Skip to main content
SpringerLink
Log in

Bacterial Communities on the Surface of the Mineral Sandy Soil from the Desert of Maine (USA)

  • Published:
Current Microbiology Aims and scope Submit manuscript

Abstract

The Desert of Maine, not a real desert, is a 160,000 m2 tourist attraction of glacial silt which resembles a desert, surrounded by a pine forest in the state of Maine located in the northeastern USA. Though not a true desert, the soil of the Desert of Maine has a sandy texture with poor water-holding abilities, nutrient retention capabilities, and a relatively low pH value (pH 5.09). Samples from this site may be of interest to examine the bacterial diversity present on mineral sandy loam soils with an acidic pH, low concentrations of organic materials though surrounded by a pine forest, and compare it with true desert soil microbial populations. Two surface sand samples from the Desert of Maine were obtained, and pyrosequencing of PCR amplified 16S rRNA genes from total extracted DNA was used to assess bacterial diversity, community structure, and the relative abundance of major bacterial taxa. We found that the soil samples from the Desert of Maine displayed high levels of bacterial diversity, with a predominance of members belonging to the Proteobacteria and Actinobacteria phyla. Bacteria from the most abundant genus, Acidiphilium, represent 12.5% of the total 16S rDNA sequences. In total, 1394 OTUs were observed in the two samples, with 668 OTUs being observed in both samples. By comparing Desert of Maine bacterial populations with studies on similar soil environments, we found that the samples contained less Acidobacteria than soils from acid soil forests, and less Firmicutes plus more Proteobacteria than oligotrophic desert soils. Interestingly, our samples were found to be highly similar in their composition to an oak forest soil in France.

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

  1. 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

    CAS  PubMed  PubMed Central  Google Scholar 

  2. Fierer N, Lauber CL, Ramirez KS, Zaneveld J, Bradford MA, Knight R (2012) Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. ISME J 6:1007–1017

    CAS  PubMed  Google Scholar 

  3. Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143–169

    CAS  PubMed  PubMed Central  Google Scholar 

  4. Petrosino JF, Highlander S, Luna RA, Gibbs RA, Versalovic J (2009) Metagenomic pyrosequencing and microbial identification. Clin Chem 55:856–866

    CAS  PubMed  PubMed Central  Google Scholar 

  5. Schloss PD (2010) The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies. PLoS Comput Biol 6:e1000844

    PubMed  PubMed Central  Google Scholar 

  6. Bahr J (2009) Amazing and unusual America. Publications International, Chicago, p 9

    Google Scholar 

  7. Griffiths RI, Thomson BC, James P, Bell T, Bailey M, Whiteley AS (2011) The bacterial biogeography of British soils. Environ Microbiol 13:1642–1654

    PubMed  Google Scholar 

  8. Crits-Christoph A, Robinson CK, Barnum T, Fricke WF, Davila AF, Jedynak B, McKay CP, Diruggiero J (2013) Colonization patterns of soil microbial communities in the Atacama Desert. Microbiome 1:28

    PubMed  PubMed Central  Google Scholar 

  9. Nacke H, Thurmer A, Wollherr A, Will C, Hodac L, Herold N, Schoning I, Schrumpf M et al (2011) Pyrosequencing-based assessment of bacterial community structure along different management types in German forest and grassland soils. PLoS ONE 6:e17000

    CAS  PubMed  PubMed Central  Google Scholar 

  10. Shah V, Shah S, Kambhampati MS, Ambrose J, Smith N, Dowd SE, McDonnell KT, Panigrahi B et al (2011) Bacterial and archaea community present in the Pine Barrens Forest of Long Island, NY: unusually high percentage of ammonia oxidizing bacteria. PLoS ONE 6:e26263

    CAS  PubMed  Google Scholar 

  11. Russo SE, Legge R, Weber KA, Brodie EL, Goldfarb KC, Benson AK, Tan S (2012) Bacterial community structure of contrasting soils underlying Bornean rain forests: inferences from microarray and next-generation sequencing methods. Soil Biol Biochem 55:48–59

