Skip to main content
SpringerLink
Log in

Inter-specific Interactions Between Carbon-limited Soil Bacteria Affect Behavior and Gene Expression

  • Soil Microbiology
  • Published:
Microbial Ecology Aims and scope Submit manuscript

Abstract

Recent publications indicate that inter-specific interactions between soil bacteria may strongly affect the behavior of the strains involved, e.g., by increased production of antibiotics or extracellular enzymes. This may point at an enhanced competitive ability due to inter-specific triggering of gene expression. However, it is not known if such inter-specific interactions also occur during competition for carbon which is the normal situation in soil. Here, we report on competitive interactions between two taxonomically non-related bacterial strains, Pseudomonas sp. A21 and Pedobacter sp. V48, that were isolated from a dune soil. The strains showed strong effects on each other’s behavior and gene expression patterns when growing together under carbon-limited conditions on agar. The most pronounced observed visual changes in mixed cultures as compared to monocultures were (1) strong inhibition of a bioindicator fungus, suggesting the production of a broad-spectrum antibiotic, and (2) the occurrence of gliding-like movement of Pedobacter cells. Two independent techniques, namely random arbitrary primed-PCR (RAP-PCR) and suppressive subtractive hybridization (SSH), identified in total 24 genes that had higher expression in mixed cultures compared to monocultures. Microbial interactions were clearly bidirectional, as differentially expressed genes were detected for both bacteria in mixed cultures. Sequence analysis of the differentially expressed genes indicated that several of them were most related to genes involved in motility and chemotaxis, secondary metabolite production and two-component signal transduction systems. The gene expression patterns suggest an interference competition strategy by the Pseudomonas strain and an escape/explorative strategy by the Pedobacter strain during confrontation with each other. Our results show that the bacterial strains can distinguish between intra- and inter-specific carbon competition.

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

Figure 1
Figure 2
Figure 3
Figure 4

References

  1. An D, Danhorn T, Fuqua C, Parsek MR (2006) Quorum sending and motility mediate interactions between Pseudomonas aeruginosa and Agrobacterium tumefaciens in biofilm cocultures. PNAS 103:3832–3833

    Google Scholar 

  2. Angell S, Bench BJ, Williams H, Watanave CMH (2006) Pyocyanin isolated from a marine microbial population: synergistic production between two distinct bacterial species and mode of action. Chem Biol 13:1349–1359

    Article  PubMed  CAS  Google Scholar 

  3. Bassler BL (1999) How bacteria talk to each other: regulation of gene expression by quorum sensing. Curr Opin Microbiol 2:582–587

    Article  PubMed  CAS  Google Scholar 

  4. Belas R, Zhulin IB, Yang Z (2008) Bacterial signaling and motility: sure bets. J Bacteriol 190:1849–1856

    Article  PubMed  CAS  Google Scholar 

  5. Bidle KL, Bartlett DH (2001) RNA arbitrarily primed PCR survey of genes regulated by TocR in the deep-sea bacterium Phytobacterium profundum Strain SS9. J Bacteriol 183:1688–1693

    Article  PubMed  CAS  Google Scholar 

  6. Bogush ML et al (1999) Identification and localization of differences between Echerichia coli and Salmonella typhimurium genome by suppressive subtractive hybridization. Mol Gen Genet 262:721–729

    Article  PubMed  CAS  Google Scholar 

  7. Chakraborty A, Das S, Majumdar S, Mukhopadhyay K, Roychoudhury S, Chaudhri K (2000) Use of RNA arbitrarily primed- PCR fingerprinting to identify Vibrio cholerae genes differentially expressed in the host following infection. Infect Immun 68:3837–3887

    Article  Google Scholar 

  8. Chang IS, Ballard JD, Krumholz LR (2003) Evidence for chimeric sequences formed during random arbitrarily primed PCR. J Microbiol Methods 54:427–431

    Article  PubMed  CAS  Google Scholar 

  9. Chia J-S, Lee Y-Y, Huang P-T, Chen J-Y (2001) Identification of stress-responsive genes in Streptococcus mutans by differential display reverse transcription-PCR. Infect Immun 69:2493–2501

    Article  PubMed  CAS  Google Scholar 

  10. De Boer W, Verheggen P, Klein Gunnewiek PJA, Kowalchuk GA, van Veen JA (2003) Microbial community composition affects soil fungistasis. Appl Environm Microbiol 69:835–844

    Article  Google Scholar 

  11. De Boer W, Wagenaar A, Gunnewiek PJA, van Veen JA (2007) In vitro suppression of fungi caused by combinations of apparently non-antagonistic soil bacteria. FEMS Microbiol Ecol 59:177–185

