Different pioneer plant species select specific rhizosphere bacterial communities in a high mountain environment

SpringerPlus

Volumn 3, Issue 1, 2014, Pages 1-10

  Ciccazzo, Sonia ^a   Esposito, Alfonso ^b   Rolli, Eleonora ^a   Zerbe, Stefan ^b   Daffonchio, Daniele ^a   Brusetti, Lorenzo ^b  

^a UNIVERSITY OF MILAN   (Italy)

^b FREE UNIVERSITY OF BOZEN BOLZANO   (Italy)

Author keywords

Alps; Bacterial community structure; Glacier forefields; Pioneer plants; Rhizobacteria

Indexed keywords

EID: 84940348890     PISSN: None     EISSN: 21931801     Source Type: Journal    
DOI: 10.1186/2193-1801-3-391     Document Type: Article

References (61)

1. Anderson MJ: A new method for non-parametric multivariate analysis of variance. Austral Ecol 2001, 26: 32-46.
2. Berg G, Smalla K: Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere. FEMS Microbiol Ecol 2009, 68: 1-13. 10. 1111/j. 1574-6941. 2009. 00654. x.
3. Bonfante P, Anca IA: Plants, mycorrhizal fungi, and bacteria: a network of interactions. Annu Rev Microbiol 2009, 63: 363-383. 10. 1146/annurev. micro. 091208. 073504.
4. Brodie E, Edwards S, Clipson N: Soil fungal community in a temperate upland grassland soil. FEMS Microbiol Ecol 2003, 45: 105-114. 10. 1016/S0168-6496(03)00126-0.
5. Cardinale M, Brusetti L, Quatrini P, Borin S, Puglia AM, Rizzi A, Zanardini E, Sorlini C, Corselli C, Daffonchio D: Comparison of different primer sets for use in automated ribosomal intergenic spacer analysis of complex bacterial communities. Appl Environ Microbiol 2004, 70: 6147-6156. 10. 1128/AEM. 70. 10. 6147-6156. 2004.
6. Carson JK, Campbell L, Rooney D, Clipson N, Gleeson DB: Minerals in soil select distinct bacterial communities in their microhabitats. FEMS Microbiol Ecol 2009, 67: 381-388. 10. 1111/j. 1574-6941. 2008. 00645. x.
7. Clarke KR: Non-parametric multivariate analyses of changes in community structure. Aust J Ecol 1993, 18: 117-143. 10. 1111/j. 1442-9993. 1993. tb00438. x.
8. Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, Tiedje JM: The ribosomal database project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 2009, 37: D141-D145. 10. 1093/nar/gkn879.
9. Costa R, Götz M, Mrotzek N, Lottmann J, Berg G, Smalla K: Effects of site and plant species on rhizosphere community structure as revealed by molecular analysis of microbial guilds. FEMS Microbiol Ecol 2006, 56: 236-249. 10. 1111/j. 1574-6941. 2005. 00026. x.
10. Dohrmann AB, Tebbe CC: Effect of elevated tropospheric ozone on the structure of bacterial communities inhabiting the rhizosphere of herbaceous plants native to Germany. Appl Environ Microbiol 2005, 71: 7750-7758. 10. 1128/AEM. 71. 12. 7750-7758. 2005.
11. Doran JW: Soil health and global sustainability: translating science into practice. Agr Ecosyst Environ 2002, 88: 119-127. 10. 1016/S0167-8809(01)00246-8.
12. Ďugova O, Barančokova M, Krajči J, Barančok P: Soil micromycetes and vegetation changes associated with vegetative cover destruction on chosen localities of Tatry Mountains - first approach. Ekologia 2013, 32: 158-172.
13. Duineveld BM, Rosado AS, van Elsas JD, van Veen JA: Analysis of the dynamics of bacterial communities in the rhizosphere of the chrysanthemum via denaturing gradient gel electrophoresis and substrate utilization patterns. Appl Environ Microbiol 1998, 64: 4950-4957.
