Bacterial community structure in the rhizosphere of three cactus species from semi-arid highlands in central Mexico

Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology

Volumn 101, Issue 4, 2012, Pages 891-904

  Aguirre Garrido, J Félix ^a   Montiel Lugo, Daniel ^a   Hernández Rodríguez, César ^b   Torres Cortes, Gloria ^c   Millán, Vicenta ^c   Toro, Nicolás ^c   Martínez Abarca, Francisco ^c   Ramírez Saad, Hugo C ^a  

^a DEPARTAMENTO DE SISTEMAS BIOLÓGICOS   (Mexico)

^b INSTITUTO POLITÉCNICO NACIONAL   (Mexico)

^c CSIC   (Spain)

Author keywords

Cactus; DGGE; Mammillaria; Metagenomic rhizosphere and NifH; Opuntia; Rhizosphere; SARST; Stenocereus

Indexed keywords

RNA 16S;

ACIDOBACTERIUM; ACTINOBACTERIA; AEROBIC BACTERIUM; ALPHAPROTEOBACTERIA; ARTICLE; BACTERIUM ISOLATE; CACTUS; COLONY FORMING UNIT; CONTROLLED STUDY; CULTURE MEDIUM; DENATURING GRADIENT GEL ELECTROPHORESIS; FIRMICUTES; FLORA; GENUS; HETEROTROPH; MAMMILLARIA CARNEA; MEXICO; MICROBIAL COMMUNITY; NITROGEN FIXATION; NONHUMAN; NUCLEOTIDE SEQUENCE; OCHROBACTRUM; OPUNTIA; OPUNTIA PILIFERA; PLANT; PRIORITY JOURNAL; PROTEOBACTERIA; RHIZOSPHERE; RNA SEQUENCE; SEASON; SEMIARID CLIMATE; SPECIES CULTIVATION; SPECIES ENDEMICITY; STENOCEREUS STELLATUS; XEROPHYTE;

BACTERIA; BIOTA; CACTACEAE; CLUSTER ANALYSIS; DNA, BACTERIAL; DNA, RIBOSOMAL; MEXICO; MOLECULAR SEQUENCE DATA; PHYLOGENY; PLANT ROOTS; RHIZOSPHERE; RNA, RIBOSOMAL, 16S; SEASONS; SEQUENCE ANALYSIS, DNA;

ACIDOBACTERIA; ACTINOBACTERIA; BACTERIA (MICROORGANISMS); CACTACEAE; FIRMICUTES; MAMMILLARIA; MAMMILLARIA CARNEA; OCHROBACTRUM; OPUNTIA; PILIFERA; PROTEOBACTERIA; STENOCEREUS; STENOCEREUS STELLATUS;

EID: 84862687738     PISSN: 00036072     EISSN: 15729699     Source Type: Journal    
DOI: 10.1007/s10482-012-9705-3     Document Type: Article

References (53)

