Metagenomic analysis of microbial community in coal samples from Kazakhstan using Illumina NGS technology
DOI:
https://doi.org/10.26577/eb-2018-3-1338Аннотация
The development of micro- and biotechnological processes for fossil energy utilization has received increasing attention in recent years. There are abundant coal resources in Kazakhstan; in particular, low-rank coal resources of lignite and leonardite. These coal types are not exploited commercially due to their low energetic power. However, they are considered as a rich source of humic substances (HS). The HS in the soil play an important role in physical and chemical quality, carbon capture and stabilization and in the inactivation of pesticides, heavy metals, as well as other polluting agents. Bioprocessing of lignite also involves the production of clean energy.
Research on coal microbes is essential for microbial ecology and applied microbiology with regard to the sustainable utilization of coal resources. Nevertheless, the inability of culturing vast amount (around 99%) of microorganisms in vitro counteract the research procedures. Currently, there is tremendous advances in using non-culturing techniques based on omics to the examination of microbial diversity of environmental compartments, such as soil, sediment, minerals, etc. Different omics tools, including FISH, SIP, next generation sequencing (NGS), microarray, mass spectrometry, etc., evolve instant results to provide comprehensive insight of the coal microbiome.
This paper discusses the findings and challenges in the study of Kazakhstan coal microbes, highlighting Illumina NGS platform. Based on the results of the metagenomic analysis of coal samples (Oikaragai, Lenger, Karaganda, Yekibastuz), 10 taxonomic groups of bacteria belonging to Proteobacteria, Tenericutes, Actinobacteria, Firmicutes, Bacteroidetes, Nitrospirae, Chloroflexi, Gemmatimonadetes, Acidobacteriaand Fusobacteria were identified and analyzed.
Key words: lignite, leonardite, microbial diversity, microbial community, metagenomics, Illumina Miseq sequencing.
Библиографиялық сілтемелер
1. Yong W., Petersen J.N., Kaufman E.N. Modeling the biological solubilization of coal in a Liquid Fluidized-Bed Reactor // Appl Biochem Biotechnol. – 1995. - Vol. 51, No. 52. - P. 437-447.
2. Xu X.H., Chen C.H., Qi H.Y. Development of coal combustion pollution control for SO2 and NOx in China // Fuel Processing Technol. – 2000. - Vol. 62, No. 2/3. - P. 153-160.
3. Yuan H., Yang J., Wang F. et al. The prospect of microbial sustainable utilization of lignite // World Science-Technology research and Development. – 2002. - Vol. 24, No. 3. - P. 13-17.
4. Dai H., Xiek U. Lignite utilization technology. – BeiJing: Coal industry press, 1998. -P. 4-7.
5. Nakagawa H., Namba A., Böhlmann M., Miura K. Hydrothermal dewatering of brown coal andcatalytic hydrothermal gasification of the organic compounds dissolving in the water using anovel Ni/carbon catalyst // Fuel. – 2004. -Vol. 83, No. 6. - P. 719-725.
6. Weber J.H. Binding and transport of metals by humic material. In: Frimmel F.H., Christman R.F., editors. Humic substances and their rolein the environment. - Chichester: John Wiley and Sons, 1988. P. 165-178.
7. Murphy E.M., Zachara J.M. The role of sorbedhumic substances onthe distribution of organic and inorganic contaminants in groundwater // Geoderma. – 1995. - Vol. 67. - Р. 103–124.
8. Christl I., Knicker H., Kogel I.K., Kretzschmar R. Chemical heterogeneityof humic substances: Characterization of size fractionsobtained by hollow-fibre ultrafiltration // Eur J Soil Sci. – 2000. - Vol. 510. - P. 617–625.
9. Piccolo A., Spaccini R., Nieder R. Sequestration of a biologicallylabile organic carbon in soils by humified organicmatter // Climatic Change. – 2004. –Vol. 67, No. 2-3. - P. 329-343.
10. Bandeira M., Mosca G., Vamerali T. Humic acids affect rootcharacteristics of fodder radish (Raphanussativus L.var.oleiformis Pers.) in metal-polluted wastes // Desalination. – 2009. - Vol. 246, No. 1-3. - P. 78-91.
