. Microbiol. 73(15), 4707–4716 (2007).
J. A. Fuerst, “The Planctomycetes: emerging models for microbial ecology, evolution and cell biology,” Microbiology, No. 141, 1493–1506 (1995).
F. W. Futterer III and E. M. Galimov, “Siberian river run-off into the Kara Sea: Characterization, quantification, variability and environmental significance,” Proc. Mar. Sci. 6, 1–9 (2003).
Bergey’s Manual of Systematic Bacteriology, Vol. 2: The Proteobacteria, Part C: The Alpha-, Beta-, Delta-, and Epsilonproteobacteria, Ed. by G. M. Garrity, D. J. Bren- ner, N. R. Krieg, et al. (Springer, New York, 2005).
F. O. Glöckner, B. M. Fuchs, and R. Amann, “Bacterioplankton compositions of lakes and oceans: a first comparison based on fluorescence in situ hybridization,” Appl. Environ. Microbiol. 65, 3721–3726 (1999).
F. O. Glöckner, M. Kube, M. Bauer, et al., “Complete genome sequence of the marine planctomycete Pirellula sp. strain 1,” Proc. Natl. Acad. Sci. U.S.A., No. 100, 8298–8303 (2003).
H. Inoue, H. Nojima, and H. Okayama, “High efficiency transformation of E. coli with plasmids,” Gene 26, 23–28 (1990).
D. L. Kirchman, “The ecology of Cytophaga-Flavobacteria in aquatic environments,” FEMS Microbiol. Ecol., No. 39, 91–100 (2002).
D. Kirchman, E. K’nees, and R. Hodson, “Leucine incorporation and its potential as a measure of protein synthesis by bacteria in natural aquatic systems,” Appl. Environ. Microbiol. 49(3), 599–607 (1985).
M. J. Larkin, L. A. Kulakov, and C. C. R. Allen, “Biodegradation by members of the genus Rhodococcus: biochemistry, physiology and genetic adaptation,” Adv. Appl. Microbiol., No. 59, 1–29 (2006).
S. Liebner, J. Harder, and D. Wagner, “Bacterial diversity and community structure in polygonal tundra soils from Samoylov Island, Lena Delta, Siberia,” Int. Microbiol. 11(3), 195–202 (2008).
K. Lysnes, I. H. Thorseth, B. O. Steinsbu, et al., “Microbial community diversity in seafloor basalt from the Arctic spreading ridges,” FEMS Microbiol. Ecol. 50(3), 213–230 (2004).
N. N. Perreault, D. T. Andersen, W. H., Pollard, et al., “Characterization of the prokaryotic diversity in cold saline perennial springs of the Canadian high Arctic,” Appl. Environ. Microbiol. 73, 1532–1543 (2007).
K. Ravenschlag, K. Sahm, J. Pernthaler, et al., “High bacterial diversity in permanently cold marine sediments,” Appl. Environ. Microbiol., No. 65, 3982–3989 (1999).
G. N. Rees and B. K. Patel, “Desulforegula conservatrix gen. nov., sp. nov., a long-chain fatty acid-oxidizing, sulfate-reducing bacterium isolated from sediments of a freshwater lake,” Int. J. Syst. Evol. Microbiol. 51(5), 1911–1926 (2001).
J. Sambrook, E. F. First, and T. Maniatis, Molecular Cloning: A Laboratory Manual (Cold Spring Harbor Lab. Press, New York, 1989).
T. Suyama, H. Hosoya, and Y. Tokiwa, “Bacterial isolates degrading aliphatic polycarbonates,” FEMS Microbiol., 255–261 (1998).
K. Tamura, J. Dudley, M. Nei, et al., “MEGA 3: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0,” Mol. Biol. Evol. 24, 1596–1599 (2007).
A. Teske, K. U. Hinrichs, V. Edgcomb, et al., “Microbial diversity of hydrothermal sediments in the Guaymas Basin: evidence for anaerobic methanotrophic communities,” Appl. Environ. Microbiol., No. 68, 1994 (2002).
H. U. Uphoff, A. Felske, W. Fehr, et al., “The microbial diversity in picoplankton enrichment cultures,” FEMS Microbiol. Ecol. 35, 249–258 (2001).
N. L. Ward, J. F. Challacombe, P. H. Janssen, et al., “Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils,” Appl. Environ. Microbiol. 75(7), 2046–2056 (2009).
D. Woebken, H. Teeling, and P. Wecker, “Fosmids of novel marine Planctomycetes from the Namibian and Oregon coast upwelling systems and their cross-comparison with planctomycete genomes,” ISME J. 1, 419–435 (2007).
J. L. Xu, J. He, Z. C. Wang, et al., “Rhodococcus qingshengii sp. nov., a carbendazim-degrading bacterium,” Int. J. Syst. Evol. Microbiol. 57,Part 12, 2754–2757 (2007).
T. I. Zemskaya, T. V. Pogodaeva, O. V. Shubenkova, et al., “Geochemical and microbiological characteristics of sediments near the Malenky mud volcano (Lake Baikal, Russia), with evidence of Archaea intermediate between the marine anaerobic methanotrophs ANME-2 and ANME-3,” Geo-Mar. Lett. 30, 411–425 (2010).
Y. Zeng, Y. Zou, B. Chen, et al., “Phylogenetic diversity of sediment bacteria in the northern Bering Sea,” Polar. Biol. 34, 907–919 (2011).
Author information
Authors and Affiliations
Corresponding author
Additional information
Original Russian Text © E.V. Mamaeva, M.Yu. Suslova, T.V. Pogodaeva, V.V. Parfenova, T.I. Zemskaya, 2014, published in Okeanologiya, 2014, Vol. 54, No. 3, pp. 338–348.
Rights and permissions
About this article
Cite this article
Mamaeva, E.V., Suslova, M.Y., Pogodaeva, T.V. et al. Microbial uncultured community of bottom sediments from the bays of Gydan and Yenisei of the Kara Sea. Oceanology 54, 308–318 (2014). https://doi.org/10.1134/S0001437014030084
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1134/S0001437014030084