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Bacterial, archaeal and eukaryotic diversity in Arctic sediment as revealed by 16S rRNA and 18S rRNA gene clone libraries analysis

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Abstract

We studied the microbial diversity in the sediment from the Kongsfjorden, Svalbard, Arctic, in the summer of 2005 based on the analysis of 16S rRNA and 18S rRNA gene clone libraries. The sequences of the cloned 16S rRNA and 18S rRNA gene inserts were used to determine the species identity or closest relatives by comparison with sequences of known species. Compared to the other samples acquired in Arctic and Antarctic, which are different from that of ours, the microbial diversity in our sediment is much higher. The bacterial sequences were grouped into 11 major lineages of the domain Bacteria: Proteobacteria (include α-, β-, γ-, δ-, and ε-Proteobacteria); Bacteroidetes; Fusobacteria; Firmicutes; Chloroflexi; Chlamydiae; Acidobacteria; Actinobacteria; Planctomycetes; Verrucomicrobiae and Lentisphaerae. Crenarchaeota were dominant in the archaeal clones containing inserts. In addition, six groups from eukaryotes including Cercozoa, Fungi, Telonema, Stramenopiles, Alveolata, and Metazoa were identified. Remarkably, the novel group Lentisphaerae was reported in Arctic sediment at the first time. Our study suggested that Arctic sediment as a unique habitat may contain substantial microbial diversity and novel species will be discovered.

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References

  • Bano N, Hollibaugh JT (2002) Phylogenetic composition of bacterioplankton assemblages from the Arctic Ocean. Appl Environ Microbiol 68:505–518

    Article  PubMed  CAS  Google Scholar 

  • Bano N, Ruffin S, Ransom B, Hollibaugh JT (2004) Phylogenetic composition of Arctic Ocean archaeal assemblages and comparison with Antarctic assemblages. Appl Environ Microbiol 70:781–789

    Article  PubMed  CAS  Google Scholar 

  • Bosshard PP, Santini Y, Gruter D, Stettler R, Bachofen R (2000) Bacterial diversity and community composition in the chemocline of the meromictic alpine Lake Cadagno as revealed by 16S rDNA analysis. FEMS Microbiol Ecol 31:173–182

    Article  PubMed  CAS  Google Scholar 

  • Bowman JP, McCuaig RD (2003) Biodiversity, community structural shifts, and biogeography of prokaryotes within Antarctic continental shelf sediment. Appl Environ Microbiol 69:2463–2483

    Article  PubMed  CAS  Google Scholar 

  • Bowmanip JP, Broww MV, Nichols DS (1997) Biodiversity and ecophysiology of bacteria associated with Antarctic sea ice. Antarct Sci 9:134–142

    Google Scholar 

  • Brinkmeyer R, Knittel K, Jurgens J, Weyland H, Amann R, Helmke E (2003) Diversity and structure of bacterial communities in Arctic versus Antarctic pack ice. Appl Environ Microbiol 69:6610–6619

    Article  PubMed  CAS  Google Scholar 

  • Cho JC, Vergin KL, Morris RM, Giovannoni SJ (2004) Lentisphaera araneosa gen. nov., sp. nov, a transparent exopolymer producing marine bacterium, and the description of a novel bacterial phylum, Lentisphaerae. Environ Microbiol 6:611–621

    Article  PubMed  CAS  Google Scholar 

  • Crosby LD, Criddle CS (2003) Understanding bias in microbial community analysis techniques due to rrn operon copy number heterogeneity. Biotechniques 34:790–794 (796, 798 passim)

    PubMed  CAS  Google Scholar 

  • Crump BC, Kling GW, Bahr M, Hobbie JE (2003) Bacterioplankton community shifts in an arctic lake correlate with seasonal changes in organic matter source. Appl Environ Microbiol 69:2253–2268

    Article  PubMed  Google Scholar 

  • DeLong EF (1992) Archaea in coastal marine environments. Proc Natl Acad Sci USA 89:5685–5689

    Article  PubMed  CAS  Google Scholar 

  • Frey JC, Rothman JM, Pell AN, Nizeyi JB, Cranfield MR, Angert ER (2006) Fecal bacterial diversity in a wild gorilla. Appl Environ Microbiol 72:3788–3792

