Skip to main content

Advertisement

SpringerLink
Log in

Characteristic microbial communities in the continuous permafrost beside the bitumen in Qinghai-Tibetan Plateau

  • Original Article
  • Published:
Environmental Earth Sciences Aims and scope Submit manuscript

Abstract

Although research on microorganisms in the global ecosystem has considerably increased, there is still incomplete understanding of the microbial communities in alpine permafrost due to the inaccessibility. In this study, the microbial composition and diversity in the continuous permafrost beside the bitumen in the Qiangtang basin (CPBQ) was investigated by 454 pyrosequencing. Among the bacterial communities, the phylum Actinobacteria was dominant, ranging from 33.42 to 48.04 %, followed by Proteobacteria and Acidobacteria. In addition to the three characteristic phyla, Planctomycetes, Chloroflexi, and Nitrospirae were also important in the CPBQ. Crenarchaeota, especially the ammonia-oxidizing archaea Soil Crenarchaeotic Group (SCG), was the main archaea in the CPBQ. Moreover, four fungal phyla, Ascomycota, Mucoromycotina, Chytridiomycota and Glomeromycota, were detected in the CPBQ. Mortierella, Fusarium, and Tetracladium were the main genera. On the average, the proportion of No_rank and unclassified sequences in bacteria and fungi were high at low taxonomic levels, which could extend the list of extreme environmental microbial candidate divisions. The demonstrations of the microbial communities in the CPBQ could provide key data to improve the knowledge of microbes in the terrestrial extreme environments.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • Acosta-Martínez V, Dowd S, Sun Y, Allen V (2008) Tag-encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use. Soil Biol Biochem 40:2762–2770. doi:10.1016/j.soilbio.2008.07.022

    Article  Google Scholar 

  • Auguet JC, Barberan A, Casamayor EO (2010) Global ecological patterns in uncultured Archaea. ISME J 4:182–190. doi:10.1038/ismej.2009.109

    Article  Google Scholar 

  • Baker BJ, Sheik CS, Taylor CA, Jain S, Bhasi A, Cavalcoli JD, Dick GJ (2013) Community transcriptomic assembly reveals microbes that contribute to deep-sea carbon and nitrogen cycling. ISME J 7:1962–1973. doi:10.1038/ismej.2013.85

    Article  Google Scholar 

  • Bates ST, Berg-Lyons D, Caporaso JG, Walters WA, Knight R, Fierer N (2011) Examining the global distribution of dominant archaeal populations in soil. ISME J 5:908–917. doi:10.1038/ismej.2010.171

    Article  Google Scholar 

  • Breuker A, Stadler S, Schippers A (2013) Microbial community analysis of deeply buried marine sediments of the New Jersey shallow shelf (IODP Expedition 313). FEMS Microbiol Ecol 85:578–592. doi:10.1111/1574-6941.12146

    Article  Google Scholar 

  • Bridge PD, Newsham KK (2009) Soil fungal community composition at Mars Oasis, a southern maritime Antarctic site, assessed by PCR amplification and cloning. Fungal Ecol 2:66–74

    Article  Google Scholar 

  • Buckles LK, Villanueva L, Weijers JW, Verschuren D, Damste JS (2013) Linking isoprenoidal GDGT membrane lipid distributions with gene abundances of ammonia-oxidizing Thaumarchaeota and uncultured crenarchaeotal groups in the water column of a tropical lake (Lake Challa, East Africa). Environ Microbiol 15:2445–2462. doi:10.1111/1462-2920.12118

    Article  Google Scholar 

  • Chu H, Fierer N, Lauber CL, Caporaso JG, Knight R, Grogan P (2010) Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomes. Environ Microbiol 12:2998–3006. doi:10.1111/j.1462-2920.2010.02277.x

    Article  Google Scholar 

  • Cui Z, Lai Q, Dong C, Shao Z (2008) Biodiversity of polycyclic aromatic hydrocarbon-degrading bacteria from deep sea sediments of the Middle Atlantic Ridge. Environ Microbiol 10:2138–2149. doi:10.1111/j.1462-2920.2008.01637.x

