Skip to main content
SpringerLink
Log in

A standardized method for the sampling of rhizosphere and rhizoplan soil bacteria associated to a herbaceous root system

  • Original Article
  • Published:
Annals of Microbiology Aims and scope Submit manuscript

Abstract

Plants-microorganisms interactions play a fundamental role in terrestrial ecosystems and various methods have been reported for plant-associated bacteria extraction. However, these methods exhibit notable variations and lack of some procedural details that may impact the interpretations of results. We propose here a standardized and detailed protocol for the independent extraction of bulk, rhizosphere and rhizoplan soil fractions. This protocol was applied to the sampling of different polluted soil fractions collected in the vicinity of Arabidopsis halleri dense root system. It allowed us to determine the cultivable bacterial densities in each fraction and to confirm the existence of a bacterial gradient linked to roots distance, with a higher amount of bacteria in the rhizospheric area. We suggest to use this unified procedure as a common basis for soil sampling and bacterial communities analysis from other roots systems.

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

Similar content being viewed by others

References

  • Aboudrar W, Schwartz C, Benizri C, Morel JL, Boularbah A (2007) Soil microbial diversity as affected by the rhizosphere of the hyperaccumulator Thlaspi caerulescens under natural conditions. Int J Phytoremediation 9:41–52

    Article  PubMed  CAS  Google Scholar 

  • Angelo-Picard C, Faure D, Carlier A, Uroz S, Raffoux A, Fray R, Dessaux Y (2004) Bacterial populations in the rhizosphere of tobacco plants producing the quorum sensing signals hexanoyl-homoserine lactone and 3-oxo-hexanoyl-homoserine lactone. FEMS Microbiol Ecol 51:19–29

    Article  PubMed  Google Scholar 

  • Angle JS, Levin MA, Gagliardi JV, McIntosh MS, Glew JG (1994) Pseudomonas aureofaciens in soil: survival and recovery efficiency. Microb Releases 2:247–254

    PubMed  CAS  Google Scholar 

  • Angle JS, Gagliardi JV, McIntosh MS, Levin MA (1996) Enumeration and expression of bacterial counts in the rhizosphere. Soil Biochem 9:233–251

    Google Scholar 

  • Bais HP, Weir TL, Perry LG, Gilroy S, Vivanco JM (2006) The role of root exudates in rhizosphere interactions with plants and other organisms. Ann Rev Plant Biol 57:233–266

    Article  CAS  Google Scholar 

  • Baudoin E, Benizri E, Guckert A (2003) Impact of artificial root exudates on the bacterial community structure in bulk soil and maize rhizosphere. Soil Biol Biochem 35:1183–1192

    Article  CAS  Google Scholar 

  • Benizri E, Piutti S, Verger S, Pages L, Vercambre G, Poessel JL, Michelot P (2005) Replant diseases: Bacterial community structure and diversity in peach rhizosphere as determined by metabolic and genetic fingerprinting. Soil Biol Biochem 37:1738–1746

    Article  CAS  Google Scholar 

  • Braud A, Jézéquel K, Bazot S, Lebeau T (2009) Enhanced phytoextraction of an agricultural Cr- and Pb-contaminated soil by bioaugmentation with siderophore-producing bacteria. Chemosphere 74:280–286

    Article  PubMed  Google Scholar 

  • Brown MRW, Winsley DBE (1969) Effect of Polysorbate 80 on cell leakage and viability of Pseudomonas aeruginosa exposed to rapid changes of pH, temperature and toxicity. J Gen Microbiol 56:99–107

    Article  PubMed  CAS  Google Scholar 

  • Canbolat MY, Bilen S, Çakmakçi R, Sahin F, Aydın A (2006) Effect of plant growth-promoting bacteria and soil compaction on barley seedling growth, nutrient uptake, soil properties and rhizosphere microflora. Biol Fertil Soils 42:350–357

    Article  CAS  Google Scholar 

  • Cavaglieri L, Orlando J, Etcheverry M (2007) Rhizosphere microbial community structure at different maize plant growth stages and root locations. Microbiol Res 164:391–399

    Article  PubMed  Google Scholar 

  • Cleyet-Marel JC, Hinsinger P (2000) Soil as a living environment, a medium to be discovered and put to good use. OCL-Ol Corps Gras Li 7:490–493