    Article  PubMed  CAS  Google Scholar 

  • Gao J, Pan H, Xiao T, Barbier G, Wang Z, Yue H, Sun S, Nitsche S, Bernadac A, Pradel N, Wu LF (2006) Isolation and characterization of novel marine Roseobacter clade members producing unique intracellular chromium-rich aggregates. Res Microbiol 157:714–719

    Article  PubMed  CAS  Google Scholar 

  • Gentile G, Giuliano L, D’Auria G, Smedile F, Azzaro M, De Domenico M, Yakimov MM (2006) Study of bacterial communities in Antarctic coastal waters by a combination of 16S rRNA and 16S rDNA sequencing. Environ Microbiol 8:2150–2161

    Article  PubMed  CAS  Google Scholar 

  • Gosink JJ, Staley JT (1995) Biodiversity of gas vacuolate bacteria from Antarctic sea ice and water. Appl Environ Microbiol 61:3486–3489

    PubMed  CAS  Google Scholar 

  • Guillou L, Eikrem W, Chretiennot-Dinet MJ, Le Gall F, Massana R, Romari K, Pedros-Alio C, Vaulot D (2004) Diversity of picoplanktonic prasinophytes assessed by direct nuclear SSU rDNA sequencing of environmental samples and novel isolates retrieved from oceanic and coastal marine ecosystems. Protist 155:193–214

    Article  PubMed  CAS  Google Scholar 

  • Head IM, Saunders JR, Pickup RW (1998) Microbial evolution, diversity, and ecology: a decade of ribosomal rna analysis of uncultivated microorganisms. Microb Ecol 35:1–21

    Article  PubMed  CAS  Google Scholar 

  • Heal OW (1999) Looking North: current issues in Arctic soil ecology. Appl Soil Ecol 11:107–109

    Article  Google Scholar 

  • Hodkinsona ID, Wookey PA (1999) Functional ecology of soil organisms in tundra ecosystems: towards the future. Appl Soil Ecol 11:111–126

    Article  Google Scholar 

  • Jiang J, Alderisio KA, Singh A, Xiao L (2005) Development of procedures for direct extraction of Cryptosporidium DNA from water concentrates and for relief of PCR inhibitors. Appl Environ Microbiol 71:1135–1141

    Article  PubMed  CAS  Google Scholar 

  • Junge K, Imhoff F, Staley T, Deming JW (2002) Phylogenetic diversity of numerically important Arctic sea-ice bacteria cultured at subzero temperature. Microb Ecol 43:315–328

    Article  PubMed  CAS  Google Scholar 

  • Kreader CA (1996) Relief of amplification inhibition in PCR with bovine serum albumin or T4 gene 32 protein. Appl Environ Microbiol 62:1102–1106

    PubMed  CAS  Google Scholar 

  • Li HR, Yu Y, Zeng YX, Chen B, Ren DM (2006) Phylogenetic analysis of bacterial diversity in Pacific Arctic sediments. Wei Sheng Wu Xue Bao 46:177–183

    PubMed  Google Scholar 

  • Lovejoy C, Massana R, Pedros-Alio C (2006) Diversity and distribution of marine microbial eukaryotes in the Arctic Ocean and adjacent seas. Appl Environ Microbiol 72:3085–3095

    Article  PubMed  CAS  Google Scholar 

  • Lozupone C, Knight R (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71:8228–8235

    Article  PubMed  CAS  Google Scholar 

  • Martin-Laurent F, Philippot L, Hallet S, Chaussod R, Germon JC, Soulas G, Catroux G (2001) DNA extraction from soils: old bias for new microbial diversity analysis methods. Appl Environ Microbiol 67:2354–2359

    Article  PubMed  CAS  Google Scholar 

  • Massana R, DeLong EF, Pedros-Alio C (2000) A few cosmopolitan phylotypes dominate planktonic archaeal assemblages in widely different oceanic provinces. Appl Environ Microbiol 66:1777–1787

    Article  PubMed  CAS  Google Scholar 

  • Massana R, Castresana J, Balague V, Guillou L, Romari K, Groisillier A, Valentin K, Pedros-Alio C (2004) Phylogenetic and ecological analysis of novel marine stramenopiles. Appl Environ Microbiol 70:3528–3534

    Article  PubMed  CAS  Google Scholar 

  • Neufeld JD, Mohn WW (2005) Unexpectedly high bacterial diversity in arctic tundra relative to boreal forest soils, revealed by serial analysis of ribosomal sequence tags. Appl Environ Microbiol 71:5710–5718

