Abstract
The ability of MALDI TOF MS (matrix-assisted laser desorption ionisation time-of-flight mass spectrometry) to identify cultivable microflora from two waste disposal sites from non-ferrous metal industry was analysed. Despite the harsh conditions (extreme pH values and heavy metal content in red mud disposal site from aluminium production or high heavy metal content in nickel sludge), relatively high numbers of bacteria were recovered. In both environments, the bacterial community was dominated by Gram-positive bacteria, especially by actinobacteria. High-quality MALDI TOF mass spectra were obtained but most of the bacteria isolates could be not identified using MALDI Biotyper software. The overall identification rate was lower than 20 %; in two of the environments tested identification rates were lower than 10 %. As a dominant bacterial species, Microbacterium spp. in drainage water from an aluminium red mud disposal site near Žiar nad Hronom, Bacillus spp. in red mud samples from the same site, and Arthrobacter spp. from nickel smelter sludge near Sereï were identified by a combination of the Biolog system and 16S rRNA sequence analysis. As the primary focus of the MALDI TOF MS-based methodology is directed towards medically important bacteria, reference database spectra expansion and refinement are needed to improve the ability of MALDI TOF MS to identify environmental bacteria, especially those from extreme environments.
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References
Anhalt, J. P., & Fenselau, C. (1975). Identification of bacteria using mass spectrometry. Analytical Chemistry, 47, 219–225. DOI: 10.1021/ac60352a007.
Bizzini, A., Jaton, K., Romo, D., Bille, J., Prod’hom, G., & Greub, G. (2011). Matrix-assisted laser desorption ionization-time of flight mass spectrometry as an alternative to 16S rRNA gene sequencing for identification of difficult-toidentify bacterial strains. Journal of Clinical Microbiology, 49, 693–696. DOI: 10.1128/jcm.01463-10.
Borsodi, A. K., Micsinai, A., Rusznyák, A., Vladár, P., Kovács, G., Tóth, E. M., & Márialigeti, K. (2005). Diversity of alkaliphilic and alkalitolerant bacteria cultivated from decomposing reed rhizomes in a Hungarian soda lake. Microbial Ecology, 50, 9-18. DOI: 10.1007/s00248-004-0063-1.
Christensen, J. J., Dargis, R., Hammer, M., Justesen, U. S., Nielsen, X. C., Kemp, M., & the Danish MALDI-TOF MS Study Group (2012). Matrix-assisted laser desorption ionization-time of flight mass spectrometry analysis of Grampositive, catalase-negative cocci not belonging to the Streptococcus or Enterococcus genus and benefits of database extension. Journal of Clinical Microbiology, 50, 1787–1791. DOI: 10.1128/jcm.06339-11.
Clarridge, J. E., III (2004). Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clinical Microbiology Reviews, 17, 840–862. DOI: 10.1128/cmr.17.4.840-862.2004.
Cobo, F. (2013). Application of MALDI-TOF mass spectrometry in clinical virology: A review. The Open Virology Journal, 7, 84–90. DOI: 10.2174/1874357920130927003.
De Bruyne, K., Slabbinck, B., Waegeman, W., Vauterin, P., De Baets, B., & Vandamme, P. (2011). Bacterial species identification from MALDI-TOF mass spectra through data analysis and machine learning. Systematic and Applied Microbiology, 34, 20–29. DOI: 10.1016/j.syapm.2010.11.003.
Edouard, S., Couderc, C., Raoult, D., & Fournier, P. E. (2012). Mass spectrometric identification of Propionibacterium isolates requires database enrichment. Advances in Microbiology, 2, 497–504. DOI: 10.4236/aim.2012.24063.
Eigner, U., Holfelder, M., Oberdorfer, K., Betz-Wild, U., Bertsch, D., & Fahr, A. M. (2009). Performance of a matrix-assisted laser desorption ionization-time-of-flight mass spectrometry system for the identification of bacterial isolates in the clinical routine laboratory. Clinical Laboratory, 55, 289–296.
Ellis, R. J., Morgan, P., Weightman, A. J., & Fry, J. C. (2003). Cultivation-dependent and -independent approaches for determining bacterial diversity in heavy-metal-contaminated soil. Applied and Environmental Microbiology, 69, 3223–3230. DOI: 10.1128/aem.69.6.3223-3230.2003.
Ferreira, L., Sánchez-Juanes, F., Muñoz-Bellido, J. L., & González-Buitrago, J. M. (2011). Rapid method for direct identification of bacteria in urine and blood culture samples by matrix-assisted laser desorption ionization time-offlight mass spectrometry: intact cell vs. extraction method. Clinical Microbiology and Infection, 17, 1007–1012. DOI: 10.1111/j.1469-0691.2010.03339.x.
Hamdy, M. K., & Williams, F. S. (2001). Bacterial amelioration of bauxite residue waste of industrial alumina plants. Journal of Industrial Microbiology and Biotechnology, 27, 228–233. DOI: 10.1038/sj.jim.7000181.
Holland, R. D., Wilkes, J. G., Rafii, F., Sutherland, J. B., Persons, C. C., Voorhees, K. J., & Lay, J. O., Jr. (1996). Rapid identification of intact whole bacteria based on spectral patterns using matrix-assisted laser desorption/ionization with time-of-flight mass spectrometry. Rapid Communications in Mass Spectrometry, 10, 1227–1232. DOI: 10.1002/(SICI)1097-0231(19960731)10:10<1227::AIDRCM659>3.0.CO;2-6.