    CAS  Google Scholar 

  12. An S, Couteau C, Luo F, Neveu J, DuBow MS (2013) Bacterial diversity of surface sand samples from the Gobi and Taklamaken deserts. Microb Ecol 66:850–860

    PubMed  Google Scholar 

  13. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB et al (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541

    CAS  PubMed  PubMed Central  Google Scholar 

  14. Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. J 17:10–12

    Google Scholar 

  15. Smeds L, Kunstner A (2011) ConDeTri–a content dependent read trimmer for Illumina data. PLoS ONE 6:e26314

    CAS  PubMed  PubMed Central  Google Scholar 

  16. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27:2194–2200

    CAS  PubMed  PubMed Central  Google Scholar 

  17. Wright ES, Yilmaz LS, Noguera DR (2012) DECIPHER, a search-based approach to chimera identification for 16S rRNA sequences. Appl Environ Microbiol 78:717–725

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P et al (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41:D590–D596

    CAS  PubMed  Google Scholar 

  19. Yilmaz P, Parfrey LW, Yarza P, Gerken J, Pruesse E, Quast C, Schweer T, Peplies J et al (2014) The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks. Nucleic Acids Res 42:D643–648

    CAS  PubMed  Google Scholar 

  20. Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460–2461

    CAS  PubMed  Google Scholar 

  21. Edgar RC (2013) UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods 10:996–998

    CAS  PubMed  Google Scholar 

  22. Schloss PD, Handelsman J (2008) A statistical toolbox for metagenomics: assessing functional diversity in microbial communities. BMC Bioinformatics 9:34

    PubMed  Google Scholar 

  23. Schloss PD, Larget BR, Handelsman J (2004) Integration of microbial ecology and statistics: a test to compare gene libraries. Appl Environ Microbiol 70:5485–5492

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  25. de Winder B, Matthijs HCP, Mur LR (1990) The effect of dehydration and ion stress on carbon dioxide fixation in drought-tolerant phototrophic micro-organisms. FEMS Microbiol Lett 74:33–38

    Google Scholar 

  26. de Winder B, Mur LR (1994) The sensitivity for salinity increase in the drought resistant cyanobacterium Crinalium epipsammum SAB 22.89. In: Stal L, Caumette P (eds) Microbial Mats, NATO ASI Series. Springer, Berlin, pp 117–123

    Google Scholar 

  27. Uroz S, Calvaruso C, Turpault MP, Frey-Klett P (2009) Mineral weathering by bacteria: ecology, actors and mechanisms. Trends Microbiol 17:378–387

    CAS  PubMed  Google Scholar 

  28. Frey B, Rieder SR, Brunner I, Plotze M, Koetzsch S, Lapanje A, Brandl H, Furrer G (2010) Weathering-associated bacteria from the Damma glacier forefield: physiological capabilities and impact on granite dissolution. Appl Environ Microbiol 76:4788–4796

    CAS  PubMed  Google Scholar 

  29. An S, Sin HH, DuBow MS (2015) Modification of atmospheric sand-associated bacterial communities during Asian sandstorms in China and South Korea. Heredity 114:460–467

    CAS  PubMed  Google Scholar 

  30. Makhalanyane TP, Valverde A, Gunnigle E, Frossard A, Ramond J, Cowan DA (2015) Microbial ecology of hot desert edaphic systems. FEMS Microbiol Rev 39:203–221

    CAS  PubMed  Google Scholar 

  31. Osman JR, Fernandes G, Regeard C, Jaubert C, DuBow MS (2018) Examination of the bacterial biodiversity of coastal eroded surface soils from the Dapani (Mayotte Island). Geomicrobiol J 35:655–665

    Google Scholar 

  32. Rousk J, Baath E, Brookes PC, Lauber CL, Lozupone C, Caporaso JG, Knight R, Fierer N (2010) Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J 4:1340–1351

