Advertisement

Journal of Soils and Sediments

, Volume 8, Issue 5, pp 349–358 | Cite as

Microbial composition and diversity of an upland red soil under long-term fertilization treatments as revealed by culture-dependent and culture-independent approaches

  • Ji-Zheng He
  • Yong Zheng
  • Cheng-Rong Chen
  • Yuan-Qiu He
  • Li-Mei Zhang
SOILS, SEC 5 • SOIL AND LANDSCAPE ECOLOGY • RESEARCH ARTICLE

Abstract

Background, aim, and scope

Fertilization is an important agricultural practice for increasing crop yields. In order to maintain the soil sustainability, it is important to monitor the effects of fertilizer applications on the shifts of soil microorganisms, which control the cycling of many nutrients in the soil. Here, culture-dependent and culture-independent approaches were used to analyze the soil bacterial and fungal quantities and community structure under seven fertilization treatments, including Control, Manure, Return (harvested peanut straw was returned to the plot), and chemical fertilizers of NPK, NP, NK, and PK. The objective of this study was to examine the effects on soil microbial composition and diversity of long-term organic and chemical fertilizer regimes in a Chinese upland red soil.

Materials and methods

Soil samples were collected from a long-term experiment station at Yingtan (28°15′N, 116°55′E), Jiangxi Province of China. The soil samples (0–20 cm) from four individual plots per treatment were collected. The total numbers of culturable bacteria and fungi were determined as colony forming units (CFUs) and selected colonies were identified on agar plates by dilution plate methods. Moreover, soil DNAs were extracted and bacterial 16S rRNA genes and fungal 18S rRNA genes were polymerase chain reaction amplified, and then analyzed by denaturing gradient gel electrophoresis (DGGE), cloning, and sequencing.

Results

The organic fertilizers, especially manure, induced the least culturable bacterial CFUs, but the highest bacterial diversity ascertained by DGGE banding patterns. Chemical fertilizers, on the other hand, had less effect on the bacterial composition and diversity, with the NK treatment having the lowest CFUs. For the fungal community, the manure treatment had the largest CFUs but much fewer DGGE bands, also with the NK treatment having the lowest CFUs. The conventional identification of representative bacterial and fungal genera showed that long-term fertilization treatments resulted in differences in soil microbial composition and diversity. In particular, 42.4% of the identified bacterial isolates were classified into members of Arthrobacter. For fungi, Aspergillus, Penicillium, and Mucor were the most prevalent three genera, which accounted for 46.6% of the total identified fungi. The long-term fertilization treatments resulted in different bacterial and fungal compositions ascertained by the culture-dependent and also the culture-independent approaches.

Discussion

It was evident that more representative fungal genera appeared in organic treatments than other treatments, indicating that culturable fungi were more sensitive to organic than to chemical fertilizers. A very notable finding was that fungal CFUs appeared maximal in organic manure treatments. This was quite different from the bacterial CFUs in the manure, indicating that bacteria and fungi responded differently to the fertilization. Similar to bacteria, the minimum fungal CFUs were also observed in the NK treatment. This result provided evidence that phosphorus could be a key factor for microorganisms in the soil. Thus, despite the fact that culture-dependent techniques are not ideal for studies of the composition of natural microbial communities when used alone, they provide one of the more useful means of understanding the growth habit, development, and potential function of microorganisms from soil habitats. A combination of culture-dependent and culture-independent approaches is likely to reveal more complete information regarding the composition of soil microbial communities.

Conclusions

Long-term fertilization had great effects on the soil bacterial and fungal communities. Organic fertilizer applications induced the least culturable bacterial CFUs but the highest bacterial diversity, while chemical fertilizer applications had less impact on soil bacterial community. The largest fungal CFUs were obtained, but much lower diversity was detected in the manure treatment. The lowest bacterial and also fungal CFUs were observed in the NK treatment. The long-term fertilization treatments resulted in different bacterial and fungal compositions ascertained by the culture-dependent and also the culture-independent approaches. Phosphorus fertilizer could be considered as a key factor to control the microbial CFUs and diversity in this Chinese upland red soil.

Recommendations and perspectives

Soil fungi seem to be a more sensitive indicator of soil fertility than soil bacteria. Since the major limitation of molecular methods in soil microbial studies is the lack of discrimination between the living and dead, or active and dormant microorganisms, both culture-dependent and culture-independent methods should be used to appropriately characterize soil microbial diversity.

Keywords

Bacterial and fungal diversity Culture-dependent method Denaturing gradient gel electrophoresis Long-term experiment Organic fertilizer Red soil 

Notes

Acknowledgments

This work was financially supported by the Chinese Academy of Sciences (KZCX2-YW-408, KZCX1-YW-603) and the Natural Science Foundation of China (50621804, 40571082).