    Google Scholar 

  • Dell’Amico E, Cavalca L, Andreoni V (2005) Analysis of rhizobacterial communities in perennial Graminaceae from polluted water meadow soil, and screening of metal-resistant, potentially plant growth-promoting bacteria. FEMS Microbiol Ecol 52:153–162

    Article  PubMed  Google Scholar 

  • Gobran GR, Clegg S (1996) A conceptual model for nutrient availability in the mineral soil-root system. Can J Soil Sci 76:125–131

    Article  Google Scholar 

  • Gremion F, Chatzinotas A, Kaufmann K, Von Sigler W, Harms H (2004) Impacts of heavy metal contamination and phytoremediation on a microbial community during a twelve-month microcosm experiment. FEMS Microbiol Ecol 48:273–283

    Article  PubMed  CAS  Google Scholar 

  • Gyaneshwar P, Naresh Kumar G, Parekh LJ, Poole PS (2002) Role of soil microorganisms in improving P nutrition of plants. Plant Soil 245:83–93

    Article  CAS  Google Scholar 

  • Han J, Xia D, Li L, Sun L, Yang K, Zhang L (2009) Diversity of culturable bacteria isolated from root domains of Moso bamboo (Phyllostachys edulis). Microb Ecol 58:363–373

    Article  PubMed  Google Scholar 

  • Harlay JL, Waid JS (1955) A method of studying active mycelia on living roots and other surfaces in the soil. Trans Br Mycol Soc 38:104–118

    Article  Google Scholar 

  • Hiltner L (1904) Uber neuere erfahrungen und probleme auf dem gebiete der bodenbakteriologie unter besonderer berucksichtigung der grundungung und brache. Arbeiten Dtsc Landwirtschaftlichen Ges 98:59–78

    Google Scholar 

  • Jeffries P, Gianinazzi S, Perotto S, Turnau K, Barea JM (2003) Interaction between selected bacterial strains and the contribution of arbuscular mycorrhizal fungi in sustainable maintenance of plant health and soil fertility. Biol Fertil Soils 37:1–16

    Google Scholar 

  • Jiang HY, Sato K (1992) Fluctuations in bacterial populations on the root surface of wheat (Triticum aestivum L.) grown under different soil conditions. Biol Fertil Soils 14:246–252

    Article  Google Scholar 

  • Kamaludeen SPB, Ramasamy K (2008) Rhizoremediation of metals: harnessing microbial communities. Indian J Microbiol 48:80–88

    Article  PubMed  CAS  Google Scholar 

  • Lock K, Janssen CR (2005) Influence of soil zinc concentrations on zinc sensitivity and functional diversity of microbial communities. Environ Pollut 136:275–281

    Article  PubMed  CAS  Google Scholar 

  • Luster J, Göttlein A, Nowack B, Sarret G (2009) Sampling, defining, characterizing and modeling the rhizosphere – the soil science tool box. Plant Soil 321:457–482

    Article  CAS  Google Scholar 

  • Lynch JM, Bragg E (1985) Advances in Soil Science. Springer-Verlag, New York

    Google Scholar 

  • Marilley E, Vogt G, Blanc M, Aragno M (1998) Bacterial diversity in the bulk soil and rhizosphere fractions of Lolium perenne and Trifolium repens as revealed by PCR restriction analysis of 16 S rDNA. Plant Soil 198:219–224

    Article  CAS  Google Scholar 

  • Mijangos I, Becerril JM, Albizu I, Epelde L, Garbisu C (2009) Effects of glyphosate on rhizosphere soil microbial communities under two different plant compositions by cultivation-dependent and -independent methodologies. Soil Biol Biochem 41:505–513

    Article  CAS  Google Scholar 

  • Nealson KH, Stahl DA (1997) Geomicrobiology: Interactions between microbes and minerals. Reviews in Mineralogy. Mineralogical Society of America, Washington

    Google Scholar 

  • Ridder-Duine AS, Kowalchuk GA, Klein Gunnewiek PJA, Smant W, van Veen JA, de Boer W (2007) Rhizosphere bacterial community composition in natural stands of Carex arenaria (sand sedge) is determined by bulk soil community composition. Soil Biol Biochem 37:349–357

