Skip to main content
SpringerLink
Log in

Microbial community and functional diversity associated with different aggregate fractions of a paddy soil fertilized with organic manure and/or NPK fertilizer for 20 years

  • SOILS, SEC 2 • GLOBAL CHANGE, ENVIRON RISK ASSESS, SUSTAINABLE LAND USE • RESEARCH ARTICLE
  • Published:
Journal of Soils and Sediments Aims and scope Submit manuscript

Abstract

Purpose

Microbial communities are sensitive to fertilizations, and the response of microbial communities to different fertilization regimes in bulk soils has been studied. However, it is unclear how microbial communities performance in soil aggregates. We determined the composition and functional diversity of the microbial community within different aggregate size fractions of a paddy soil fertilized with organic manure (OM) or/and mineral NPK fertilizer (NPK/NPKO) for 20 years, along with a control (no fertilizer, NoF).

Materials and methods

Soils were sampled in late December 2010 from a long-term experimental site established from an uncultivated wasteland in 1990. Five aggregate fractions, i.e., large macroaggregates (>2 mm), macroaggregates (1–2 mm), small macroaggregates (0.25–1 mm), microaggregates (0.053–0.25 mm), and non-aggregated silt and clay particles (<0.053 mm), respectively, were obtained by wet sieving. Microbial community composition was estimated based on phospholipid fatty acids (PLFAs) analysis. Microbial functional diversity was evaluated using the community level physiological profile method by Biolog Eco-microplate.

Results and discussion

The PLFA signature analysis revealed that microbial biomass tended to decrease with decreasing aggregate size. The application of fertilizer significantly increased the microbial biomass of large macroaggregates relative to the NoF treatment, but there was no significant difference among aggregates of the three fertilization treatments. Average well color development (AWCD) as well as all the functional diversity indices was almost highest in large macroaggregates and microaggregates of NoF, OM, and NPK treatments and in microaggregates of NPKO treatment, while all of them were lowest in silt and clay particles. NPKO treatment led to the greatest microbial functional diversity. AWCD values and McIntosh index (U) of most aggregates under the NPK treatment were significantly increased. The OM treatment did not significantly affect microbial functional diversity associated with different aggregate fractions.

Conclusions

Aggregate fractions and fertilization significantly affected microbial community composition and functional diversity. Soil organic C and carbon to nitrogen (C/N) ratio dominated microbial community composition and metabolic profile associated with different aggregates, respectively.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  • Angers DA, Giroux M (1996) Recently deposited organic matter in soil water-stable aggregates. Soil Sci Soc Am J 60:1547–1551

    Article  CAS  Google Scholar 

  • Baldock JA, Oades JM, Waters AG, Peng X, Vassallo AM, Wilson MA (1992) Aspects of the chemical structure of soil organic materials as revealed by solid-state 13C NMR spectroscopy. Biogeochemistry 16:1–42

    Article  CAS  Google Scholar 

  • Barthes B, Roose E (2002) Aggregate stability as an indicator of soil susceptibility to runoff and erosion; validation at several levels. Catena 47:133–149

    Article  Google Scholar 

  • Bending GD, Turner MK, Jones JE (2002) Interactions between crop residue and soil organic matter quality and the functional diversity of soil microbial communities. Soil Biol Biochem 34:1073–1082

    Article  CAS  Google Scholar 

  • Bhattacharyya R, Prakash V, Kundu S, Srivastva AK, Gupta HS, Mitra S (2010) Long term effects of fertilization on carbon and nitrogen sequestration and aggregate associated carbon and nitrogen in the Indian sub-Himalayas. Nutr Cycl Agroecosys 86:1–16

    Article  CAS  Google Scholar 

  • Bligh EG, Dyer WJ (1959) A rapid method of total lipid extraction and purification. Can J Biochem Physiol 37:911–917

    Article  CAS  Google Scholar 

  • Bossio DA, Scow KM (1998) Impacts of carbon and flooding on soil microbial communities: Phospholipid fatty acid profiles and substrate utilization patterns. Microb Ecol 35:265–278

