COMPARISON OF C AND N MINERALIZATION AND METAGENOME ANALYSIS OF RHIZOSPHERE SOILS BELONGING TO DIFFERENT Colchicum L. SPECIES

Year 2022, , 1 - 13, 15.04.2022

İpek Ekici , Cengiz Darıcı , Zahraddeen Sanı Sadık Dinçer

https://doi.org/10.23902/trkjnat.971156

Cited By: 1

Abstract

This study is aimed at determining the characteristics and microbiota of soil upon which some Turkish Colchicum (Colchicaceae) species naturally grows. For this aim the rhizosphere soil samples of Colchicum balansae Planch., Colchicum triphyllum Kunze and Colchicum variegatum L. were analysed in this research. The carbon mineralization rate of C. balansae soil at p<0.05 is significantly different from that of the other two soils. In terms of nitrogen mineralization, significant difference exists between all the three soils (p<0.001). Colchicum variegatum rhizosphere was found to have the highest bacterial diversity. The results revealed that 254 bacterial species were common to the three rhizosphere soils, 35.60% of the bacterial species were unique to C. variegatum soil while 21.89% and 22.67% of the bacterial species were unique to C. balansae and C. triphyllum soil respectively. It was found that C. variegatum and C. balansae collected from areas close to each other had the highest number of common bacterial species, while C. triphyllum from the distant region shared 75 with C. variegatum and 19 with C. balansae. Metagenomics analysis reveals that in the rhizophere of C. variegatum, C. balansae and C. triphyllum, Actinobacteria is dominant at phylum level. Likewise, in C. variegatum soil, Nitrosocosmicus and halophilic Halobacter were found to be the dominant archaea. In the soils of C. triphyllum and C. balansae Saccharomycetales were detected, while Cryptococcus neoformans var. grubii H99 was exclusively detected in C. balansae soil. Significant difference (p<0.05) was observed in C. variegatum rhizosphere soil in terms of organic carbon (C%) and carbon mineralization from the other two soil samples. Significant differences were observed in all three soils in terms of nitrogen content, and the C. triphyllum rhizosphere soil was significantly different from the others in terms of available phosphorus content (p<0.05). This study showed that biological as well as the physico-chemical properties of the rhizosphere soil regulate soil microbial diversity and density and by extension influences their activity which evidently manifests itself in carbon and nitrogen mineralisation.