    Article  PubMed  CAS  Google Scholar 

  • Neufeld JD, Yu Z, Lam W, Mohn WW (2004) Serial analysis of ribosomal sequence tags (SARST): a high-throughput method for profiling complex microbial communities. Environ Microbiol 6:131–144

    Article  PubMed  CAS  Google Scholar 

  • Priscu JC, Fritsen CH, Adams EE, Giovannoni SJ, Paerl HW, McKay CP, Doran PT, Gordon DA, Lanoil BD, Pinckney JL (1998) Perennial Antarctic lake ice: an oasis for life in a polar desert. Science 280:2095–2098

    Article  PubMed  CAS  Google Scholar 

  • Purdy KJ, Nedwell DB, Embley TM (2003) Analysis of the sulfate-reducing bacterial and methanogenic archaeal populations in contrasting Antarctic sediments. Appl Environ Microbiol 69:3181–3191

    Article  PubMed  CAS  Google Scholar 

  • Purkhold U, Wagner M, Timmermann G, Pommerening-Roser A, Koops HP (2003) 16S rRNA and amoA-based phylogeny of 12 novel betaproteobacterial ammonia-oxidizing isolates: extension of the dataset and proposal of a new lineage within the nitrosomonads. Int J Syst Evol Microbiol 53:1485–1494

    Article  PubMed  CAS  Google Scholar 

  • Rappe MS, Giovannoni SJ (2003) The uncultured microbial majority. Annu Rev Microbiol 57:369–394

    Article  PubMed  CAS  Google Scholar 

  • Ravenschlag K, Sahm K, Pernthaler J, Amann R (1999) High bacterial diversity in permanently cold marine sediments. Appl Environ Microbiol 65:3982–3989

    PubMed  CAS  Google Scholar 

  • Schloss PD, Handelsman J (2005) Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71:1501–1506

    Article  PubMed  CAS  Google Scholar 

  • Smith JJ, Tow LA, Stafford W, Cary C, Cowan DA (2006) Bacterial diversity in three different Antarctic cold desert mineral soils. Microb Ecol 51:413–421

    Article  PubMed  Google Scholar 

  • Spiegelman D, Whissell G, Greer CW (2005) A survey of the methods for the characterization of microbial consortia and communities. Can J Microbiol 51:355–386

    Article  PubMed  CAS  Google Scholar 

  • Staley JT, Gosink JJ (1999) Poles apart: biodiversity and biogeography of sea ice bacteria. Annu Rev Microbiol 53:189–215

    Article  PubMed  CAS  Google Scholar 

  • Stoeck T, Epstein S (2003) Novel eukaryotic lineages inferred from small-subunit rRNA analyses of oxygen-depleted marine environments. Appl Environ Microbiol 69:2657–2663

    Article  PubMed  CAS  Google Scholar 

  • Torsvik V, Goksoyr J, Daae FL (1990) High diversity in DNA of soil bacteria. Appl Environ Microbiol 56:782–787

    PubMed  CAS  Google Scholar 

  • Wallenstein MD, McMahon S, Schimel J (2007) Bacterial and fungal community structure in Arctic tundra tussock and shrub soils. FEMS Microbiol Ecol 59:428–435

    Article  PubMed  CAS  Google Scholar 

  • von Wintzingerode F, Gobel UB, Stackebrandt E (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21:213–229

    Article  Google Scholar 

Download references

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Authors and Affiliations

  1. Department of Medical Microbiology and Parasitology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China

    Fei Tian, Yu-Feng Yao & Xiao-Kui Guo

  2. State Oceanic Administration Key Laboratory for Polar Science, Polar Research Institute of China, 200136, Shanghai, China

    Yong Yu, Bo Chen & Huirong Li

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  1. Fei Tian
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  2. Yong Yu
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  3. Bo Chen
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  4. Huirong Li
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  5. Yu-Feng Yao
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  6. Xiao-Kui Guo
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Correspondence to Xiao-Kui Guo.

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Tian, F., Yu, Y., Chen, B. et al. Bacterial, archaeal and eukaryotic diversity in Arctic sediment as revealed by 16S rRNA and 18S rRNA gene clone libraries analysis. Polar Biol 32, 93–103 (2009). https://doi.org/10.1007/s00300-008-0509-x

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