    Article  PubMed  Google Scholar 

  12. Demoling F, Figueroa D, Bååth E (2007) Comparison of factors limiting bacterial growth in different soils. Soil Biol Biochem 39:2485–2495

    Article  CAS  Google Scholar 

  13. Diatchenko L et al (1996) Suppression subtractive hybridization: a method for generating regulated or tissue-specific cDNA probes and libraries. PNAS 93:6025–6030

    Article  PubMed  CAS  Google Scholar 

  14. Diatchenko L, Chenchi A, Siebert P (1998) Suppression subtractive hybridization: a method for generating subtracted cDNA libraries starting from poly (A) or total RNA. In: Siebert P, Larrik J (eds) RT-PCR methods for gene cloning and analysis. BioTechniques Books, MA, pp 213–239

    Google Scholar 

  15. Dubuis C, Haas D (2007) Cross-species GacA-controlled induction of antibiosis in Pseudomonas. Appl Environm Microbiol 73:650–654

    Article  CAS  Google Scholar 

  16. Dubuis C, Keel C, Haas D (2007) Dialogues of root-colonizing biocontrol pseudomonads. Eur J Plant Pathol 119:311–328

    Article  Google Scholar 

  17. Dutta R, Qin L, Inouye M (1999) Histidine kinase: diversity of domain organization. Molec Microbiol 34:633–640

    Article  CAS  Google Scholar 

  18. Frias-Lopez J, Bonheyo GT, Fouke BW (2004) Identification of differential gens expression in bacteria associated with coral black band disease by using RNA-Arbitrarily primed PCR. Appl Environ Microbiol 70:3687–3694

    Article  PubMed  CAS  Google Scholar 

  19. Fong KP, Chung WO, Lamont RJ, Demunth DR (2001) Intra-and interspecies regulation of gene expression by actinobacillus actinomycetomcomitans LuxS. Infection Immunity 69:7625–7634

    Article  PubMed  CAS  Google Scholar 

  20. Harrison F, Paul J, Massey RC, Buckling A (2008) Interspecific competition and siderophore-mediated cooperation in Pseudomonas aeruginosa. ISME Journal 2:49–55

    Article  PubMed  Google Scholar 

  21. Harschey RM (2003) Bacterial motility on a surface: many ways to a common goal. Annu Rev Microbiol 57:249–273

    Article  Google Scholar 

  22. Heeb S, Blumer C, Haas D (2002) A regulatory RNA as a mediator in GacA/RsmA-dependent global control of exoproduct formation in Pseudomonas fluorescens CHA0. J Bacteriol 184:1046–1056

    Article  PubMed  CAS  Google Scholar 

  23. Holmsrom K, Gram L (2003) Elucidation of the Vibrio anguillarum genetic response to the potential fish probiont Pseudomonas fluorescens AH2 using RAP-arbitrarily primed PCR. J Bacteriol 185:831–842

    Article  Google Scholar 

  24. Kanagasabhapathy M, Nagata S (2008) Cross-species induction of antibacterial activity produced by epibiotic bacteria isolated from Indian marine sponge Pseudoceratina purpurea. World J Microbiol Biotechnol 24:687–691

    Article  CAS  Google Scholar 

  25. Kill K, Ferchaud JP, David C, Binnewies TT, Wu H et al (2005) Genome update: distribution of two-component transduction system in 250 bacterial genomes. Microbiology 151:3447–3452

    Article  Google Scholar 

  26. Kim J-D, Kim B, Lee C-G (2007) Alga-lytic activity of Pseudomonas fluorescens against red tide causing marine alga Heterosigma akashiwo. Biol Control 41:296–303

    Article  Google Scholar 

  27. Khorchid A, Ikura M (2005) Bacterial histidine kinase as signal sensor and transducer. Inter IJBCB 38:307–312

    Google Scholar 

  28. Lang AS, Beatty JT (2002) A bacterial signal transduction system controls genetic exchange and motility. J Bacteriol 184:913–918

    Article  PubMed  CAS  Google Scholar 

  29. Li S, Xiao X, Li J, Luo J, Wang F (2006) Identification of genes regulated by changing salinity in the deep-sea bacterium Shewanella sp. WP3 using RNA arbitrarily primed PCR. Extremophiles 10:97–104

    Article  PubMed  CAS  Google Scholar 

  30. Meunier L, Prefontainen G, Van Munster M, Brousseau R, Masson L (2006) Transcriptional response of Choristoneura fumiferana to sublethal exposure of Cry1Ab protoxin from Bacillus thuringiensis. Insect Molec Biol 15:475–483