14. Edwards IP, Bürgmann H, Miniaci C, Zeyer J: Variation in microbial community composition and culturability in the rhizosphere ofLeucanthemopsis alpina(L.) Heywood and adjacent bare soil along an alpine chronosequence. Microb Ecol 2006, 52: 679-692. 10. 1007/s00248-006-9097-x.
15. Edwards A, Rassner SME, Anesio AM, Worgan HJ, Irvine-Fynn TDL, Williams HW, Sattler B, Griffith GW: Contrasts between the cryoconite and ice-marginal bacterial communities of Svalbard glaciers. Polar Res 2013, 32: 19468.
16. Esposito A, Ciccazzo S, Borruso L, Zerbe S, Daffonchio D, Brusetti L: A three-scale analysis of bacterial communities involved in rocks colonization and soil formation in high mountain environments. Curr Microbiol 2013, 67: 472-479. 10. 1007/s00284-013-0391-9.
17. Fisher MM, Triplett EW: Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities. Appl Environ Microbiol 1999, 65: 4630-4636.
18. Garbeva P, van Elsas JD, van Veen JA: Rhizosphere microbial community and its response to plant species and soil history. Plant Soil 2008, 302: 19-32. 10. 1007/s11104-007-9432-0.
19. Grayston SJ, Wang S, Campbell CD, Edwards AC: Selective influence of plant species on microbial diversity in the rhizosphere. Soil Biol Biochem 1998, 30: 369-378. 10. 1016/S0038-0717(97)00124-7.
20. Gurtler V, Stanisich VA: New approaches to typing and identification of bacteria using the 16S-23S rDNA spacer region. Microbiol 1996, 142: 3-16. 10. 1099/13500872-142-1-3.
21. Habler G, Thöni M, Grasemann B: Cretaceous metamorphism in the Austroalpine Matsch Unit (Eastern Alps): the interrelation between deformation and chemical equilibration processes. Mineral Petrol 2009, 97: 149-171. 10. 1007/s00710-009-0094-x.
22. Haichar FZ, Marol C, Berge O, Rangel-Castro JI, Prosser JI, Balesdent J, Heulin T, Achouak W: Plant host habitat and root exudates shape soil bacterial community structure. ISME J 2008, 2: 1221-1230. 10. 1038/ismej. 2008. 80.
23. Hamady M, Lozupone C, Knight R: Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME J 2010, 4: 17-27. 10. 1038/ismej. 2009. 97.
24. Hammer Ø, Harper DAT, Ryan PD: PAST: Paleontological statistics software package for education and data analysis. Palaeontol Electron 2001, 4: 1-9.
25. Hansel CM, Fendorf S, Jardine PM, Francis CF: Changes in bacterial and archaeal community structure and functional diversity along a geochemically variable soil profile. Appl Environ Microbiol 2008, 74: 1620-1633. 10. 1128/AEM. 01787-07.
26. Hayat R, Ali S, Amara U, Khalid R, Ahmed I: Soil beneficial bacteria and their role in plant growth promotion: a review. Ann Microbiol 2010, 60: 579-598. 10. 1007/s13213-010-0117-1.
27. Huang XF, Chaparro JM, Reardon KF, Zhang R, Shen Q, Vivanco JM: Rhizosphere interactions: root exudates, microbes, and microbial communities. Botany 2014, 92: 267-275. 10. 1139/cjb-2013-0225.
28. Kennedy NM, Gleeson DE, Connolly J, Clipson NJW: Seasonal and management influences on bacterial community structure in an upland grassland soil. FEMS Microbiol Ecol 2005, 53: 329-337. 10. 1016/j. femsec. 2005. 01. 013.
29. Knelman JE, Legg TM, O'Neill SP, Washenberger CL, González A, Cleveland CC, Nemergut DR: Bacterial community structure and function change in association with colonizer plants during early primary succession in a glacier forefield. Soil Biol Biochem 2012, 46: 172-180.
30. Knoll C, Kerschner H: A glacier inventory for South Tyrol, Italy, based on airborne laser-scanner data. Ann Glaciol 2010, 50: 46-52. 10. 3189/172756410790595903.
