Biotic stress shifted structure and abundance of enterobacteriaceae in the lettuce microbiome

PLoS ONE

Volumn 10, Issue 2, 2015, Pages

  Erlacher, Armin ^a,b   Cardinale, Massimiliano ^a,b   Grube, Martin ^b   Berg, Gabriele ^a  

^a GRAZ UNIVERSITY OF TECHNOLOGY   (Austria)

^b UNIVERSITY OF GRAZ   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S;

16S RRNA GENE; AMPLICON; ARTICLE; BACTERIAL STRAIN; BACTERIAL STRUCTURES; BIOTIC STRESS; CONTROLLED STUDY; ENTEROBACTERIACEAE; ESCHERICHIA COLI; FUNGAL STRAIN; GASTROPOD; GENE LIBRARY; INOCULATION; LETTUCE; LIFESTYLE; MESOCOSM; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; NONHUMAN; PLANT LEAF; PLANT MICROORGANISM INTERACTION; POPULATION ABUNDANCE; RHIZOSPHERE; SOIL MICROFLORA; STRUCTURE ANALYSIS; ANIMAL; ANTIBIOSIS; CLASSIFICATION; GENETICS; METAGENOME; MICROBIOLOGY; MICROFLORA; PARASITOLOGY;

BACTERIA (MICROORGANISMS); ENTEROBACTERIACEAE; ESCHERICHIA COLI; FUNGI; GASTROPODA; LACTUCA;

ANIMALS; ANTIBIOSIS; ENTEROBACTERIACEAE; GASTROPODA; LETTUCE; METAGENOME; MICROBIOTA; PLANT LEAVES; RHIZOSPHERE; RNA, RIBOSOMAL, 16S; SOIL MICROBIOLOGY;

EID: 84923913672     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0118068     Document Type: Article

References (44)