1. 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 60:453-461
2. Bais HP, Weir TL, Perry LG, Gilroy S, Vivanco JM (2006) The role of root exudates in rhizosphere interactions with plants and other organisms. Annu Rev Plant Biol 57:234-266
3. Bashan Y, Rojas A, Puente ME (1999) Improved establishment and development of three cacti species inoculated with Azospirillum brasiliense transplanted into disturbed urban desert soil. Can J Microbiol 45:441-451
4. 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 68:1-13
5. Caballero JM, Onofre J, de los Santos P, Martinez L (2007) The tomato rhizosphere, an environment rich in nitrogen-fixing burkholderia species with capabilities of interest for agriculture and bioremediation. Appl Environ Microbiol 73:5308-5319 (Pubitemid 47326664)
6. Carrillo-García A, Bashan Y, Díaz-Rivera E, Bethlenfalvay GJ (2000) Effects of resource-islands soils, competition and inoculation with Azospirillum on survival and growth of Pachycereus pringlei, the giant cactus of the Sonoran desert. Restor Ecol 8:65-73 (Pubitemid 30306283)
7. Casas A, Barbera G (2002). Mesoamerican domestication and diffusion. In: Park S Nobel (ed) Cacti: Biology and uses, University of California Press. USA, pp 143-162
8. Chakraborty U, Chakraborty BN, Basnet M, Chakraborty AP (2009) Evaluation of Ochrobactrum anthropi TRS-2 and its talc based formulation for enhancement of growth of tea plants and management of brown root rot disease. J Appl Microbiol 107:625-634
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 8:514-525
10. Chun J, Lee JH, Jung Y, Kim M, Kim S, Kim BK, Lim YW (2007) EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 57:2259-2261 (Pubitemid 350031697)
11. Dávila P, Arizmendi M, Valiente-Banuet A, Villaseñor J, Casas A, Lira R (2002) Biological diversity in the Tehuacan-Cuicatlan valley. Mex Biodivrs Conserv 11:421-442
12. Enge K, Whiteford S (1989) The keepers of water and earth: Mexican rural social organization and irrigation, pp 179-222. University of Texas Press, Austin
13. Felsenstein J. (1993). Phylip (Phylogeny Inference Package) version 3.57c. Dept. of Genetics, University of Washington, Seattle. http://evolution.genetics.washington.edu/phylip.html
14. Felske A, Engelen B, Nübel U, Backhaus H (1996) Direct ribosome isolation from soil to extract bacterial rRNA for community analysis. Appl Environ Microbiol 62:4162-4167 (Pubitemid 26371520)
15. Haichar FE, Marol C, Berge O, Rangel-Castro JI, Prosser JI, Balesdent J, Heulin T, Achouak W (2008) Plant host habitat and root exudates shape soil bacterial community structure. ISME J 2:1221-1230
16. Herman RP, Provencio K, Torrez R, Seager GM (1994) Seasonal and spatial population dynamics of the nitrogenefficient guild in a desert Baja grassland. Appl Environ Microbiol 60:1160-1165 (Pubitemid 24113930)
17. Holland S (2003) Analytic Rarefaction. http://www.uga.edu/strata/ software/index.html
18. Huber T, Faulkner G, Hugenholtz P (2004) Bellerophon; a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20:2317-2319 (Pubitemid 39341624)
19. Instituto Nacional de Estadística, Geografía e Informática (2005) Carta Topográfica, 1:250,000. Oaxaca, E 14-9. (INEGI). www.inegi.org.mx
20. Jones K, Bangs D (1985) Nitrogen fixation by free living heterotrophic bacteria in oak forest: the effect of liming. Soil Biol Biochem 17:705-709
21. Kempers AJ (1974) Determination of sub-microquantities of ammonium and nitrates in soils with phenol, sodium nitroprusside and hypochlorite. Geoderma 12:201-206
22. Kumar S, Dudley J, Nei M, Tamura K (2008) MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform 9:299-306 (Pubitemid 351890826)
23. Kysela DT, Palacios C, Sogin ML (2005) Serial analysis of V6 ribosomal sequence tags (SARST-V6): a method for efficient, high-throughput analysis of microbial community composition. Environ Microbiol 7:356-364 (Pubitemid 40290124)
24. Lebuhn M, Achouak W, Schloter M, Berge O, Meier H, Barakat M, Hartmann A, Heulin T (2000) Taxonomic characterization of Ochrobactrum sp. isolates from soil samples and wheat roots, and description of Ochrobactrum tritici sp. nov. and Ochrobactrum grignonense sp. nov. Int J Syst Evol Microbiol 50:2207-2223 (Pubitemid 32049574)
25. López-Galindo F, Muñoz-Iniestra D, Hernández-Moreno M, Soler-Aburto A, Castillo López MC, Hernández-Arzate I (2003) Análisis integral de la toposecuencia y su influencia en la distribución de la vegetación y la degradación del suelo en la subcuenca de Zapotitlán de las Salinas, Puebla. Boletín de la Sociedad Geológica Mexicana LVI, pp 19-41
26. Mnasri B, Tajini F, Trabelsi M, Aouani ME, Mhamdi R (2007) Rhizobium gallicum as an efficient symbiont for bean cultivation. Agron Sustain Dev 27:331-336 (Pubitemid 350308273)
27. Muyzer G, Brinkhoff T, Nübel U, Santegoeds C, Schäfer H, Wawer C (1998) Denaturing Gradient Gel Electrophoresis (DGGE) in Microbial Ecology. Chap. 3.4.4. In: Akkermans ADL, van Elsas JD, de Bruijn FJ (eds) Molecular Microbial Ecology Manual. Kluwer Academic Publishers, Dordrecht, pp 1-27