References

  1. Bridge P, Spooner B (2001) Soil fungi: diversity and detection. Plant Soil 232:147–154CrossRefGoogle Scholar
  2. Cai ZC, Qin SW (2006) Dynamics of crop yields and soil organic carbon in a long-term fertilization experiment in the Huang-Huai-Hai Plain of China. Geoderma 136:708–715CrossRefGoogle Scholar
  3. Cernansky S, Urik M, Sevc J, Khun M (2007) Biosorption and biovolatilization of arsenic by heat-resistant fungi. Environ Sci Pollut Res 14:31–35CrossRefGoogle Scholar
  4. Davis KER, Joseph SJ, Janssen PH (2005) Effects of growth medium, inoculum size, and incubation time on culturability and isolation of soil bacteria. Appl Environ Microbiol 71:826–834CrossRefGoogle Scholar
  5. Deacon LJ, Pryce-Miller EJ, Frankland JC, Bainbridge BW, Moore PD, Robinson CH (2006) Diversity and function of decomposer fungi from a grassland soil. Soil Biol Biochem 38:7–20CrossRefGoogle Scholar
  6. Ellis RJ, Neish B, Trett MW, Best JG, Weightman AJ, Morgan P, Fry JC (2001) Comparison of microbial and meiofaunal community analyses for determining impact of heavy metal contamination. J Microbiol Methods 45:171–185CrossRefGoogle Scholar
  7. Ellis RJ, Morgan P, Weightman AJ, Fry JC (2003) Cultivation-dependent and -independent approaches for determining bacterial diversity in heavy-metal-contaminated soil. Appl Environ Microbiol 69:3223–3230CrossRefGoogle Scholar
  8. Enwall K, Philippot L, Hallin S (2005) Activity and composition of the denitrifying bacterial community respond differently to long-term fertilization. Appl Environ Microbiol 71:8335–8343CrossRefGoogle Scholar
  9. Ge Y, Zhang JB, Zhang LM, Yang M, He JZ (2008) Long-term fertilization regimes and diversity of an agricultural affect bacterial community structure soil in northern China. J Soils Sediments 8:43–50CrossRefGoogle Scholar
  10. Girvan MS, Bullimore J, Pretty JN, Osborn AM, Ball AS (2003) Soil type is the primary determinant of the composition of the total and active bacterial communities in arable soils. Appl Environ Microbiol 69:1800–1809CrossRefGoogle Scholar
  11. He JZ, Xu ZH, Hughes J (2006) Molecular bacterial diversity of a forest soil under residue management regimes in subtropical Australia. FEMS Microbiol Ecol 55:38–47CrossRefGoogle Scholar
  12. He JZ, Shen JP, Zhang LM, Zhu YG, Zheng YM, Xu MG, Di HJ (2007) Quantitative analyses of the abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea of a Chinese upland red soil under long-term fertilization practices. Environ Microbiol 9:2364–2374CrossRefGoogle Scholar
  13. Herai Y, Kouno K, Hashimoto M, Nagaoka T (2006) Relationships between microbial biomass nitrogen, nitrate leaching and nitrogen uptake by corn in a compost and chemical fertilizer-amended regosol. Soil Sci Plant Nutr 52:186–194Google Scholar
  14. Holt JG, Krieg NR, Sneath PHA, Staley JT, William ST (1994) Bergey’s manual of determinative bacteriology. Williams and Wilkins, Baltimore, USAGoogle Scholar
  15. Karlen DL, Ditzler CA, Andrews SS (2003) Soil quality: why and how? Geoderma 114:145–156CrossRefGoogle Scholar
  16. Kennedy AC (1999) Bacterial diversity in agroecosystems. Agric Ecosyst Environ 74:65–76CrossRefGoogle Scholar
  17. Kirk JL, Beaudette LA, Hart M, Moutoglis P, Klironomos JN, Lee H, Trevors JT (2004) Methods of studying soil microbial diversity. J Microbiol Meth 58:169–188CrossRefGoogle Scholar
  18. Kostanjsek R, Lapanje A, Drobne D, Perovic S, Perovic A, Zidar P, Strus J, Hollert H, Karaman G (2005) Bacterial community structure analyses to assess pollution of water and sediments in the Lake Shkodra/Skadar, Balkan Peninsula. Environ Sci Pollut Res 12:361–368CrossRefGoogle Scholar
  19. Mallarino AP, Borges R (2006) Phosphorus and potassium distribution in soil following long-term deep-band fertilization in different tillage systems. Soil Sci Soc Am J 70:702–707CrossRefGoogle Scholar
  20. May LA, Smiley B, Schmidt MG (2001) Comparative denaturing gradient gel electrophoresis analysis of fungal communities associated with whole plant corn silage. Can J Microbiol 47:829–841CrossRefGoogle Scholar
  21. Muyzer G (1999) DGGE/TGGE a method for identifying genes from natural ecosystems. Curr Opin Microbiol 2:317–322CrossRefGoogle Scholar
  22. Muyzer G, Dewaal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59:695–700Google Scholar
