Genomic Analysis of Plant-Associated Bacteria and Their Potential in Enhancing Phytoremediation Efficiency

• Autorzy: Piński A. , Hupert-Kocurek K.

Identyfikatory

DOI

10.12911/22998993/74281

• Języki publikacji: EN

Abstrakty

EN

Phytoremediation is an emerging technology that uses plants in order to cleanup pollutants including xenobiotics and heavy metals from soil, water and air. Inoculation of plants with plant growth promoting endophytic and rhizospheric bacteria can enhance efficiency of phytoremediation. Genomic analysis of four plant-associated strains belonging to the Stenotrophomonas maltophilia species revealed the presence of genes encoding proteins involved in plant growth promotion, biocontrol of phytopathogens, biodegradation of xenobiotics, heavy metals resistance and plant-bacteria-environment interaction. The results of this analysis suggest great potential of bacteria belonging to Stenotrophomonas maltophilia species in enhancing phytoremediation efficiency.

Słowa kluczowe

EN

endophytic bacteria; rhizospheric bacteria; Stenotrophomonas maltophilia; heavy metals; phytoremediation; xenobiotics

• Wydawca: Polskie Towarzystwo Inżynierii Ekologicznej ; Lublin University of Technology
• Czasopismo: Journal of Ecological Engineering
• Rocznik: 2017
• Tom: Vol. 18, nr 4
• Strony: 152--159
• Opis fizyczny: Bibliogr. 43 poz., tab., rys.

Twórcy

autor

Piński A.

• The University of Silesia in Katowice, Faculty of Biology and Environmental Protection, Jagiellonska 28, 40-032 Katowice, Poland

autor

Hupert-Kocurek K.

• The University of Silesia in Katowice, Faculty of Biology and Environmental Protection, Jagiellonska 28, 40-032 Katowice, Poland