28. Ngom A, Nakagawa Y, Sawada H, Tsukahara J, Wakabayashi S, Uchiumi T, Nuntagij A, Kotepong S, Suzuki A, Higashi S, Abe M (2004) A novel symbiotic nitrogen-fixing member of the Ochrobactrum clade isolated from root nodules of Acacia mangium. J Gen Appl Microbiol 50:17-27 (Pubitemid 38519461)
29. Nunan N, Daniell TJ, Singh BK, Papert A, McNicol JW, Prosser JI (2005) Links between plant and rhizoplane bacterial communities in grassland soils, characterized using molecular techniques. Appl Environ Microbiol 71:6784-6792 (Pubitemid 43194165)
30. Príncipe A, Alvarez F, Castro MG, Zachi L, Fischer SE, Mori GB, Jofr E (2007) Biocontrol and PGPR features in native strains isolated from saline soils of Argentina. Curr Microbiol 55:314-322 (Pubitemid 47460530)
31. Puente ME, Bashan Y (1993) Effect of inoculation with Azospirillum brasilense strains on the germination and seedlings growth of the giant columnar Cardon cactus (Pachycereus pringlei). Symbiosis 15:49-60
32. Puente ME, Ching Li Y, Bashan Y (2009) Rock-degrading endophytic bacteria in cacti. Environ Exp Bot 66:389-401
33. Ramírez-Saad H, Akkermans W, Akkermans ADL (1996) DNA Extraction from Actinorhizal Nodules. Chap. 1.4.4. In: Manual Molecular Microbial Ecology, Akkermans ADL, van Elsas JD, de Bruijn F (eds) Kluwer Academic Publishers. The Netherlands, Dordrecht, pp 1-11
34. Ramírez-Saad HC, Janse J, Akkermans ADL (1998) Root nodules of Ceanothus caeruleus contain both the N2-fixing Frankia endophyte and a phylogenetically related Nod-/Fix-actinomycete. Can J Microbiol 44:140-148
35. Ramírez-Saad HC, Sessitsch A, de Vos WM, Akkermans ADL (2000) Bacterial community changes and enrichment of uncultured Burkholderia-like bacteria induced by chlorinated benzoates in a Peat-forest soil-microcosm. Syst Appl Microbiol 23:591-598 (Pubitemid 32110952)
36. Recagno E (2001) Conocimiento y conservación de las Mamilarias endémicas del valle de Tehuacán-Cuicatlán. Informe de Proyecto R166, CONABIO, Mexico pp 3-7
37. Rennie RJ (1981) A single medium for the isolation of acetylene reducing (dinitrogen fixing) bacteria from soil. Can J Microbiol 27:8-14 (Pubitemid 11100677)
38. Ros M, Pascual JA, Moreno JL, Hernandez MT, Garcia C (2009) Evaluation of microbial community activity, abundance and structure in a semiarid soil under cadmium pollution at laboratory level. Water Air Soil Pollut 203:229-242
39. Rosselló-Mora R, Aman R (2001) The species concept for prokaryotes. FEMS Microbiol Rev 25:39-67 (Pubitemid 32057196)
40. Rzedowski J (1991) Diversidad y orígenes de la flora fanerogámica de México. Acta Bot Mex 14:3-21
41. Sanguinetti CJ, Dias Nieto E, Simpson AJG (1994) Rapid silver staning and recovery of PCR products separated on polyacrilamyde gels. Biotechniques 17:915-919
42. 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 (Pubitemid 39279626)
43. Singleton DR, Furlong MA, Rathbun SL, Whitman WB (2001) Quantitative comparison of 16S rRNA gene sequence libraries from enviromental samples. Appl Environ Microbiol 67:4374-4376 (Pubitemid 33641744)
44. Sliwinski MK, Goodman RM (2003) Comparison of Crenarchaeal consortia inhabiting the rhizosphere of diverse terrestrial plants with those in bulk soil in native environments. Appl Environ Microbiol 70:1821-1826 (Pubitemid 38365168)
45. Smalla K, Wieland G, Buchner A, Zock A, Parzy J, Kaiser S, Roskot N, Heuer H, Berg G (2001) Bulk and rhizosphere soil bacterial communities studied by denaturing gradient gel electrophoresis: plant-dependent enrichment and seasonal shifts revealed. Appl Environ Microbiol 67:4742-4751 (Pubitemid 33646108)
46. Somers E, Vanderleyden J, Srinivisam M (2004) Rhizosphere bacterial signaling: a love parade beneath our feet. Crit Rev Microbiol 30:205-240 (Pubitemid 39557581)
47. Stotzky G (1997) Soil as an Environment for Microbial Life. In: Van Elsas JD, Trevors JT, Wellington EMH (eds) Modern Soil Microbiology, pp 1-20. Marcel Dekker Inc, New York
48. Tripathi AK, Verma SC, Chowdhury SP, Lebuhn M, Gattinger A, Schloter M (2006) Ochrobactrum oryzae sp. nov., an endophytic bacterial species isolated from deep-water rice in India. Int J Syst Evol Microbiol 56:1677-1680 (Pubitemid 44097183)
49. Trubat R, Cortina J, Vilagrosa A (2010) Nursery fertilization affects seedling traits but not field performance in Quercus suber L. J Arid Environ 74:491-497
50. Trujillo ME, Willems A, Abril A, Planchuelo AM, Rivas R, Ludeña D, Mateos PF, Martínez-Molina E, Velázquez E (2005) Nodulation of Lupinus albus by strains of Ochrobactrum lupini sp. nov. Appl Environ Microbiol 71:1318-1327 (Pubitemid 40396671)
51. Yechieli A, Oren A, Yair A (1995) The effect of water distribution on bacterial numbers and microbial activity along a hill slope, northern Negev. Isr Adv Geoecol 28:193-207
52. Zhang Z, Schwartz S, Wagner L, Miller W (2000) A greedy algorithm for aligning DNA sequences. J Comput Biol 7:203-214 (Pubitemid 30412170)
53. Zurdo-Piñeiro JL, Rivas R, Trujillo ME, Vizcaíno N, Carrasco JA, Chamber M, Palomares A, Mateos PF, Martínez-Molina E, Velázquez E (2007) Ochrobactrum cytisi sp. nov., isolated from nodules of Cytisus scoparius in Spain. Int J Syst Evol Microbiol 57:784-788 (Pubitemid 46711960)