Changes in the bacterial populations of the highly alkaline saline soil of the former lake Texcoco (Mexico) following flooding

Extremophiles

Volumn 13, Issue 4, 2009, Pages 609-621

  Valenzuela Encinas, César ^a   Neria González, Isabel ^a   Alcántara Hernández, Rocio J ^a   Estrada Alvarado, Isabel ^b   Zavala Díaz de la Serna, Francisco Javier ^a   Dendooven, Luc ^a   Marsch, Rodolfo ^a  

^a DEPARTAMENTO DE FÍSICA   (Mexico)

^b INSTITUTO TECNOLÓGICO DE SONORA   (Mexico)

Author keywords

16S rDNA; Alkaline saline soil; Bacterial community; Clone library

Indexed keywords

ACIDOBACTERIA; ACTINOBACTERIA; ACTINOMYCETALES; BACTERIA (MICROORGANISMS); BACTEROIDETES; BURKHOLDERIALES; CLOSTRIDIALES; CYANOBACTERIA; FIRMICUTES; GAMMAPROTEOBACTERIA; MYXOCOCCALES; OSCILLATORIALES; PROTEOBACTERIA; PSEUDOMONADALES; RHIZOBIALES; RHODOBACTERALES; RHODOSPIRILLALES; SPHINGOBACTERIALES; SPHINGOMONADALES; XANTHOMONADALES;

EID: 70349443435     PISSN: 14310651     EISSN: 14334909     Source Type: Journal    
DOI: 10.1007/s00792-009-0244-4     Document Type: Article

References (80)