    Article  Google Scholar 

  • Das N, Chandran P (2011) Microbial degradation of petroleum hydrocarbon contaminants: an overview. Biotechnol Res Int 2011:941810. doi:10.4061/2011/941810

    Google Scholar 

  • Dedysh SN (2011) Cultivating uncultured bacteria from northern wetlands: knowledge gained and remaining gaps. Front Microbiol 2:184. doi:10.3389/fmicb.2011.00184

    Article  Google Scholar 

  • Fierer N, Bradford MA, Jackson RB (2007) Toward an ecological classification of soil bacteria. Ecology 88:1354–1364

    Article  Google Scholar 

  • Frumkin H, Hess J, Vindigni S (2009) Energy and public health: the challenge of peak petroleum. Public Health Rep 124:5–19

    Google Scholar 

  • Gao B, Gupta RS (2005) Conserved indels in protein sequences that are characteristic of the phylum Actinobacteria. Int J Syst Evol Microbiol 55:2401–2412. doi:10.1099/ijs.0.63785-0

    Article  Google Scholar 

  • Gibson J et al (2014) Simultaneous assessment of the macrobiome and microbiome in a bulk sample of tropical arthropods through DNA metasystematics. Proc Natl Acad Sci USA. doi:10.1073/pnas.1406468111

    Google Scholar 

  • Goecks J, Nekrutenko A, Taylor J, Galaxy T (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 11:R86. doi:10.1186/gb-2010-11-8-r86

    Article  Google Scholar 

  • Hadziavdic K, Lekang K, Lanzen A, Jonassen I, Thompson EM, Troedsson C (2014) Characterization of the 18S rRNA gene for designing universal eukaryote specific primers. PLoS One 9:e87624. doi:10.1371/journal.pone.0087624

    Article  Google Scholar 

  • He JL, Wang J, Fu XG, Zheng CG, Chen YT (2012) Assessing the conditions favorable for the occurrence of gas hydrate in the Tuonamu area Qiangtang basin, Qinghai-Tibetan, China. Energ Convers Manage 53:11–18. doi:10.1016/j.enconman.2011.08.012

    Article  Google Scholar 

  • Ivanova AO, Dedysh SN (2012) Abundance, diversity, and depth distribution of planctomycetes in acidic northern wetlands. Front Microbiol 3:5. doi:10.3389/fmicb.2012.00005

    Article  Google Scholar 

  • Johnson RJ, Smith BE, Sutton PA, McGenity TJ, Rowland SJ, Whitby C (2011) Microbial biodegradation of aromatic alkanoic naphthenic acids is affected by the degree of alkyl side chain branching. ISME J 5:486–496. doi:10.1038/ismej.2010.146

    Article  Google Scholar 

  • Jones RT, Robeson MS, Lauber CL, Hamady M, Knight R, Fierer N (2009) A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses. ISME J 3:442–453. doi:10.1038/ismej.2008.127

    Article  Google Scholar 

  • Kim M, Morrison M, Yu Z (2011) Evaluation of different partial 16S rRNA gene sequence regions for phylogenetic analysis of microbiomes. J Microbiol Methods 84:81–87. doi:10.1016/j.mimet.2010.10.020

    Article  Google Scholar 

  • Kochkina G et al (2012) Ancient fungi in Antarctic permafrost environments. FEMS Microbiol Ecol 82:501–509. doi:10.1111/j.1574-6941.2012.01442.x

    Article  Google Scholar 

  • Kuffner M et al (2012) Effects of season and experimental warming on the bacterial community in a temperate mountain forest soil assessed by 16S rRNA gene pyrosequencing. FEMS Microbiol Ecol 82:551–562. doi:10.1111/j.1574-6941.2012.01420.x

    Article  Google Scholar 

  • Lauber CL, Hamady M, Knight R, Fierer N (2009) Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol 75:5111–5120. doi:10.1128/AEM.00335-09

    Article  Google Scholar 

  • Li Y, Wang C, Li Y, Ma C, Wang L, Peng S (2010) The Cretaceous tectonic event in the Qiangtang Basin and its implications for hydrocarbon accumulation. Petrol Sci 7:466–471. doi:10.1007/s12182-010-0096-7

