Plant community effects on the diversity and pathogen suppressive activity of soil streptomycetes

Applied Soil Ecology

Volumn 46, Issue 1, 2010, Pages 35-42

  Bakker, Matthew G ^a   Glover, Jerry D ^b   Mai, John G ^b   Kinkel, Linda L ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

^b THE LAND INSTITUTE   (United States)

Author keywords

Diversity; Land use change; Pathogen suppression; Prairie; Streptomycete

Indexed keywords

STREPTOMYCETACEAE; STREPTOMYCINEAE;

EID: 77955981506     PISSN: 09291393     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.apsoil.2010.06.003     Document Type: Article

References (59)

1. Anderson A.S., Wellington E.M.H. The taxonomy of Streptomyces and related genera. Int. J. Syst. Evol. Microbiol. 2001, 51:797-814.
2. Angell S., Bench B.J., Williams H., Watanabe C.M.H. Pyocyanin isolated from a marine microbial population: synergistic production between two distinct bacterial species and mode of action. Chem. Biol. 2006, 13:1349-1359.
3. Bentley S.D., Chater K.F., Cerdeno-Tarraga A.M., Challis G.L., Thomson N.R., James K.D., Harris D.E., Quail M.A., Kieser H., Harper D., Bateman A., Brown S., Chandra G., Chen C.W., Collins M., Cronin A., Fraser A., Goble A., Hidalgo J., Hornsby T., Howarth S., Huang C.H., Kieser T., Larke L., Murphy L., Oliver K., O'Neil S., Rabbinowitsch E., Rajandream M.A., Rutherford K., Rutter S., Seeger K., Saunders D., Sharp S., Squares R., Squares S., Taylor K., Warren T., Wietzorrek A., Woodward J., Barrell B.G., Parkhill J., Hopwood D.A. Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 2002, 417:141-147.
4. Bergsma-Vlami M., Prins M.E., Raaijmakers J.M. Influence of plant species on population dynamics, genotypic diversity and antibiotic production in the rhizosphere by indigenous Pseudomonas spp. FEMS Microbiol. Ecol. 2005, 52:59-69.
5. Bowden R.D., Davidson E., Savage K., Arabia C., Steudler P. Chronic nitrogen additions reduce total soil respiration and microbial respiration in temperate forest soils at the Harvard Forest. Forest Ecol. Manage. 2004, 196:43-56.
6. Challis G.L., Hopwood D.A. Synergy and contingency as driving forces for the evolution of multiple secondary metabolite production by Streptomyces species. Proc. Natl. Acad. Sci. U.S.A. 2003, 100:14555-14561.
7. Chamberlain K., Crawford D.L. In vitro and in vivo antagonism of pathogenic turf grass fungi by Streptomyces hygroscopicus strains YCED9 and WYE53. J. Ind. Microbiol. Biotechnol. 1999, 23:641-646.
8. Compton J.E., Watrud L.S., Porteous L.A., DeGrood S. Response of soil microbial biomass and community composition to chronic nitrogen additions at Harvard forest. Forest Ecol. Manage. 2004, 196:143-158.
9. Culman S.W., DuPont S.T., Glover J.D., Buckley D.H., Fick G.W., Ferris H., Crews T.E. Long-term impacts of high-input annual cropping and unfertilized perennial grass production on soil properties and belowground food webs in Kansas, USA. Agric. Ecosyst. Environ. 2010, 137:13-24.
10. da Rocha U.N., van Overbeek L., van Elsas J.D. Exploration of hitherto-uncultured bacteria from the rhizosphere. FEMS Microbiol. Ecol. 2009, 69:313-328.
11. Davelos Baines A.L., Xiao K., Kinkel L.L. Lack of correspondence between genetic and phenotypic groups amongst soil-borne streptomycetes. FEMS Microbiol. Ecol. 2007, 59:564-575.
12. DeForest J.L., Zak D.R., Pregitzer K.S., Burton A.J. Atmospheric nitrate deposition, microbial community composition, and enzyme activity in northern hardwood forests. Soil Sci. Soc. Am. J. 2004, 68:132-138.
13. de Werra P., Baehler E., Huser A., Keel C., Maurhofer M. Detection of plant-modulated alterations in antifungal gene expression in Pseudomonas fluorescens CHA0 on roots by flow cytometry. Appl. Environ. Microbiol. 2008, 74:1339-1349.
14. Ducklow H. Microbial services: challenges for microbial ecologists in a changing world. Aquat. Microbiol. Ecol. 2008, 53:13-19.
15. DuPont S.T., Culman S.T., Ferris H., Buckley D.H., Glover J.D. No-tillage conversion of harvested perennial grassland to annual cropland reduces root biomass, decreases active carbon stocks, and impacts soil biota. Agric. Ecosyst. Environ. 2010, 137:25-32.