1. Abed RMM, Kohls K, de Beer D (2007) Effect of salinity changes on the bacterial diversity, photosynthesis and oxygen consumption of cyanobacterial mats from an intertidal flat of the Arabian Gulf. Environ Microbiol 9:1384-1392
2. Ait Tayeb L, Ageron E, Grimont F, Grimont PAD (2005) Molecular phylogeny of the genus Pseudomonas based on rpoB sequences and application for the identification of isolates. Res Microbiol 156:763-773
3. Alazard D, Badillo C, Fardeau M, Cayol J, Thomas P, Roldan T, Tholozan JL, Ollivier B (2007) Tindallia texcoconensis sp. nov., a new haloalkaliphilic bacterium isolated from lake Texcoco, Mexico. Extremophiles 11:33-39
4. 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. Nucleic Acids Res 25:3389-3402
5. Arahal D, Ventosa A (2006) The family Halomonadaceae. In: The Prokaryotes, vol 6, 3rd edn, pp 811-835
6. Asker D, Beppu T, Ueda K (2007) Unique diversity of carotenoid-producing bacteria isolated from Misasa, a radioactive site in Japan. Appl Microbiol Biotechnol 77:383-392
7. 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
8. 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
9. Bernard L, Mougel C, Maron PA, Nowak V, Lévêque J, Henault C, Haichar F, Berge O, Marol C, Balesdent J, Gibiat F, Lemanceau P, Ranjard L (2007) Dynamics and identification of soil microbial populations actively assimilating carbon from 13C-labelled wheat residue as estimated by DNA- and RNA-SIP techniques. Environ Microbiol 9:752-764
10. Buonaurio R, Stravato VM, Kosako Y, Fujiwara N, Naka T, Kobayashi K, Cappelli C, Yabuuchi E (2002) Sphingomonas melonis sp. nov., a novel pathogen that causes brown spots on yellow Spanish melon fruits. Int J Syst Evol Microbiol 52:2081-2087
11. Cao X, Liu X, Dong X (2003) Alkaliphilus crotonatoxidans sp. nov., a strictly anaerobic, crotonate-dismutating bacterium isolated from a methanogenic environment. Int J Syst Evol Microbiol 53:971-975
12. Choi DH, Cho BC (2005) Idiomarina seosinensis sp. nov., isolated from hypersaline water of a solar saltern in Korea. Int J Syst Evol Microbiol 55:379-383
13. Cole JR, Chai B, Marsh TL, Farris RJ, Wang Q, Kulam SA, Chandra S, McGarrell DM, 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. Nucleic Acids Res 31:442-443
14. 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
15. De Champs C, Le Seaux S, Dubost JJ, Boisgard S, Sauvezie B, Sirot J (2000) Isolation of Pantoea agglomerans in two cases of septic monoarthritis after plant thorn and wood sliver injuries. J Clin Microbiol 38:460-461
16. Duckworth AW, Grant WD, Jones BE, van Steenbergen R (1996) Phylogenetic diversity of soda lake alkaliphiles. FEMS Microbiol Ecol 19:181-191
17. Edwards U, Rogall T, Blocker H, Emde M, Bottger E (1989) Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA. Nucleic Acids Res 17:7843-7853
18. Egli T, Auling G (2005) Chelatococcus. In: Bergey's Manual® of Systematic Bacteriology, pp 433-437
19. Eichorst SA, Breznak JA, Schmidt TM (2007) Isolation and characterization of soil bacteria that define Terriglobus gen. nov., in the phylum Acidobacteria. Appl Environ Microbiol 73:2708-2717
20. Foti MJ, Sorokin DY, Zacharova EE, Pimenov NV, Kuenen JG, Muyzer G (2008) Bacterial diversity and activity along a salinity gradient in soda lakes of the Kulunda Steppe (Altai, Russia). Extremophiles 12:133-145
21. Francis CA, Obraztsova AY, Tebo BM (2000) Dissimilatory metal reduction by the facultative anaerobe Pantoea agglomerans SP1. Appl Environ Microbiol 66:543-548
22. Gauthier MJ, Lafay B, Christen R, Fernandez L, Acquaviva M, Bonin P, Bertrand JC (1992) Marinobacter hydrocarbonoclasticus gen. nov., sp. nov., a new, extremely halotolerant, hydrocarbon-degrading marine bacterium. Int J Syst Bacteriol 42:568-576