    Article  Google Scholar 

  • Li X, Gai J, Cai X, Li X, Christie P, Zhang F, Zhang J (2014) Molecular diversity of arbuscular mycorrhizal fungi associated with two co-occurring perennial plant species on a Tibetan altitudinal gradient. Mycorrhiza 24:95–107. doi:10.1007/s00572-013-0518-7

    Article  Google Scholar 

  • Logares R et al (2013) Biogeography of bacterial communities exposed to progressive long-term environmental change. ISME J 7:937–948. doi:10.1038/ismej.2012.168

    Article  Google Scholar 

  • Margesin R (2009) Fungi in permafrost 16 doi:10.1007/978-3-540-69371-0

  • Margesin R, Miteva V (2011) Diversity and ecology of psychrophilic microorganisms. Res Microbiol 162:346–361. doi:10.1016/j.resmic.2010.12.004

    Article  Google Scholar 

  • Nicol GW, Leininger S, Schleper C, Prosser JI (2008) The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria. Environ Microbiol 10:2966–2978. doi:10.1111/j.1462-2920.2008.01701.x

    Article  Google Scholar 

  • Offre P, Spang A, Schleper C (2013) Archaea in biogeochemical cycles Annu Rev Microbiol 67:437–457. doi:10.1146/annurev-micro-092412-155614

    Article  Google Scholar 

  • Ollivier J et al (2013) Bacterial community structure in soils of the Tibetan Plateau affected by discontinuous permafrost or seasonal freezing. Biol Fert Soils 50:555–559. doi:10.1007/s00374-013-0869-4

    Article  Google Scholar 

  • Prosser JI, Nicol GW (2008) Relative contributions of archaea and bacteria to aerobic ammonia oxidation in the environment. Environ Microbiol 10:2931–2941. doi:10.1111/j.1462-2920.2008.01775.x

    Article  Google Scholar 

  • Rousk J et al (2010) Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J 4:1340–1351. doi:10.1038/ismej.2010.58

    Article  Google Scholar 

  • Schidlowski M (2001) Carbon isotopes as biogeochemical recorders of life over 3.8 Ga of Earth history: evolution of a concept. Precambrian Res 106:117–134. doi:10.1016/S0301-9268(00)00128-5

    Article  Google Scholar 

  • Schippers A, Kock D, Hoft C, Koweker G, Siegert M (2012) Quantification of microbial communities in subsurface marine sediments of the Black Sea and off Namibia. Front Microbiol 3. doi:10.3389/Fmicb.2012.00016

  • Silva CC et al (2013) Identification of genes and pathways related to phenol degradation in metagenomic libraries from petroleum refinery wastewater. PLoS ONE 8:e61811. doi:10.1371/journal.pone.0061811

    Article  Google Scholar 

  • Stan-Lotter H, Fendrihan S (2012) Adaption of microbial life to environmental extremes : novel research results and application. Springer, New York

    Book  Google Scholar 

  • Sun B, Wang F, Jiang YJ, Li Y, Dong ZX, Li ZP, Zhang XX (2014) A long- term field experiment of soil transplantation demonstrating the role of contemporary geographic separation in shaping soil microbial community structure. Ecol Evol 4:1073–1087. doi:10.1002/Ece3.1006

    Article  Google Scholar 

  • Tang YQ, Li Y, Zhao JY, Chi CQ, Huang LX, Dong HP, Wu XL (2012) Microbial communities in long-term, water-flooded petroleum reservoirs with different in situ temperatures in the Huabei Oilfield, China. PLoS One 7:e33535. doi:10.1371/journal.pone.0033535

    Article  Google Scholar 

  • Teske A, Sorensen KB (2008) Uncultured archaea in deep marine subsurface sediments: have we caught them all? ISME J 2:3–18. doi:10.1038/ismej.2007.90

    Article  Google Scholar 

  • Tischer K et al (2013) Microbial communities along biogeochemical gradients in a hydrocarbon-contaminated aquifer. Environ Microbiol 15:2603–2615. doi:10.1111/1462-2920.12168

    Article  Google Scholar 

  • Tripathi BM, Kim M, Lai-Hoe A, Shukor NA, Rahim RA, Go R, Adams JM (2013) pH dominates variation in tropical soil archaeal diversity and community structure. FEMS Microbiol Ecol 86:303–311. doi:10.1111/1574-6941.12163

