Abstract
The Qinghai-Tibet Plateau is sensitive to climate change, with ecosystems that are important with respect to scientific research. Here high-throughput DNA pyrosequencing was used to assess bacterial diversity within different alpine grassland ecosystems of the Qinghai-Tibet Plateau, China. In total, 34,759 sequences were obtained for the three ecosystems––alpine cold swamp meadow (ASM), alpine cold meadow (AM), alpine sandy grassland (ASG), and 31 phyla and a small number of unclassified bacteria were detected. The bacterial community structures were different for each alpine grassland ecosystem. The Proteobacteria and Acidobacteria were the predominant phyla in all three ecosystems. Besides this, Actinobacteria and Chloroflexi were abundant in ASM, Bacteroidetes, Gemmatimonadetes and Verrucomicrobia were abundant in AM, and Actinobacteria were abundant in ASG. In addition, the functional bacterial genera also differed with each alpine grassland ecosystem. The ASM contained more nitrifying bacteria, methane-oxidizing bacteria and sulfur- and sulfate-reducing bacteria, whereas the ASG ecosystem contained more nitrogen-fixing bacteria. Pyrosequencing provided a greater insight into bacterial diversity within different alpine grassland ecosystems than previously possible, and gave key data for the involvement of bacteria in the protection of alpine grassland ecosystems of the Qinghai-Tibet Plateau, China.
Similar content being viewed by others
References
Bardgett RD, Leemans DK, Cook R, Hobbs PJ (1997) Seasonality of soil biota of grazed and ungrazed hill grasslands. Soil Biol Biochem 29(8):1285–1294
Beniston M (2003) Climatic change in mountain regions: a review of possible impacts. Climatic Change 59(1–2):5–31
Clark FE, Pawl EA (1970) The microflora of grassland. Adv Agron 22:375–435
Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, Tiedje JM (2009) The ribosomal database project: improved alignments and new tools for rRNA analysis. Nucl Acid Res 37:141–145
Costello EK, Schmidt SK (2006) Microbial diversity in alpine tundra wet meadow soil: novel Chloroflexi from a cold, water-saturated environment. Environ Microbiol 8(8):1471–1486
Fierer N, Jackson RB (2006) The diversity and biogeography of soil bacterial communities. Proc Nat Acad Sci USA 103(3):626–631
Gans J, Wolinsky M, Dunbar J (2005) Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 309:1387–1390
Gao B, Gupta RS (2005) Conserved indels in protein sequences that are characteristic of the phylum Actinobacteria. Int J Syst Evol Microbiol 55(6):2401–2412
Glöckner J, Kube M, Shrestha PM, Weber M, Glöckner FO, Reinhardt R, Liesack W (2010) Phylogenetic diversity and metagenomics of candidate division OP3. Environ Microbiol 12(5):1218–1229
Guo Z, Niu F, Zhan H, Wu Q (2007) Changes of grassland ecosystem due to degradation of permafrost frozen soil in the Qinghai Tibet Plateau. Acta Ecol Sin 27:3294–3301
Horner-Devine MC, Lage M, Hughes JB, Bohannan BJM (2004) A taxa-area relationship for bacteria. Nature 432:750–753
Hugenholtz P, Pitulle C, Hershberger KL, Pace NR (1998) Novel division level bacterial diversity in a Yellowstone hot spring. J Bacteriol 180(2):366–376
IPCC (2007) Climate change 2007: mitigation of climate change. Contribution of working group III to the fourth assessment report of the intergovernmental panel on climate change. Cambridge University Press, Cambridge
Klein JA, Harte J, Zhao X (2004) Experimental warming causes large and rapid species loss, dampened by simulated grazing, on the Tibetan Plateau. Ecol Lett 7(12):1170–1179
Klein JA, Harte J, Zhao X (2007) Experimental warming, not grazing, decreases rangeland quality on the Tibetan plateau. Ecol Appl 17(2):541–557
Klironomos JN (2002) Feedback with soil biota contributes to plant rarity and invasiveness in communities. Nature 417:67–70
Knoblauch C, Zimmermann U, Blumenberg M, Michaelis W, Pfeiffer E (2008) Methane turnover and temperature response of methane-oxidizing bacteria in permafrost-affected soils of northeast Siberia. Soil Biol Biochem 40(12):3004–3013
Kuivila KM, Murray JW, Devol AH (1989) Methane production, sulfate reduction and competition for substrates in the sediments of Lake Washington. Geochim Cosmochim Acta 53(2):409–416
Lipson DA, Schmidt SK (2004) Seasonal changes in an alpine soil bacterial community in the Colorado Rocky mountains. Appl Environ Microbiol 70(5):2867–2879
