مقایسه روش‌های HRM و DGGE جهت بررسی ترکیب جوامع باکتریایی خاک در کاربری‌های اراضی مختلف

نوع مقاله : مقاله پژوهشی

نویسندگان

1 استادیار گروه علوم خاک- دانشگاه جیرفت

2 استاد گروه علوم خاک- دانشگاه فردوسی مشهد

3 دانشیار گروه علوم خاک- دانشگاه فردوسی مشهد

4 استادیار دانشکده کشاورزی و منابع طبیعی- دانشگاه آزاد اسلامی واحد کرج

چکیده

تغییر کاربری اراضی یکی از مهمترین فاکتورهایی است که جوامع ریزجانداران خاک را تحت تأثیر قرار داده که نقش محوری در اکثر فرایندهای بیوژئوشیمیایی و اکولوژیکی ایفا می‌کنند. به‌منظور بررسی تأثیر تغییر کاربری اراضی (از مراتع بوته‌زار به کشاورزی) روی ترکیب جوامع باکتریایی خاک، مطالعه‌ای با استفاده از آنالیز تفکیک‌پذیری بالای ذوب (HRM) و ‌روش ژل الکتروفورز با شیب واسرشت­ساز (DGGE) در سه کاربری اراضی باغی، زراعی و مرتع بوته‌زار در دشت جیرفت انجام شد. برای آنالیز HRM از نرم‎‌افزار جانبی دستگاه Real-time PCR که مجهز به این تکنیک است، استفاده شد. DGGE با استفاده از سیستم جهانی تشخیص جهش انجام شد. نتایج تکنیک HRM و همپنین نتایج رج‌بندی با استفاده از روش مقیاس‌بندی چند بعدی غیرمتریک (NMDS) و بر پایه حضور یا عدم حضور باندهای DGGE در نمونه‌های خاک نشان دادند که تغییر کاربری اراضی از مراتع بوته‌زار به کشاورزی (باغ و زراعی) سبب تغییر معنی‌دار در ترکیب جوامع باکتریایی خاک شده است. همچنین با توجه به نتایج هر دو روش، ترکیب جوامع باکتریایی خاک در کاربری­های اراضی کشاورزی (باغ و زراعی) نسبت به کاربری مرتع بوته‌زار دارای شباهت بیشتری بود. از آنجایی که آنالیز HRM در مقایسه با تکنیک DGGE کم هزینه­تر، راحت­تر و دارای انحراف کمتر می­باشد، جهت مقایسه ترکیب جوامع باکتریایی خاک بین نمونه‌های مختلف پیشنهاد می­شود.

کلیدواژه‌ها

موضوعات

عنوان مقاله [English]

Comparison of HRM and DGGE methods to study the composition of soil bacterial communities indifferent land uses

نویسندگان [English]

  • ghobad jalali 1
  • Amir Lakzian 2
  • Alireza Astaraei 3
  • Mahboobe Mazhari 4
1 Assistant Professor, Department of Soil Science, University of Jiroft
2 Professor, Department of Soil Science, Ferdowsi University of Mashhad
3 Associate Professor, Department of Soil Science, Ferdowsi University of Mashhad
4 Assistant Professor, Faculty of Agriculture and Natural Resources, Karaj Islamic Azad University
چکیده [English]

Land use change is one of the most important factors influencing soil microbial communities which play a pivotal role in most biogeochemical and ecological processes. In order to determine the effect of land use on the composition of soil bacterial communities, High Resolution Melt (HRM) analysis and Denaturing Gradient Gel Electrophoresis (DGGE) were used in three different land uses (orchard land, farmland and shrub land) in Jiroft plain, Iran. In the case of HRM analysis, a real-time PCR device equipped with this technique was used. DGGE technique via DCodeTM Universal Mutation Detection System was conducted to evaluate the composition of soil bacterial communities. The results of HRM as well as the ordination results based on the presence or absence of DGGE bands in soil samples using non-metric multidimensional scaling (NMDS) method showed that the land-use change from shrub land to agriculture (orchard and farm) had a significant effect on the soil bacterial community composition. According to the results of both methods, the soil bacterial community composition in agricultural lands (orchard and farm) was more similar than shrub land. Since HRM analysis is less expensive, easier and has less bias compared to DGGE technique, it is recommended to compare the composition of soil bacterial communities in different samples.

