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Bacterial Diversity of Surface Sand Samples from the Gobi and Taklamaken Deserts

  • Environmental Microbiology
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Abstract

Arid regions represent nearly 30 % of the Earth's terrestrial surface, but their microbial biodiversity is not yet well characterized. The surface sands of deserts, a subset of arid regions, are generally subjected to large temperature fluctuations plus high UV light exposure and are low in organic matter. We examined surface sand samples from the Taklamaken (China, three samples) and Gobi (Mongolia, two samples) deserts, using pyrosequencing of PCR-amplified 16S V1/V2 rDNA sequences from total extracted DNA in order to gain an assessment of the bacterial population diversity. In total, 4,088 OTUs (using ≥97 % sequence similarity levels), with Chao1 estimates varying from 1,172 to 2,425 OTUs per sample, were discernable. These could be grouped into 102 families belonging to 15 phyla, with OTUs belonging to the Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria phyla being the most abundant. The bacterial population composition was statistically different among the samples, though members from 30 genera were found to be common among the five samples. An increase in phylotype numbers with increasing C/N ratio was noted, suggesting a possible role in the bacterial richness of these desert sand environments. Our results imply an unexpectedly large bacterial diversity residing in the harsh environment of these two Asian deserts, worthy of further investigation.

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References

  1. Bhatnagar A, Bhatnagar M (2005) Microbial diversity in desert ecosystems. Curr Sci 89:91–100

    Google Scholar 

  2. Lima DM, Oliveira RQ, Uetanabaro AP, Goes-Neto A, Rosa CA, Assis SA (2009) Thermostable inulinases secreted by yeast and yeast-like strains from the Brazilian semi-arid region. Int J Food Sci Nutr 60(Suppl 7):63–71

    Article  CAS  PubMed  Google Scholar 

  3. Neveu J, Regeard C, DuBow MS (2011) Isolation and characterization of two serine proteases from metagenomic libraries of the Gobi and Death Valley deserts. Appl Microbiol Biot 91:635–644

    Article  CAS  Google Scholar 

  4. Pointing SB, Chan Y, Lacap DC, Lau MC, Jurgens JA, Farrell RL (2009) Highly specialized microbial diversity in hyper-arid polar desert. Proc Natl Acad Sci USA 106:19964–19969

    Google Scholar 

  5. Drees KP, Neilson JW, Betancourt JL, Quade J, Henderson DA, Pryor BM et al (2006) Bacterial community structure in the hyperarid core of the Atacama Desert, Chile. Appl Environ Microbiol 72:7902–7908

    Google Scholar 

  6. Neilson JW, Quade J, Ortiz M, Nelson WM, Legatzki A, Tian F et al (2012) Life at the hyperarid margin: novel bacterial diversity in arid soils of the Atacama Desert, Chile. Extremophiles 16:553–566

    Article  PubMed  Google Scholar 

  7. Liu M, Dai J, Liu Y, Cai F, Wang Y, Fang C (2011) Desertibacter roseus gen. nov., sp. nov., a gamma radiation-resistant bacterium in the family Rhodospirillaceae, isolated from desert sand. Int J Syst Evol Microbiol 61:1109–1113

    Article  CAS  PubMed  Google Scholar 

  8. Zhang L, Wu GL, Wang Y, Dai J, Fang CX (2010) Bacillus deserti sp. nov., a novel bacterium isolated from the desert of Xinjiang, China. A Van Leeuw 99:221–229

    Article  Google Scholar 

  9. Liu M, Liu Y, Wang Y, Luo X, Dai J, Fang C (2010) Lysobacter xinjiangensis sp. nov., a moderately thermotolerant and alkalitolerant bacterium isolated from gamma-irradiated sand soil sample. Int J Syst Evol Microbiol 61:433–437

    Article  PubMed  Google Scholar 

  10. An H, Xu M, Dai J, Wang Y, Cai F, Qi H et al (2010) Sphingomonas xinjiangensis sp. nov., isolated from the desert of Xinjiang, China. Int J Syst Evol Microbiol 61:1865–1869

    Article  PubMed  Google Scholar 

  11. Zha Y, Gao J (1997) Characteristics of desertification and its rehabilitation in China. J Arid Environ 37:419–432

    Article  Google Scholar 

  12. Ma J, Ding Z, Edmunds WM, Gates JB, Huang T (2009) Limits to recharge of groundwater from Tibetan Plateau to the Gobi Desert, implications for water management in the mountain front. J Hydrol 364:128–141