    PubMed  Google Scholar 

  33. Centeno CM, Legendre P, Beltran Y, Alcantara-Hernandez RJ, Lidstrom UE, Ashby MN, Falcon LI (2012) Microbialite genetic diversity and composition relate to environmental variables. FEMS Microbiol Ecol 82:724–735

    CAS  PubMed  Google Scholar 

  34. Fierer N, Leff JW, Adams BJ, Nielsen UN, Bates ST, Lauber CL, Owens S, Gilbert JA et al (2012) Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proc Natl Acad Sci USA 109:21390–21395

    CAS  PubMed  PubMed Central  Google Scholar 

  35. Osborne CA, Zwart AB, Broadhurst LM, Young AG, Richardson AE (2011) The influence of sampling strategies and spatial variation on the detected soil bacterial communities under three different land-use types. FEMS Microbiol Ecol 78:70–79

    CAS  PubMed  Google Scholar 

  36. Uroz S, Buee M, Murat C, Frey-Klett P, Martin F (2010) Pyrosequencing reveals a contrasted bacterial diversity between oak rhizosphere and surrounding soil. Environ Microbiol Rep 2:281–288

    CAS  PubMed  Google Scholar 

  37. Winsley T, van Dorst JM, Brown MV, Ferrari BC (2012) Capturing greater 16S rRNA gene sequence diversity within the domain bacteria. Appl Environ Microbiol 78:5938–5941

    CAS  PubMed  PubMed Central  Google Scholar 

  38. Andrew DR, Fitak RR, Munguia-Vega A, Racolta A, Martinson VG, Dontsova K (2012) Abiotic factors shape microbial diversity in Sonoran Desert soils. Appl Environ Microbiol 78:7527–7537

    CAS  PubMed  PubMed Central  Google Scholar 

  39. Lee CK, Barbier BA, Bottos EM, McDonald IR, Cary SC (2012) The Inter-Valley Soil Comparative Survey: the ecology of Dry Valley edaphic microbial communities. ISME J 6:1046–1057

    CAS  PubMed  Google Scholar 

  40. Tiao G, Lee CK, McDonald IR, Cowan DA, Cary SC (2012) Rapid microbial response to the presence of an ancient relic in the Antarctic Dry Valleys. Nat Commun 3:660

    PubMed  Google Scholar 

  41. 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

    CAS  PubMed  Google Scholar 

  42. Osman JR, DuBow MS (2018) Bacterial communities on the surface of oligotrophic (nutrient-poor) soils. Curr Top Biotechnol 9:31–44

    Google Scholar 

  43. Lacap DC, Warren-Rhodes KA, McKay CP, Pointing SB (2011) Cyanobacteria and chloroflexi-dominated hypolithic colonization of quartz at the hyper-arid core of the Atacama Desert, Chile. Extremophiles 15:31–38

    PubMed  Google Scholar 

  44. Ley RE, Harris JK, Wilcox J, Spear JR, Miller SR, Bebout BM, Maresca JA, Bryant DA et al (2006) Unexpected diversity and complexity of the Guerrero Negro hypersaline microbial mat. Appl Environ Microbiol 72:3685–3695

    CAS  PubMed  PubMed Central  Google Scholar 

  45. Freeman KR, Pescador MY, Reed SC, Costello EK, Robeson MS, Schmidt SK (2009) Soil CO2 flux and photoautotrophic community composition in high-elevation, 'barren' soil. Environ Microbiol 11:674–686

    CAS  PubMed  Google Scholar 

  46. Reis VM, Teixeira KRS (2015) Nitrogen fixing bacteria in the family Acetobacteraceae and their role in agriculture. J Basic Microbiol 55:931–949

    CAS  PubMed  PubMed Central  Google Scholar 

  47. Koberl M, Muller H, Ramadan EM, Berg G (2011) Desert farming benefits from microbial potential in arid soils and promotes diversity and plant health. PLoS ONE 6:e24452

    PubMed  PubMed Central  Google Scholar 

  48. Harrison PJ (1981) Acidiphilium cryptum gen. nov., sp. nov., heterotrophic bacterium from acidic mineral environments. Int J Syst Bacteriol 31:327–332