    Article  CAS  Google Scholar 

  31. Nagel A, Fleming JT, Sayler GS (1999) Reduction of false positives in prokaryotic mRNA differential display. BioTechniques 26:641–648

    PubMed  CAS  Google Scholar 

  32. Nguyen B, Bowers RM, Wahlund TM, Read BA (2005) Suppressive subtractive hybridization of and differences in gene expression content of calcifying and noncalcifying cultures of Emiliana huxleyi strain 1516. Appl Environ Microbiol 71:2564–2575

    Article  PubMed  CAS  Google Scholar 

  33. Oliva AA, Swann JW (2001) Increased yield of PCR products by addition of T4 gene 32 protein to the SMART tm PCR cDNA synthesis system. BioTechniques 31:81–86

    Google Scholar 

  34. Parret AHA, de Mot R (2002) Escherichia coli's uropathogenic-specific protein: a bacteriocin promoting infectivity. Microbiology 148:1604–1606

    PubMed  CAS  Google Scholar 

  35. Rao D, Webb JS, Kjellberg S (2005) Competitive interactions in mixed-species biofilm containing the marine bacterium Pseudoalteromonas tunicate. Appl Environ Microbiol 71:1729–1736

    Article  PubMed  CAS  Google Scholar 

  36. Rebrikov DV, Britanova OV, Gurskaya NG, Lukyanova KA, Tarabykin VS, Vukyanov SA (2000) Mirror orientation selection (MOS): a method for elimination false positive clones from libraries generated by suppression subtractive hybridization. Nucleic Acid Res 28:20

    Article  Google Scholar 

  37. Riedel K, Hentzer M, Geisenberger O, Huber B, Steidle A, Wu H, Holby N, Givskov M, Molin S, Eberl L (2001) N-Acylchomoserine-lactone-mediated communication between Pseudomonas aeruginosa and Burkholderia cepacia in mixed biofilms. Microbiology 147:3249–3262

    PubMed  CAS  Google Scholar 

  38. Saunders NFW, Goodchild A, Reftry M, Guilhaus M, Curmi PMG, Cavicchioli R (2005) Predicted roles for hypothetical proteins in the low-temperature expressed proteome of Antarctic archeon. J Proteome Research 4:464–472

    Article  CAS  Google Scholar 

  39. Shepard BD, Gilmore MS (1999) Identification of aerobically and anaerobically induced genes in Enterococcus faecalis by random arbitrarily primed PCR. Appl Environ Microbiol 65:1470–1476

    Google Scholar 

  40. Taga ME, Bassler BL (2003) Chemical communication among bacteria. PNAS 100:14549–14554

    Article  PubMed  CAS  Google Scholar 

  41. Varga A, Jame D (2006) Real-time PCR and SYBR Green I melting curve analysis for identification of Plum pox virus strain C, EA and W: effect of amplicon size melt rate, and dye translocation. J Virol Methods 132:146–153

    Article  PubMed  CAS  Google Scholar 

  42. Williams P (2007) Quorum sensing, communication and cross-kingdom signalling in the bacterial world. Microbiol 153:3923–3938

    Article  CAS  Google Scholar 

  43. Winstanley C (2002) Spot the difference: application of subtractive hybridization to the study of bacterial pathogens. J Med Microbiol 51:459–467

    PubMed  CAS  Google Scholar 

  44. Zhang Q, Melcher U, Zhou L, Najar FZ, Roe BA, Fletcher J (2005) Genomic comparison of plant pathogenic and nonpathogenic Serratia marcesens strain by suppressive subtractive hybridization. Appl Environ Microbiol 71:7716–7723

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgment

This work is supported by The Netherlands Organization for Scientific research (NWO). The authors thank Wiecher Smant for ergosterol determination and Adam Ostrowski for his help in Q-PCR analysis. This is publication No. 4440 NIOO-KNAW of the Netherlands Institute of Ecology.

Author information

Authors and Affiliations

  1. Netherlands Institute of Ecology (NIOO-KNAW), Center for Terrestrial Ecology, Heteren, The Netherlands

    Paolina Garbeva & Wietse de Boer

  2. P.O. Box 40, Heteren, 6666ZG, The Netherlands

    Paolina Garbeva

Authors
  1. Paolina Garbeva
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Wietse de Boer
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Paolina Garbeva.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Garbeva, P., de Boer, W. Inter-specific Interactions Between Carbon-limited Soil Bacteria Affect Behavior and Gene Expression. Microb Ecol 58, 36–46 (2009). https://doi.org/10.1007/s00248-009-9502-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00248-009-9502-3

Keywords

Search

Navigation