1. Olaimat AN, Holley RA (2012) Factors influencing the microbial safety of fresh produce: a review. Food Microbiol 32: 1-19. doi: 10.1016/j.fm.2012.04.016 PMID: 22850369
2. Brandl MT (2006) Fitness of human enteric pathogens on plants and implications for food safety. Annu Rev Phytopathol 44: 367-392. PMID: 16704355
3. Moyne AL, Harris LJ, Marco ML (2013) Assessments of total and viable Escherichia coli O157:H7 on field and laboratory grown lettuce. PLoS One 8: e70643. doi: 10.1371/journal.pone.0070643 PMID: 23936235
4. Teplitski M, Warriner K, Bartz J, Schneider KR (2011) Untangling metabolic and communication networks: interactions of enterics with phytobacteria and their implications in produce safety. Trends Microbiol 19: 121-127. doi: 10.1016/j.tim.2010.11.007 PMID: 21177108
5. Hou Z, Fink RC, Sugawara M, Diez-Gonzalez F, Sadowsky MJ (2013) Transcriptional and functional responses of Escherichia coli O157:H7 growing in the lettuce rhizoplane. Food Microbiol 2: 136-142.
6. Rastogi G, Sbodio A, Tech JJ, Suslow TV, Coaker GL, et al. (2012) Leaf microbiota in an agroecosystem: spatiotemporal variation in bacterial community composition on field-grown lettuce. ISME J 6: 1812-1822. doi: 10.1038/ismej.2012.32 PMID: 22534606
7. Rastogi G, Coaker GL, Leveau JH (2013) New insights into the structure and function of phyllosphere microbiota through high?throughput molecular approaches. FEMS Microbiol Lett 348: 1-10. doi: 10. 1111/1574-6968.12225 PMID: 23895412
8. Hunter PJ, Hand P, Pink D, Whipps JM, Bending GD (2010) Both leaf properties and microbe-microbe interactions influence within-species variation in bacterial population diversity and structure in the lettuce (Lactuca species) phyllosphere. Appl Environ Microbiol 76: 8117-8125. doi: 10.1128/AEM. 01321-10 PMID: 20952648
9. Berendsen RL, Pieterse CM, Bakker PA (2012) The rhizosphere microbiome and plant health. Trends Plant Sci 17: 478-86. doi: 10.1016/j.tplants.2012.04.001 PMID: 22564542
10. Hirsch PR, Mauchline TH (2012) Who's who in the plant root microbiome? Nat Biotechnol 30: 961-962. doi: 10.1038/nbt.2387 PMID: 23051815
11. Berg G, Smalla K (2009) Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere. FEMS Microbiol Ecol 68: 1-13. doi: 10.1111/j.1574-6941. 2009.00654.x PMID: 19243436
12. Lundberg DS, Lebeis SL, Paredes SH, Yourstone S, Gehring J, et al. (2013) Defining the core Arabidopsis thaliana root microbiome. Nature 488: 86-90.
13. Leff JW, Fierer N (2013) Bacterial communities associated with the surfaces of fresh fruits and vegetables. PLoS One 8: e59310. doi: 10.1371/journal.pone.0059310 PMID: 23544058
14. Berg G, Eberl L, Hartmann A (2005) The rhizosphere as a reservoir for opportunistic human pathogenic bacteria. Environ Microbiol 7: 1673-1685. PMID: 16232283
15. Mendes R, Garbeva P, Raaijmakers JM (2013) The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiol Ecol 37: 634-663.
16. Pagaling E, Strathdee F, Spears BM, Cates ME, Allen RJ, et al. (2014) Community history affects the predictability of microbial ecosystem development. ISME J 8: 19-30. doi: 10.1038/ismej.2013.150 PMID: 23985743
17. Grosch R, Schneider JHM, Kofoet A (2004) Characterisation of Rhizoctonia solani anastomosis groups causing bottom rot in field grown lettuce in Germany. Eur J Plant Pathol 110: 53-62.
18. Raid RN (1997) Bottom rot. In: Davis RM, Subbarao KV, Raid RN, Kurtz EA, editors. Compendium of lettuce diseases. Saint Paul: APS Press. pp. 15-16.
19. Fredericks DN, Relman DA (1996) Sequence-based identification of microbial pathogens: a reconsideration of Koch's postulates. Clin Microbiol Rev 9: 18-33. PMID: 8665474
20. Clemente JC, Ursell LK, Parfrey LW, Knight R (2012) The impact of the gut microbiota on human health: an integrative view. Cell 148: 1258-1270. doi: 10.1016/j.cell.2012.01.035 PMID: 22424233
21. Blaser M, Bork P, Fraser C, Knight R, Wang J (2013) The microbiome explored: recent insights and future challenges. Nat Rev Microbiol 11: 213-217. doi: 10.1038/nrmicro2973 PMID: 23377500
22. Ramírez-Puebla ST, Servín-Garcidueñas LE, Jiménez-Marín B, Bolaños LM, Rosenblueth M, et al. (2013) Gut and root microbiota commonalities. Appl Environ Microbiol 79: 2-9. doi: 10.1128/AEM. 02553-12 PMID: 23104406
23. Chowdhury SP, Dietel K, Rändler M, Schmid M, Junge H, et al. (2014) Effects of Bacillus amyloliquefaciens FZB42 on lettuce growth and health under pathogen pressure and its impact on the rhizosphere bacterial community. PLoS One 8: e68818.