McKenna P, Hoffmann C, Minkah N, Aye PP, Lackner A, Liu ZZ, Lozupone CA, Hamady M, Knight R, Bushman FD (2008) The macaque gut microbiome in health, lentiviral infection, and chronic enterocolitis. PLoS Pathog 4:22–28
Oakley BB, Fiedler TL, Marrazzo JM, Fredricks DN (2008) Diversity of human vaginal bacterial communities and their association with clinically-defined bacterial vaginosis. Appl Environ Microbiol 74(15):4898–4909
Philippot L, Hallin S, Börjesson G, Baggs EM (2009) Biochemical cycling in the rhizosphere having an impact on global change. Plant Soil 321(1–2):61–81
Popp TJ, Chanton JP, Whiting GJ, Grant N (2000) Evaluation of methane oxidation in the rhizosphere of a Carex dominated fen in north-central Alberta, Canada. Biogeochemistry 51(3):259–281
Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Pelies J, Glockner FO (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucl Acid Res 35(21):7188–7196
Roesch LF, Fulthorpe RR, Riva A, Casella G, Hadwin AK, Kent AD, Daroub SH, Camargo FAO, Farmerie WG, Triplett EW (2007) Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J 1:283–290
Roslev P, King GM (1996) Regulation of methane oxidation in a freshwater wetland by water table changes and anoxia. FEMS Microbiol Ecol 19(2):105–115
Schloss PD, Handelsman J (2006) Introducing SONS, a tool for operational taxonomic unit-based comparisons of microbial community memberships and structures. Appl Environ Microbiol 72(10):6773–6779
Schweitzer JA, Bailey JK, Fischer DG, LeRoy CJ, Lonsdorf EV, Whitham TG, Hart SC (2008) Plant–soil–microorganism interactions: heritable relationship between plant genotype and associated soil microorganisms. Ecology 89(3):773–781
Sogin ML, Morrison HG, Huber JA, Welch MD, Huse SM, Neal PR, Arrieta JM, Herndl GJ (2006) Microbial diversity in the deep sea and the underexplored ‘rare biosphere’. Proc Nat Acad Sci USA 103(32):12115–12120
Sun H, Zheng D (1996) Formation and evolution of Qinghai-Xizang Plateau. Shanghai Science and Technology Press, Shanghai
Torsvik V, Øvreas L (2002) Microbial diversity and function in soil: from genes to ecosystems. Curr Opin Microbiol 5(1):240–245
Uroz S, Buée M, Murat C, Frey-Klett P, Martin F (2010) Pyrosequencing reveals a contrasted bacterial diversity between oak rhizosphere and surrounding soil. Environ Microbiol Rep 2(2):281–288
Van Der Heijden MGA, Bardgett RD, Van Straalen NM (2008) The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. Ecol Lett 11(3):296–310
Vladár P, Rusznyák A, Márialigeti K, Borsodi AK (2008) Diversity of sulfate-reducing bacteria inhabiting the rhizosphere of Phragmites australis in Lake Velencei (Hungary) revealed by a combined cultivation-based and molecular approach. Microbial Ecol 56(1):64–75
Watanabe K, Nagao N, Toda T, Kurosawa N (2009) The dominant bacteria shifted from the order ‘‘Lactobacillales’’ to Bacillales and Actinomycetales during a start-up period of large-scale, completely-mixed composting reactor using plastic bottle flakes as bulking agent. World J Microbiol Biotechnol 25(5):803–811
Yang Z, Ou YH, Xu X, Zhao L, Song M, Zhou C (2010) Effects of permafrost degradation on ecosystems. Acta Ecologica Sinica 30(1):33–39
Zhang XS, Yang DA, Zhou GS, Liu CY, Zhang J (1996) Model expectation of impacts of global climate change on biomes of the Tibetan Plateau. In: Omasa K, Kai K, Taoda H, Uchijima Z, Yoshino M (eds) Climate change and plants in East Asia. Springer-Verlag, Tokyo, pp 25–38
Zhang Y, Wang H, Li D, Xiao Q, Liu X (2005) Molecular diversity and phylogenetic analysis of nitrogen-fixing (nifH) genes in alp prairie soil of Sanjiangyuan natural reserve. Acta Microbiol Sin 45(2):166–171
Zhang Y, Li D, Wang H, Xiao Q, Liu X (2006) The diversity of denitrifying bacteria in the alpine meadow soil of Sanjiangyuan natural reserve in Tibet Plateau. Chin Sci Bull 51(10):1245
Acknowledgments
This project was supported by National Basic Research Program (973) of China (No. 2012CB026105), National Natural Science Foundation of China (No. 31170465, 31100365), China Postdoctoral Science Fund (No. 2012M512053), Foundation for Excellent Youth Scholars of CAREERI, CAS, and UK BBSRC China Partnering Grant BB/J020419/1.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Zhang, W., Wu, X., Liu, G. et al. Tag-encoded pyrosequencing analysis of bacterial diversity within different alpine grassland ecosystems of the Qinghai-Tibet Plateau, China. Environ Earth Sci 72, 779–786 (2014). https://doi.org/10.1007/s12665-013-3001-z
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12665-013-3001-z