11. Badis A., Ferradji F.Z., Boucherit A., Fodil D., Boutoumi H. Characterization and biodegradation of soil humic acids and preliminary identification of decolorizing actinomycetes at Mitidja plain soil (Algeria) // Microbiol Res. - 2009. - Vol. 3, No. 13. - P. 997-1007.
12. Barros L., Canellas L.P., Lopes F., Oliveira N., Lazaro E., Piccolo A. Bioactivity of chemically transformed humic matterfrom vermicompost on plant root growth // Agric Food Chem. - 2010. - Vol. 58, No. 6. - P. 3681-3688.
13. Fakoussa R.M. Investigation with microbial conversion of nationalcoals. - PhD thesis, University Bonn, 1981. - P. 634-642
14. Cohen M.S., Gabriele P.D. Degradation of coal by the fungi Polyporus versicolor and Poriamonticola // Appl Environ Microbiol. - 1982. - Vol. 51. - P. 437–447.
15. Fakoussa R.M, Hofrichter M. Biotechnology and microbiology of coal degradation // Appl. Microbiol. Biotechnol., - 1999. - Vol. 52. - P. 25–40.
16. Gupta A., Birenda K. Biogasification of coal using different sources of microorganisms // Fuel. – 2000. -Vol. 79. - P. 103–105.
17. Helena M., Kamila P., Anna P. Microbial degradation of low rank coals // Fuel Process Technol. – 2002. - Vol. 77/78. - P. 17–23.
18. Crowford D.L., Gupta R.K. Characterization of extracellular bacterial enzymes which depolymerize a soluble lignite coal polymer // Fuel - 1991. - Vol. 70. - P. 577–580.
19. Polman J.K., Brechkenridge C.R., Stoner D.L.. Biologically derived value-added products from coal // Appl Biochem Biotechnol. - 1995. - Vol. 54. - P. 249–255.
20. Davison B.H., Nicklaous D.M., Misra A., Lewis S.N., Faison BD. Utilization of microbially solubilized coal // Appl Biochem Biotechnol. - 1990. -Vol. 24, No 25. - P. 447–56.
21. Hess M., et al. Metagenomic discovery of biomass-degrading genes and genomes from cow rumen // Science. – 2011. - Vol. 331, No. 6016. - P. 463-467.
22. Avershina E., Trine F., Knut R. De novo Semi-alignment of 16S rRNA gene sequences for deep phylogenetic characterization of next generation sequencing data // Microbes and Environments. – 2013. - Vol. 28, No. 2. - P. 211-216.
23. Caporaso J.G., et al. Global patterns of 16S rRNA diversity at a depth of millions of period per sample // Proceedings of the National Academy of Sciences. - 2011. – Vol. 108. - P. 4516-4522.
24. Youssef N., et al. Comparison of species richness estimates using nearlyhed fragments and simulated pyrosequencing-fusion fragments in 16S rRNA gene-based environmental surveys // Applied and environmental microbiology. – 2009. - Vol. 75, No. 16. - P. 5227-5236.
25. Asnicar F., Weingart G., Tickle T.L, et al. Compact graphical representation of phylogenetic data and metadata with GraPhlAn. - PeerJ, 2015. - P. 1029.
26. DeSantis T.Z., et al. NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes // Nucleic acids research. – 2006. - Vol. 34., Suppl. 2. – Р. 394-399.
27. Brian О.D., Bergman N.H., Phillippy A.P. Interactive metagenomic visualization in a Web browser // BMC bioinformatics. – 2011. - Vol. 12, No. 1. - P. 385.
28. Bulgarelli D., Garrido-Oter R., Münch P.C., et al. Structure and function of the bacterial root microbiota in wild and domesticated barley // Cell host & microbe. - 2015. - Vol. 17, No. 3. – P.392-403.
29. Li B., et al. Characterization of tetracycline resistant bacterial community in saline activated sludge using batch stress incubation with high-throughput sequencing analysis // Water research. – 2013. - Vol. 47, No. 13. - P. 4207-4216.
