Metagenomic Analysis Reveals Correlation Between Microbiome Structure and Leonardite Characteristics from Kazakhstan Coal Deposits

A. A. Zhubanova; Q. Xiaohui; P. S. Ualieva; G. Zh. Abdieva; K. T. Tastambek; G. K. Kayrmanova; N. Sh. Akimbekov

doi:10.18321/ectj823

Authors

A. A. Zhubanova Scientific Research Institute of Biology and Biotechnology Problems, 71 al-Farabi ave., Almaty, Kazakhstan; Scientific Research Institute of Ecology Problems, 71 al-Farabi ave., Almaty, Kazakhstan; al-Farabi Kazakh National University, 71 al-Farabi ave., Almaty, Kazakhstan
Q. Xiaohui al-Farabi Kazakh National University, 71 al-Farabi ave., Almaty, Kazakhstan
P. S. Ualieva Scientific Research Institute of Ecology Problems, 71 al-Farabi ave., Almaty, Kazakhstan; al-Farabi Kazakh National University, 71 al-Farabi ave., Almaty, Kazakhstan
G. Zh. Abdieva Scientific Research Institute of Ecology Problems, 71 al-Farabi ave., Almaty, Kazakhstan; al-Farabi Kazakh National University, 71 al-Farabi ave., Almaty, Kazakhstan
K. T. Tastambek Scientific Research Institute of Ecology Problems, 71 al-Farabi ave., Almaty, Kazakhstan; al-Farabi Kazakh National University, 71 al-Farabi ave., Almaty, Kazakhstan
G. K. Kayrmanova Scientific Research Institute of Ecology Problems, 71 al-Farabi ave., Almaty, Kazakhstan; al-Farabi Kazakh National University, 71 al-Farabi ave., Almaty, Kazakhstan
N. Sh. Akimbekov Scientific Research Institute of Biology and Biotechnology Problems, 71 al-Farabi ave., Almaty, Kazakhstan; Scientific Research Institute of Ecology Problems, 71 al-Farabi ave., Almaty, Kazakhstan; al-Farabi Kazakh National University, 71 al-Farabi ave., Almaty, Kazakhstan

DOI:

https://doi.org/10.18321/ectj823

Keywords:

leonardite, coal characteristics, microbial diversity, microbial community, metagenomics

Abstract

Coal microbial communities have not been well examined, despite their importance in the formation and maintenance of terrestrial ecosystems. Microorganisms are geographically versatile, exhibit wide morphological diversity and provide a rich platform for studying energy and carbon flows through different ecosystems. The coal characteristics, in turn, are important environmental factors that control the composition, structure and activity of terrestrial bio-communities through various endogenous physiological and biochemical processes. The total phylogenetic structure of prokaryotes is closely related to their functional diversity and, ultimately, to the variety of environmental conditions in oxidized coal (leonardite). Metagenomic studies in this area attempt to assess the relationship between the coal properties and its microbiome. The microbial community of the coal profiles, collected from various Kazakhstan coal deposits, have been studied in detail for the first time using high-throughput sequencing. As part of this study, a wide range of leonardites generated in various bioclimatic and geomorphological conditions are considered. A comprehensive characterization of the phylogenetic structure and diversity of coal was given on the basis of the 16S rDNA gene analysis. The revealed features of the prokaryotic composition can be used as bioindicators of the leonardite condition. In addition, metagenomic characteristics of coals of different origin can serve as valuable platform to assess the terrestrial ecosystem health.

References

(1). S.L. Bend, Fuel 71 (1992) 851–870. Crossref DOI: https://doi.org/10.1016/0016-2361(92)90234-F

(2). M.J. Ghani, M.I. Rajoka, K. Akhtar, Biotechnol. Bioproc. E 20 (2015) 634–642. Crossref DOI: https://doi.org/10.1007/s12257-015-0162-5

(3). D.E.A. Catcheside, J.P. Ralph, Bioconversion of Coal by Fungi BT – Industrial Applications, in: H.D. Osiewacz (Ed.), Springer Berlin Heidelberg, Berlin, Heidelberg, 2002. P. 343– 354. Crossref DOI: https://doi.org/10.1007/978-3-662-10378-4_17

(4). R.M. Fakoussa, M. Hofrichter, Appl. Microbiol. Biot. 52 (1999) 25–40. Crossref DOI: https://doi.org/10.1007/s002530051483

(5). A.Y. Malik, M. Ali, A. Jamal, M.I. Ali, Geomicrobiol. J. 34 (2017) 109–118. Crossref DOI: https://doi.org/10.1080/01490451.2016.1143538

(6). A.J. Grethlein, M.K. Jain, Trends Biotechnol. 10 (1992) 418–423. Crossref DOI: https://doi.org/10.1016/0167-7799(92)90290-C

(7). E.P. Barnhart, E.P. Weeks, E.J.P. Jones, D.J. Ritter, J.C. McIntosh, A.C. Clark, L.F. Ruppert, A.B. Cunningham, D.S. Vinson, W. Orem, M.W. Fields, Int. J. Coal Geol.162 (2016) 14–26. Crossref DOI: https://doi.org/10.1016/j.coal.2016.05.001

(8). I. Romanowska, B. Strzelecki, S. Bielecki, Fuel Process. Technol. 131 (2015) 430–436. Crossref DOI: https://doi.org/10.1016/j.fuproc.2014.12.019