Keywords

C. balansae, C. variegatum, C. triphyllum, Soil, carbon and nitrogen mineralization, Microbiota, Rhizosphere

Supporting Institution

Çukurova University Research Projects Unit

Project Number

FYL-2020-12926

References

• 1. Alali, F.Q., Tawaha, K. & El-Elimat, T. 2007. Determination of (-)-demecolcine and (-)-colchicine content in selected Jordanian Colchicum species. Pharmazie, 62(10): 739-42.
• 2. Alef, K. & Nannipieri, P. 1995. Soil respiration, pp. 214-215. In: Alef, K., Nannipieri, P. (Eds). Methods in applied soil microbiology and biochemistry. Academic press, New york.
• 3. Allison, L. & Moodie, C. 1965. Carbonate. pp. 1379-1398. In: In: Black, C., Evans, D., Ensminger, L., White, J., Clark, F., Dinauer, R. (Eds). Methods of soil Analysis. American society of Agronomy Inc., Wisconsin.
• 4. Ayilara, M.S., Olanrewaju, O. S., Babalola, O. O. & Odeyemi, O. 2020. Waste Management through Composting: Challenges and Potentials. Sustainability, 12: 4456.
• 5. Barns, S., Cain, E., Sommerville, L. & Kuske, C. R. 2007. Acidobacteria phylum sequences in uranium-contaminated subsurface sediments greatly expand the known diversity within the phylum. Applied and Environmental Microbiology, 73(9): 3113.
• 6. Bashan, Y. & de-Bashan, L. 2010. How the plant growth-promoting bacterium Azospirillum promotes plant growth—A critical assessment. Advances in Agronomy, 108, 77-136.
• 7. Berg, G., Rybakova, D., Grube, M. & Köberl, M. 2016. The plant microbiome explored: Implications for experimental botany. Journal of Experimental Botany, 67(4): 995-1002.
• 8. Berg, M., Kiers, E., Driessen, G., Van Der Heijden, M., Kooi, B., Kuenen, F., Lieftıng, M., Verhoef, H. & Ellers, J. 2010. Adapt or disperse: Understanding species persistence in a changing world. Global Change Biology, 16(2): 587-598.
• 9. Bolyen, E., Rideout, J.R., Dillon, M.R., Bokulich, N.A., Abnet, C.C., Al-Ghalith, G.A., Alexander, H., Alm, E.J., Arumugam, M., Asnicar, F., Bai, Y,, Bisanz, J.E., Bittinger, K., Brejnrod, A., Brislawn, C.J., Brown, C.T., Callahan, B.J., Caraballo-Rodríguez, A.M., Chase, J., Cope, E.K., Da Silva, R., Diener, C., Dorrestein, P.C., Douglas, G.M., Durall, D.M., Duvallet, C., Edwardson, C.F., Ernst, M., Estaki, M., Fouquier, J., Gauglitz, J.M., Gibbons, S.M., Gibson, D.L., Gonzalez, A., Gorlick, K., Guo, J., Hillmann, B., Holmes, S., Holste, H., Huttenhower, C., Huttley, G.A., Janssen, S., Jarmusch, A.K., Jiang, L., Kaehler, B.D., Kang, K.B., Keefe, C.R., Keim, P., Kelley, S.T., Knights, D., Koester, I., Kosciolek, T., Kreps, J., Langille, M.G.I., Lee, J., Ley, R., Liu, Y.X., Loftfield, E., Lozupone, C., Maher, M., Marotz, C., Martin, B.D., McDonald, D., McIver, L.J., Melnik, A.V., Metcalf, J.L., Morgan, S.C., Morton, J.T., Naimey, A.T., Navas-Molina, J.A., Nothias, L.F., Orchanian, S.B., Pearson, T., Peoples, S.L., Petras, D., Preuss, M.L., Pruesse, E., Rasmussen, L.B., Rivers, A., Robeson, M.S., Rosenthal, P., Segata, N., Shaffer, M., Shiffer, A., Sinha, R., Song, S.J., Spear, J.R., Swafford, A.D., Thompson, L.R., Torres, P.J., Trinh, P., Tripathi, A., Turnbaugh, P.J., Ul-Hasan, S., van der Hooft, J.J.J., Vargas, F., Vázquez-Baeza, Y., Vogtmann, E., von Hippel. M., Walters, W., Wan, Y., Wang, M., Warren, J., Weber, K.C., Williamson, C.H.D., Willis, A.D., Xu, Z.Z., Zaneveld, J.R., Zhang, Y., Zhu, Q., Knight, R. & Caporaso, J.G. 2019. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology, 37, 852-857.
