Skip to main content
SpringerLink
Log in

Phylogenetic analysis of the archaeal community in an alkaline-saline soil of the former lake Texcoco (Mexico)

  • Original Paper
  • Published:
Extremophiles Aims and scope Submit manuscript

Abstract

The soil of the former lake Texcoco is an extreme environment localized in the valley of Mexico City, Mexico. It is highly saline and alkaline, where Na+, Cl−, HCO −3 and CO 2−3 are the predominant ions, with a pH ranging from 9.8 to 11.7 and electrolytic conductivities in saturation extracts from 22 to 150 dS m−1. Metagenomic DNA from the archaeal community was extracted directly from soil and used as template to amplify 16S ribosomal gene by PCR. PCR products were used to construct gene libraries. The ribosomal library showed that the archaeal diversity included Natronococcus sp., Natronolimnobius sp., Natronobacterium sp., Natrinema sp., Natronomonas sp., Halovivax sp., “Halalkalicoccus jeotgali” and novel clades within the family of Halobacteriaceae. Four clones could not be classified. It was found that the archaeal diversity in an alkaline-saline soil of the former lake Texcoco, Mexico, was low, but showed yet uncharacterized and unclassified species.

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

Similar content being viewed by others

References

  • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl Acids Res 25:3389–3402

    Article  PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Beltrán-Hernández RI, Coss-Muñoz E, Luna-Guido ML, Mercado-García F, Siebe C, Dendooven L (1999) Carbon and nitrogen dynamics in alkaline saline soil of the former Lake Texcoco (Mexico) as affected by application of sewage sludge. Eur J Soil Sci 50:601–608

    Article  Google Scholar 

  • Beltrán-Hernández RI, Luna-Guido ML, Dendooven L (2007) Emission of carbon dioxide and dynamics of inorganic N in a gradient of alkaline saline soils of the former lake Texcoco. Appl Soil Ecol 35:390–403

    Article  Google Scholar 

  • Benlloch S, Lopez-Lopez A, Casamayor EO, Ovreas L, Goddard V, Daae FL, Smerdon G, Massana R, Joint I, Thingstad F, Pedros-Alio C, Rodriguez-Valera F (2002) Prokaryotic genetic diversity throughout the salinity gradient of a coastal solar saltern. Environ Microbiol 4:349–360

    Article  PubMed  Google Scholar 

  • Castillo AM, Gutierrez MC, Kamekura M, Ma Y, Cowan DA, Jones BE, Grant WD, Ventosa A (2006) Halovivax asiaticus gen. nov., sp. nov., a novel extremely halophilic archaeon isolated from Inner Mongolia, China. Int J Syst Evol Micr 56:765–770

    Article  CAS  Google Scholar 

  • Cole JR, Chai B, Marsh TL, Farris RJ, Wang Q, Kulam SA, Chandra S, McGarrell DM, T. Schmidt M, Garrity GM, Tiedje JM (2003) The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucl Acids Res 31:442–443

    Article  PubMed  CAS  Google Scholar 

  • Conde E, Cardenas M, Ponce-Mendoza A, Luna-Guido ML, Cruz-Mondragon C, Dendooven L (2005) The impacts of inorganic nitrogen application on mineralization of 14C-labelled maize and glucose, and on priming effect in saline alkaline soil. Soil Biol Biochem 37:681–691

    Article  CAS  Google Scholar 

  • Cytryn E, Minz D, Oremland RS, Cohen Y (2000) Distribution and diversity of archaea corresponding to the limnological cycle of a hypersaline stratified lake (Solar Lake, Sinai, Egypt). Appl Environ Microbiol 66:3269–3276

    Article  PubMed  CAS  Google Scholar 

  • Demergasso C, Casamayor EO, Chong G, Galleguillos P, Escudero L, Pedros-Alio C (2004) Distribution of prokaryotic genetic diversity in athalassohaline lakes of the Atacama Desert, Northern Chile. FEMS Microbiol Ecol 48:57–69