    Article  Google Scholar 

  • Walker T, Adams AR (1958) Studies on soil organic matter: I. Influence of phosphorus content of parent materials on accumulations of carbon, nitrogen, sulfur, and organic phosphorus in grassland soils. Soil Sci 85:307–318

    Article  Google Scholar 

  • Wang C et al (2008) Constraints on the early uplift history of the Tibetan Plateau. Proc Natl Acad Sci USA 105:4987–4992. doi:10.1073/pnas.0703595105

    Article  Google Scholar 

  • Willerslev E et al (2004) Long-term persistence of bacterial DNA. Curr Biol 14:R9–10

    Article  Google Scholar 

  • Wong FK, Lacap DC, Lau MC, Aitchison JC, Cowan DA, Pointing SB (2010) Hypolithic microbial community of quartz pavement in the high-altitude tundra of central Tibet. Microb Ecol 60:730–739. doi:10.1007/s00248-010-9653-2

    Article  Google Scholar 

  • Xiong J et al (2012) Geographic distance and pH drive bacterial distribution in alkaline lake sediments across Tibetan Plateau. Environ Microbiol 14:2457–2466. doi:10.1111/j.1462-2920.2012.02799.x

    Article  Google Scholar 

  • Yu S, Li S, Tang Y, Wu X (2011) Succession of bacterial community along with the removal of heavy crude oil pollutants by multiple biostimulation treatments in the Yellow River Delta, China. J Environ Sci 23:1533–1543. doi:10.1016/s1001-0742(10)60585-2

    Article  Google Scholar 

  • Yuan Y, Si G, Wang J, Luo T, Zhang G (2014) Bacterial community in alpine grasslands along an altitudinal gradient on the Tibetan Plateau. FEMS Microbiol Ecol 87:121–132. doi:10.1111/1574-6941.12197

    Article  Google Scholar 

  • Zhalnina K, de Quadros PD, Camargo FA, Triplett EW (2012) Drivers of archaeal ammonia-oxidizing communities in soil. Front Microbiol 3:210. doi:10.3389/fmicb.2012.00210

    Article  Google Scholar 

  • Zhang XF, Zhao L, Xu SJ Jr, Liu YZ, Liu HY, Cheng GD (2013) Soil moisture effect on bacterial and fungal community in Beilu River (Tibetan Plateau) permafrost soils with different vegetation types. J Appl Microbiol 114:1054–1065. doi:10.1111/jam.12106

    Article  Google Scholar 

  • Zhang W, Wu XK, Liu GX, Dong ZB, Zhang GS, Chen T, Dyson PJ (2014) Tag-encoded pyrosequencing analysis of bacterial diversity within different alpine grassland ecosystems of the Qinghai-Tibet Plateau, China. Environ Earth Sci 72:779–786. doi:10.1007/s12665-013-3001-z

    Article  Google Scholar 

  • Zheng Y et al (2014) Ammonia oxidizers and denitrifiers in response to reciprocal elevation translocation in an alpine meadow on the Tibetan Plateau. J Soil Sediment 14:1189–1199. doi:10.1007/s11368-014-0867-7

    Article  Google Scholar 

Download references

Acknowledgments

This work was supported by Natural Science Foundation of China (NSFC Grant #31100061).

Author information

Authors and Affiliations

  1. State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China

    Nan Jiang, Lijun Chen, Kai Wei, Jiao Feng & Jihui Tian

  2. Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China

    Yang Li

  3. Petroleum Exploration and Production Research Institute, Sinopec, Beijing, 100083, China

    Chenggang Zheng

Authors
  1. Nan Jiang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yang Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Chenggang Zheng
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Lijun Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Kai Wei
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Jiao Feng
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Jihui Tian
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Nan Jiang.

Additional information

Nan Jiang and Yang Li are contributed equally to this work.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Jiang, N., Li, Y., Zheng, C. et al. Characteristic microbial communities in the continuous permafrost beside the bitumen in Qinghai-Tibetan Plateau. Environ Earth Sci 74, 1343–1352 (2015). https://doi.org/10.1007/s12665-015-4124-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12665-015-4124-1

Keywords

Search

Navigation