    Google Scholar 

  49. Wichlacz PL, Unz RF, Langworthy TA (1986) Acidiphilium angustum sp. nov., Acidiphilium facilis sp. nov., and Acidiphilium rubrum sp. nov.: Acidophilic heterotrophic bacteria isolated from acidic coal mine drainage. Int J Syst Evol Microbiol 36:197–201

    Google Scholar 

  50. Sanchez-Andrea I, Rodriguez N, Amils R, Sanz JL (2011) Microbial diversity in anaerobic sediments at Rio Tinto, a naturally acidic environment with a high heavy metal content. Appl Environ Microbiol 77:6085–6093

    CAS  PubMed  Google Scholar 

  51. Kan J, Chellamuthu P, Obraztsova A, Moore JE, Nealson KH (2011) Diverse bacterial groups are associated with corrosive lesions at a Granite Mountain Record Vault (GMRV). J Appl Microbiol 111:329–337

    CAS  PubMed  Google Scholar 

  52. Wu Y, Tan L, Liu W, Wang B, Wang J, Cai Y, Lin X (2015) Profiling bacterial diversity in a limestone cave of the western Loess Plateau of China. Front Microbiol 6:244

    PubMed  Google Scholar 

  53. Pointing SB, Belnap J (2012) Microbial colonization and controls in dryland systems. Nat Rev Microbiol 10:551–562

    CAS  PubMed  Google Scholar 

  54. Lepleux C, Turpault MP, Oger P, Frey-Klett P, Uroz S (2012) Correlation of the abundance of betaproteobacteria on mineral surfaces with mineral weathering in forest soils. Appl Environ Microbiol 78:7114–7119

    CAS  PubMed  Google Scholar 

  55. Schutte UM, Abdo Z, Foster J, Ravel J, Bunge J, Solheim B, Forney LJ (2010) Bacterial diversity in a glacier foreland of the high Arctic. Mol Ecol 19(Suppl 1):54–66

    PubMed  Google Scholar 

  56. de Gannes V, Eudoxie G, Hickey WJ (2013) Prokaryotic successions and diversity in composts as revealed by 454-pyrosequencing. Bioresour Technol 133:573–580

    PubMed  Google Scholar 

  57. Hartmann M, Frey B, Mayer J, Mader P, Widmer F (2015) Distinct soil microbial diversity under long-term organic and conventional farming. ISME J 9:1177–1194

    PubMed  Google Scholar 

Download references

Acknowledgements

We thank Ginger and Gary Currens from the Desert of Maine for their help in obtaining the sand samples, the Reviewers for their insightful comments and questions, and all the members of the Laboratoire de Génomique et Biodiversité Microbienne des Biofilms (LGBMB) of the Institute for Integrative Biology of the Cell (I2BC) for interesting discussions, comments, and suggestions. YW was a doctoral scholarship recipient from the China Scholarship Council (CSC). JO was a doctoral scholarship recipient from CONICYT Becas Chile. This work was supported by the Centre National de la Recherche Scientifique (CNRS), France.

Author information

Author notes

  1. Jorge R. Osman

    Present address: Laboratoire de Géologie de Lyon, Université Claude Bernard Lyon-1, UMR5276, Lyon, France

  2. Yang Wang and Jorge R. Osman contributed equally to this work.

Authors and Affiliations

  1. Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Univ Paris-Sud, Bâtiment 409, 91405, Orsay, France

    Yang Wang, Jorge R. Osman & Michael S. DuBow

Authors
  1. Yang Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jorge R. Osman
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Michael S. DuBow
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Michael S. DuBow.

Ethics declarations

Conflict of interest:

The authors declare that they have no conflict of interest.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Wang, Y., Osman, J.R. & DuBow, M.S. Bacterial Communities on the Surface of the Mineral Sandy Soil from the Desert of Maine (USA). Curr Microbiol 77, 1429–1437 (2020). https://doi.org/10.1007/s00284-020-01946-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00284-020-01946-z

Search

Navigation