16. Edwards U., Rogall T., Blocker H., Emde M., Bottger E.C. Isolation and direct complete nucleotide determination of entire genes - characterization of a gene coding for 16s-ribosomal RNA. Nucleic Acids Res. 1989, 17:7843-7853.
17. El-Tarabily K.A., Hardy G.E.S.J., Sivasithamparam K., Hussein A.M., Kurtboke D.I. The potential for the biological control of cavity-spot disease of carrots, caused by Pythium coloratum, by streptomycete and non-streptomycete actinomycetes. New Phytol. 1997, 137:495-507.
18. Emmert E.A.B., Handelsman J. Biocontrol of plant disease: a (Gram-) positive perspective. FEMS Microbiol. Lett. 1999, 171:1-9.
19. Ghini R., Morandi M.A.B. Biotic and abiotic factors associated with soil suppressiveness to Rhizoctonia solani. Sci. Agric. 2006, 63:153-160.
20. Glover J.D., Culman S.T., DuPont S.T., Broussard W., Young L., Mangan M.E., Mai J.G., Crews T.E., DeHaan L.R., Buckley D.H., Ferris H., Turner R.E., Reynolds H.L., Wyse D.L. Harvested perennial grasslands provide ecological benchmarks for agricultural sustainability. Agric. Ecosyst. Environ. 2010, 137:3-12.
21. Guetsky R., Shtienberg D., Elad Y., Fischer E., Dinoor A. Improving biological control by combining biocontrol agents each with several mechanisms of disease suppression. Phytopathology 2002, 92:976-985.
22. Hansen S.K., Rainey P.B., Haagensen J.A.J., Molin S. Evolution of species interactions in a biofilm community. Nature 2007, 445:533-536.
23. Hjort K., Lembke A., Speksnijder A., Smalla K., Jansson J.K. Community structure of actively growing bacterial populations in plant pathogen suppressive soil. Microbiol. Ecol. 2007, 53:399-413.
24. Horinouchi S., Beppu T. A-factor as a microbial hormone that controls cellular differentiation and secondary metabolism in Streptomyces griseus. Mol. Microbiol. 1994, 12:859-864.
25. Jones C.R., Samac D.A. Biological control of fungi causing alfalfa seedling damping-off with a disease-suppressive strain of Streptomyces. Biol. Control 1996, 7:196-204.
26. Joseph S.J., Hugenholtz P., Sangwan P., Osborne C.A., Janssen P.H. Laboratory cultivation of widespread and previously uncultured soil bacteria. Appl. Environ. Microbiol. 2003, 9:7210-7215.
27. Kataoka M., Ueda K., Kudo T., Seki T., Yoshida T. Application of the variable region in 16S rDNA to create an index for rapid species identification in the genus Streptomyces. FEMS Microbiol. Lett. 1997, 151:249-255.
28. Kieser T., Bibb M., Buttner J., Chater M.J., Hopwood K.F. Practical Streptomyces Genetics 2000, Norwich, The John Innes Foundation, 613 pp.
29. Kuster E., Williams S.T. Selection of media for isolation of Streptomyces. Nature 1964, 202:928-929.
30. Larkin M.A., Blackshields G., Brown N.P., Chenna R., McGettigan P.A., McWilliam H., Valentin F., Wallace I.M., Wilm A., Lopez R., Thompson J.D., Gibson T.J., Higgins D.G. Clustal W and Clustal X version 2.0. Bioinformatics 2007, 23:2947-2948.
31. Lauber C.L., Hamady M., Knight R., Fierer N. Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl. Environ. Microbiol. 2009, 75:5111-5120.
32. Liu D., Anderson N.A., Kinkel L.L. Biological control of potato scab in the field with antagonistic Streptomyces scabies. Phytopathology 1995, 85:827-831.
33. Mazzola M., Funnell D.L., Raaijmakers J.M. Wheat cultivar-specific selection of 2,4-diacetylphloroglucinol-producing fluorescent Pseudomonas species from resident soil populations. Microbiol. Ecol. 2004, 48:338-348.
34. Marshall K.C., Alexander M. Competition between soil bacteria and Fusarium. Plant Soil 1960, 12:143-153.
35. Neefs J.M., Vandepeer Y., Hendriks L., Dewachter R. Compilation of small ribosomal-subunit RNA sequences. Nucleic Acids Res. 1990, 18:2237-2317.
36. Nemergut D.R., Townsend A.R., Sattin S.R., Freeman K.R., Fierer N., Neff J.C., Bowman W.D., Schadt C.W., Weintraub M.N., Schmidt S.K. The effects of chronic nitrogen fertilization on alpine tundra soil microbial communities: implications for carbon and nitrogen cycling. Environ. Microbiol. 2008, 10:3093-3105.
37. Okubara P.A., Bonsall R.F. Accumulation of Pseudomonas-derived 2,4-diacetylphloroglucinol on wheat seedling roots is influenced by host cultivar. Biol. Control 2008, 46:322-331.