کلیدواژه‌ها [English]

  • Genomic DNA from soil
  • Soil bacterial 16S rDNA
  • Real-time PCR
  • Non-metric multidimensional scaling (NMDS)

مراجع

  1. 1. بنایی، ح.م. 1380. نقشه منابع و استعداد خاک‎های ایران. مؤسسه تحقیقات خاک و آب. تهران، ایران.

    1. طباطبایی، م. و پورمظاهری، ه. 1391. متاژنومیکس و کاربرد آن در شناسایی تنوع ژنتیکی اکوسیستم‌های میکروبی. مجله ژنتیک نوین، دوره هفتم، شماره 4. صفحه 324-313.
    2. نوری دلویی، م.ر. و فرجی، ک. 1394. فن ذوب DNA با تفکیک بالا و کاربردهای راهبردی آن به‌ویژه در ژنتیک مولکولی. فصلنامه افق دانش، دوره 22، شماره 1. صفحه 88-77.
    3. Ahmad Suleiman A.K., Pylro V.S., and Wurdig Roesch L.F. 2017. Replacement of native vegetation alters the soil microbial structure in the Pampa biome. Scientia Agricola, 74: 77-84.
    4. Bevivino A., Paganin P., Bacci G., Florio A., Pellicer M.S., Papaleo M.C., Mengoni A. Ledda L., Fani R., Benedetti A., and Dalmastri C. 2014. Soil bacterial community response to differences in agricultural management along with seasonal changes in a Mediterranean region. PLoS ONE, 9(8): e105515.
    5. Bossio, D.A., Girvan, M.S., Verchot, L., Bullimore, J., Borelli, T., Albrecht, A., Scow, K.M., Ball, A.S., Pretty, J.N., and Osborn, A.M. 2005. Soil microbial community response to land use change in an agricultural landscape of Western Kenya. Microbial Ecology, 49: 50-62.
    6. Bouyoucos G.J. 1962. Hydrometer method improved for making particle size analyses of soils. Agronomy Journal, 54: 464-465.
    7. Bremner J.M. 1960. Determination of nitrogen in soil by the Kjeldahl method. The Journal of Agricultural Science, 55: 11-33.
    8. Crecchio, C., Gelsomino, A., Ambrosoli, R., Minati, J.L. and Ruggiero, P. 2004. Functional and molecular responses of soil microbial communities under differing soil management practices. Soil Biology and Biochemistry, 36: 1873-1883.
    9. De Lipthay, J.R., Enzinger, C., Johnsen, K., Aamand, J., and Sorensen, S.J. 2004. Impact of DNA extraction method on bacterial community composition measured by denaturing gradient gel electrophoresis. Soil Biology and Biochemistry, 36: 1607-1614.
    10. Ding, G.C., Piceno, Y.M., Heuer, H., Weinert, N., Dohrmann, A.B., Carrillo, A., Andersen, G.L., Castellanos, T., Tebbe, C.C., and Smalla, K. 2013. Changes of soil bacterial diversity as a consequence of agricultural land use in a semiarid ecosystem. PLoS ONE, 8(3): e59497.
    11. Fierer N., Jackson J.A., Vilgalys R., and Jackson R.B. 2005. Assessment of Soil Microbial Community Structure by Use of Taxon-Specific Quantitative PCR Assays. Applied and Environmental Microbiology, 71: 4117-4120.
    12. Foti M., Sorokin D.Y., Lomans B., Mussman M., Zacharova E.E., Pimenov N.V., Kuenen J.G., and Muyzer G. 2007. Diversity, activity, and abundance of sulfate-reducing bacteria in saline and hypersaline soda lakes. Applied Environmental Microbiology, 73: 2093-2100.
    13. Govaerts B., Mezzalama M., Unno Y., Sayre K.D., Luna-Guido M., Vanherck K., Dendooven L., and Deckers, J. 2007. Influence of tillage, residue management, and crop rotation on soil microbial biomass and catabolic diversity. Applied Soil Ecology, 37: 18-30.
    14. Helmke P.A., and Sparks D.L. 1996. Lithium, sodium, potassium, rubidium, and cesium. In: Sparks D.L. (Ed.), Methods of Soil Analysis-Part 3. Chemical Methods-SSSA Book Series No. 5. Soil Science Society of America and American Society of Agronomy, Madison, Wisconsin, USA, pp. 551-574.
