تاثیر کاربری اراضی روی فراوانی نسبی و ترکیب جوامع باکتریایی خاک

نوع مقاله: مقاله پژوهشی

نویسندگان

1 دانشگاه فردوسی مشهد

2 عضو هیات علمی گروه علوم خاک-دانشگاه فردوسی مشهد

3 عضو هیات علمی گروه علوم خاک- دانشگاه فردوسی مشهد

4 عضو هیات علمی گروه زیست‌شناسی- دانشگاه فردوسی مشهد

5 عضو هیات علمی گروه گیاهپزشکی، مرکز تحقیقات و آموزش کشاورزی و منابع طبیعی جنوب استان کرمان

6 عضو هیات علمی گروه علوم خاک- دانشگاه ولیعصر (عج) رفسنجان

چکیده

تغییر کاربری اراضی یکی از مهم‌ترین فاکتورهایی بوده که ضمن اثرگذاری روی جوامع ریزجانداران خاک، نقش محوری در اکثر فرآیندهای بیوژئوشیمیایی و اکولوژیکی ایفا می‌کنند. به‌منظور بررسی تأثیر تغییر کاربری اراضی (از مراتع بوته‌زار به کشاورزی) روی فراوانی نسبی و ترکیب جوامع باکتریایی خاک، مطالعه‌ای با استفاده از روش‌ Real-time PCR در سه کاربری اراضی (باغ، زراعی و بوته‌زار) در دشت جیرفت انجام شد. در هر کاربری 12 نمونه خاک سطحی از عمق 10 سانتی‌متری جمع‌آوری و برخی از ویژگی‌های فیزیکی و شیمیایی آن‌ها‌ اندازه‌گیری شدند. استخراج و خالص‌سازی DNA از نمونه‌های خاک با استفاده از کیت نوکلئواسپین سویل (NucleoSpin® Soil kit) انجام شد. با استفاده از دستگاه Real-time PCR و طبق روش منحنی استاندارد نسبی، مقایسه کمّی غلظت نسبی و دمای ذوب قطعات 16S rDNA باکتریایی خاک به‌ترتیب برای بررسی فراوانی نسبی و ترکیب جوامع باکتریایی خاک در کاربری‌های اراضی مختلف انجام شد. نتایج بررسی غلظت و کیفیت DNA های استخراج شده از نمونه‌های خاک نشان داد که استخراج و خالص‌سازی DNA با استفاده از کیت نوکلئواسپین سویل مطلوب بود. نتایج آنالیز واریانس یک طرفه ناپارامتریک کروسکال والیس (در سطح آماری پنج درصد) نشان داد که کاربری اراضی روی فراوانی نسبی و ترکیب جوامع باکتریایی خاک اثر معنی‌دار داشت؛ به‌طوری‌که میانگین فراوانی نسبی جوامع باکتریایی خاک در کاربری باغ بیش‌تر و با دو کاربری دیگر تفاوت معنی‌دار داشت. هم‌چنین ترکیب جوامع باکتریایی خاک در کاربری بوته‌زار با دو کاربری دیگر تفاوت معنیدار داشت. به‌طورکلی در دشت جیرفت تغییر کاربری اراضی از بوته‌زار به باغ و از بوته‌زار به باغ و زراعی به‌ترتیب سبب افزایش فراوانی نسبی و تغییر معنی‌دار ترکیب جوامع باکتریایی خاک شده است.