    Article  CAS  Google Scholar 

  • Bossio DA, Scow KM, Gunapala N, Graham KJ (1998) Determinants of soil microbial communities: effects of agricultural management, season, and soil type on phospholipid fatty acid profiles. Microb Ecol 36:1–12

    Article  CAS  Google Scholar 

  • Brant JB, Sulzman EW, Myrold DD (2006) Microbial community utilization of added carbon substrates in response to long-term carbon input manipulation. Soil Biol Biochem 38:2219–2232

    Article  CAS  Google Scholar 

  • Briar SS, Fonte SJ, Park I, Six J, Scow K, Ferris H (2011) The distribution of nematodes and soil microbial communities across soil aggregate fractions and farm management systems. Soil Biol Biochem 43:905–914

    Article  CAS  Google Scholar 

  • Cambardella CA, Elliott ET (1993) Carbon and nitrogen distribution in aggregates from cultivated and native grassland soils. Soil Sci Soc Am J 57:1071–1076

    Article  CAS  Google Scholar 

  • Campbell CD, Grayston SJ, Hirst DJ (1997) Use of rhizosphere carbon sources in sole carbon source tests to discriminate soil microbial communities. J Microbiol Methods 30:33–41

    Article  Google Scholar 

  • Chen Y, Zhang XD, He HB, Xie HT, Yan Y, Zhu P, Ren J, Wang LC (2010) Carbon and nitrogen pools in different aggregates of a Chinese Mollisol as influenced by long-term fertilization. J Soils Sediments 10:1018–1026

    Article  CAS  Google Scholar 

  • Chen XF, Li ZP, Liu M, Jiang CY (2013) Effects of different fertilizations on organic carbon and nitrogen Contents in water-stable aggregates and microbial biomass content in paddy soil of subtropical China. Agric Sci Chin 46:950–960

    CAS  Google Scholar 

  • Degens BP (1998) Microbial functional diversity can be influenced by the addition of simple organic substrates to soil. Soil Biol Biochem 30:1981–1988

    Article  CAS  Google Scholar 

  • Elliott ET (1986) Aggregate structure and carbon, nitrogen, and phosphorus in native and cultivated soils. Soil Sci Soc Am J 50:627–633

    Article  Google Scholar 

  • Fierer N, Schimel JP, Holden PA (2003) Variations in microbial community composition through two soil depth profiles. Soil Biol Biochem 35:167–176

    Article  CAS  Google Scholar 

  • Fontaine S, Mariotti A, Abbadie L (2003) The priming effect of organic matter: a question of microbial competition? Soil Biol Biochem 35:837–843

    Article  CAS  Google Scholar 

  • Frostegård Å, Bååth E, Tunlid A (1993) Shifts in the structure of soil microbial communities in limed forests as revealed by phospholipid fatty acid analysis. Soil Biol Biochem 25:723–730

    Article  Google Scholar 

  • Garland JL (1996) Analytical approaches to the characterization of samples of microbial communities using patterns of potential C source utilization. Soil Biol Biochem 28:213–221

    Article  CAS  Google Scholar 

  • Garland JL, Mills AL (1991) Classification and characterization of heterotrophic microbial communities on the basis of patterns of community-level-sole-carbon-source-utilization. Appl Environ Microbiol 57:2351–2359

    CAS  Google Scholar 

  • Gartzia-Bengoetxea N, González-Arias A, Merino A, Martínez de Arano I (2009) Soil organic matter in soil physical fractions in adjacent semi-natural and cultivated stands in temperate Atlantic forests. Soil Biol Biochem 41:1674–1683

    Article  CAS  Google Scholar 

  • Haynes RJ, Swift RS (1990) Stability of soil aggregates in relation to organic constituents and soil water content. J Soil Sc 41:73–83

    Article  CAS  Google Scholar 

  • Helgason BL, Walleyb FL, Germidab JJ (2010) No-till soil management increases microbial biomass and alters community profiles in soil aggregates. Appl Soil Eco 46:390–397