    15. Hernesmaa, A., Björklöf, K., Kiikkilä, O., Fritze, H., Haahtela, K., and Romantschuk, M. 2005. Structure and function of microbial communities in the rhizosphere of Scots pine after tree-felling. Soil Biology and Biochemistry, 37: 777-785.
    16. Hjelms M.H., Hansen L.H., Blum J., Feld L., Holben W.E., and Jacobsen C.S. 2014. High-Resolution Melt Analysis for Rapid Comparison of Bacterial Community Compositions. Applied and Environmental Microbiology, 80: 3568-3575.
    17. Hoshino, Y.T., and Matsumoto, N. 2007. DNA- versus RNA-based denaturing gradient gel electrophoresis profiles of a bacterial community during replenishment after soil fumigation. Soil Biology and Biochemistry, 39: 434-444.
    18. Hu J., Lin X., Wang J., Dai J., Chen R., Zhang J., and Wong, M.H. 2011. Microbial functional diversity, metabolic quotient, and invertase activity of a sandy loam soil as affected by long-term application of organic amendment and mineral fertilizer. Journal of Soils and Sediments, 11: 271-278.
    19. Kent, A.D., and Triplett, E.W. 2002. Microbial communities and their interactions in soil and rhizosphere ecosystems. Annual Review of Microbiology, 56: 211-236.
    20. Knauth S., Schmidt H., and Tippkootter R. 2012. Comparison of commercial kits for the extraction of DNA from paddy soils. Letters in Applied Microbiology, 56: 222-228.
    21. Kolb S., Knief C., Stubner S., and Conrad R. 2003. Quantitative detection of methanotrophs in soil by novel pmoA-targeted real-time PCR assays. Applied Environmental Microbiology, 69: 2423-2429.
    22. Lauber C.L., Ramirez K.S., Aanderud Z., Lennon J., and Fierer N. 2013. Temporal variability in soil microbial communities across land-use types. ISME Journal, 7: 1641-1650.
    23. Lauber C.L., Strickland M.S., Bradford M.A., and Fierer N. 2008. The influence of soil properties on the structure of bacterial and fungal communities across land-use types. Soil Biology and Biochemistry, 40: 2407-2415.
    24. Lindsay W.L., and Norvell W.A. 1978. Development of a DTPA Soil Test for Zinc, Iron, Manganese, and Copper. Soil Science Society of America Journal, 42(3): 421-428.
    25. Liu, E., Yan, C., Mei, X., He, W., Bing, S.H., Ding, L., Liu, Q., Liu, S., and Fan, T. 2010. Long term effect of chemical fertilizer, straw, and manure on soil chemical and biological properties in northwest China, Geoderma, 158: 173-180.
    26. Loeppert R.H., and Suarez, D.L. 1996. Carbonate and gypsum. In: Sparks D.L. (Ed.), Methods of Soil Analysis-Part 3. Chemical Methods-SSSA Book Series No. 5. Soil Science Society of America and American Society of Agronomy, Madison, Wisconsin, USA, pp. 437-474.
    27. Long, L.K., Yao, Q., Guo, J., Yang, R.H., Huang, Y.H., and Zhu, H.H. 2010. Molecular community analysis of arbuscular mycorrhizal fungi associated with five selected plant species from heavy metal polluted soils. European Journal of Soil Biology, 46:288-294.
    28. Marschner P., Yang C-H., Lieberei R., and Crowley D.E. 2001. Soil and plant specific effects on bacterial community composition in the rhizosphere. Soil Biology and Biochemistry, 33: 1437-1445.
    29. Muyzer, G., de Waal, E.C., and Uitterlinden, A.G. 1993. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Applied and Environmental Microbiology, 59: 695-700.
    30. Nakatsu, C.H. 2007. Soil microbial community analysis using denaturing gradient gel electrophoresis. Soil Science Society of America Journal, 71: 562-571.
