Taxonomic structure of bacterial communities of rhizospheric soil under bog plants

Abstract

For the first time, the ratio of large taxa and the genera spectrum in the prokaryotic complex of the rhizosphere soil under typical plants of bogs were revealed by high-performance sequencing. The dominance of acidobatheria and alpha-proteobacteria was established with a low proportion of other taxa (less than 10%). Among the 24 bacterial genera found, representatives of the phylums Acidobacteria and Actinobacteria, as well as the Alphaproteobacteria class, predominate. Common bacterial genera were identified in rhizosphere soil under plants and surface layers of peat. Representatives of most of these bacteria are adapted to grow in an acidic environment and at low temperatures. Their functioning is determined by the use of various sugars, polysaccharides, aromatic compounds, organic and amino acids. Bacteria of the genera Cytophaga and Acidothermus are capable of cellulose destruction, Occallatibacter - chitin, Nocardia - humic substances and lignin.

References

1. Bondoso J., Albuquerque L., Nobre M.F. et al. Aquisphaera giovannonii gen. nov., sp. nov., a planctomycetes isolated from a freshwater aquarium // Int. J. Syst. Evol. Microbiol. 2011. Vol. 61, N 12.

2. Bragina A., Berg C., Cardinale M. et al. Sphagnum mosses harbour highly specific bacterial diversity during their whole lifecycle // ISME J. 2012. N 6.

3. Bragina A., Berg C., Berg G. The core microbiome bonds the Alpine bog vegetation to a transkingdom metacommunity // Molec. Ecol. 2015. Vol. 24.

4. Chin K.J., Liesack W., Janssen P.H. Opitutus terrae gen. nov., sp. nov., to accommodate novel strains of the division “Verrucomicrobia” isolated from rice paddy soil // Int. J. Syst. Evol. Microbiol. 2001. Vol. 51.

5. Dedysh S.N. Cultivating uncultured bacteria from northern wetlands: knowledge gained and remaining gaps // Front. Microbiol. 2011. N 2. doi:10.3389/fmicb.2011.00184

6. Dedysh S.N., Pankratov T.A., Belova S.E. et al. Phylogenetic analysis and in situ identification of Bacteria community composition in an acidic Sphagnum peat bog // Appl. Environ. Microbiol. 2006. Vol. 72, N 3.

7. Falagan C., Johnson D.B. Acidibacterferrireducens gen. nov., sp. nov.; an acidophilic ferric iron-reduction gammaproteobacterium // Extremophilus. 2014. Vol. 18, N 6.

8. Foesel B.U., Mayer S., Luckner M. et al. Occallatibacter riparius gen. nov., sp. nov. and Occallatibacter avannae sp. nov., acidobacteria isolated from Namibian soils, and emended description of the family Acidobacteriaceae // Int. J. Syst. Evol. Microbiol. 2016. Vol. 66, N 1.

9. Jones F.P., Clark I.M., King R. et al. Novel European free-living, non-diazotrophic Bradyrhizobium isolates from contrasting soils that lack nodulation and nitrogen fixation genes — a genome comparison // Sci. Rep. 2016. Vol. 6. Article number: 25858.

10. Kampfer P., Young C.C., Arun A.B. et al. Pseudolabrys taiwanensis gen. nov., sp. nov., an alphaproteobacterium isolated from soil // Int. J. Syst. Evol. Microbiol. 2006. Vol. 56, N 10.

11. Kishimoto N., Kosako N., Wakao N. et al. Transfer of Acidiphilium facilis and Acidiphilium aminolytica to the genus Acidocella gen. nov., and emendation of the genus Acidiphilium // Syst. Appl. Microbiol. 1995. Vol. 18, N 1.

12. Kulichevskaya I.S., Danilova O.V, Tereshina V.M. et al. Descriptions of Roseiarcus fermentans gen. nov., sp. nov., a bacteriochlorophyll containing fermentative bacterium phylogenetically related to alphaproteobacterial methanotrophs, and of the family Roseiarcaceae fam. nov. // Int. J. Syst. Evol. Microbiol. 2014. Vol. 64.

13. Kulichevskaya I.S., Ivanova A.O., Baulina O.l. et al. Singulisphaera acidiphila gen. nov., sp. nov., a nonfilamentous, Isosphaera-like planctomycete from acidic northern wetlands // Int. J. Syst. Evol. Microbiol. 2008. Vol. 58, N5.

14. Kulichevskaya I.S., Kostina L.A., Valaskova V.W. et al. Acidicapsa borealis gen. nov., sp. nov. and Acidicapsa ligni sp. nov., subdivision 1 Acidobacteria from Sphagnum peat and decaying wood I I Int. J. Syst. Evol. Microbiol. 2012. Vol. 62, N7.