    Article  CAS  PubMed  Google Scholar 

  • Desmarais D, Jablonski PE, Fedarko NS, Roberts MF (1997) 2-Sulfotrehalose, a novel osmolyte in haloalkaliphilic archaea. J Bacteriol 179:3146–3153

    PubMed  CAS  Google Scholar 

  • Dojka MA, Harris JK, Pace NR (2000) Expanding the known diversity and environmental distribution of an uncultured phylogenetic division of Bacteria. Appl Environ Microbiol 66:1617–1621

    Article  PubMed  CAS  Google Scholar 

  • Dojka MA, Hugenholtz P, Haack SK, Pace NR (1998) Microbial diversity in a hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation. Appl Environ Microbiol 64:3869–3877

    PubMed  CAS  Google Scholar 

  • Duckworth AW, Grant WD, Jones BE, van Steenbergen R (1996) Phylogenetic diversity of soda lake alkaliphiles. FEMS Microbiol Ecol 19:181–191

    Article  CAS  Google Scholar 

  • Feng J, Zhou P, Zhou Y-G, Liu S-J, Warren-Rhodes K (2005) Halorubrum alkaliphilum sp. nov., a novel haloalkaliphile isolated from a soda lake in Xinjiang, China. Int J Syst Evol Microbiol 55:149–152

    Article  PubMed  CAS  Google Scholar 

  • Grant S, Sorokin DY, Grant WD, Jones BE, Heaphy S (2004) A phylogenetic analysis of Wadi el Natrun soda lake cellulase enrichment cultures and identification of cellulase genes from these cultures. Extremophiles 8:421–429

    Article  PubMed  CAS  Google Scholar 

  • Guo C, Sun W, Harsh JB, Ogram A (1997) Hybridization analysis of microbial DNA from fuel oil-contaminated and noncontaminated soil. Microb Ecol 34:178–187

    Article  PubMed  CAS  Google Scholar 

  • Hezayen FF, Tindall BJ, Steinbuchel A, Rehm BHA (2002) Characterization of a novel halophilic archaeon, Halobiforma haloterrestris gen. nov., sp. nov. and transfer of Natronobacterium nitratireducens to Halobiforma nitratireducens comb. nov. Int J Syst Evol Micr 52:2271–2280

    Article  CAS  Google Scholar 

  • Hugenholtz P, Goebel BM, Pace NR (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180:4765–4774

    PubMed  CAS  Google Scholar 

  • Humayoun SB, Bano N, Hollibaugh JT (2003) Depth distribution of microbial diversity in mono lake, a meromictic soda lake in California. Appl Environ Microbiol 69:1030–1042

    Article  PubMed  CAS  Google Scholar 

  • Itoh T, Yamaguchi T, Zhou P, Takashina T (2005) Natronolimnobius baerhuensis gen. nov., sp. nov. and Natronolimnobius innermongolicus sp. nov., novel haloalkaliphilic archaea isolated from soda lakes in Inner Mongolia, China. Extremophiles 9:111–116

    Article  PubMed  CAS  Google Scholar 

  • Jan Roblero J, Magos X, Hernández-Rodríguez C, Le Borgne S (2004) Phylogenic analysis of bacterial populations in waters of the former Texcoco Lake, Mexico. Can J Microbial 50:1049–1059

    Article  CAS  Google Scholar 

  • Jiang H, Dong H, Yu B, Liu X, Li Y, Ji S, Zhang CL (2007) Microbial response to salinity change in Lake Chaka, a hypersaline lake on Tibetan plateau. Environ Microbiol 9:2603–2621

    Article  PubMed  CAS  Google Scholar 

  • Kamekura M, Dyall-Smith ML (1995) Taxonomy of the family halobacteriaceae and the description of two new genera Halorubrobacterium and Natrialba. J Gen Appl Microbiol 41:333–350