    Article  Google Scholar 

  • Hu JL, Lin XG, Wang JH, Dai J, Chen RR, Zhang JB, Wong MH (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. J Soils Sediments 11:271–280

    Article  CAS  Google Scholar 

  • Huang S, Peng XX, Huang QR, Zhang WJ (2010) Soil aggregation and organic carbon fractions affected by long-term fertilization in a red soil of subtropical China. Geoderma 154:364–369

    Article  CAS  Google Scholar 

  • Jiang YJ, Sun B, Jin C, Wang F (2013) Soil aggregate stratification of nematodes and microbial communities affects the metabolic quotient in an acid soil. Soil Biol Biochem 60:1–9

    Article  Google Scholar 

  • Lazcano C, Gómez-Brandón M, Revilla P, Domínguez J (2013) Short-term effects of organic and inorganic fertilizers on soil microbial community structure and function. Biol Fert Soils 49:723–733

    Article  CAS  Google Scholar 

  • Lu RK (1999) Analytical methods for soil and agricultural chemistry. China Agricultural Scientech Press, Beijing

    Google Scholar 

  • Lv MR, Li ZP, Che YP, Han FX (2011) Soil organic C, nutrients, microbial biomass, and grain yield of rice (Oryza sativa L.) after 18 years of fertilizer application to an infertile paddy soil. Biol Fert Soils 47:777–783

    Article  CAS  Google Scholar 

  • Majumder B, Ruehlmann J, Kuzyakov Y (2010) Effects of aggregation processes on distribution of aggregate size fractions and organic C content of a long-term fertilized soil. Eur J Soil Biol 46:365–370

    Article  Google Scholar 

  • Marschner P, Kandeler E, Marschner B (2003) Structure and function of the soil microbial community in a long-term fertilizer experiment. Soil Biol Biochem 35:453–461

    Article  CAS  Google Scholar 

  • Mondini C, Cayuela ML, Sanchez-Monedero MA, Roig A, Brookes PC (2006) Soil microbial biomass activation by trace amounts of readily available substrate. Biol Fertil Soils 42:542–549

    Article  Google Scholar 

  • R Development Core Team (2006) R, a Language and Environment for Statistical Computing. R 21. Foundation for Statistical Computing, Vienna, Austria

  • Sexstone AJ, Revsbech NP, Parkin TB, Tiedje JM (1985) Direct measurement of oxygen profiles and denitrification rates in soil aggregates. Soil Sci Soc Am J 49:645–651

    Article  CAS  Google Scholar 

  • Six J, Elliott ET, Paustian K (2000a) Soil macroaggregate turnover and microaggregate formation: a mechanism for C sequestration under no-tillage agriculture. Soil Biol Biochem 32:2099–2103

    Article  CAS  Google Scholar 

  • Six J, Paustian K, Elliott ET, Combrink C (2000b) Soil structure and organic matter. I. Distribution of aggregate-size classes and aggregate-associated carbon. Soil Sci Soc Am J 64:681–689

    Article  CAS  Google Scholar 

  • Smith P, Powlson DS, Glendining MJ, Smith JU (1997) Potential for carbon sequestration in European soil preliminary estimates for five scenarios using results from long-term experiments. Glob Change Biol 3:67–79

    Article  Google Scholar 

  • Spring S, Schulze R, Overmann J, Schleifer KH (2000) Identification and characterization of ecologically significant prokaryotes in the sediment of freshwater lakes: Molecular and cultivation studies. FEMS Microbiol Rev 24:573–590

    Article  CAS  Google Scholar 

  • Stahl PD, Klug MJ (1996) Characterization and differentiation of filamentous fungi based on fatty acid composition. Appl Environ Microbiol 62:4136–4146

    CAS  Google Scholar 

  • Sundh I, Nilsson M, Borga P (1997) Variation in microbial community structure in two boreal peatlands as determined by analysis of phospholipid fatty acid profiles. Appl Environ Microbiol 63:1476–1482

    CAS  Google Scholar 

  • Tisdall JM (1994) Possible role of soil microorganisms in aggregation in soils. Plant Soil 159:115–121