23. Goncalves ER, Rosato YB (2002) Phylogenetic analysis of Xanthomonas species based upon 16S-23S rDNA intergenic spacer sequences. Int J Syst Evol Microbiol 52:355-361
24. González JM, Covert JS, Whitman WB, Henriksen JR, Mayer F, Scharf B, Schmitt R, Buchan A, Fuhrman JA, Kiene RP, Moran MA (2003) Silicibacter pomeroyi sp. nov. and Roseovarius nubinhibens sp. nov., dimethylsulfoniopropionate-demethylating bacteria from marine environments. Int J Syst Evol Microbiol 53:1261-1269
25. Gorlenko V, Tsapin A, Namsaraev Z, Teal T, Tourova T, Engler D, Mielke R, Nealson K (2004) Anaerobranca californiensis sp.nov., an anaerobic, alkalithermophilic, fermentative bacterium isolated froma hot spring on Mono lake. Int J Syst Evol Micriobiol 54:739-743
26. Gutiérrez-Castorena MC, Stoops G, Ortíz-Solorio CA, López-Avila G (2005) Amorphous silica materials in soils and sediments of the Ex-Lago de Texcoco, Mexico: an explanation for its subsidence. Catena 60:205-226
27. Horikoshi K (1999) Alkaliphiles: some applications of their products for biotechnology. Microbiol Mol Biol Rev 63:735-750
28. 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
29. Imhoff JF, Süling J (1996) The phylogenetic relationship among Ectothiorhodospiraceae: a reevaluation of their taxonomy on the basis of 16S rDNA analyses. Arch Microbiol 165:106-113
30. Ivanova EP, Romanenko LA, Chun J, Matte MH, Matte GR, Mikhailov VV, Svetashev VI, Huq A, Maugel T, Colwell RR (2000) Idiomarina gen. nov., comprising novel indigenous deep-sea bacteria from the Pacific Ocean, including descriptions of two species, Idiomarina abyssalis sp. nov. and Idiomarina zobellii sp. nov. Int J Syst Evol Microbiol 50:901-907
31. 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 Microbiol 50:1049-1059
32. Janssen PH (2006) Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl Environ Microbiol 72:1719-1728
33. 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
34. Jones FB, Retting SL, Eugste HP (1967) Silica in alkaline brines. Science 158:1310-1314
35. Kaneko T, Nakamura Y, Sato S, Asamizu E, Kato T, Sasamoto S, Watanabe A, Idesawa K, Ishikawa A, Kawashima K, Kimura T, Kishida Y, Kiyokawa C, Kohara M, Matsumoto M, Matsuno A, Mochizuki Y, Nakayama S, Nakazaki N, Shimpo S, Sugimoto M, Takeuchi C, Yamada M, Tabata S (2000) Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti. DNA Res 7:331-338
36. Kersters K, Vos P, Gillis M, Swings J, Vandamme P, Stackebrandt E (2006) Introduction to the Proteobacteria. In: The Prokaryotes, vol 5, 3rd edn, pp 3-37
37. 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 rDNA-based analysis, and related to physicochemical gradients. Environ Microbiol 6:622-637
38. Kong YH, Beer M, Seviour RJ, Lindrea KC, Rees GA (2002) Role of "G-bacteria" in anaerobic substrate uptake in a SBR with no phosphorus removal. Water Sci Technol 46:171-178
39. Kumar S, Tamura K, Jakobsen I, Nei M (2001) MEGA2: molecular evolutionary genetics analysis software. Arizona State University, Tempe
40. La H-J, Im W-T, Ten LN, Kang MS, Shin D-Y, Lee S-T (2005) Paracoccus koreensis sp. nov., isolated from anaerobic granules in an upflow anaerobic sludge blanket (UASB) reactor. Int J Syst Evol Microbiol 55:1657-1660
41. 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
42. Luna-Guido ML, Beltrán-Hernández RI, Solís-Ceballos NA, Hernández-Chávez N, Mercado-García F, Catt JA, Olalde-Portugal V, Dendooven L (2000) Chemical and biological characteristics of alkaline saline soils from the former Lake Texcoco as affected by artificial drainage. Biol Fertil Soils 32:102-108
43. Luna-Guido ML, Beltrán-Hernández RI, Dendooven L (2001) Dynamics of 14C-labelled glucose in alkaline saline soil. Soil Biol Biochem 33:707-719
44. Ma Y, Xue Y, Grant WD, Collins NC, Duckworth AW, van Steenbergen RP, Jones BE (2004a) Alkalimonas amylolytica gen. nov., sp. nov., and Alkalimonas delamerensis gen. nov., sp. nov., novel alkaliphilic bacteria from soda lakes in China and East Africa. Extremophiles 8:193-200
