Plant and Soil

, Volume 357, Issue 1–2, pp 275–288 | Cite as

Bacterial community in the rhizosphere of the cactus species Mammillaria carnea during dry and rainy seasons assessed by deep sequencing

  • G. Torres-Cortés
  • V. Millán
  • A. J. Fernández-González
  • J. F. Aguirre-Garrido
  • H. C. Ramírez-Saad
  • M. Fernández-López
  • N. Toro
  • F. Martínez-Abarca
Regular Article


Background and aims

The Tehuacán-Cuitcatlán reserve is an area of unique plant biodiversity mostly in the form of xerophytes, with exceptionally high numbers of rare and endemic species. This endemism results partly from the characteristics of the climate of this area, with two distinct seasons: rainy and dry seasons. Although rhizosphere communities must be critical in the function of this ecosystem, understanding the structure of these communities is currently limited. This is the first molecular study of the microbial diversity present in the rhizosphere of Mamillaria carnea.


Total DNA was obtained from soil and rhizosphere samples at three locations in the Tehuacán Cuicatlán Reserve, during dry and rainy seasons. Temperature gradient gel electrophoresisis (TGGE) fingerprinting, 16S rRNA gene libraries and pyrosequencing were used to investigate bacterial diversity in the rhizosphere of Mammillaria carnea and changes in the microbial community between seasons.


Deep sequencing data reveal a higher level of biodiversity in the dry season. Statistical analyses based on these data indicates that the composition of the bacterial community differed between both seasons affecting to members of the phyla Acidobacteria, Cyanobacteria, Gemmatimonadetes, Plantomycetes, Actinobacteria and Firmicutes. In addition, the depth of sequencing performed (>24,000 reads) enables detection of changes in the relative abundance of lower bacterial taxa (novel bacterial phylotypes) indicative of the increase of specific bacterial populations due to the season.


This study states the basis of the bacterial diversity in the rhizosphere of cacti in semi-arid environments and it is a sequence-based demonstration of community shifts in different seasons.


Microbial community Soil bacteria 16S rRNA analysis Mammillaria carnea Tehuacán Cuicatlán reserve 454-pyrosequencing 



This work was supported by research projects BIO2003-02473, OAPN21/2007, BIO2008-00740 and CSD 2009-0006 of the Consolider-Ingenio 2010 program from the Ministerio de Ciencia e Innovación; P08-CVI-03549 from Consejería de Innovación, Ciencia y Empresa of Junta de Andalucía including ERDF (European Regional Development Fund); and the BBVA Foundation (BBVA BIOCON 04-084 Project). G.T.C. and A.J.F.G. were supported by CSIC predoctoral and FPU fellowships, respectively, from the Ministerio de Ciencia e Innovación. V.M. and J.F.A.G. were supported by the mentioned BBVA Project. We are grateful to J.I. Jiménez-Zurdo and A. Schüβler for critical reading of the manuscript.