Bibliografia

• 1. Alavi, P., Muller, H., Cardinale, M., Zachow, C., Sanches, M., Martinez, L., Berg, G. 2013. The DSF quorum sensing system controls the positive influence of Stenotrophomonas maltophilia on plants. PLoS ONE, 8(7), 1–9.
• 2. Alavi, P., Starcher, M. R., Thallinger, G. G., Zachow, C., Müller, H., Berg, G. 2014. Stenotrophomonas comparative genomics reveals genes and functions that differentiate beneficial and pathogenic bacteria. BMC Genomics, 15, 482.
• 3. Ali, S., Duan, J., Charles, T. C., Glick, B. R. 2014. A bioinformatics approach to the determination of genes involved in endophytic behavior in Burkholderia spp. Journal of Theoretical Biology, 343, 193–198.
• 4. Bondarczuk, K., Piotrowska-Seget, Z. 2013. Molecular basis of active copper resistance mechanisms in Gram-negative bacteria. Cell Biology and Toxicology, 29, 397–405.
• 5. Byung, P., Karpinets, T. V. 2010. CAZymes Analysis Toolkit (CAT): Web service for searching and analyzing carbohydrate-active enzymes in a newly sequenced organism using CAZy database. Glycobiology, 20(12), 1574–1584.
• 6. Compant, S., Clément, C., Sessitsch, A. 2010. Plant growth-promoting bacteria in the rhizo- and endosphere of plants: Their role, colonization, mechanisms involved and prospects for utilization. Soil Biology Biochemistry, 42, 669–678.
• 7. Finn, R. D., Attwood, T. K., Babbitt, P. C., Bateman, A., Bork, P., Bridge, J., … Mitchell, A. L. 2017. InterPro in 2017 - beyond protein family and domain annotations. Nucleic Acids Research, 45, 190–199.
• 8. Gandhi, N. U., Chandra, S. B. (2012). A comparative analysis of three classes of bacterial non-specific acid phosphatases and archaeal phosphoesterases: evolutionary perspective. Acta Inform Med, 20(3), 167–173.
• 9. García-León, G., Hernández, A., Hernando-Amado, S., Alavi, P., Berg, G., Martínez, L. 2014. A function of SmeDEF, the major quinolone resistance determinant of Stenotrophomonas maltophilia, is the colonization of plant roots. Applied and Environmental Microbiology, 80(15), 4559–4565.
• 10. García, C. A., Alcaraz, E. S., Franco, M. A., Rossi, B. N. P. De. 2015. Iron is a signal for Stenotrophomonas maltophilia biofilm formation, oxidative stress response, OMPs expression, and virulence. Frontiers in Microbiology, 6, 1–14.
• 11. Ghosh, A., Das, P. 2013. Optimization of copper bioremediation by Stenotrophomonas maltophilia PD2. Journal of Environmental Chemical Engineering, 1(3), 159–163.
• 12. Guzik, U., Greń, I., Wojcieszyńska, D., Sylwia, Ł. 2009. Isolation and characterization of a novel strain of Stenotrophomonas maltophilia possessing various dioxygenases for monocyclic hydrocarbon degradation. Brazilian Journal of Microbiology, 40, 285–291.
• 13. Guzik, U., Hupert-Kocurek, K., Sitnik, M., Wojcieszyńska, D. 2013. High activity catechol 1.2-dioxygenase from Stenotrophomonas maltophilia strain KB2 as a useful tool in cis,cis-muconic acid production. Antonie van Leeuwenhoek, 103, 1297–1307.
• 14. Higashi, K., Ishigure, H., Demizu, R., Uemura, T., Nishino, K., Yamaguchi, A., … Igarashi, K. 2008. Identification of a spermidine excretion protein complex (MdtJI) in Escherichia coli. Journal of Bacteriology, 190(3), 872–878.
• 15. Huang, X., Liu, J., Ding, J., He, Q., Xiong, R. 2009. The investigation of nematocidal activity in Stenotrophomonas maltophilia G2 and characterization of a novel virulence serine protease. Canadian Journal of Microbiology, 942, 934–942.
• 16. Huedo, P., Yero, D., Martínez-servat, S., Estibariz, I., Planell, R., Martínez, P., Ruyra, À. (2014). Two different rpf clusters distributed among a population of Stenotrophomonas maltophilia clinical strains display differential diffusible signal factor production and virulence regulation. Journal of Bacteriology, 196(13), 2431–2442.
• 17. Itoh, Y., Rice, J. D., Goller, C., Pannuri, A., Taylor, J., Meisner, J., … Romeo, T. 2008. Roles of pgaABCD genes in synthesis, modification, and export of the Escherichia coli biofilm adhesin poly-beta-1.6-n-acetyl-d-glucosamine. Journal of Bacteriology, 190(10), 3670–3680.
• 18. Iwagami, S., Yang, K., Davies, J. (2000). Characterization of the protocatechuic acid catabolic gene cluster from Streptomyces sp. strain 2065. Applied and Environmental Microbiology, 66(4), 1499–1508.
• 19. Kanehisa, M., Furumichi, M., Tanabe, M., Sato, Y., Morishima, K. 2017. KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Research, 45, 353–361.
• 20. Kearse, M., Moir, R., Wilson, A., Stones-Havas, S., Sturrock, S., Buxton, S., … Drummond, A. 2012. Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics, 28(12), 1647–1649.