45. Ma Y, Zhang W, Xue Y, Zhou P, Ventosa A, Grant WD (2004b) Bacterial diversity of the Inner Mongolian Baer Soda Lake as revealed by 16S rRNA gene sequence analysis. Extremophiles 8:45-51
46. Martínez-Cánovas MJ, Bejar V, Martínez-Checa F, Paez R, Quesada E (2004) Idiomarina fontislapidosi sp. nov. and Idiomarina ramblicola sp. nov., isolated from inland hypersaline habitats in Spain. Int J Syst Evol Microbiol 54:1793-1797
47. Maszenan AM, Seviour RJ, Patel BKC, Rees GN, McDougall BM (1997) Amaricoccus gen. nov, a gram-negative coccus occurring in regular packages or tetrads, isolated from activated sludge biomass, and descriptions of Amaricoccus veronensis sp. nov, Amaricoccus tamworthensis sp. nov, Amaricoccus macauensis sp. nov, and Amaricoccus kaplicensis sp. nov. Int J Syst Bacteriol 47:727-734
48. Mesbah N, Abou-El-Ela S, Wiegel J (2007) Novel and unexpected prokaryotic diversity in water and sediments of the alkaline, hypersaline lakes of the Wadi An Natrun, Egypt. Microb Ecol 54:598-617
49. Mohamed NM, Enticknap JJ, Lohr JE, McIntosh SM, Hill RT (2008) Changes in bacterial communities of the marine sponge Mycale laxissima on transfer into aquaculture. Appl Environ Microbiol 74:1209-1222
50. Quaiser A, Ochsenreiter T, Lanz C, Schuster SC, Treusch AH, Eck J, Schleper C (2003) Acidobacteria form a coherent but highly diverse group within the bacterial domain: evidence from environmental genomics. Mol Microbiol 50:563-575
51. Rainey FA, Ward-Rainey N, Gliesche CG, Stackebrandt E (1998) Phylogenetic analysis and intrageneric structure of the genus Hyphomicrobium and the related genus Filomicrobium. Int J Syst Bacteriol 48:635-639
52. Ramana VV, Sasikala C, Ramana CV (2008) Rhodobacter maris sp. nov., a phototrophic alphaproteobacterium isolated from a marine habitat of India. Int J Syst Evol Microbiol 58:1719-1722
53. Rees HC, Grant WD, Jones BE, Heaphy S (2004) Diversity of Kenyan soda lake alkaliphiles assesses by molecular methods. Extremophiles 8:63-71
54. Ridge JP, Lin M, Larsen EI, Fegan M, McEwan AG, Sly LI (2007) A multicopper oxidase is essential for manganese oxidation and laccase-like activity in Pedomicrobium sp. ACM 3067. Environ Microbiol 9:944-953
55. Rossello-Mora R, Amann R (2001) The species concept for prokaryotes. FEMS Microbiol Rev 25:39-67
56. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual. 2nd edn. Cold Spring Harbor Laboratory Press, New York, pp I.25-I.28
57. Santos P, Pinhal I, Rainey FA, Empadinhas N, Costa J, Fields B, Benson R, Veríssimo A, Da Costa MS (2003) Gamma-Proteobacteria Aquicella lusitana gen. nov., sp. nov., and Aquicella siphonis sp. nov. Infect Protozoa and require activated charcoal for growth in laboratory media. Appl Environ Microbiol 69:6533-6540
58. Schloss PD, Handelsman J (2005) Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71:1501-1506
59. Scholten JCM, Joye SB, Hollibaugh JT, Murrell JC (2005) Molecular analysis of the sulfate-reducing and archaeal community in a meromictic soda lake (mono Lake, California) by targeting 16S rRNA, mcrA, apsA and dsrAB genes. Microb Ecol 50:29-39
60. Shrestha PM, Noll M, Liesack W (2007) Phylogenetic identity, growth-response time and rRNA operon copy number of soil bacteria indicate different stages of community succession. Environ Microbiol 9:2464-2474
61. Sorokin DY, Foti M, Pinkart HC, Muyzer G (2007) Sulfur-oxidizing bacteria in Soap Lake (Washington State), a meromictic, halosaline lake with an unprecedented high sulphide content. Appl Environ Microbiol 73:451-455
62. Stevens H, Stubner M, Simon M, Brinkhoff T (2005) Phylogeny of Proteobacteria and Bacteroidetes from oxic habitats of a tidal flat ecosystem. FEMS Microbiol Ecol 54:351-365