Supplementary material

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  1. Angel R, Soares MI, Ungar ED, Gillor O (2010) Biogeography of soil archaea and bacteria along a steep precipitation gradient. ISME J 4:553–563PubMedCrossRefGoogle Scholar
  2. Audic S, Claverie JM (1997) The significance of digital gene expression profiles. Genome Res 7:986–995PubMedGoogle Scholar
  3. Bachar A, Al-Ashhab A, Soares MI, Sklarz MY, Angel R, Ungar ED, Gillor O (2010) Soil microbial abundance and diversity along a low precipitation gradient. Microb Ecol 60:453–461PubMedCrossRefGoogle Scholar
  4. Bahl J, Lau MC, Smith GJ, Vijaykrishna D, Cary SC, Lacap DC, Lee CK, Papke RT, Warren-Rhodes KA, Wong FK, McKay CP, Pointing SB (2011) Ancient origins determine global biogeography of hot and cold desert cyanobacteria. Nat Commun 25:163CrossRefGoogle Scholar
  5. Baker G, Smith JJ, Cowan DA (2003) Review and re-analysis of domain-specific 16S primers. J Microbiol Methods 55:541–555PubMedCrossRefGoogle Scholar
  6. Berg G, Smalla K (2009) Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere. FEMS Microbiol Ecol 68:1–13PubMedCrossRefGoogle Scholar
  7. Binladen J, Gilbert MT, Bollback JP, Panitz F, Bendixen C, Nielsen R, Willerslev E (2007) The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PLoS One 2:e197PubMedCrossRefGoogle Scholar
  8. Castro HF, Classen AT, Austin EE, Norby RJ, Schadt CW (2010) Soil microbial community responses to multiple experimental climate change drivers. Appl Environ Microbiol 76:999–1007PubMedCrossRefGoogle Scholar
  9. Chanal A, Chapon V, Benzerara K, Barakat M, Christen R, Achouak W, Barras F, Heulin T (2006) The desert of Tataouine: an extreme environment that hosts a wide diversity of microorganisms and radiotolerant bacteria. Environ Microbiol 8:514–525PubMedCrossRefGoogle Scholar
  10. Chao A, Bunge J (2002) Estimating the number of species in a stochastic abundance model. Biometrics 58:531–539PubMedCrossRefGoogle Scholar
  11. Chow ML, Radomski CC, McDermott JM, Davies J, Axelrood PE (2002) Molecular characterization of bacterial diversity in Lodgepole pine (Pinus contorta) rhizosphere soils from British Columbia forest soils differing in disturbance and geographic source. FEMS Microbiol Ecol 42:347–357PubMedCrossRefGoogle Scholar
  12. Clarke KR (1993) Non-parametric multivariate analysis of changes in community structure. Austr J Ecol 18:117–143CrossRefGoogle Scholar
  13. 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. Nucleic Acids Res 37:D141–D145PubMedCrossRefGoogle Scholar
  14. Cruz-Martínez K, Suttle KB, Brodie EL, Power ME, Andersen GL, Banfield JF (2009) Despite strong seasonal responses, soil microbial consortia are more resilient to long-term changes in rainfall than overlying grassland. ISME J 3:738–744PubMedCrossRefGoogle Scholar
  15. Dávila P, Arizmendi M, Valiente-Banuet A, Villaseñor J, Casas A, Lira R (2002) Biological diversity in the Tehuacan-Cuicatlan Valley, México. Biodiv Conserv 11:421–442CrossRefGoogle Scholar
  16. Elshahed MS, Youssef NH, Spain AM, Sheik C, Najar FZ, Sukharnikov LO, Roe BA, Davis JP, Schloss PD, Bailey VL, Krumholz LR (2008) Novelty and uniqueness patterns of rare members of the soil biosphere. Appl Environ Microbiol 74:5422–5428PubMedCrossRefGoogle Scholar
  17. Enge K, Whiteford S (1989) The keepers of water and earth: Mexican rural social organization and irrigation. University of Texas Press, AustinGoogle Scholar
  18. Felsenstein J (2005) PHYLIP (Phylogeny Inference Package). Version 3.6. Department of Genome Sciences, University of Washington, Seattle (distributed by the author)Google Scholar
  19. Fierer N, Jackson RB (2006) The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci USA 103:626–631PubMedCrossRefGoogle Scholar
  20. Fierer N, Bradford MA, Jackson RB (2007) Toward an ecological classification of soil bacteria. Ecology 88:1354–1364PubMedCrossRefGoogle Scholar
  21. Green J, Bohannan BJM (2006) Spatial scaling of microbial biodiversity. Trends Ecol Evol 21:501–507PubMedCrossRefGoogle Scholar
  22. Green SJ, Blackford C, Bucki P, Jahnke LL, Prufert-Bebout L (2008) A salinity and sulfate manipulation of hypersaline microbial mats reveals stasis in the cyanobacterial community structure. ISME J 2:457–470PubMedCrossRefGoogle Scholar