31. Kowalchuk GA, Buma DS, de Boer W, Klinkhamer PGL, van Veen JA: Effects of above-ground plant species composition and diversity on the diversity of soil-borne microorganisms. Anton Leeuw Int J G 2002, 81: 509-520. 10. 1023/A: 1020565523615.
32. Kuramae E, Gamper H, van Veen J, Kowalchuk GA: Soil and plant factors driving the community of soil-borne microorganisms across chronosequences of secondary succession of chalk grasslands with a neutral pH. FEMS Microbiol Ecol 2011, 77: 285-294. 10. 1111/j. 1574-6941. 2011. 01110. x.
33. Kuramae EE, Yergeau E, Wong LC, Pijl AS, van Veen JA, Kowalchuk GA: Soil characteristics more strongly influence soil bacterial communities than land-use type. FEMS Microbiol Ecol 2012, 79: 12-24. 10. 1111/j. 1574-6941. 2011. 01192. x.
34. Kuske CR, Ticknor LO, Miller ME, Dunbar JM, Davis JA, Barns SM, Belnap J: Comparison of soil bacterial communities in rhizosphere of three plant species and the interspaces in an arid grassland. Appl Environ Microbiol 2002, 68: 1854-1863. 10. 1128/AEM. 68. 4. 1854-1863. 2002.
35. Kytöviita MM, Vestberg M, Tuomi J: A test of mutual aid in common mycorrhizal networks: established vegetation negates benefit in seedlings. Ecology 2003, 84: 898-906. 10. 1890/0012-9658(2003)084[0898: ATOMAI]2. 0. CO;2.
36. Ladygina N, Hedlund K: Plant species influence microbial diversity and carbon allocation in the rhizosphere. Soil BiolBiochem 2010, 42: 162-168. 10. 1016/j. soilbio. 2009. 10. 009.
37. Lane DJ: 16S/23S rRNA sequencing. Nucleic acid techniques in bacterial systematics. In Modern microbiological methods. Edited by: Stackebrandt E, Goodfellow M. Chichester, UK: J Wiley & Sons; 1991: 133.
38. Lauber CL, Strickland MS, Bradford MA, Fierer N: The influence of soil properties on the structure of bacterial and fungal communities across land-use types. Soil Biol Biochem 2008, 40: 2407-2415. 10. 1016/j. soilbio. 2008. 05. 021.
39. Lozupone C, Knight R: UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 2005, 71: 8228-8235. 10. 1128/AEM. 71. 12. 8228-8235. 2005.
40. Marschner P, Yang CH, Lieberei R, Crowley DE: Soil and plant specific effects on bacterial community composition in the rhizosphere. Soil Biol Biochem 2001, 33: 1437-1445. 10. 1016/S0038-0717(01)00052-9.
41. Marschner P, Crowley D, Yang CH: Development of specific rhizosphere bacterial communities in relation to plant species, nutrition and soil type. Plant Soil 2004, 261: 199-208.
42. Mattheus JA: The ecology of recently-deglaciated terrain: a geoecological approach to glacier forelands and primary succession. Cambridge University Press, Cambridge, UK; 1992.
43. Miniaci C, Bunge M, Duc L, Edwards I, Bürgmann H, Zeyer J: Effects of pioneering plants on microbial structures and functions in a glacier forefild. Biol Fertil Soils 2007, 44: 289-297. 10. 1007/s00374-007-0203-0.
44. Muyzer G, De Waal EC, Uitierlinden AG: Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 1993, 59: 695-700.
45. Quaiser A, Ochsenreiter T, Lanz C, Schuster SC, Treusch AH, Eck J, Schleper C: Acidobacteria form a coherent but highly diverse group within the bacterial domain: evidence from environmental genomics. Mol Microbiol 2003, 50: 563-575. 10. 1046/j. 1365-2958. 2003. 03707. x.
46. R Core Team: R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria; 2012.
47. Ranjard L, Brothier E, Nazaret S: Sequencing bands of RISA fingerprints for the characterization and the microscale distribution of soil bacterial populations responding to mercury spiking. Appl Environ Microbiol 2000, 66: 5334-5339. 10. 1128/AEM. 66. 12. 5334-5339. 2000.
