Lysis efficiency of standard DNA extraction methods for Halococcus spp. in an organic rich environment
Tóm tắt
The extraction of nucleic acids from a given environment marks a crucial and essential starting point in any molecular investigation. Members of Halococcus spp. are known for their rigid cell walls, and are thus difficult to lyse and could potentially be overlooked in an environment. Furthermore, the lack of a suitable lysis method hinders subsequent molecular analysis. The effects of six different DNA extraction methods were tested on Halococcus hamelinensis, Halococcus saccharolyticus and Halobacterium salinarum NRC-1 as well as on an organic rich, highly carbonated sediment from stromatolites spiked with Halococcus hamelinensis. The methods tested were based on physical disruption (boiling and freeze/thawing), chemical lysis (Triton X-100, potassium ethyl xanthogenate (XS) buffer and CTAB) and on enzymatic lysis (lysozyme). Results showed that boiling and freeze/thawing had little effect on the lysis of both Halococcus strains. Methods based on chemical lysis (Triton X-100, XS-buffer, and CTAB) showed the best results, however, Triton X-100 treatment failed to produce visible DNA fragments. Using a combination of bead beating, chemical lysis with lysozyme, and thermal shock, lysis of cells was achieved however DNA was badly sheared. Lysis of cells and DNA extraction of samples from spiked sediment proved to be difficult, with the XS-buffer method indicating the best results. This study provides an evaluation of six commonly used methods of cell lysis and DNA extraction of Halococcus spp., and the suitability of the resulting DNA for molecular analysis.
Tài liệu tham khảo
Antón J, Rosselló-Mora R, Rodríguez-Valera F, Amann R (2000) Extremely halophilic bacteria in crystallizer ponds from solar salterns. Appl Environ Microbiol 66:3052–3057
Benlloch S, Acinas SG, Antón J, López-López A, Luz SP, Rodríguez-Valera F (2001) Archaeal biodiversity in crystallizer ponds from a solar saltern: culture versus PCR. Microb Ecol 41:12–19
Bickley J, Short JK, McDowell DG, Parkes HC (1996) Polymerase chain reaction (PCR) detection of Listeria monocytogenes in diluted milk and reversal of PCR inhibition caused by calcium ions. Lett Appl Microbiol 22:153–158
Burns BP, Goh F, Allen MA, Neilan BA (2004) Microbial diversity of extant stromatolites in the hypersaline marine environment of Shark Bay, Australia. Environ Microbiol 6:1096–1101
DasSarma S, Fleischmann EM, Rodríguez-Valera F (1995) Halophiles. In: Robb FT (ed) Archaea: a laboratory manual. CSHL Press, Cold Spring Harbor, USA, pp 225–230
DeLong EF (1992) Archaea in coastal marine environments. Proc Natl Acad Sci USA 89:5685–5689
Fortin N, Beaumier D, Lee K, Greer CW (2004) Soil washing improves the recovery of total community DNA from polluted and high organic content sediments. J Microbiol Meth 56:181–191
Gabig-Ciminska M, Liu Y, Enfors SO (2005) Gene-based identification of bacterial colonies with an electric chip. Anal Biochem 345:270–276
Goh F, Leuko S, Allen MA, Bowman JP, Kamekura M, Neilan BA, Burns BP (2006) Halococcus hamelinensis sp. nov., a novel halophilic archaeon isolated from stromatolites in Shark Bay, Australia. Int J Syst Evol Microbiol 56:1323–1329
Harju S, Fedosyuk H, Peterson KR (2004) Rapid isolation of yeast genomic DNA: bust’n grab. BMC Biotechnol 4:8
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
Kandler O, König H (1998) Cell wall polymers in Archaea (Archaebacteria). Cell Mol Life Sci 54:305–308
Kuske CR, Banton KL, Adorada DL, Stark PC, Hill KK, Jackson PJ (1998) Small-scale DNA sample preparation method for field PCR detection of microbial cells and spores in soil. Appl Environ Microbiol 64:2463–2472
Leff LG, Dana JR, McArthur JV, Shimkets LJ (1995) Comparison of methods of DNA extraction from stream sediments. Appl Environ Microbiol 61:1141–1143
Leuko S, Goh F, Allen MA, Burns BP, Walter MR, Neilan BA (2007) Analysis of intergenic spacer region length polymorphisms to investigate the halophilic archaeal diversity of stromatolites and microbial mats. Extremophiles 11:203–210