    31. Olsen S.R., and Sommers L.E. 1982. Phosphorus. In: Page A.L. (Ed.), Methods of Soil Analysis-Part 2. Chemical and Microbiological Properties-Agronomy Monograph 9, 2nd Ed. Soil Science Society of America and American Society of Agronomy, Madison, Wisconsin, USA, pp. 403-430.
    32. Rhoades J.D. 1996. Salinity: Electrical conductivity and total dissolved solids. In: Sparks D.L. (Ed.), Methods of Soil Analysis-Part 3. Chemical Methods-SSSA Book Series No. 5. Soil Science Society of America and American Society of Agronomy, Madison, Wisconsin, USA, pp. 417-435.
    33. Ritz, K., Mac Nicol, J.W., Nunan, N., Grayston, S., Millard, P., Atkinson, A., Gollotte, A., Habeshaw, D., Boag, B., and Clegg, C.D. 2004. Spatial structure in soil chemical and microbiological properties in upland grassland. FEMS Microbiology Ecology, 49: 191-205.
    34. Shen, J.P., Zhang, L.M., Guo, J.F., Ray, J.L., and He, J.Z. 2010. Impact of long-term fertilization practices on the abundance and composition of soil bacterial communities in Northeast China, Applied Soil Ecology, 46: 119-24.
    35. Smit, E., Leeflang, P., Gommans, S., van den Broek, J., van Mil, S., and Wernars, K. 2001. Diversity and seasonal fluctuations of the dominant members of the bacterial soil community in a wheat field as determined by cultivation and molecular methods. Applied and Environmental Microbiology, 67: 2284-2291.
    36. Soni R., and Goel R. 2010. Triphasic approach to assessment of bacterial population in different soil systems. Ekologija, 56: 99-104.
    37. Tao, S.Q., Xia, Q., Zhu, L., Chen, J.J., Wang, Y.N., and Qin, B. 2012. Analysis of the bacterial communities in lime concretion black soil upon the incorporation of crop residues. Open Journal of Soil Science, 9: 312-319.
    38. Tebbe C.C., and Schloter M. 2007. Discerning the diversity of soil prokaryotes (Bacteria and Archaea) and their impact on agriculture. In: Benckiser G. and Schnell S. (Ed.), Biodiversity in agricultural production systems. CRC Press, Taylor and Francis Group, UK, pp. 81-100.
    39. Thomas G.W. 1996. Soil pH and soil acidity. In: Sparks D.L. (Ed.), Methods of Soil Analysis-Part 3. Chemical Methods-SSSA Book Series No. 5. Soil Science Society of America and American Society of Agronomy, Madison, Wisconsin, USA, pp. 475-490.
    40. Wakelin, S.A., Macdonald, L.M., Rogers, S.L., Gregg, A.L., Bolger, T.P., and Baldock, J.A. 2008. Habitat selective factors influencing the structural composition and functional capacity of microbial communities in agricultural soils. Soil Biology and Biochemistry, 40: 803-813.
    41. Walkley A., and Black I.A. 1934. An examination of the Degtjareff method for determining soil organic matter, and a proposed modification of the chromic acid titration method. Soil Science, 37: 29-38.
    42. Wallis, P.D., Haynes, R.J., Hunter, C.H., and Morris, C.D. 2010. Effect of land use and management on soil bacterial biodiversity as measured by PCR-DGGE. Applied Soil Ecology, 46: 147-150.
    43. Webster G., Embley T.M., and Prosser J.I. 2002. Grassland management regimens reduce small-scale heterogeneity and species diversity of ß-Proteobacterial ammonia oxidizer populations. Applied Environment Microbiology, 68: 20-30.
    44. Xue D., Yao H., and Huang C. 2006. Microbial biomass, N mineralization and nitrification, enzyme activities, and microbial community diversity in tea orchard soils. Plant and Soil, 288: 319-331.
زیست شناسی خاک
دوره 10، شماره 1
فروردین 1401
صفحه 49-64

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