  23. Hartmann M, Widmer F (2006) Community structure analyses are more sensitive to differences in soil bacterial communities than anonymous diversity indices. Appl Environ Microbiol 72:7804–7812PubMedCrossRefGoogle Scholar
  24. Hawkins BA, Field R, Cornell HV, Currie DJ, Guegan JF, Kaufman DM, Kerr JT, Mittelbach GG, Oberdorff T, O’Brien EM, Porter EE, Turner JRG (2003) Energy, water, and broad-scale geographic patterns of species richness. Ecology 84:3105–3117CrossRefGoogle Scholar
  25. He J, Xu Z, Hughes J (2006) Molecular bacterial diversity of a forest soil under residue management regimes in subtropical Australia. FEMS Microbiol Ecol 55:38–47PubMedCrossRefGoogle Scholar
  26. Janssen PH (2006) Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl Environ Microbiol 72:1719–1728PubMedCrossRefGoogle Scholar
  27. 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 3:442–453PubMedCrossRefGoogle Scholar
  28. Karthikeyan N, Prasanna R, Nain L, Kaushik BD (2007) Evaluating the potential of plant growth promoting cyanobacteria as inoculants for wheat. Eur J Soil Biol 43:23–30CrossRefGoogle Scholar
  29. Katoh K, Toh H (2008) Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform 9:286–298PubMedCrossRefGoogle Scholar
  30. Kempers AJ (1974) Determination of sub-microquantities of ammonium and nitrates in soils with phenol, sodiumnitroprusside and hypochlorite. Geoderma 12:201–206CrossRefGoogle Scholar
  31. Köberl M, Müller H, Ramadan EM, Berg G (2011) Desert farming benefits from microbial potential in arid soils and promotes diversity and plant health. PLoS One 6:e24452PubMedCrossRefGoogle Scholar
  32. Kolton M, Meller Harel Y, Pasternak Z, Graber ER, Elad Y, Cytryn E (2007) Impact of biochar application to soil on the root-associated bacterial community structure of fully developed greenhouse pepper plants. Appl Environ Microbiol 77:4924–4930CrossRefGoogle Scholar
  33. Kumar S, Nei M, Dudley J, Tamura K (2008) MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform 9:299–306PubMedCrossRefGoogle Scholar
  34. Moissl C, Osman S, La Duc MT, Dekas A, Brodie E, DeSantis T, Venkateswaran K (2007) Molecular bacterial community analysis of clean rooms where spacecraft are assembled. FEMS Microbiol Ecol 61:509–521PubMedCrossRefGoogle Scholar
  35. Morales SE, Cosart TF, Johnson JV, Holben WE (2009) Extensive phylogenetic analysis of a soil bacterial community illustrates extreme taxon evenness and the effects of amplicon length, degree of coverage, and DNA fractionation on classification and ecological parameters. Appl Environ Microbiol 75:668–675PubMedCrossRefGoogle Scholar
  36. Muyzer G, de Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59:695–700PubMedGoogle Scholar
  37. Nacke H, Thürmer A, Wollherr A, Will C, Hodac L, Herold N, Schöning I, Schrumpf M, Daniel R (2011) Pyrosequencing-based assessment of bacterial community structure along different management types in German forest and grassland soils. PLoS One 6:e17000PubMedCrossRefGoogle Scholar
  38. Osborn AM, Moore ER, Timmis KN (2000) An evaluation of terminal-restriction fragment length polymorphism (T-RFLP) analysis for the study of microbial community structure and dynamics. Environ Microbiol 2:39–50PubMedCrossRefGoogle Scholar
  39. Porteous LA, Armstrong JL, Seidler RJ, Watrud LS (1994) An effective method to extract DNA from environmental samples for polymerase chain reaction amplification and DNA fingerprint analysis. Curr Microbiol 29:301–307PubMedCrossRefGoogle Scholar
  40. Prasanna R, Jaiswal P, Nayak S, Sood A, Kaushik BD (2009) Cyanobacterial diversity in the rhizosphere of rice and its ecological significance. Indian J Microbiol 49:89–97CrossRefGoogle Scholar
  41. Price MN, Dehal PS, Arkin AP (2009) FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 26:1641–1650PubMedCrossRefGoogle Scholar
  42. Rivera-Aguilar V, Godinez-Alvarez H, Moreno-Torres R, Rodriguez-Zaragoza S (2009) Soil physico-chemical properties affecting the distribution of biological soil crusts along an environmental transect at Zapotitlan drylands. Mexico J Arid Environ 73:1023–1028CrossRefGoogle Scholar
  43. Roesch LF, Fulthorpe RR, Riva A, Casella G, Hadwin AK, Kent AD, Daroub SH, Camargo FA, Farmerie WG, Triplett EW (2007) Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J 1:283–290PubMedGoogle Scholar
  44. Rosselló-Mora R, Aman R (2001) The species concept for prokaryotes. FEMS Microbiol Rev 25:39–67PubMedCrossRefGoogle Scholar