Liesack W, Weyland H, Stackebrandt E (1991) Potential risks of gene amplification by PCR as determined by 16S rDNA analysis of a mixed-culture of strict barophilic Bacteria. Microb Ecol 21:191–198
Luna GM, Dell’Anno A, Danovaro R (2006) DNA extraction procedure: a critical issue for bacterial diversity assessment in marine sediments. Environ Microbiol 8:308–320
Malik M, Kain J, Pettigrew C, Ogram A (1994) Purification and molecular analysis of microbial DNA from compost. J Microbiol Meth 20:183–196
Martin-Laurent F, Philippot L, Hallet S, Chaussod R, Germon JC, Soulas G, Catroux G (2001) DNA extraction from soils: old bias for new microbial diversity analysis methods. Appl Environ Microbiol 67:2354–2359
Miller DN, Bryant JE, Madsen EL, Ghiorse WC (1999) Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples. Appl Environ Microbiol 65:4715–4724
Mormile MR, Biesen MA, Gutierrez MC, Ventosa A, Pavlovich JB, Onstott TC, Fredrickson JK (2003) Isolation of Halobacterium salinarum retrieved directly from halite brine inclusions. Environ Microbiol 5:1094–1102
O’Mahony J, Hill C (2004) Rapid real-time PCR assay for detection and quantitation of Mycobacterium avium subsp. paratuberculosis DNA in artificially contaminated milk. Appl Environ Microbiol 70:4561–4568
Ochsenreiter T, Pfeifer F, Schleper C (2002) Diversity of Archaea in hypersaline environments characterized by molecular-phylogenetic and cultivation studies. Extremophiles 6:267–274
Ogram A, Sayler GS, Barkay T (1987) The extraction and purification of microbial DNA from sediments. J Microbiol Meth 7:57–66
Oren A (1994) The ecology of the extremely halophilic archaea. FEMS Microbiol Rev 13:415–440
Oren A, Gavrieli I, Gavrieli J, Kohen M, Lati J, Aharoni M (2006) Microbial communities in the Dead Sea—past, present and future. In: Gunde-Cimerman N, Oren A, Plemenitaš A (eds) Adaptation to life at high salt concentrations in Archaea, Bacteria and Eukarya. Springer, The Netherlands, pp 29–40
Papineau D, Walker JJ, Mojzsis SJ, Pace NR (2005) Composition and structure of microbial communities from stromatolites of Hamelin Pool in Shark Bay, Western Australia. Appl Environ Microbiol 71:4822–4832
Purdy KJ (2005) Nucleic acid recovery from complex environmental samples. In: Leadbetter JR (ed) Methods of enzymology, vol 397. Elsevier, New York, pp 271–292
Radax C, Gruber C, Stan-Lotter H (2001) Novel haloarchaeal 16S rRNA gene sequences from alpine permo-triassic rock salt. Extremophiles 5:221–228
Rodríguez-Valera F, Ruiz-Berraquero F, Ramos-Cormenzana A (1979) Isolation of extreme halophiles from seawater. Appl Environ Microbiol 38:164–165
Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Habor Laboratory Press, Cold Spring Harbor, NY
Smalla K, Cresswell N, Mendonca-Hagler C, Wolters A, van Elsas JD (1993) Rapid DNA extraction protocol from soil for polymerase chain reaction-mediated amplification. J Appl Bacteriol 74:78–85
Stan-Lotter H, Pfaffenhuemer M, Legat A, Busse HJ, Radax C, Gruber C (2002) Halococcus dombrowskii sp. nov., an archaeal isolate from a Permian alpine salt deposit. Int J Syst Evol Microbiol 52:1807–1814
Stan-Lotter H, Leuko S, Legat A, Fendrihan S (2006) The assessment of the viability of halophilic microorganisms In: Rainy FA, Oren A (eds) Methods in microbiology, vol 35. Academic, London, pp 569–584
Tillett D, Neilan BA (2000) Xanthogenate nucleic acid isolation from cultured and environmental cyanobacteria. J Phycol 36:251–258
Tsai YL, Olson BH (1991) Rapid method for direct extraction of DNA from soil and sediments. Appl Environ Microbiol 57:1070–1074
Wilson K (1990) Preparation of genomic DNA from bacteria In: Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K (eds) Current protocols in molecular biology. Wiley, New York, pp 2.4.1–2.4.2
Wilson IG (1997) Inhibition and facilitation of nucleic acid amplification. Appl Environ Microbiol 63:3741–3751
v. Wintzingerode F, Göbel UB, Stackebrandt E (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21:213–229
Zhou J, Bruns MA, Tiedje JM (1996) DNA recovery from soils of diverse composition. Appl Environ Microbiol 62:316–322