30. Lundberg D.S., et al. Practical innovations for high-throughput amplicon sequencing // Nature methods. – 2013. - Vol. 10, No. 10. - P. 999-1002.
31. Lozupone C., Rob K. UniFrac: a new phylogenetic method for comparison microbial communities // Applied and environmental microbiology. – 2015. - Vol. 71, No. 12. - P. 8228-8235.
References
1. Avershina E., Trine F., and Knut R. (2013) De novo Semi-alignment of 16S rRNA Gene Sequences for Deep Phylogenetic Characterization of Next Generation Sequencing Data. Microbes and Environments vol. 28 no. 2, pp. 211-216.
2. Asnicar F, Weingart G, Tickle T.L, et al. (2015) Compact graphical representation of phylogenetic data and metadata with GraPhlAn [J]. PeerJ, p. 1029.
3. Bandeira M., Mosca G., Vamerali T. (2009) Humic acids affect rootcharacteristics of fodder radish (Raphanussativus L. var.oleiformis Pers.) in metal-polluted wastes. Desalination.,vol. 246, no. 1-3, pp. 78-91.
4. Badis A., Ferradji F.Z., Boucherit A., Fodil D., Boutoumi H. (2009) Characterization and biodegradation of soil humic acids andpreliminary identification of decolorizing actinomycetes atMitidja plain soil (Algeria). Microbiol Res.,vol. 3, no. 13, pp. 997-1007.
5. Barros L., Canellas L.P., Lopes F., Oliveira N., Lazaro E., Piccolo A. (2010) Bioactivity of chemically transformed humic matterfrom vermicompost on plant root growth. Agric FoodChem., vol. 58, no. 6, pp. 3681-3688.
6. Bulgarelli D, Garrido-Oter R, Münch P C, et al. (2015) Structure and function of the bacterial root microbiota in wild and domesticated barley [J]. Cell host & microbe, vol. 17, no. 3, 392-403.
7. Caporaso, J. Gregory, et al. (2011) Global patterns of 16S rRNA diversity at a depth of millions of period per sample. Proceedings of the National Academy of Sciences 108. Suk 1, pp. 4516-4522.
8. Christl I., Knicker H., Kogel I.K., Kretzschmar R. (2000) Chemical heterogeneityof humic substances: Characterization of size fractionsobtained by hollow-fibre ultrafiltration.Eur J Soil Sci.,vol . 510, pp. 617–25.
9. Cohen M.S., Gabriele P.D. (1982) Degradation of coal by the fungi Polyporus versicolor and Poriamonticola. Appl Environ Microbiol., vol. 51, pp. 437–47.
10. Crowford DL., Gupta R.K. (1991) Characterization of extracellular bacterial enzymes which depolymerize a soluble lignite coal polymer. Fuel.,vol. 70, pp. 577–80.
11. DeSantis, T.Z., et al. (2006) NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic acids research 34. Suppl 2, W394-W399.
12. Dai H., Xiek U. (1998) Lignite utilization technology. BeiJing.. Coal industry press. vol. 23 pp. 4-7.
13. Davison B.H., Nicklaous D.M., Misra A., Lewis S.N., Faison B.D. (1990) Utilization of microbially solubilized coal. Appl Biochem Biotechnol., vol. 24, no 25, pp. 447–56.
14. Fakoussa R.M. (1981) Investigation with microbial conversion of nationalcoals. PhD thesis, University Bonn. vol. 20, no. 4, pp. 634-642
15. Fakoussa R.M, Hofrichter M. (1999) Biotechnology and microbiology of coal degradation. ApplMicrobiolBiotechnol., vol. 52, pp. 25–40.
16. Gupta A., Birenda K. (2000) Biogasification of coal using different sources of micro-organisms. Fuel., vol. 79, pp. 103–5.
17. Nakagawa H., Namba A., Böhlmann M., Miura K. (2004) Hydrothermal dewatering of brown coal andcatalytic hydrothermal gasification of the organic compounds dissolving in the water using anovel Ni/carbon catalyst. Fuel., vol. 83, no. 6, pp. 719-725.