15. Kulichevskaya I.S., Pankratov T.A., Dedysh S.N. Detection of representatives of the Planctomycetes in Sphagnum peat bogs by molecular and cultivation approaches // Microbiology. 2006. Vol. 75.

16. Kulichevskaya I.S., Suzina N.E., Liesack W., Dedysh S.N. Bryobacter aggregatus gen. nov., sp. nov., a peat-inhabiting, aerobic chemoorganotroph from subdivision 3 of the Acidobacteria 11 Int. J. Syst. Evol. Microbiol. 2010. Vol. 60.

17. Leys N.M., Ryngaert A., Bastiaens L. et al. Occurrence and community composition of fast-growing Mycobacterium in soils contaminated with polycyclic aromatic hydrocarbons // FEMS Microbiol. Ecol. 2005. Vol. 51, N 3.

18. Mohagheghi A. Isolation and characterization of Acidothermus cellulolyticus gen. nov., sp. nov., a new genus of thermophilic, acidophilic, cellulolytic bacteria // Int. J. Syst. Bacteriol. 1986. Vol. 36.

19. Monciardini P., Cavaletti L., Schumann P. et al. Conexibacter woesei gen. nov., sp. nov., a novel representative of a deep evolutionary line of descent within the class Actinobacteria // Int. J. Syst. Evol. Microbiol. 2003. Vol. 53, N 2.

20. Okamura K., Kawai A., Yamada T. et al. Acidipila rosea gen. nov., sp. nov., an acidophilic chemoorganotrophic bacterium belonging to the phylum Acidobacteria // FEMS Microbiology Letters. 2011. Vol. 317, N 2. doi.org/ 10.1111/j. 1574-6968.2011.02224.x

21. Pankratov T.A., Dedysh S.N. Granulicella paludicola gen. nov., sp. nov., G.pectinivovorans sp. nov., G. aggregans sp. nov. and G. rosea sp. nov., novel acidophilic, polymer-degrading acidobacteria from Sphagnum peat bogs // Int. J. Syst. Evol. Microbiol. 2010. Vol. 60.

22. Pankratov Т.А., Serkebaeva Y.M., Kulichevskaya LS. et al. Substrate-induced growth and isolation of Acidobacteria from acidic Sphagnum peat // Int. J. Syst. Evol. Microbiol. 2008. Vol. 2.

23. Pankratov T.A., Tindall B.J., Liesack W., Dedysh S.N. Mucilaginibacter paludis gen. nov., sp., nov., and Mucilaginibacter gracilis, pectinxylan and laminarindegrading members of the family Sphingobacteraceae from acidic Sphagnum peat bog 11 Int. J. Syst. Evol. Microbiol. 2007. Vol. 57, N 10.

24. Sangwan P., Chen X., Hugenholtz P., Janssen P.H. Chthoniobacter flavus gen. nov., sp. nov., the First Pure Culture Representative of Subdivision Two, Spartobacteria classis nov., of the Phylum Verrucomicrobia // Appl. Environ. Microbiol. 2004. Vol. 70, N 10.

25. Seki T., Matsumoto A., Shimada R. et al. Conexibacter arvalis sp. nov., isolated from a cultivated field soil sample // Int. J. Syst. Evol. Microbiol. 2012. Vol. 62, N 10.

26. Serkebaeva Y.M., Kim Y., Liesack W, Dedysh S.N. Pyrosequencing-based assessment of the Bacteria diversity in surface and subsurface peat layers of a northern wetland, with focus on poorly studied phyla and candidate divisions // PLOS ONE. 2013. Vol. 8, N 5: e63994. doi: 10.1371/journal.pone.0063994

27. Singleton D.R., Furlong M.A., Peacock A.D. et al. Solirubrobacterpauli gen. nov., sp. nov., a mesophilic bacterium within the Rubrobacteridae related to common soil clones I I Int. J. Syst. Evol. Microbiol. 2003. Vol. 53, N 2.

28. Sizova M. V., Panikov N.S., Spiridonova E.M. et al. Novel facultative anaerobic acidotolerant Telmatospirillum siberiense gen. nov., sp. nov. isolated from mesotrophic fen // Syst. Appl. Microbiol. 2007. Vol. 30, N 3.

29. Talia P., Sede S.M., Campos E. et al. Biodiversity characterization of cellulolytic bacteria present on native Chaco soil by comparison of ribosomal RNA genes // Res. Microbiol. 2012. Vol. 163, N 3.

30. Upton M. Combined molecular ecological and confocal laser scanning microscopic analysis of peat bog methanogen populations // FEMS Microbiol. Letters. 2000. Vol. 193, N 2.

31. Vaninsberghe D., Maas K.R., Cardenas E. et al. Non-symbiotic Bradyrhizobium ecotypes dominate North American forest soils // ISME J. 2015. Vol. 9.