24. Erlacher A, Cardinale M, Grosch R, Grube M, Berg G (2014) The impact of the pathogen Rhizoctonia solani and its beneficial counterpart Bacillus amyloliquefaciens on the indigenous lettuce microbiome. Front Microbiol 5: 175. doi: 10.3389/fmicb.2014.00175 PMID: 24795707
25. Bragina A, Berg C, Cardinale M, Shcherbakov A, Chebotar V, et al. (2012) Sphagnum mosses harbour highly specific bacterial diversity during their whole lifecycle. ISME J 6: 802-813. doi: 10.1038/ismej. 2011.151 PMID: 22094342
26. Schwieger F, Tebbe CC (1998) A new approach to utilize PCR-single-strand-conformation polymorphism for 16S rRNA gene-based microbial community analysis. Appl Environ Microbiol 64: 4870-4876. PMID: 9835576
27. Rossmann B, Müller H, Smalla K, Mpiira S, Tumuhairwe JB, et al. (2012) Banana-associated microbial communities in Uganda are highly diverse but dominated by Enterobacteriaceae. Appl Environ Microbiol 78: 4933-4941. doi: 10.1128/AEM.00772-12 PMID: 22562988
28. Berg G, Krechel A, Ditz M, Faupel A, Ulrich A, Hallmann J. (2005) Comparison of endophytic and ectophytic potato-associated bacterial communities and their antagonistic activity against plant pathogenic fungi. FEMS Microbiol Ecol 51: 215-229. PMID: 16329870
29. Mühling M, Woolven-Allen J, Murrell JC, Joint I (2008) Improved group-specific PCR primers for denaturing gradient gel electrophoresis analysis of the genetic diversity of complex microbial communities. ISME J 2: 379-392. doi: 10.1038/ismej.2007.97 PMID: 18340335
30. Binh CT, Heuer H, Gomes NC, Kaupenjohann M, Smalla K (2010) Similar bacterial community structure and high abundance of sulfonamide resistance genes in field-scale manures. In: Dellaguardia CS, editor. Manure: management, uses and environmental impacts. Hauppauge: Nova Science Publishers. pp. 141-166.
31. Heuer H, Krsek M, Baker P, Smalla K, Wellington EM (1997) Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients. Appl Environ Microbiol 63: 3233-3241. PMID: 9251210
32. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, et al. (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7: 335-336. doi: 10.1038/nmeth.f.303 PMID: 20383131
33. Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73: 5261-5267. PMID: 17586664
34. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13: 2498-2504. PMID: 14597658
35. Handschur M, Pinar G, Gallist B, Lubitz W, Haslberger AG (2005) Culture free DGGE and cloning based monitoring of changes in bacterial communities of salad due to processing. Food Chem Toxicol 43: 1595-1605. PMID: 15993997
36. Cardinale M, Vieira de Castro J, Müller H, Berg G, Grube M (2008) In situ analysis of the bacterial community associated with the reindeer lichen Cladonia arbuscula reveals predominance of Alphaproteobacteria. FEMS Microbiol Ecol 66: 63-71. doi: 10.1111/j.1574-6941.2008.00546.x PMID: 18631179
37. Amann RI, Binder BJ, Olson RJ, Chisholm SW, Devereux R, et al. (1990) Combination of 16S rRNAtargeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl Environ Microbiol 56: 1919-1925. PMID: 2200342
38. Berg G, Krechel A, Ditz M, Sikora RA, Ulrich A, Hallmann J (2005) Endophytic and ectophytic potato-associated bacterial communities differ in structure and antagonistic function against plant pathogenic fungi. FEMS Microbiol Ecol 51: 215-229. PMID: 16329870
39. Reisberg EE, Hildebrandt U, Riederer M, Hentschel U (2013) Distinct phyllosphere bacterial communities on Arabidopsis wax mutant leaves. PLoS One 8: e78613. doi: 10.1371/journal.pone.0078613 PMID: 24223831
40. Franz E, Visser AA, Van Diepeningen AD, Klerks MM, Termorshuizen AJ, et al. (2007) Quantification of contamination of lettuce by GFP-expressing Escherichia coli O157:H7 and Salmonella enterica serovar typhimurium. Food Microbiol 24: 106-112. PMID: 16943102
41. Connell JH (1978) Diversity in tropical rain forests and coral reefs. Science 199: 1302-1310. PMID: 17840770
42. Fox JW (2013) The intermediate disturbance hypothesis is broadly defined, substantive issues are key: a reply to Sheil and Burslem. Trends Ecol Evol 28: 572-573. doi: 10.1016/j.tree.2013.07.008 PMID: 23968969
43. Hanski I, von Hertzen L, Fyhrquist N, Koskinen K, Torppa K, et al. (2012) Environmental biodiversity, human microbiota, and allergy are interrelated. Proc Natl Acad Sci USA 109: 8334-8339. doi: 10.1073/ pnas.1205624109 PMID: 22566627
44. Doreswamy V, Peden DB (2011) Modulation of asthma by endotoxin. Clin Exp Allergy 41: 9-19. doi: 10.1111/j.1365-2222.2010.03628.x PMID: 20977505