(9). Y. David, M.G. Baylon, S.D.V.N. Pamidimarri, K.A. Baritugo, C.G. Chae, Y.J. Kim, T.W. Kim, M.S. Kim, J.G. Na, S.J. Park, Biotechnol. Bioproc. E. 22 (2017) 178–185. Crossref DOI: https://doi.org/10.1007/s12257-016-0263-9

(10). C. Sergaki, B. Lagunas, I. Lidbury, M.L. Gifford, P. Schafer, Front. Plant Sci. 9 (2018) 1205. Crossref DOI: https://doi.org/10.3389/fpls.2018.01205

(11). J.K. Jansson, K.S. Hofmockel, Curr. Opin. Microbiol. 43 (2018) 162–168. Crossref DOI: https://doi.org/10.1016/j.mib.2018.01.013

(12). M.A. Lever, A. Torti, P. Eickenbusch, A.B. Michaud, T. Santl-Temkiv, B.B. Jorgensen, Front. Microbiol. 6 (2015) 476. Crossref DOI: https://doi.org/10.3389/fmicb.2015.00476

(13). K. Minas, C.J. Newbold, N.R. McEwan, K.P. Scott, FEMS Microbiol. Lett. 325 (2011) 162– 169. Crossref DOI: https://doi.org/10.1111/j.1574-6968.2011.02424.x

(14). T. Magoc, S.L. Salzberg, Bioinformatics 27 (2011) 2957–2963. Crossref DOI: https://doi.org/10.1093/bioinformatics/btr507

(15). N.A. Bokulich, S. Subramanian, J.J. Faith, D. Gevers, J.I. Gordon, R. Knight, D.A. Mills, J.G. Caporaso, Nat. Methods 10 (2013) 57–59. Crossref DOI: https://doi.org/10.1038/nmeth.2276

(16). J.G. Caporaso, J. Kuczynski, J. Stombaugh, K. Bittinger, F.D. Bushman, E.K. Costello, N. Fierer, A.G. Pena, J.K. Goodrich, J.I. Gordon, Nat. Methods 7 (2010) 335–336. Crossref DOI: https://doi.org/10.1038/nmeth.f.303

(17). R.C. Edgar, B.J. Haas, J.C. Clemente, C. Quince, R. Knight, Bioinformatics 27 (2011) 2194–2200. Crossref DOI: https://doi.org/10.1093/bioinformatics/btr381

(18). B.J. Haas, D. Gevers, A.M. Earl, M. Feldgarden, D.V. Ward, G. Giannoukos, D. Ciulla, D. Tabbaa, S.K. Highlander, E. Sodergen, Genome Res. 21 (2011) 494–504. Crossref DOI: https://doi.org/10.1101/gr.112730.110

(19). R.C. Edgar, Nat. Methods 10 (2013) 996–998. Crossref DOI: https://doi.org/10.1038/nmeth.2604

(20). T.Z. DeSantis, P. Hugenholtz, N. Larsen, M. Rojas, E.L. Brodie, K. Keller, T. Huber, D. Dalevi, P. Hu, G.L. Andersen, Appl. Environ. Microb. 72 (2006) 5069–5072. Crossref DOI: https://doi.org/10.1128/AEM.03006-05

(21). Q. Wang, G.M. Garrity, J.M. Tiedje, J.R. Cole, Appl. Environ. Microb. 73 (2007) 5261–5267. Crossref DOI: https://doi.org/10.1128/AEM.00062-07

(22). R.C. Edgar, Nucleic Acids Res. 32 (2004) 1792– 1797. Crossref DOI: https://doi.org/10.1093/nar/gkh340

(23). H. Daims, The Family Nitrospiraceae BT – The Prokaryotes: Other Major Lineages of Bacteria and The Archaea, in: E. Rosenberg, E.F. DeLong, S. Lory, E. Stackebrandt, et al. (Eds.), Springer Berlin Heidelberg, Berlin, Heidelberg, 2014. P. 733–749. Crossref

(24). S.G. Dastager, S. Krishnamurthi, N. Rameshkumar, M. Dharne, The Family Micrococcaceae BT – The Prokaryotes: Actinobacteria, in: E. Rosenberg, E.F. DeLong, S. Lory, E. Stackebrandt, et al. (Eds.), Springer Berlin Heidelberg, Berlin, Heidelberg, 2014. P. 455–498. Crossref DOI: https://doi.org/10.1007/978-3-642-30138-4_168

(25). M. Satomi, The Family Shewanellaceae BT – The Prokaryotes: Gammaproteobacteria, in: E. Rosenberg, E.F. DeLong, S. Lory, E. Stackebrandt, et al. (Eds.), Springer Berlin Heidelberg, Berlin, Heidelberg, 2014. P. 597– 625. Crossref DOI: https://doi.org/10.1007/978-3-642-38922-1_226

(26). A. Willems, The Family Phyllobacteriaceae BT – The Prokaryotes: Alphaproteobacteria and Betaproteobacteria, in: E. Rosenberg, E.F. DeLong, S. Lory, E. Stackebrandt, et al. (Eds.), Springer Berlin Heidelberg, Berlin, Heidelberg, 2014. P. 355–418. Crossref DOI: https://doi.org/10.1007/978-3-642-30197-1_298