18. Weber J.H. Binding and transport of metals by humic material. In: Frimmel F.H., Christman R.F., editors. (1988) Humic substances and their rolein the environment. Chichester: John Wiley and Sons. pp. 165–78.
19. Murphy E.M., Zachara J.M. (1995) The role of sorbedhumic substances onthe distribution of organic and inorganic contaminants in groundwater. Geoderma., vol. 67, pp. 103–24.
20. Piccolo A., Spaccini R., Nieder R. (2004) Sequestration of a biologicallylabile organic carbon in soils by humified organicmatter. Climatic Change., vol .67, no. 2-3, pp. 329-343.
21. Helena M., Kamila P., Anna P. (2002) Microbial degradation of low rank coals. Fuel Process Technol. vol. 77/78, pp. 17–23.
22. Hess M., et al. (2011) Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science. vol. 331, no. 6016, pp. 463-467.
23. Yong W., Petersen J.N., Kaufman E.N. (1995) Modeling the biological solubilization of coal in a Liquid Fluidized-Bed Reactor. ApplBiochemBiotechnol.vol. 51, no. 52, pp. 437–47.
24. Lundberg D.S., et al. (2013) Practical innovations for high-throughput amplicon sequencing. Nature methods vol. 10, no. 10, pp. 999-1002.
25. Lozupone, Catherine, and Rob Knight. (2015) UniFrac: a new phylogenetic method for comparison microbial communities. Applied and environmental microbiology vol. 71, no. 12, pp. 8228-8235.
26. Brian О.D., Bergman N.H., Phillippy A.P. (2011) Interactive metagenomic visualization in a Web browser. BMC bioinformatics vol. 12, no. 1, p. 385.
27. Polman J.K., Brechkenridge C.R., Stoner D.L. (1995). Biologically derived value-added products from coal. Appl Biochem Biotechnol., vol. 54, pp. 249–55.
28. Xu X.H., Chen C.H., Qi H.Y. (2000) Development of coal combustion pollution control for SO2 and NOx in China. Fuel Processing Technol.,vol. 62, no. 2/3, pp. 153-160.
29. Youssef N., et al. (2009) Comparison of species richness estimates using nearlyhed fragments and simulated pyrosequencing-fusion fragments in 16S rRNA gene-based environmental surveys. Applied and environmental microbiology. vol. 75, no. 16, pp. 5227-5236.
30. Yuan H., Yang J., Wang F. et al. (2002) The prospect of microbial sustainable utilization of lignite. World Science-Technology research and Development., vol. 24 no. 3, pp. 13 - 17.
31. Li B., et al. (2013) Characterization of tetracycline resistant bacterial community in saline activated sludge using batch stress incubation with high-throughput sequencing analysis. Water research, vol. 47, no. 13, pp. 4207-4216.
2. Xu X.H., Chen C.H., Qi H.Y. Development of coal combustion pollution control for SO2 and NOx in China // Fuel Processing Technol. – 2000. - Vol. 62, No. 2/3. - P. 153-160.
3. Yuan H., Yang J., Wang F. et al. The prospect of microbial sustainable utilization of lignite // World Science-Technology research and Development. – 2002. - Vol. 24, No. 3. - P. 13-17.
4. Dai H., Xiek U. Lignite utilization technology. – BeiJing: Coal industry press, 1998. -P. 4-7.
5. Nakagawa H., Namba A., Böhlmann M., Miura K. Hydrothermal dewatering of brown coal andcatalytic hydrothermal gasification of the organic compounds dissolving in the water using anovel Ni/carbon catalyst // Fuel. – 2004. -Vol. 83, No. 6. - P. 719-725.
6. Weber J.H. Binding and transport of metals by humic material. In: Frimmel F.H., Christman R.F., editors. Humic substances and their rolein the environment. - Chichester: John Wiley and Sons, 1988. P. 165-178.
7. Murphy E.M., Zachara J.M. The role of sorbedhumic substances onthe distribution of organic and inorganic contaminants in groundwater // Geoderma. – 1995. - Vol. 67. - Р. 103–124.