  23. Nubel U, Engelen B, Felske A, Snaidr J, Wieshuber A, Amann RI, Ludwig W, Backhaus H (1996) Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis. J Bacteriol 178:5636–5643Google Scholar
  24. Palmroth MRT, Koskinen PEP, Pichtel J, Vaajasaari K, Joutti A, Tuhkanen TA, Puhakka JA (2006) Field-scale assessment of phytotreatment of soil contaminated with weathered hydrocarbons and heavy metals. J Soils Sediments 6:128–136CrossRefGoogle Scholar
  25. Pernes-Debuyser A, Tessier D (2004) Soil physical properties affected by long-term fertilization. Eur J Soil Sci 55:505–512CrossRefGoogle Scholar
  26. Ratcliff AW, Busse MD, Shestak CJ (2006) Changes in microbial community structure following herbicide (glyphosate) additions to forest soils. Appl Soil Ecol 34:114–124CrossRefGoogle Scholar
  27. Sessitsch A, Weilharter A, Gerzabek MH, Kirchmann H, Kandeler E (2001) Microbial population structures in soil particle size fractions of a long-term fertilizer field experiment. Appl Environ Microbiol 67:4215–4224CrossRefGoogle Scholar
  28. Shen JP, Zhang LM, Zhu YG, Zhang JB, He JZ (2008) Abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea communities of an alkaline sandy loam. Environ Microbiol 10:1601–1611CrossRefGoogle Scholar
  29. Simek M, Hopkins DW, Kalcik J, Picek T, Santruckova H, Stana J, Travnik K (1999) Biological and chemical properties of arable soils affected by long-term organic and inorganic fertilizer applications. Biol Fertil Soils 29:300–308CrossRefGoogle Scholar
  30. Smit E, Leeflang P, Glandorf B, van Elsas JD, Wernars K (1999) Analysis of fungal diversity in the wheat rhizosphere by sequencing of cloned PCR-amplified genes encoding 18S rRNA and temperature gradient gel electrophoresis. Appl Environ Microbiol 65:2614–2621Google Scholar
  31. Thompson IP, Bailey MJ, Ellis RJ, Maguire N, Meharg AA (1998) Response of soil microbial communities to single and multiple doses of an organic pollutant. Soil Biol Biochem 31:95–105CrossRefGoogle Scholar
  32. Torsvik V, Daae FL, Sandaa RA, Ovreas L (1998) Novel techniques for analysing microbial diversity in natural and perturbed environments. J Biotechnol 64:53–62CrossRefGoogle Scholar
  33. Vainio EJ, Hantula J (2000) Direct analysis of wood-inhabiting fungi using denaturing gradient gel electrophoresis of amplified ribosomal DNA. Mycol Res 104:927–936CrossRefGoogle Scholar
  34. Vieira FCS, Nahas E (2005) Comparison of microbial numbers in soils by using various culture media and temperatures. Microbiol Res 160:197–202CrossRefGoogle Scholar
  35. Wei JC (1979) Manual of determinative mycology. Shanghai Science and Technology, Shanghai, ChinaGoogle Scholar
  36. Weissenhorn I, Leyval C (1996) Spore germination of arbuscular mycorrhizal fungi in soils differing in heavy metal content and other parameters. Eur J Soil Biol 32:165–172Google Scholar
  37. Westergaard K, Muller AK, Christensen S, Bloem J, Sorensen SJ (2001) Effects of tylosin as a disturbance on the soil microbial community. Soil Biol Biochem 33:2061–2071CrossRefGoogle Scholar
  38. Xu GH, Zheng HY (1986) Handbook of analysis methods of soil microbiology. Agricultural, Beijing, ChinaGoogle Scholar
  39. Xu ZH, Chen CR (2006) Fingerprinting global climate change and forest management within rhizosphere carbon and nutrient cycling processes. Environ Sci Pollut Res 13:293–298CrossRefGoogle Scholar
  40. Young AL (2006) Enhanced co-metabolism of TCDD in the presence of high concentrations of phenoxy herbicides. Environ Sci Pollut Res 13:149–150CrossRefGoogle Scholar
  41. Zhong WH, Cai ZC (2007) Long-term effects of inorganic fertilizers on microbial biomass and community functional diversity in a paddy soil derived from quaternary red clay. Appl Soil Ecol 36:84–91CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • Ji-Zheng He
    • 1
  • Yong Zheng
    • 1
    • 3
  • Cheng-Rong Chen
    • 2
  • Yuan-Qiu He
    • 4
  • Li-Mei Zhang
    • 1
  1. 1.State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-environmental SciencesChinese Academy of SciencesBeijingChina
  2. 2.Centre for Forestry & Horticultural Research, School of ScienceGriffith UniversityQueenslandAustralia
  3. 3.Graduate University, Chinese Academy of SciencesBeijingChina
  4. 4.Institute of Soil ScienceChinese Academy of SciencesNanjingChina

Personalised recommendations