• 21. Kerepesi, C., Bánky, D., Grolmusz, V. 2014. AmphoraNet: The webserver implementation of the AMPHORA2 metagenomic work flow suite. Gene, 533(2), 538–540.
• 22. Kupferschmied, P., Maurhofer, M., Keel, C. 2013. Promise for plant pest control: root-associated pseudomonads with insecticidal activities. Frontiers in Plant Science, 4, 287.
• 23. Liaqat, F., Eltem, R. (2016). Identification and characterization of endophytic bacteria isolated from in vitro cultures of peach and pear rootstocks. 3 Biotech, 6(2), 1–8.
• 24. Ma, Y., Rajkumar, M., Zhang, C., Freitas, H. 2016. Beneficial role of bacterial endophytes in heavy metal phytoremediation. Journal of Environmental Management, 174, 14–25.
• 25. Mcguinness, M., Dowling, D. 2009. Plant-associated bacterial degradation of toxic organic compounds in soil. International Journal of Environmental Research and Public Health, 6, 2226–2247.
• 26. Miller-Fleming, L., Olin-Sandoval, V. 2015. Remaining mysteries of molecular biology: the role of polyamines in the cell. Journal of Molecular Biology, 427(21), 3389–3406.
• 27. Mukherjee, P., Roy, P. 2016. Genomic potential of Stenotrophomonas maltophilia in bioremediation with an assessment of its multifaceted role in our environment. Frontiers in Microbiology, 7, 1–14.
• 28. Pedrosa, F. O., Monteiro, R. A., Wassem, R., Cruz, L. M., Ayub, R. A., Colauto, N. B., … Souza, E. M. 2011. Genome of Herbaspirillum seropedicae strain SmR1, a specialized diazotrophic endophyte of tropical grasses. PLoS Genetics, 7(5).
• 29. Purushotham, P., Arun, P. V. P. S., Prakash, J. S. S., Podile, A. R. 2012. Chitin binding proteins act synergistically with chitinases in Serratia proteamaculans 568. PLoS ONE, 7(5), 1–10.
• 30. Reinhold-Hurek, B., Hurek, T. 2011. Living inside plants: Bacterial endophytes. Current Opinion in Plant Biology, 14, 435–443.
• 31. Silver, S., Phung, L. T. 1996. Bacterial heavy metal resistance: new surprises. Annual Review of Microbiology, 50, 753–789.
• 32. Singh, P., Kumar, V., Agrawal, S. 2014. Evaluation of phytase producing bacteria for their plant growth promoting activities. International Journal of Microbiology.
• 33. Taghavi, S., van der Lelie, D. 2010. Genome sequence of the plant growth-promoting endophytic bacterium Enterobacter sp. 638. Molecular Microbial Ecology of the Rhizosphere, 2(5), 899–908.
• 34. Wang, L., Jeon, B., Sahin, O., Zhang, Q. 2009. Identification of an arsenic resistance and arsenic-sensing system in Campylobacter jejuni. Applied and Environmental Microbiology, 75(15), 5064–5073.
• 35. Wang, M., Xing, Y., Wang, J., Xu, Y., Wang, G. 2014. The role of the chi1 gene from the endophytic bacteria Serratia proteamaculans 336x in the biological control of wheat take-all. Canadian Journal of Microbiology, 60(8), 533–40.
• 36. Wang, S., Ng, T. B., Chen, T., Lin, D., Wu, J., Rao, P., Ye, X. (2005). First report of a novel plant lysozyme with both antifungal and antibacterial activities. Biochemical and Biophysical Research Communications, 327(3), 820–827.
• 37. Wang, Y., Zheng, X., Hu, Q., Zheng, Y. 2015. Degradation of abamectin by newly isolated Stenotrophomonas maltophilia ZJB-14120 and characterization of its abamectin-tolerance mechanism. Research in Microbiologoy, 166(5), 1–11.
• 38. Wattam, A. R., Abraham, D., Dalay, O., Disz, T. L., Driscoll, T., Gabbard, J. L., … Sobral, B. W. 2014. PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Research, 42, 581–591.
• 39. Weber, T., Blin, K., Duddela, S., Krug, D., Kim, H. U., Bruccoleri, R., … Medema, M. H. 2015. antiSMASH 3.0 - a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Research, 43, 237–243.
• 40. Wu, Y., Wang, Y., Li, J., Hu, J., Chen, K., Wei, Y., … Yang, H. 2015. Draft genome sequence of Stenotrophomonas maltophilia strain B418, a promising agent for biocontrol of plant pathogens and root-knot nematode. Genome Announcements, 3(1), 1998–1999.
• 41. Xie, J., Shi, H., Du, Z., Wang, T., Liu, X., Chen, S. 2016. Comparative genomic and functional analysis reveal conservation of plant growth promoting traits in Paenibacillus polymyxa and its closely related species. Scientific Reports, 1–12.
• 42. Yu, N. Y., Wagner, J. R., Laird, M. R., Melli, G., Rey, S., Lo, R., … Brinkman, F. S. L. 2010. PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics, 26(13), 1608–1615.
• 43. Zhang, Z., Yuen, G. Y. 1999. The role of chitinase production by Stenotrophomonas maltophilia strain C3 in biological control of Bipolaris sorokiniana. Phytopathology, 90(4), 384–389.

Uwagi

Opracowanie ze środków MNiSW w ramach umowy 812/P-DUN/2016 na działalność upowszechniającą naukę (zadania 2017).