    Article  Google Scholar 

  13. Li X, Yan P, Wu L (2003) Resources of medicinal plants living in sands in Xinjian areas. Prim J Chinese Materia Medica 17:54–56

    Google Scholar 

  14. Xia X, Chen H, Wang P (2004) Aerosol properties in a Chinese semiarid region. Atmos Environ 38:4571–4581

    Article  CAS  Google Scholar 

  15. Zhou J, Bruns MA, Tiedje JM (1996) DNA recovery from soils of diverse composition. Appl Environ Microbiol 62:316–322

    Google Scholar 

  16. Reasoner D, Geldreich E (1985) A new medium for the enumeration and subculture of bacteria from potable water. Appl Environ Microbiol 49:1–7

    Google Scholar 

  17. Hamady M, Walker JJ, Harris JK, Gold NJ, Knight R (2008) Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat Methods 5:235–237

    Google Scholar 

  18. Binladen J, Gilbert MT, Bollback JP, Panitz F, Bendixen C, Nielsen R et al (2007) The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PLoS One 2:e197

    Google Scholar 

  19. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K et al (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72:5069–5072

    Google Scholar 

  20. Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:5261–5267

    Google Scholar 

  21. Liu Z, Lozupone C, Hamady M, Bushman FD, Knight R (2007) Short pyrosequencing reads suffice for accurate microbial community analysis. Nucl Acids Res 35:e120

    Google Scholar 

  22. Mori H, Maruyama F, Kurokawa K (2010) VITCOMIC: visualization tool for taxonomic compositions of microbial communities based on 16S rRNA gene sequences. BMC Bioinfo 11:332

    Article  Google Scholar 

  23. Giongo A, Crabb DB, Davis-Richardson AG, Chauliac D, Mobberley JM, Gano KA et al (2010) PANGEA: pipeline for analysis of next generation amplicons. ISME J 4:852–861

    Google Scholar 

  24. Chao A, Shen T-J (2010) Program SPADE (Species Prediction And Diversity Estimation). Program and User's Guide published at http://chao.stat.nthu.edu.tw. Accessed 12 Oct 2010

  25. Chessel D, Dufour AB, Thioulouse J (2004) The ade4 package-I: one-table methods. R news 4:5–10

    Google Scholar 

  26. Huse SM, Huber JA, Morrison HG, Sogin ML, Welch DM (2007) Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol 8:R143

    Google Scholar 

  27. Teixeira LC, Peixoto RS, Cury JC, Sul WJ, Pellizari VH, Tiedje J et al (2010) Bacterial diversity in rhizosphere soil from Antarctic vascular plants of Admiralty Bay, maritime Antarctica. ISME J 4:989–1001

    Google Scholar 

  28. Guss AM, Roeselers G, Newton IL, Young CR, Klepac-Ceraj V, Lory S et al (2011) Phylogenetic and metabolic diversity of bacteria associated with cystic fibrosis. ISME J 5:20–29

    Google Scholar 

  29. 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

    Google Scholar 

  30. Noha HY, Couger MB, Mostafa SE, Niyaz A (2010) Fine-scale bacterial beta diversity within a complex ecosystem (Zodletone Spring, OK, USA): the role of the rare biosphere. PLoS One 5:e12414

    Google Scholar 

  31. Nemergut DR, Costello EK, Hamady M, Lozupone C, Jiang L, Schmidt SK et al (2010) Global patterns in the biogeography of bacterial taxa. Environ Microbiol 13:135–144

    Google Scholar 

  32. Fulthorpe RR, Roesch LF, Riva A, Triplett EW (2008) Distantly sampled soils carry few species in common. ISME J 2:901–910

    Google Scholar 

  33. Kirchman DL (2012) Processes in microbial ecology. Oxford University Press Inc., New York

    Google Scholar 

  34. Bachar A, Al-Ashhab A, Soares MI, Sklarz MY, Angel R, Ungar ED et al (2010) Soil microbial abundance and diversity along a low precipitation gradient. Microb Ecol 60:453–461

    Google Scholar 

  35. Angel R, Soares MI, Ungar ED, Gillor O (2010) Biogeography of soil archaea and bacteria along a steep precipitation gradient. ISME J 4:553–563