    Article  CAS  Google Scholar 

  • Kamekura M, Dyall-Smith ML, Upasani V, Ventosa A, Kates M (1997) Diversity of alkaliphilic halobacteria: proposals for transfer of Natronobacterium vacuolatum, Natronobacterium magadii, and Natronobacterium pharaonis to Halorubrum, Natrialba, and Natronomonas gen. nov., respectively, as Halorubrum vacuolatum comb. nov., Natrialba magadii comb. nov., and Natronomonas pharaonis comb. nov., respectively. Int J Syst Bacteriol 47:853–857

    PubMed  CAS  Google Scholar 

  • Kanal H, Kobayashi T, Aono R, Kudo T (1995) Natronococcus amylolyticus sp. nov., a haloalkaliphilic archaeon. Int J Syst Bacteriol 45:762–766

    PubMed  CAS  Google Scholar 

  • Koizumi Y, Kojima H, Oguri K, Kitazato H, Fukui M (2004) Vertical and temporal shifts in microbial communities in the water column and sediment of saline meromictic Lake Kaiike (Japan), as determined by a 16S rRNA-based analysis and related to physicochemical gradients. Environ Microbiol 6:622–637

    Article  PubMed  CAS  Google Scholar 

  • Kumar S, Tamura K, Jakobsen I, Nei M (2001) MEGA2: molecular evolutionary genetics analysis software. Arizona State University, Tempe

    Google Scholar 

  • Lizama C, Monteoliva-Sanchez M, Prado B, Ramos-Cormenzana A, Weckesser J, Campos V (2001) Taxonomic study of extreme halophilic archaea isolated from the “Salar de Atacama”, Chile. Syst Appl Microbiol 24:464–474

    Article  PubMed  CAS  Google Scholar 

  • Luna-Guido ML, Beltrán-Hernández RI, Dendooven L (2001) Dynamics of 14C-labelled glucose in alkaline saline soil. Soil Biol Biochem 33:707–719

    Article  CAS  Google Scholar 

  • Luna-Guido ML, Beltrán-Hernández RI, Solís-Ceballos NA, Hernández-Chávez N, Mercado-García F, Catt JA, Olalde-Portugal V, Dendooven1 L (2000) Chemical and biological characteristics of alkaline saline soils from the former Lake Texcoco as affected by artificial drainage. Biol Fert Soils 32:102–108

    Article  CAS  Google Scholar 

  • Ma Y, Zhang W, Xue Y, Zhou P, Ventosa A, Grant W (2004) Bacterial diversity of the Inner Mongolian Baer Soda Lake as revealed by 16S rRNA gene sequence analyses. Extremophiles 8:45–51

    Article  PubMed  CAS  Google Scholar 

  • Maturrano L, Santos F, Rossello-Mora R, Anton J (2006) Microbial diversity in Maras Salterns, a hypersaline environment in the peruvian andes. Appl Environ Microbiol 72:3887–3895

    Article  PubMed  CAS  Google Scholar 

  • McGenity TJ, Gemmell RT, Grant WD (1998) Proposal of a new halobacterial genus Natrinema gen. nov., with two species Natrinema pellirubrum nom. nov. and Natrinema pallidum nom. nov. Int J Syst Bacteriol 48:1187–1196

    Article  PubMed  Google Scholar 

  • Nuttall SD, Dyall-Smith ML (1993) Ch2, a novel halophilic archaeon from an Australian solar saltern. Int J Syst Bacteriol 43:729–734

    PubMed  CAS  Google Scholar 

  • Ochsenreiter T, Pfeifer F, Schleper C (2002) Diversity of Archaea in hypersaline environments characterized by molecular-phylogenetic and cultivation studies. Extremophiles 6:267–274

    Article  PubMed  CAS  Google Scholar 

  • Rossello-Mora R, Amann R (2001) The species concept for prokaryotes. FEMS Microbiol Rev 25:39–67

    Article  PubMed  CAS  Google Scholar 

  • Sambrook J, Fritseh EF, Maniatis T (1989) Molecular cloning: a laboratory manual. 2nd ed. Cold Spring Harbor Laboratory, New York, pp I.25–I.28

    Google Scholar 

  • Stackebrandt E, Goebel BM (1994) Taxonomic note: a place for DNA–DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44:846–849