کلیدواژه‌ها


عنوان مقاله [English]

The impact of land use on the relative abundance and composition of soil bacterial communities

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 relative abundance and composition of soil bacterial communities by using Real-time PCR, a study was carried out in three different land uses (orchard land, farmland and shrubland) in Jiroft plain, Iran. 12 surface soil samples were collected from each land use and some soil physicochemical properties were measured. The NucleoSpin® Soil kit was used for extraction and purification of DNA from soil samples. Quantitative comparison of the concentration and melting temperature of 16S rDNA amplicons, respectively, for assessment of the relative abundance and composition of soil bacterial communities in different land uses were performed by using Real-time PCR system and based on the relative standard curve method. The results related to the concentration and quality of soil DNA indicated that extraction of DNA from soil samples by using NucleoSpin® Soil kit was favorable. As the results of Kruskal-Wallis nonparametric ANOVA showed, land use had significant effect on the relative abundance and composition of soil bacterial communities at the level of 5%. Means comparison showed that the relative abundance of soil bacterial communities in orchard land use was higher than that of two other land uses. Furthermore, the composition of soil bacterial communities in orchard and farm land uses was significantly different from shrub one. It can be concluded that land-use changes in Jiroft plain from shrubland to orchard land, and from shrubland to orchard land and farmland have caused an increase in the relative abundance as well as a significant change in the composition of soil bacterial communities, respectively.

کلیدواژه‌ها [English]

  • genomic DNA from soil
  • soil bacterial 16S rDNA
  • Real-time PCR
  • Jiroft plain
References

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.

Banaei, H.M. 2001. Map of Iran's soil resources and talent. Soil and Water Research Institute, Iran. (In Persian)

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.

Bouyoucos G.J. 1962. Hydrometer method improved for making particle size analyses of soils. Agronomy Journal, 54: 464-465.

Bremner J.M. 1960. Determination of nitrogen in soil by the Kjeldahl method. The Journal of Agricultural Science, 55: 11-33.

Bustin S.A., Benes V., Garson J.A., Hellemans J., Huggett J., Kubista M., Mueller R., Nolan T., Pfaffl M.W., Shipley G.L.,Vandesompele J. and Wittwer C.T. 2009. The MIQE Guidelines: Minimum Information for Publication of Quantitative Real-Time PCR Experiments. Clinical Chemistry, 55: 611-622.

Curtis T.P., Sloan W.T., and Scannell J.W. 2002. Estimating prokaryotic diversity and its limits. Proceedings of the National Academy of Sciences of the United States of America, 99: 10494-10499.

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.

Dong X., Ying Y.H., Yong G.E., and Yong H.C. 2008. Soil microbial community structure in diverse land use systems: A comparative study using Biolog, DGGE, and PLFA analyses. Pedosphere, 18(5): 653-663.

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.

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 and Environmental Microbiology, 73: 2093-2100.

Geography Organization of Armed Forces. 2005. Gazetteer of villages in Kerman province: the city of Jiroft. Vol. 5. 506p. (In Persian)

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.

Heid C.A., Stevens J., Livak K.J., and Williams P.M. 1996. Real-time quantitative PCR. Genome Resarch, 6: 986-994.

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.

Hermansson A., and Lindgren P-E. 2001. Quantification of Ammonia-Oxidizing Bacteria in Arable Soil by Real-Time PCR. Applied and Environmental Microbiology, 67: 972-976.

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.

Hoseini M., Montazeri F., Foroughmand A.M., Dehghani M.R., and Ghadimi H.R. 2014. Introduction to Genetic Testing – Applications, Advantages and Disadvantages. Genetics in the Third Millennium, 12(2): 3544-3563. (In Persian)

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.

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.

Hussain Q., Pan G.X., Liu Y.Z., Zhang A., Li L.Q., Zhang X.H., and Jin Z.J. 2012. Microbial community dynamics and function associated with rhizosphere over periods of rice growth. Plant, Soil and Environment, 58: 55-61.

Jangid K., Williams M.A., Franzluebbers A.J., Sanderlin J.S., Reeves J.H., Jenkins M.B., Endale D.M., Coleman D.C., and Whitman W.B. 2008. Relative impacts of land-use, management intensity and fertilization upon soil microbial community structure in agricultural systems. Soil Biology and Biochemistry, 40: 2843-2853.