    Google Scholar 

  36. Fierer N, Jackson RB (2006) The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci USA 103:626–631

    Google Scholar 

  37. Bell C, McIntyre N, Cox S, Tissue D, Zak J (2008) Soil microbial responses to temporal variations of moisture and temperature in a Chihuahuan Desert grassland. Microb Ecol 56:153–167

    Google Scholar 

  38. Bowker MA, Reed SC, Belnap J, Phillips SL (2002) Temporal variation in community composition, pigmentation, and F(v)/F(m) of desert cyanobacterial soil crusts. Microb Ecol 43:13–25

    Google Scholar 

  39. Wang Y, Zhang K, Cai F, Zhang L, Tang Y, Dai J et al (2010) Pontibacter xinjiangensis sp. nov., in the phylum ‘Bacteroidetes’, and reclassification of [Effluviibacter] roseus as Pontibacter roseus comb. nov. Int J Syst Evol Microbiol 60:99–103

  40. Zhou Y, Wang X, Liu H, Zhang KY, Zhang YQ, Lai R et al (2007) Pontibacter akesuensis sp. nov., isolated from a desert soil in China. Int J Syst Evol Microbiol 57:321–325

    Google Scholar 

  41. Zhang L, Zhang Q, Luo X, Tang Y, Dai J, Li Y et al (2008) Pontibacter korlensis sp. nov., isolated from the desert of Xinjiang, China. Int J Syst Evol Microbiol 58:1210–1214

    Google Scholar 

  42. Lim JM, Jeon CO, Lee SS, Park DJ, Xu LH, Jiang CL et al (2008) Reclassification of Salegentibacter catena Ying et al. 2007 as Salinimicrobium catena gen. nov., comb. nov. and description of Salinimicrobium xinjiangense sp. nov., a halophilic bacterium isolated from Xinjiang Province in China. Int J Syst Evol Microbiol 58:438–442

  43. Kellogg CA, Griffin DW, Garrison VH, Peak KK, Royall N, Smith RR et al (2004) Characterization of aerosolized bacteria and fungi from desert dust events in Mali, West Africa. Aerobiologia 20:99–110

    Article  Google Scholar 

  44. Griffina DW, Kubilayb N, Koc-akb M, Graya MA (2007) Airborne desert dust and aeromicrobiology over the Turkish Mediterranean coastline. Atmos Environ 41:4050–4062

    Article  Google Scholar 

  45. Lee DW, Lee SD (2010) Marmoricola scoriae sp. nov., isolated from volcanic ash. Int J Syst Evol Microbiol 60:2135–2139

    Google Scholar 

  46. Urzi C, Salamone P, Schumann P, Stackebrandt E (2000) Marmoricola aurantiacus gen. nov., sp. nov., a coccoid member of the family Nocardioidaceae isolated from a marble statue. Int J Syst Evol Microbiol 50:529–536

    Article  CAS  PubMed  Google Scholar 

  47. Lee SD (2007) Marmoricola aequoreus sp. nov., a novel actinobacterium isolated from marine sediment. Int J Syst Evol Microbiol 57:1391–1395

    Article  PubMed  Google Scholar 

  48. Dastager SG, Lee JC, Ju YJ, Park DJ, Kim CJ (2008) Marmoricola bigeumensis sp. nov., a member of the family Nocardioidaceae. Int J Syst Evol Microbiol 58:1060–1063

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

We thank Barry Holland (Institut de Génétique et Microbiologie, Université Paris-Sud, France) and Denis Faure (Institut des Sciences du Végétal, CNRS, Gif-sur-Yvette, France) for interesting discussions and the reviewers for their insightful comments and suggestions. This work was supported by the Centre National de la Recherche Scientifique, France and by the AQUAPHAGE program of the Agence Nationale de la Recherche, France.

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Authors and Affiliations

  1. Univ. Paris-Sud, Laboratoire de Génomique et Biodiversité Microbienne des Biofilms (LGBMB), Institut de Génétique et Microbiologie, CNRS UMR 8621, Bâtiment 409, 91405, Orsay, France

    Shu An, Cécile Couteau, Fan Luo, Julie Neveu & Michael S. DuBow

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  1. Shu An
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  2. Cécile Couteau
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Correspondence to Michael S. DuBow.

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An, S., Couteau, C., Luo, F. et al. Bacterial Diversity of Surface Sand Samples from the Gobi and Taklamaken Deserts. Microb Ecol 66, 850–860 (2013). https://doi.org/10.1007/s00248-013-0276-2

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  • DOI: https://doi.org/10.1007/s00248-013-0276-2

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