    CAS  Google Scholar 

  • Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10:512–526

    PubMed  CAS  Google Scholar 

  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl Acids Res 25:4876–4882

    Article  PubMed  CAS  Google Scholar 

  • Tian X, Xu Y, Liu H, Zhou P (1997) New species of Natronobacterium. Acta Microbiol Sin 37:1–6

    CAS  Google Scholar 

  • Tindall BJ (2004) Prokaryotic diversity in the antarctic: The Tip of the Iceberg. Microb Ecol 47:271–283

    Article  PubMed  CAS  Google Scholar 

  • Vega-Jarquin C, Garcia-Mendoza M, Jablonowski N, Luna-Guido M, Dendooven L (2003) Rapid immobilization of applied nitrogen in saline–alkaline soils. Plant Soil 256:379–388

    Article  CAS  Google Scholar 

  • Vreeland R, Straight S, Krammes J, Dougherty K, Rosenzweig W, Kamekura M (2002) Halosimplex carlsbadense gen. nov., sp. nov., a unique halophilic archaeon, with three 16S rRNA genes, that grows only in defined medium with glycerol and acetate or pyruvate. Extremophiles 6:445–452

    Article  PubMed  CAS  Google Scholar 

  • Walsh DA, Papke RT, Doolittle WF (2005) Archaeal diversity along a soil salinity gradient prone to disturbance. Environ Microbiol 7:1655–1666

    Article  PubMed  CAS  Google Scholar 

  • Ward DM, Weller R, Bateson MM (1990) 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 345:63–65

    Article  PubMed  CAS  Google Scholar 

  • Xue Y, Fan H, Ventosa A, Grant WD, Jones BE, Cowan DA, Ma Y (2005) Halalkalicoccus tibetensis gen. nov., sp. nov., representing a novel genus of haloalkaliphilic archaea. Int J Syst Evol Micr 55:2501–2505

    Article  CAS  Google Scholar 

  • Yang Y, Cui H-L, Zhou P-J, Liu SJ (2006) Halobacterium jilantaiense sp. nov., a halophilic archaeon isolated from a saline lake in Inner Mongolia, China. Int J Syst Evol Microbiol 56:2353–2355

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

This work was funded by “Secretaria de medio ambiente y recursos naturals” (SEMARNAT) project SEMARNAT-2004-C01-257 and “Consejo Nacional de Ciencia y Tecnología” (CONACYT) project SEP-2004-C01-479991.I.N. -G. received a postdoctoral grant from Cinvestav while C.V. -E. and R.A. -H. received grant-aided support from CONACYT.

Author information

Authors and Affiliations

  1. Departamento de Biotecnología y Bioingeniería, Cinvestav, Campus Zacatenco, Apartado Postal 14-740, Mexico, DF, 07360, Mexico

    César Valenzuela-Encinas, Isabel Neria-González, Rocio J. Alcántara-Hernández, J. Arturo Enríquez-Aragón, César Hernández-Rodríguez, Luc Dendooven & Rodolfo Marsch

  2. Departamento de Biotecnología y Ciencias Alimentarias, Instituto Tecnológico de Sonora, México, Cd. Obregon, Sonora, 85000, Mexico

    Isabel Estrada-Alvarado

Authors
  1. César Valenzuela-Encinas
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Isabel Neria-González
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Rocio J. Alcántara-Hernández
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. J. Arturo Enríquez-Aragón
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Isabel Estrada-Alvarado
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. César Hernández-Rodríguez
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Luc Dendooven
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Rodolfo Marsch
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Rodolfo Marsch.

Additional information

Communicated by K. Horikoshi.

César Valenzuela-Encinas and Isabel Neria-González contributed equally to this publication.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Valenzuela-Encinas, C., Neria-González, I., Alcántara-Hernández, R.J. et al. Phylogenetic analysis of the archaeal community in an alkaline-saline soil of the former lake Texcoco (Mexico). Extremophiles 12, 247–254 (2008). https://doi.org/10.1007/s00792-007-0121-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00792-007-0121-y

Keywords

Search

Navigation