Kamaa M., Mburu H., Blanchart E., Chibole L., Chotte J.L., Kibunja C., and Lesueur D. 2011. Effects of organic and inorganic fertilization on soil bacterial and fungal microbial diversity in the Kabete long term trial, Kenya. Biology and Fertility of Soils, 47: 315-321.

Kennedy A.C., and Gewin V.L. 1997. Soil microbial diversity: present and future considerations. Soil Science, 162: 607-617.

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.

Klein D. 2002. Quantification using real-time PCR technology: applications and limitations. Trends in Molecular Medicine, 8: 257-260.

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.

Koberl M., Muller H., Ramadan E.M., and Berg G. 2011. Desert farming benefits from microbial potential in arid soils and promotes diversity and plant health. PLOS ONE, 6(9): e24452.

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.

Kristof Verthe D.S., Reheul D., Bulcke R., Siciliano S.D., Verstraete W., and Top E.M. 2003. Effect of long-term herbicide applications on the bacterial community structure and function in an agricultural soil. FEMS Microbiology Ecology, 46: 139-146.

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.

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.

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.

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.

Mamnoon B., Naserpour Farivar T., and Karimi Arzenani M. 2015. Application of Rapid and Sensitive Real Time PCR Technique in Detection of DNA Impurities in Recombinant Interferon. Journal of Fasa University of Medical Sciences, 4(4): 382-391. (In Persian)

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.

Miethling R., Ahrends K., and Tebbe C.C. 2003. Structural differences in the rhizosphere communities of legumes are not equally reflected in community level physiological profiles. Soil Biology and Biochemistry, 35: 1405-1410.

Mohammadi J. 2006. Pedometrics, Vol 1: Classical statistic. Pelk press, Iran, 250p. (In Persian)

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.

Nagy M.L., Perez A., and Garcia-Pichel F. 2005. The prokaryotic diversity of biological soil crusts in the Sonoran Desert (Organ Pipe Cactus National Monument, AZ). FEMS Microbiology Ecology, 54: 233-245.

Noori-Daloii M.R., and Faraji K. 2016. High Resolution Melt Analysis (HRM) and its Strategic Applications Especially in Molecular Genetics. Quarterly of the Horizon of Medical Sciences, 22(1): 77-88. (In Persian).

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.

Peixoto R.S., Coutinho H.L.D., Rumjanek N.G., Macrae A., and Rosado A.S. 2002. Use of rpoB and 16S rRNA genes to analyse bacterial diversity of a tropical soil using PCR and DGGE. Letters in Applied Microbiology, 35: 316-320.

Ranjard L., Lejon D.P.H., Mougel C., Schehrer L., Merdinoglu D., and Chaussod R. 2003. Sampling strategy in molecular microbial ecology: influence of soil sample size on DNA fingerprinting analysis of fungal and bacterial communities. Environmental Microbiology, 5: 1111-1120.

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.

Soni R., and Goel R. 2010. Triphasic approach to assessment of bacterial population in different soil systems. Ekologija, 56: 99-104.

Tabatabaei M., and Pourmazaheri H. 2013. Metagenomics and its application in identification of genetic diversity of microbial ecosystems. Modern Genetics Journal, 7(4): 313-324. (In Persian)

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.

Tevfik Dorak, M. (Ed.). 2007.Real-time PCR. CRC Press, Taylor and Francis Group, UK, 333p.

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.

Waid J.S. 1999. Does soil biodiversity depend upon metabiotic activity and influences? Applied Soil Ecology, 13: 151-158.

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.

Wang G., Liu J., Qi X., Jin J., Wang Y., and Liu X. 2008. Effects of fertilization on bacterial community structure and function in a black soil of Dehui region estimated by Biolog and PCR-DGGE methods. Acta Ecologica Sinica, 28: 220-226.

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.

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.

Yao H., Bowman D., and Shi W. 2006. Soil microbial community structure and diversity in a turfgrass chronosequence: land-use change versus turfgrass management. Applied Soil Ecology, 34: 209-218.