    Article  Google Scholar 

  • Seguin V, Courchesne F, Gagnon C, Martin RR, Naftel SJ, Skinner W (2005) Mineral weathering in the rhizosphere of forested soils. In: Huang PM, Gobran GR (eds) Biogeochemistry of trace elements in the rhizosphere. Elsevier, Amsterdam, pp 29–55

    Chapter  Google Scholar 

  • Smalla K, Wieland G, Buchner A, Zock A, Parzy J, Kaiser S, Roskot N, Heuer H, Berg G (2001) Bulk and rhizosphere soil bacterial communities studied by denaturing gradient gel electrophoresis: plant-dependent enrichment and seasonal shifts revealed. Appl Environ Microbiol 67:4742–4751

    Article  PubMed  CAS  Google Scholar 

  • Taylor JP, Wilson B, Mills MS, Burns RG (2002) Comparison of microbial numbers and enzymatic activities in surface soils and subsoils using various techniques. Soil Biol Biochem 34:387–401

    Article  CAS  Google Scholar 

  • Tedla T, Stanghellini ME (1992) Bacterial population dynamics and interactions with Pythium apanidermatum in intact rhizosphere soil. Phytopathol 82:652–656

    Article  Google Scholar 

  • Timonin MI (1946) Microflora of the rhizosphere in relation to the manganese deficiency disease of oats. Soil Sci Soc Am Proc 11:284–292

    Article  Google Scholar 

  • Turpault MP (2006) Sampling of rhizosphere soil for physicochemical and mineralogical analyses by physical separation based on drying and shaking. In: Luster J, Finlay R (eds) Handbook of methods used in rhizosphere research. Swiss Federal Research Institute WSL, Birmensdorf, pp 196–197

    Google Scholar 

  • Vásquez-Murrieta MS, Migueles-Garduño I, Franco-Hernández O, Govaerts B, Dendooven L (2006) C and N mineralization and microbial biomass in heavy-metal contaminated soil. Eur J Soil Biol 42:89–98

    Article  Google Scholar 

  • Yang J, Kloepper JW, Ryu CM (2009) Rhizosphere bacteria help plants tolerate abiotic stress. Trends Plant Sci 14:1–4

    Article  PubMed  CAS  Google Scholar 

  • Zeng GM, Shi JG, Yuan XZ, Liu J, Zhang ZB, Huang GH, Li JB, Xi BD, Liu LH (2006) Effects of Tween 80 and rhamnolipid on the extracellular enzymes of Penicillium simplicissimum isolated from compost. Enzym Microb Tech 39:1451–1456

    Article  Google Scholar 

  • Zhuang X, Chen J, Shim H, Bai Z (2007) New advances in plant growth-promoting rhizobacteria for bioremediation. Environ Int 33:406–413

    Article  PubMed  Google Scholar 

Download references

Acknowledgements

This work was supported by Région Picardie. C.D.C. Barillot was co-granted by Agence Nationale de la Recherche et de la Technologie (ANRT) and by Institut National de l’Environnement Industriel et des Risques (INERIS).

Author information

Authors and Affiliations

  1. Equipe Transformations Intégrées de la Matière Renouvelable, EA 4297, Université de Technologie de Compiègne, UTC, BP 20529, 60205, Compiègne, Cedex, France

    Cindy D. C. Barillot, Claude-Olivier Sarde & Nelly Cochet

  2. Parc Technologique Alata, INERIS, DRC-TPPD, BP2, 60550, Verneuil en Halatte, Cedex, France

    Cindy D. C. Barillot, Valerie Bert & Eric Tarnaud

Authors
  1. Cindy D. C. Barillot
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Claude-Olivier Sarde
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Valerie Bert
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Eric Tarnaud
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Nelly Cochet
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Nelly Cochet.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Barillot, C.D.C., Sarde, CO., Bert, V. et al. A standardized method for the sampling of rhizosphere and rhizoplan soil bacteria associated to a herbaceous root system. Ann Microbiol 63, 471–476 (2013). https://doi.org/10.1007/s13213-012-0491-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s13213-012-0491-y

Keywords

Search

Navigation