    Google Scholar 

  • Tisdall JM, Oades JM (1982) Organic matter and water-stable aggregates in soils. J Soil Sci 33:141–163

    Article  CAS  Google Scholar 

  • Väisänen RK, Roberts MS, Garland JL, Frey SD, Dawson LA (2005) Physiological and molecular characterization of microbial communities associated with different water-stable aggregate size classes. Soil Biol Biochem 37:2007–2016

    Article  Google Scholar 

  • Wang X, Yost RS, Linquist BA (2001) Soil aggregate size affects phosphorus desorption from highly weathered soils and plant growth. Soil Sci Soc Am J 65:139–146

    Article  CAS  Google Scholar 

  • Widmer F, Fließbach A, Laczkó E, Schulze-Aurich J, Zeyer J (2001) Assessing soil biological characteristics: a comparison of bulk soil community DNA-, PLFA-, and Biolog ™-analyses. Soil Biol Biochem 33:1029–1036

    Article  CAS  Google Scholar 

  • Wu XC, Li ZP, Zhang TL (2009) Nutrient cycling and balance of paddy fields with different long-term fertilization management in red soil region. Soils 41:377–383

    CAS  Google Scholar 

  • Yan H, Zhong WH, Li ZP, Cai ZC (2008) Effects of long-term fertilization on phospholipid fatty acids and enzyme activities in paddy red soil. Chin J Ecol 19:71–75

    CAS  Google Scholar 

  • Yang ZH, Singh BR, Hansen S (2007) Aggregate associated carbon, nitrogen and sulfur and their ratios in long-term fertilized soils. Soil Till Res 95:161–171

    Article  Google Scholar 

  • Young IM, Crawford JW, Nunan N, Otten W, Spiers A (2008) Microbial distribution in soils: Physics and scaling. Adv Agron 100:81–121

    Article  Google Scholar 

  • Zak JC, Willig MR, Moorhead DL, Wildman HG (1994) Functional diversity of microbial communities: a quantitative approach. Soil Biol Biochem 26:1101–1108

    Article  Google Scholar 

  • Zelles L, Bai QY, Beck T, Beese F (1992) Signature fatty acids in phospholipids and lipopolysaccharides as indicators of microbial biomass and community structure in agricultural soils. Soil Biol Biochem 24:317–323

    Article  CAS  Google Scholar 

  • Zhang QC, Wang GH, Yao HY (2007) Phospholipid fatty acid patterns of microbial communities in paddy soil under different fertilizer treatments. J Environ Sci 19:55–59

    Article  Google Scholar 

  • Zhong WH, Gu T, Wang W, Zhang B, Lin XG, Huang QR, Shen WS (2010) The effects of mineral fertilizer and organic manure on soil microbial community and diversity. Plant Soil 326:511–522

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This study was supported by the National Natural Science Foundation of China (no. 41171233 and 41001143). In addition, we thank the anonymous reviewers and editors for their helpful comments regarding the manuscript.

Author information

Authors and Affiliations

  1. State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No. 71, East Beijing Road, P.O. box 821, Nanjing, 210008, China

    Xiaofen Chen, Zhongpei Li, Ming Liu, Chunyu Jiang & Yuping Che

  2. University of Chinese Academy of Sciences, Beijing, 100049, China

    Xiaofen Chen & Zhongpei Li

Authors
  1. Xiaofen Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Zhongpei Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ming Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Chunyu Jiang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Yuping Che
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Zhongpei Li.

Additional information

Responsible Editor: Chengrong Chen

Electronic supplementary material

Below is the link to the electronic supplementary material.

Table S1

(DOCX 16 kb)

Table S2

(DOCX 14 kb)

Table S3

(DOCX 13 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Chen, X., Li, Z., Liu, M. et al. Microbial community and functional diversity associated with different aggregate fractions of a paddy soil fertilized with organic manure and/or NPK fertilizer for 20 years. J Soils Sediments 15, 292–301 (2015). https://doi.org/10.1007/s11368-014-0981-6

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11368-014-0981-6

Keywords

Search

Navigation