63. Sullivan RF, Holtman MA, Zylstra GJ, White JF, Kobayashi DY (2003) Taxonomic positioning of two biological control agents for plant diseases as Lysobacter enzymogenes based on phylogenetic analysis of 16S rDNA, fatty acid composition and phenotypic characteristics. J Appl Microbiol 94:1079-1086
64. Takai K, Moser DP, Onstott TC, Spoelstra N, Pfiffner SM, Dohnalkova A, Fredrickson JK (2001) Alkaliphilus transvaalensis gen. nov., sp. nov., an extremely alkaliphilic bacterium isolated from a deep South African gold mine. Int J Syst Evol Microbiol 51:1245-1256
65. 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
66. 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. Nucleic Acids Res 25:4876-4882
67. Tourova TP, Spiridonova EM, Berg IA, Slobodova NV, Boulygina ES, Sorokin DY (2007) Phylogeny and evolution of the family Ectothiorhodospiraceae based on comparison of 16S rRNA, cbbL and nifH gene sequences. Int J Syst Evol Microbiol 57:2387-2398
68. Valenzuela-Encinas C, Neria-González I, Alcántara-Hernández R, Enríquez-Aragón J, Estrada-Alvarado I, Hernández-Rodríguez C, Dendooven L, Marsch R (2008) Phylogenetic analysis of the archaeal community in an alkaline-saline soil of the former lake Texcoco (Mexico). Extremophiles 12:247-254
69. van Trappen S, Mergaert J, Swings J (2004) Loktanella salsilacus gen. nov., sp. nov., Loktanella fryxellensis sp. nov and Loktanella vestfoldensis sp. nov., new members of the Rhodobacter group, isolated from microbial mats in Antarctic lakes. Int J Syst Evol Microbiol 54:1263-1269
70. 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
71. Vingadassalom D, Kolb A, Mayer C, Rybkine T, Collatz E, Podglajen I (2005) An unusual primary sigma factor in the Bacteroidetes phylum. Mol Microbiol 56:888-902
72. Wani AA, Surakasi VP, Siddharth J, Raghavan RG, Patole MS, Ranade D, Shouche YS (2006) Molecular analysis of microbial diversity associated with the Lonar soda lake in India: an impact crater in a basalt area. Res Microbiol 157:928-937
73. Wu QL, Zwart G, Schauer M, Kamst-van Agterveld MP, Hahn MW (2006) Bacterioplankton community composition along a salinity gradient of sixteen high-mountain lakes located on the Tibetan Plateau, China. Appl Environ Microbiol 72:5478-5485
74. Xie C-H, Yokota A (2004) Transfer of Hyphomicrobium indicum to the genus Photobacterium as Photobacterium indicum comb. nov. Int J Syst Evol Microbiol 54:2113-2116
75. Yabuuchi E, Yamamoto H, Terakubo S, Okamura N, Naka T, Fujiwara N, Kobayashi K, Kosako Y, Hiraishi A (2001) Proposal of Sphingomonas wittichii sp. nov. for strain RW1(T), known as a dibenzo-p-dioxin metabolizer. Int J Syst Evol Microbiol 51:281-292
76. Ye Q, Roh Y, Carroll SL, Blair B, Zhou J, Zhang CL, Fields MW (2004) Alkaline anaerobic respiration: isolation and characterization of a novel alkaliphilic and metal-reducing bacterium. Appl Environ Microbiol 70:5595-5602
77. Yoon J-H, Yeo S-H, Kim I-G, Oh T-K (2004) Marinobacter flavimaris sp. nov. and Marinobacter daepoensis sp. nov., slightly halophilic organisms isolated from sea water of the Yellow Sea in Korea. Int J Syst Evol Microbiol 54:1799-1803
78. Yu Z, Morrison M (2004) Comparisons of different hypervariable regions of rrs genes for use in fingerprinting of microbial communities by PCR-denaturing gradient gel electrophoresis. Appl Environ Microbiol 70:4800-4806
79. Yu F, Zaleta-Rivera K, Zhu X, Huffman J, Millet JC, Harris SD, Yuen G, Li XC, Du L (2007) Structure and biosynthesis of heat-stable antifungal factor (HSAF), a broad-spectrum antimycotic with a novel mode of action. Antimicrob Agents Chemother 51:64-72
80. Zeevaert L (1949) An investigation of the engineering characteristics of the volcanic lacustrine clay deposits beneath Mexico City. PhD thesis, University of Illinois, USA