• 10. Bouyoucos, G. 1951. A Recalibration of the Hydrometer Method for Making Mechanical Analysis of Soils1. Agronomy Journal, 43(9): 434-438.
• 11. Braga, R., Dourado, M. & Araújo, W. 2016. Microbial interactions: Ecology in a molecular perspective. Brazilian Journal of Microbiology, 47, 86-98.
• 12. Bremmer, J. 1965. Total nitrogen. pp 1149-1178. In: Black, C., Evans, D., Ensminger, L., White, J., Clark, F. & Dinauer, R. (Eds). Methods of soil analysis. American society of Agronomy Inc., Madison.
• 13. Campbell, B. 2014. The family Acidobacteriaceae. pp 405-415. In Rosenberg, E., Delong, E., Lory, S., Stackebrandt, E. & Thompson, E. (Eds). The prokaryotes. Springer, Berlin.
• 14. Chaparro, J., Badri, D., Bakker, M., Sugiyama, A., Manter, D. & Vivanco, J. 2013. Root exudation of phytochemicals in Arabidopsis follows specific patterns that are developmentally programmed and correlate with soil microbial functions. PloS One, 8(2): e55731.
• 15. Classen, A., Sundqvist, M., Henning, J., Newman, G., Moore, J., Cregger, M., Moorhead, L. & Patterson, C. 2015. Direct and indirect effects of climate change on soil microbial and soil microbial-plant interactions: What lies ahead? Ecosphere, 6(8): 1-21.
• 16. Compant, S., Samad, A., Faist, H. & Sessitsch, A. 2019. A review on the plant microbiome: Ecology, functions, and emerging trends in microbial application. Journal of Advanced Research, 19, 29-37.
• 17. Costa, E., Pérez, J. & Kreft, J. 2006. Why is metabolic labour divided in nitrification? Trends in Microbiology, 14(5): 213-219.
• 18. Daims, H., Lebedeva, E, Pjevac, P., Han, P., Herbold, C., Albertsen, M., Jehmlich, N., Palatinszky, M., Vierheilig, J., Bulaev, A., Kirkegaard, R., von Bergen, M., Rattei, T., Bendinger, B., Nielsen, P. & Wagner, M. 2015. Complete nitrification banny Nitrospira bacteria. Nature, 528(7583): 504-509.
• 19. Demiralay, I. 1993. Toprak fiziksel analizleri. Atatürk üniversitesi Ziraat fakültesi yayınları, 131 pp.
• 20. Duchaufour, P. 1970. Précis de Pédologie. Masson et Cie, Paris, 435-436 pp.
• 21. Evans, W.C. 2002. Trease and Evans. Pharmacognosy, WB Saunders. Edinburgh, London: 72 pp.
• 22. Fukami, J., Cerezini, P., & Hungria, M. 2018. Azospirillum: Benefits that go far beyond biological nitrogen fixation. AMB Express, 8, 73. https://doi.org/10.1186/s13568-018-0608-1
• 23. Gökçeoğlu, M. 1979. Bazı bitki organlarındaki azot, fosfor ve potasyumun bir vegetasyon periyodundaki değişimi. Doğa tarım ve ormancılık, 3, 192-199.
• 24. Hassani, M., Durán, P. & Hacquard, S. 2018. Microbial interactions within the plant holobiont. Microbiome, 6, 58.
• 25. Hogan, C. 2010. Bacteria. In: Draggon, S. (Eds). Encyclopaedia of Earth. National council for science and the environment, Washington DC. http://editors.eol.org/eoearth/wiki/Bacteria (Date accessed: 18.09.2017)
• 26. Jackson, M. 1958. Soil chemical analysis. Prentice Hall Inc, Engle-wood Cliffs, 111-133 pp.
• 27. Katsy, E. 2014. Plasmid rearrangements and changes in cell-surface architecture and social behaviour of Azospirillum brasilense, 81-97. In: Katsy, E (Eds). Plasticity in plant-growth-promoting and phytopathogenic bacteria. Springer, New york.
• 28. Kielak, A., Barreto, C., Kowalchuk, G., van Veen, J. & Kuramae, E. 2016. The Ecology of Acidobacteria: Moving beyond Genes and Genomes. Frontiers in Microbiology, 7, 744.