8. Christl I., Knicker H., Kogel I.K., Kretzschmar R. Chemical heterogeneityof humic substances: Characterization of size fractionsobtained by hollow-fibre ultrafiltration // Eur J Soil Sci. – 2000. - Vol. 510. - P. 617–625.
9. Piccolo A., Spaccini R., Nieder R. Sequestration of a biologicallylabile organic carbon in soils by humified organicmatter // Climatic Change. – 2004. –Vol. 67, No. 2-3. - P. 329-343.
10. Bandeira M., Mosca G., Vamerali T. Humic acids affect rootcharacteristics of fodder radish (Raphanussativus L.var.oleiformis Pers.) in metal-polluted wastes // Desalination. – 2009. - Vol. 246, No. 1-3. - P. 78-91.
11. Badis A., Ferradji F.Z., Boucherit A., Fodil D., Boutoumi H. Characterization and biodegradation of soil humic acids and preliminary identification of decolorizing actinomycetes at Mitidja plain soil (Algeria) // Microbiol Res. - 2009. - Vol. 3, No. 13. - P. 997-1007.
12. Barros L., Canellas L.P., Lopes F., Oliveira N., Lazaro E., Piccolo A. Bioactivity of chemically transformed humic matterfrom vermicompost on plant root growth // Agric Food Chem. - 2010. - Vol. 58, No. 6. - P. 3681-3688.
13. Fakoussa R.M. Investigation with microbial conversion of nationalcoals. - PhD thesis, University Bonn, 1981. - P. 634-642
14. Cohen M.S., Gabriele P.D. Degradation of coal by the fungi Polyporus versicolor and Poriamonticola // Appl Environ Microbiol. - 1982. - Vol. 51. - P. 437–447.
15. Fakoussa R.M, Hofrichter M. Biotechnology and microbiology of coal degradation // Appl. Microbiol. Biotechnol., - 1999. - Vol. 52. - P. 25–40.
16. Gupta A., Birenda K. Biogasification of coal using different sources of microorganisms // Fuel. – 2000. -Vol. 79. - P. 103–105.
17. Helena M., Kamila P., Anna P. Microbial degradation of low rank coals // Fuel Process Technol. – 2002. - Vol. 77/78. - P. 17–23.
18. Crowford D.L., Gupta R.K. Characterization of extracellular bacterial enzymes which depolymerize a soluble lignite coal polymer // Fuel - 1991. - Vol. 70. - P. 577–580.
19. Polman J.K., Brechkenridge C.R., Stoner D.L.. Biologically derived value-added products from coal // Appl Biochem Biotechnol. - 1995. - Vol. 54. - P. 249–255.
20. Davison B.H., Nicklaous D.M., Misra A., Lewis S.N., Faison BD. Utilization of microbially solubilized coal // Appl Biochem Biotechnol. - 1990. -Vol. 24, No 25. - P. 447–56.
21. Hess M., et al. Metagenomic discovery of biomass-degrading genes and genomes from cow rumen // Science. – 2011. - Vol. 331, No. 6016. - P. 463-467.
22. Avershina E., Trine F., Knut R. De novo Semi-alignment of 16S rRNA gene sequences for deep phylogenetic characterization of next generation sequencing data // Microbes and Environments. – 2013. - Vol. 28, No. 2. - P. 211-216.
23. Caporaso J.G., et al. Global patterns of 16S rRNA diversity at a depth of millions of period per sample // Proceedings of the National Academy of Sciences. - 2011. – Vol. 108. - P. 4516-4522.
24. Youssef N., et al. Comparison of species richness estimates using nearlyhed fragments and simulated pyrosequencing-fusion fragments in 16S rRNA gene-based environmental surveys // Applied and environmental microbiology. – 2009. - Vol. 75, No. 16. - P. 5227-5236.
25. Asnicar F., Weingart G., Tickle T.L, et al. Compact graphical representation of phylogenetic data and metadata with GraPhlAn. - PeerJ, 2015. - P. 1029.
26. DeSantis T.Z., et al. NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes // Nucleic acids research. – 2006. - Vol. 34., Suppl. 2. – Р. 394-399.