  45. Saul-Tcherkas V, Steinberger Y (2011) Soil microbial diversity in the vicinity of a Negev Desert shrub-Reaumuria negevensis. Microb Ecol 61:64–81PubMedCrossRefGoogle Scholar
  46. Schloss PD, Handelsman J (2005) Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71:1501–1506PubMedCrossRefGoogle Scholar
  47. Schloss PD, Handelsman J (2006) Toward a census of bacteria in soil. PLoS Comput Biol 2:e92PubMedCrossRefGoogle Scholar
  48. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF (2009) Introducing MOTHUR: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541PubMedCrossRefGoogle Scholar
  49. Sergeeva E, Liaimer A, Bergman B (2002) Evidence for production of the phytohormone indole-3-acetic acid by cyanobacteria. Planta 215:229–238PubMedCrossRefGoogle Scholar
  50. Singleton DR, Furlong MA, Rathbun SL, Whitman WB (2001) Quantitative comparisons of 16S rDNA sequence libraries from environmental samples. Appl Environ Microbiol 67:4373–4376CrossRefGoogle Scholar
  51. Smith CE (1965) Flora Tehuacán Valley. Fieldiana Botany 31:101–143Google Scholar
  52. Somers E, Vanderleyden J, Srinivasan M (2004) Rhizosphere bacterial signalling: a love parade beneath our feet. Crit Rev Microbiol 30:205–240PubMedCrossRefGoogle Scholar
  53. Tamames J, Abellán JJ, Pignatelli M, Camacho A, Moya A (2010) Environmental distribution of prokaryotic taxa. BMC Microbiol 10:85PubMedCrossRefGoogle Scholar
  54. Tarlera S, Jangid K, Ivester AH, Whitman WB, Williams MA (2008) Microbial community succession and bacterial diversity in soils during 77,000 years of ecosystem development. FEMS Microbiol Ecol 64:129–140PubMedCrossRefGoogle Scholar
  55. Tracy CR, Streten-Joyce C, Dalton R, Nussear KE, Gibb KS, Christian KA (2010) Microclimate and limits to photosynthesis in a diverse community of hypolithic cyanobacteria in northern Australia. Environ Microbiol 12:592–607PubMedCrossRefGoogle Scholar
  56. van Dillewijn P, Villadas PJ, Toro N (2002) Effect of a Sinorhizobium meliloti strain with a modified putA gene on the rhizosphere microbial community of alfalfa. Appl Environ Microbiol 68:4201–4208PubMedCrossRefGoogle Scholar
  57. Vessey JK (2003) Plant growth promoting rhizobacteria as biofertilizers. Plant Soil 255:571–586CrossRefGoogle Scholar
  58. Villadas PJ, Fernández-López M, Ramírez-Saad H, Toro N (2007) Rhizosphere-bacterial community in Eperua falcata (Caesalpiniaceae) a putative nitrogen-fixing tree from French Guiana rainforest. Microb Ecol 53:317–327PubMedCrossRefGoogle Scholar
  59. Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. App Environ Microbiol 73:5261–5267CrossRefGoogle Scholar
  60. Warren-Rhodes KA, Rhodes KL, Pointing SB, Ewing SA, Lacap DC, Gomez-Silva B, Amundson R, Friedmann EI, McKay CP (2006) Hypolithic cyanobacteria, dry limit of photosynthesis, and microbial ecology in the hyperarid Atacama Desert. Microb Ecol 52:389–398PubMedCrossRefGoogle Scholar
  61. 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 60:730–739PubMedCrossRefGoogle Scholar
  62. Yarza P, Ludwig W, Euzéby J, Amann R, Schleifer KH, Glöckner FO, Rosselló-Mora R (2010) Update of the all-species living tree project based on 16S and 23S rRNA sequence analyses. Syst Appl Microbiol 33:291–299PubMedCrossRefGoogle Scholar
  63. Youssef N, Sheik CS, Krumholz LR, Najar FZ, Roe BA, Elshahed MS (2009) Comparison of species richness estimates obtained using nearly complete fragments and simulated pyrosequencing-generated fragments in 16S rRNA gene-based environmental surveys. Appl Environ Microbiol 75:5227–5236PubMedCrossRefGoogle Scholar
  64. Zhou J, Xia B, Treves DS, Wu LY, Marsh TL, O’Neill RV, Palumbo AV, Tiedje JM (2002) Spatial and resource factors influencing high microbial diversity in soil. Appl Environ Microbiol 68:326–334PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2012

Authors and Affiliations

  • G. Torres-Cortés
    • 1
    • 3
  • V. Millán
    • 1
  • A. J. Fernández-González
    • 1
  • J. F. Aguirre-Garrido
    • 2
  • H. C. Ramírez-Saad
    • 2
  • M. Fernández-López
    • 1
  • N. Toro
    • 1
  • F. Martínez-Abarca
    • 1
  1. 1.Departamento de Microbiología y Sistemas Simbióticos, Estación Experimental del ZaidínConsejo Superior de Investigaciones CientíficasGranadaSpain
  2. 2.Departamento de Sistemas BiológicosUniversidad Autónoma MetropolitanaMéxicoMexico
  3. 3.GeneticsUniversity of Munich (LMU)MartinsriedGermany

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