Kaprelyants, A. S., & Kell, D. B. (1993). Dormancy in stationary-phase cultures of Micrococcus luteus: Flow cytometric analysis of starvation and resuscitation. Applied and Environmental Microbiology, 59, 3187–3196.
Keys, C. J., Dare, D. J., Sutton, H., Wells, G., Lunt, M., McKenna, T., McDowall, M., & Shah, H. N. (2004). Compilation of a MALDI-TOF mass spectral database for the rapid screening and characterisation of bacteria implicated in human infectious diseases. Infection, Genetics and Evolution, 4, 221–242. DOI: 10.1016/j.meegid.2004.02.004.
Kim, O. S., Cho, Y. J., Lee, K., Yoon, S. H., Kim, M., Na, H., Park, S. C., Jeon, Y. S., Lee, J. H., Yi, H., Won, S., & Chun, J. (2012). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. International Journal of Systematic and Evolutionary Microbiology, 62, 716–721. DOI: 10.1099/ijs.0.038075-0.
Koubek, J., Uhlik, O., Jecna, K., Junkova, P., Vrkoslavova, J., Lipov, J., Kurzawova, V., Macek, T., & Mackova, M. (2012). Whole-cell MALDI-TOF: Rapid screening method in environmental microbiology. International Biodeterioration & Biodegradation, 69, 82–86. DOI: 10.1016/j.ibiod.2011.12.007.
Krader, P., & Emerson, D. (2004). Identification of archaea and some extremophilic bacteria using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. Extremophiles, 8, 259–268. DOI: 10.1007/s00792-004-0382-7.
Logan, N. A. (2012). Bacillus and relatives in foodborne illness. Journal of Applied Microbiology, 112, 417–429. DOI: 10.1111/j.1365-2672.2011.05204.x.
Margesin, R., Płaza, G. A., & Kasenbacher, S. (2011). Characterization of bacterial communities at heavy-metal-contaminated sites. Chemosphere, 82, 1583–1588. DOI: 10.1016/j.chemosphere.2010.11.056.
Martiny, D., Busson, L., Wybo, I., Ait El Haj, R., Dediste, A., & Vandenberg, O. (2012). Comparison of the Microflex LT and Vitek MS systems for routine identification of bacteria by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Journal of Clinical Microbiology, 50, 1313–1325. DOI: 10.1128/jcm.05971-11.
Mengoni, A., Barzanti, R., Gonnelli, C., Gabbrielli, R., & Bazzicalupo, M. (2001). Characterization of nickel-resistant bacteria isolated from serpentine soil. Environmental Microbiology, 3, 691–698. DOI: 10.1046/j.1462-2920.2001.00243.x.
Michaeli, E., Boltižiar, M., Solár, V., & Ivanová, M. (2012). The landfill of industrial waste - lúženec near the former Nickel Smelter at Sered’ Town as an example of environmental load. Životné prostredie, 46, 63–68. (in Slovak)
Sauer, S., Freiwald, A., Maier, T., Kube, M., Reinhardt, R., Kostrzewa, M., & Geider, K. (2008). Classification and identification of bacteria by mass spectrometry and computational analysis. PLoS ONE, 3, e2843. DOI: 10.1371/journal.pone.0002843.
Su, J., Wu, Y., Ma, X., Zhang, G., Feng, H., & Zhang, Y. (2004). Soil microbial counts and identification of culturable bacteria in an extreme by arid zone. Folia Microbiologica, 49, 423–429. DOI: 10.1007/bf02931604.
Van Belkum, A., Welker, M., Erhard, M., & Chatellier, S. (2012). Biomedical mass spectrometry in today’s and tomorrow’s clinical microbiology laboratories. Journal of Clinical Microbiology, 50, 1513–1517. DOI: 10.1128/jcm.00420-12.
Vargha, M., Takáts, Z., Konopka, A., & Nakatsu, C. H. (2006). Optimization of MALDI-TOF MS for strain level differentiation of Arthrobacter isolates. Journal of Microbiological Methods, 66, 399–409. DOI: 10.1016/j.mimet.2006.01.006.
Van Veen, S. Q., Claas, E. C. J., & Kuijper, E. J. (2010). High-throughput identification of bacteria and yeast by matrix-assisted laser desorption ionization-time of flight mass spectrometry in conventional medical microbiology laboratories. Journal of Clinical Microbiology, 48, 900–907. DOI: 10.1128/jcm.02071-09.
Wang, Y. P., Shi, J. Y., Wang, H., Lin, Q., Chen, X. C., & Chen, Y. X. (2007). The influence of soil heavy metals pollution on soil microbial biomass, enzyme activity, and community composition near a copper smelter. Ecotoxicology and Environmental Safety, 67, 75–81. DOI: 10.1016/j.ecoenv.2006.03.007.
Weisburg, W. G., Barns, S. M., Pelletier, D. A., & Lane, D. J. (1991). 16S ribosomal DNA amplification for phylogenetic study. Journal of Bacteriology, 173, 697–703.
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Kopcakova, A., Stramova, Z., Kvasnova, S. et al. Need for database extension for reliable identification of bacteria from extreme environments using MALDI TOF mass spectrometry. Chem. Pap. 68, 1435–1442 (2014). https://doi.org/10.2478/s11696-014-0612-0
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DOI: https://doi.org/10.2478/s11696-014-0612-0