27. Brian О.D., Bergman N.H., Phillippy A.P. Interactive metagenomic visualization in a Web browser // BMC bioinformatics. – 2011. - Vol. 12, No. 1. - P. 385.
28. Bulgarelli D., Garrido-Oter R., Münch P.C., et al. Structure and function of the bacterial root microbiota in wild and domesticated barley // Cell host & microbe. - 2015. - Vol. 17, No. 3. – P.392-403.
29. Li B., et al. Characterization of tetracycline resistant bacterial community in saline activated sludge using batch stress incubation with high-throughput sequencing analysis // Water research. – 2013. - Vol. 47, No. 13. - P. 4207-4216.
30. Lundberg D.S., et al. Practical innovations for high-throughput amplicon sequencing // Nature methods. – 2013. - Vol. 10, No. 10. - P. 999-1002.
31. Lozupone C., Rob K. UniFrac: a new phylogenetic method for comparison microbial communities // Applied and environmental microbiology. – 2015. - Vol. 71, No. 12. - P. 8228-8235.
References
1. Avershina E., Trine F., and Knut R. (2013) De novo Semi-alignment of 16S rRNA Gene Sequences for Deep Phylogenetic Characterization of Next Generation Sequencing Data. Microbes and Environments vol. 28 no. 2, pp. 211-216.
2. Asnicar F, Weingart G, Tickle T.L, et al. (2015) Compact graphical representation of phylogenetic data and metadata with GraPhlAn [J]. PeerJ, p. 1029.
3. Bandeira M., Mosca G., Vamerali T. (2009) Humic acids affect rootcharacteristics of fodder radish (Raphanussativus L. var.oleiformis Pers.) in metal-polluted wastes. Desalination.,vol. 246, no. 1-3, pp. 78-91.
4. Badis A., Ferradji F.Z., Boucherit A., Fodil D., Boutoumi H. (2009) Characterization and biodegradation of soil humic acids andpreliminary identification of decolorizing actinomycetes atMitidja plain soil (Algeria). Microbiol Res.,vol. 3, no. 13, pp. 997-1007.
5. Barros L., Canellas L.P., Lopes F., Oliveira N., Lazaro E., Piccolo A. (2010) Bioactivity of chemically transformed humic matterfrom vermicompost on plant root growth. Agric FoodChem., vol. 58, no. 6, pp. 3681-3688.
6. Bulgarelli D, Garrido-Oter R, Münch P C, et al. (2015) Structure and function of the bacterial root microbiota in wild and domesticated barley [J]. Cell host & microbe, vol. 17, no. 3, 392-403.
7. Caporaso, J. Gregory, et al. (2011) Global patterns of 16S rRNA diversity at a depth of millions of period per sample. Proceedings of the National Academy of Sciences 108. Suk 1, pp. 4516-4522.
8. Christl I., Knicker H., Kogel I.K., Kretzschmar R. (2000) Chemical heterogeneityof humic substances: Characterization of size fractionsobtained by hollow-fibre ultrafiltration.Eur J Soil Sci.,vol . 510, pp. 617–25.
9. Cohen M.S., Gabriele P.D. (1982) Degradation of coal by the fungi Polyporus versicolor and Poriamonticola. Appl Environ Microbiol., vol. 51, pp. 437–47.
10. Crowford DL., Gupta R.K. (1991) Characterization of extracellular bacterial enzymes which depolymerize a soluble lignite coal polymer. Fuel.,vol. 70, pp. 577–80.
11. DeSantis, T.Z., et al. (2006) NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic acids research 34. Suppl 2, W394-W399.
12. Dai H., Xiek U. (1998) Lignite utilization technology. BeiJing.. Coal industry press. vol. 23 pp. 4-7.
13. Davison B.H., Nicklaous D.M., Misra A., Lewis S.N., Faison B.D. (1990) Utilization of microbially solubilized coal. Appl Biochem Biotechnol., vol. 24, no 25, pp. 447–56.