48. Rees GN, Baldwin DS, Watson GO, Perryman S, Nielsen DL: Ordination and significance testing of microbial community composition derived from terminal restriction fragment length polymorphisms: application of multivariate statistics. Antonie van Leeuwenhoek 2004, 86: 339-347. 10. 1007/s10482-004-0498-x.
49. Rhodes M, Knelman J, Lynch RC, Darcy JL, Nemergut DR, Schmidt SK: Structure and function of prokaryotic communities in soils of polar and high elevation deserts. In The Prokaryotes. Edited by: Rosenberg E, DeLong E, Lory S, Stackebrandt E, Thompson F. Berlin: Springer-Verlag; 2012: 201-213.
50. Roy J, Albert CH, Ibanez S, Saccone P, Zinger L, Choler P, Clément JC, Lavergne S, Geremia RA: Microbes on the cliff: alpine cushion plants structure bacterial and fungal communities. Front Microbiol 2013, 4: 64.
51. Sass AM, Sass H, Coolen MJ, Cypionka H, Overmann J: Microbial communities in the chemocline of a hypersaline deep-sea basin (Urania basin, Mediterranean Sea). Appl Environ Microbiol 2001, 67: 5392-5402. 10. 1128/AEM. 67. 12. 5392-5402. 2001.
52. Schutter ME, Sandeno JM, Dick RP: Seasonal, soil type, and alternative management influences on microbial communities of vegetable cropping systems. Biol Fertil Soils 2001, 34: 397-410. 10. 1007/s00374-001-0423-7.
53. Singh BK, Millard P, Whiteley AS, Murrell JC: Unravelling rhizosphere-microbial interactions: opportunities and limitations. Trends Microbiol 2004, 12: 386-393. 10. 1016/j. tim. 2004. 06. 008.
54. Smalla K, Wieland G, Buchner A, Zock A, Parzy J, Kaiser S, Roskot N, Heuer H, Berg G: Bulk and rhizosphere soil bacterial communities studied by Denaturing Gradient Gel Electrophoresis: plant-dependent enrichment and seasonal shifts revealed. Appl Environ Microbiol 2001, 67: 4742-4751. 10. 1128/AEM. 67. 10. 4742-4751. 2001.
55. Smit E, Leeflang P, Gommans S, van Den Broek J, van Mil S, Wernars K: Diversity and seasonal fluctuations of the dominant members of the bacterial soil community in a wheat field as determined by cultivation and molecular methods. Appl Environ Microbiol 2001, 67: 2284-2291. 10. 1128/AEM. 67. 5. 2284-2291. 2001.
56. Steer J, Harris JA: Shifts in the microbial community in rhizosphere and non-rhizosphere soils during the growth ofAgrostis stolonifera. Soil Biol Biochem 2000, 32: 869-878. 10. 1016/S0038-0717(99)00219-9.
57. Steven B, Leveille R, Pollard WH, Whyte LG: Microbial ecology and biodiversity in permafrost. Extremophiles 2006, 10: 259-267. 10. 1007/s00792-006-0506-3.
58. Tscherko D, Hammesfahr U, Marx MC, Kandeler E: Shifts in rhizosphere microbial communities and enzyme activity ofPoa alpinaacross an alpine chronosequence. Soil Biol Biochem 2004, 36: 1685-1698. 10. 1016/j. soilbio. 2004. 07. 004.
59. Tscherko D, Hammesfahr U, Zeltner G, Kandeler E, Böcker R: Plant succession and rhizosphere microbial communities in a recently deglaciated alpine terrain. Basic Appl Ecol 2005, 6: 367-383. 10. 1016/j. baae. 2005. 02. 004.
60. Whittaker RH: Vegetation of the Siskiyou mountains, Oregon and California. Ecol Monograph 1960, 30: 279-338. 10. 2307/1943563.
61. Wu T, Chellemi DO, Graham JH, Martin KJ, Rosskopf EN: Comparison of soil bacterial communities under diverse agricultural land management and crop production practices. Microb Ecol 2008, 55: 293-310. 10. 1007/s00248-007-9276-4.