• 29. Kishimoto, N., Kosako, Y. & Tano, T. 1991. Acidobacterium capsulatum gen. nov., sp. nov.: An acidophilic chemoorganotrophic bacterium containing menaquinone from acidic mineral environment. Current Microbiology, 22, 1-7.
• 30. Koch, H., Lücker, S., Albertsen, M., Kitzinger, K., Herbold, C., Spieck, E., Nielsen, P. H., Wagner, M. & Daims, H. 2015. Expanded metabolic versatility of ubiquitous nitrite-oxidizing bacteria from the genus Nitrospira. Proceedings of the National Academy of Sciences, 112(36): 11371-11376.
• 31. Lakshmanan, V., Selvaraj, G. & Bais, H. 2014. Functional soil microbiome: Belowground solutions to an aboveground problem. Plant Physiology, 166(2): 689-700.
• 32. Lemee, G. 1967. Investigations sur la mineralization de L’azote et son evolution annuelle dans des humus forestiers in situ. Oecologia, 2, 285-324.
• 33. Madigan, M., Martinko, J. & Parker, J. 2003. Brock biology of microorganisms. Prentice Hall,Pearson Education Inc., New York, 606-620 pp.
• 34. Mendes, R. & Raaijmakers, J. 2015. Cross-kingdom similarities in microbiome functions. The ISME Journal, 9(9): 1905-1907.
• 35. Olsen, S. 1954. Estimation of available phosphorus in soils by extraction with sodium bicarbonate. USDA circular Nr 939, US Govt. Print. Office, Washington, D.C.
• 36. Palomo, A., Jane Fowler, S., Gülay, A., Rasmussen, S., Sicheritz-Ponten, T. & Smets, B. 2016. Metagenomic analysis of rapid gravity sand filter microbial communities suggests novel physiology of Nitrospira spp. The ISME Journal, 10(11): 2569-2581.
• 37. Persson, K. 2007. Nomenclatural synopsis of the genus Colchicum (Colchicaceae), with some new species and combinations. Botanische Jahrbücher Für Systematik, Pflanzengeschichte Und Pflanzengeographie, 127(2): 165-242.
• 38. Pester, M., Maixner, F., Berry, D., Rattei, T., Koch, H., Lücker, S., Nowka, B., Richter, A., Spieck, E., Lebedeva, E., Loy, A., Wagner, M. & Daims, H. 2014. NxrB encoding the beta subunit of nitrite oxidoreductase as functional and phylogenetic marker for nitrite-oxidizing Nitrospira. Environmental Microbiology, 16(10): 3055-3071.
• 39. Rodriguez-Caballero, A., Ribera, A., Balcázar, J. & Pijuan, M. 2013. Nitritation versus full nitrification of ammonium-rich wastewater: Comparison in terms of nitrous and nitric oxides emissions. Bioresource Technology, 139, 195-202.
• 40. Rosenberg, E. 2013. The Prokaryotes: Alphaproteobacteria and Betaproteobacteria (p. 1012). https://doi.org/10.1007/978-3-642-30197-1
• 41. Thrall, P., Hochberg, M., Burdon, J. & Bever, J. 2007. Coevolution of symbiotic mutualists and parasites in a community context. Trends in Ecology & Evolution, 22(3): 120-126.
• 42. Toplan, G.G., Gurer, C. & Mat, A. 2016. Importance of Colchicum species in modern therapy and its significance in Turkey. Journal of the Faculty of Pharmacy of İstanbul University, 46(2): 129-144.
• 43. Uysal, E. & Kaya, E. 2019. Türkiye’de doğal olarak yetişen kır sümbülü (Bellevalia spp.) türlerinin yetiştiği topraklara ait özellikler. Mediterrenean Agricultural sciences, 32, 35-41.
• 44. van der Putten, W., Bardgett, R., Bever, J., Bezemer, T., Casper, B., Fukami, T., Kardol, P., Klironomos, J., Kulmatiski, A., Schweitzer, J., Suding, K., Van de Voorde, T. & Wardle, D. 2013. Plant–soil feedbacks: The past, the present and future challenges. Journal of Ecology, 101(2): 265-276.
• 45. van Kessel, M., Speth, D., Albertsen, M., Nielsen, P., Op den Camp, H., Kartal, B., Jetten, M. & Lücker, S. 2015. Complete nitrification by a single microorganism. Nature, 528(7583): 555-559.