14. Fakoussa R.M. (1981) Investigation with microbial conversion of nationalcoals. PhD thesis, University Bonn. vol. 20, no. 4, pp. 634-642
15. Fakoussa R.M, Hofrichter M. (1999) Biotechnology and microbiology of coal degradation. ApplMicrobiolBiotechnol., vol. 52, pp. 25–40.
16. Gupta A., Birenda K. (2000) Biogasification of coal using different sources of micro-organisms. Fuel., vol. 79, pp. 103–5.
17. Nakagawa H., Namba A., Böhlmann M., Miura K. (2004) Hydrothermal dewatering of brown coal andcatalytic hydrothermal gasification of the organic compounds dissolving in the water using anovel Ni/carbon catalyst. Fuel., vol. 83, no. 6, pp. 719-725.
18. Weber J.H. Binding and transport of metals by humic material. In: Frimmel F.H., Christman R.F., editors. (1988) Humic substances and their rolein the environment. Chichester: John Wiley and Sons. pp. 165–78.
19. Murphy E.M., Zachara J.M. (1995) The role of sorbedhumic substances onthe distribution of organic and inorganic contaminants in groundwater. Geoderma., vol. 67, pp. 103–24.
20. Piccolo A., Spaccini R., Nieder R. (2004) Sequestration of a biologicallylabile organic carbon in soils by humified organicmatter. Climatic Change., vol .67, no. 2-3, pp. 329-343.
21. Helena M., Kamila P., Anna P. (2002) Microbial degradation of low rank coals. Fuel Process Technol. vol. 77/78, pp. 17–23.
22. Hess M., et al. (2011) Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science. vol. 331, no. 6016, pp. 463-467.
23. Yong W., Petersen J.N., Kaufman E.N. (1995) Modeling the biological solubilization of coal in a Liquid Fluidized-Bed Reactor. ApplBiochemBiotechnol.vol. 51, no. 52, pp. 437–47.
24. Lundberg D.S., et al. (2013) Practical innovations for high-throughput amplicon sequencing. Nature methods vol. 10, no. 10, pp. 999-1002.
25. Lozupone, Catherine, and Rob Knight. (2015) UniFrac: a new phylogenetic method for comparison microbial communities. Applied and environmental microbiology vol. 71, no. 12, pp. 8228-8235.
26. Brian О.D., Bergman N.H., Phillippy A.P. (2011) Interactive metagenomic visualization in a Web browser. BMC bioinformatics vol. 12, no. 1, p. 385.
27. Polman J.K., Brechkenridge C.R., Stoner D.L. (1995). Biologically derived value-added products from coal. Appl Biochem Biotechnol., vol. 54, pp. 249–55.
28. Xu X.H., Chen C.H., Qi H.Y. (2000) Development of coal combustion pollution control for SO2 and NOx in China. Fuel Processing Technol.,vol. 62, no. 2/3, pp. 153-160.
29. Youssef N., et al. (2009) Comparison of species richness estimates using nearlyhed fragments and simulated pyrosequencing-fusion fragments in 16S rRNA gene-based environmental surveys. Applied and environmental microbiology. vol. 75, no. 16, pp. 5227-5236.
30. Yuan H., Yang J., Wang F. et al. (2002) The prospect of microbial sustainable utilization of lignite. World Science-Technology research and Development., vol. 24 no. 3, pp. 13 - 17.
31. Li B., et al. (2013) Characterization of tetracycline resistant bacterial community in saline activated sludge using batch stress incubation with high-throughput sequencing analysis. Water research, vol. 47, no. 13, pp. 4207-4216.
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Как цитировать
Аkimbekov N. S., Qiao, X., Tastambek K. Т., Digel, L., Abdieva, G. Z., Ualieva, P. S., Berdikulov, B., & Zhubanova, A. A. (2018). Metagenomic analysis of microbial community in coal samples from Kazakhstan using Illumina NGS technology. ҚазҰУ Хабаршысы. Биология сериясы, 76(3), 28–39. https://doi.org/10.26577/eb-2018-3-1338
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МОЛЕКУЛЯРНАЯ БИОЛОГИЯ И ГЕНЕТИКА