38. Perez C., Dill-Macky R., Kinkel L.L. Management of soil microbial communities to enhance populations of Fusarium graminearum antagonists in soil. Plant Soil 2008, 302:53-69.
39. Raaijmakers J.M., Weller D.M. Natural plant protection by 2,4-diacetylphloroglucinol -producing Pseudomonas spp. in take-all decline soils. Mol. Plant-Microbe Interact. 1998, 11:144-152.
40. Ruddick S.M., Williams S.T. Studies on the ecology of actinomycetes in soil. V. Some factors influencing the dispersal and adsorption of spores in soil. Soil Biol. Biochem. 1972, 4:93-103.
41. Ryan A.D., Kinkel L.L., Schottel J.L. Effect of pathogen isolate, potato cultivar, and antagonist strain on potato scab severity and biological control. Biocontrol Sci. Technol. 2004, 4:301.
42. Samac D.A., Willert A.M., McBride M.J., Kinkel L.L. Effect of antibiotic-producing Streptomyces on nodulation and leaf spot in alfalfa. Appl. Soil Ecol. 2003, 22:55-66.
43. Samac D.A., Kinkel L.L. Suppression of the root-lesion nematode (Pratylenchus penetrans) in alfalfa (Medicago sativa) by Streptomyces spp. Plant Soil 2001, 235:35-44.
44. Sarathchandra S.U., Ghani A., Yeates G.W., Burch G., Cox N.R. Effect of nitrogen and phosphate fertilisers on microbial and nematode diversity in pasture soils. Soil Biol. Biochem. 2001, 33:953-964.
45. Schlatter D.C., Fubuh A., Xiao K., Hernandez D., Hobbie S., Kinkel L.L. Influence of carbon source amendments on population density, resource use, and antibiotic phenotypes of soilborne Streptomyces. Phytopathology 2008, 98:S140-S141.
46. Schloss P.D., Westcott S.L., Ryabin T., Hall J.R., Hartmann M., Hollister E.B., Lesniewski R.A., Oakley B.B., Parks D.H., Robinson C.J., Sahl J.W., Stres B., Thallinger G.G., Van Horn D.J., Weber C.F. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 2009, 75:7537-7541.
47. Shennan C. Biotic interactions, ecological knowledge and agriculture. Philos. Trans. R. Soc. Lond.: B 2008, 363:717-739.
48. Stackebrandt E., Witt D., Kemmerling C., Kroppenstedt R., Liesack W. Designation of streptomycete 16s and 23s ribosomal-RNA-based target regions for oligonucleotide probes. Appl. Environ. Microbiol. 1991, 57:1468-1477.
49. Thompson J.N. The evolution of species interactions. Science 1999, 284:2116-2118.
50. Tilman D., Reich P.B., Knops J., Wedin D., Mielke T., Lehman C. Diversity and productivity in a long-term grassland experiment. Science 2001, 294:843-845.
51. van Elsas J.D., Garbeva P., Salles J. Effects of agronomical measures on the microbial diversity of soils as related to the suppression of soil-borne plant pathogens. Biodegradation 2002, 13:29-40.
52. Wang Q., Garrity G.M., Tiedje J.M., Cole J.R. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 2007, 73:5261-5267.
53. Wang Q.K., Wang S.L., Liu Y.X. Responses to N and P fertilization in a young Eucalyptus dunnii plantation: Microbial properties, enzyme activities and dissolved organic matter. Appl. Soil Ecol. 2008, 40:484-490.
54. Weller D.M., Raaijmakers J.M., Gardener B.B.M., Thomashow L.S. Microbial populations responsible for specific soil suppressiveness to plant pathogens. Annu. Rev. Phytopathol. 2002, 40:309-348.
55. Wiggins B.E., Kinkel L.L. Green manures and crop sequences influence alfalfa root rot and pathogen inhibitory activity among soil-borne streptomycetes. Plant Soil 2005, 268:271-283.
56. Wiggins B.E., Kinkel L.L. Green manures and crop sequences influence potato diseases and pathogen inhibitory activity of indigenous streptomycetes. Phytopathology 2005, 95:178-185.
57. Xiao K., Kinkel L.L., Samac D.A. Biological control of Phytophthora root rots on alfalfa and soybean with Streptomyces. Biol. Control 2002, 23:285-295.
58. Yuan W.M., Crawford D.L. Characterization of Streptomyces lydicus WYEC108 as a potential biocontrol agent against fungal root and seed rots. Appl. Environ. Microbiol. 1995, 61:3119-3128.
59. Zhou J., Xia B., Treves D.S., Wu L.Y., Marsh T.L., O'Neill R.V., Palumbo A.V., Tiedje J.M. Spatial and resource factors influencing high microbial diversity in soil. Appl. Environ. Microbiol. 2002, 68:326-334.