Illumina amplicon sequencing of 16S rRNA tag reveals bacterial community development in the rhizosphere of apple nurseries at a replant disease site and a new planting site

PLoS ONE

Volumn 9, Issue 10, 2014, Pages

  Sun, Jian ^a   Zhang, Qiang ^a   Zhou, Jia ^a   Wei, Qinping ^a  

^a INSTITUTE OF PLANT AND ENVIRONMENT PROTECTION   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BETA FRUCTOFURANOSIDASE; CELLULASE; RNA 16S; UREASE; SOIL;

ACIDOBACTERIA; ACTINOBACTERIA; AMPLICON; APPLE; ARTICLE; BACTERIUM; BACTEROIDETES; CHINA; CONTROLLED STUDY; ENZYME ACTIVITY; GEMMATIMONADETES; GENETIC ANALYZER; GROWTH RATE; LYSOBACTER; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; NONHUMAN; PROTEOBACTERIA; PSEUDOMONAS; RHIZOSPHERE; RNA SEQUENCE; SPECIES COMPOSITION; SPECIES RICHNESS; VERRUCOMICROBIA; BIODIVERSITY; BIOMASS; GENETICS; GROWTH, DEVELOPMENT AND AGING; MALUS; MICROBIOLOGY; PHYLOGENY; PLANT DISEASE; PRINCIPAL COMPONENT ANALYSIS; PROCEDURES; SEEDLING; SEQUENCE ANALYSIS; SOIL; SPECIES DIFFERENCE;

BACTERIA (MICROORGANISMS); MALUS X DOMESTICA;

BACTERIA; BIODIVERSITY; BIOMASS; MALUS; PHYLOGENY; PLANT DISEASES; PRINCIPAL COMPONENT ANALYSIS; RHIZOSPHERE; RNA, RIBOSOMAL, 16S; SEEDLINGS; SEQUENCE ANALYSIS, RNA; SOIL; SPECIES SPECIFICITY;

EID: 84910009572     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0111744     Document Type: Article

References (56)

1. Mazzola M, Granatstein DM, Elfving DC, Mullinix K, Gu Y (2002) Cultural management of microbial community structure to enhance growth of apple in replant soils. Phytopathology 92: 1363-1366.
2. Mazzola M (1998) Elucidation of the microbial complex having a causal role in the development of apple replant disease in Washington. Phytopathology 88: 930-938.
3. Fan H, Zhao Z, Liu H, Zhao G, Zhang X, et al. (2008) Changes of Soil Nutrition in Root Zone and Their Effects on Growth of the Replanted Apple. Acta Horticulturae Sinica 12: 3.
4. Mazzola M, Gu Y (2000) Impact of wheat cultivation on microbial communities from replant soils and apple growth in greenhouse trials. Phytopathology 90: 114-119.
5. Mazzola M, Mullinix K (2005) Comparative field efficacy of management strategies containing Brassica napus seed meal or green manure for the control of apple replant disease. Plant Dis 89: 1207-1213.
6. Wilson S, Andrews P, Nair TS (2004) Non-fumigant management of apple replant disease. Sci Hortic-Amsterdam 102: 221-231.
7. Hofmann A, Wittenmayer L, Arnold G, Schieber A, Merbach W (2012) Root exudation of phloridzin by apple seedlings (Malus x domestica Borkh.) with symptoms of apple replant disease. Journal of Applied Botany and Food Quality 82: 193-198.
8. Utkhede RS, Smith EM (1993) Biotic and abiotic causes of replant problems of fruit trees. III International Symposium on Replant Problems 363. 25-32.
9. Rumberger A, Yao S, Merwin IA, Nelson EB, Thies JE (2004) Rootstock genotype and orchard replant position rather than soil fumigation or compost amendment determine tree growth and rhizosphere bacterial community composition in an apple replant soil. Plant Soil 264: 247-260.
10. Mazzola M, Manici LM (2012) Apple replant disease: role of microbial ecology in cause and control. Annu Rev Phytopathol 50: 45-65.
11. Yim B, Smalla K, Winkelmann T (2013) Evaluation of apple replant problems based on different soil disinfection treatments-links to soil microbial community structure? Plant Soil 1-15.
12. Covey Jr RP, Benson NR, Haglund WA (1979) Effect of soil fumigation on the apple replant disease in Washington [USA]. Phytopathology 69.
13. Manici LM, Kelderer M, Franke-Whittle IH, Rühmer T, Baab G, et al. (2013) Relationship between root-endophytic microbial communities and replant disease in specialized apple growing areas in Europe. Appl Soil Ecol 72: 207-214.
14. Cardenas E, Tiedje JM (2008) New tools for discovering and characterizing microbial diversity. Curr Opin Biotech 19: 544-549.
15. Smalla K, Oros-Sichler M, Milling A, Heuer H, Baumgarte S, et al. (2007) Bacterial diversity of soils assessed by DGGE, T-RFLP and SSCP fingerprints of PCR-amplified 16S rRNA gene fragments: do the different methods provide similar results? J Microbiol Meth 69: 470-479.
16. Hirsch PR, Mauchline TH, Clark IM (2010) Culture-independent molecular techniques for soil microbial ecology. Soil Biology and Biochemistry 42: 878-887.
17. Drenovsky RE, Elliott GN, Graham KJ, Scow KM (2004) Comparison of phospholipid fatty acid (PLFA) and total soil fatty acid methyl esters (TSFAME) for characterizing soil microbial communities. Soil Biology and Biochemistry 36: 1793-1800.
18. Ronaghi M, Uhlén M, Nyrén P (1998) A sequencing method based on real-time pyrophosphate. Science 281: 363-365.
19. Lee OO, Wang Y, Yang J, Lafi FF, Al-Suwailem A, et al. (2010) Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea. The ISME journal 5: 650-664.
20. Mazzola M, Strauss SL (2013) Resilience of orchard replant soils to pathogen re-infestation in response to Brassicaceae seed meal amendment. Aspects of Applied Biology 119: 69-77.
21. Gołe¸biewski M, Deja-Sikora E, Cichosz M, Tretyn A, Wróbel B (2014) 16S rDNA Pyrosequencing Analysis of Bacterial Community in Heavy Metals Polluted Soils. Microbial Ecol 1-13.
22. Qian X, Gu J, Sun W, Li Y, Fu Q, et al. (2014) Changes in the soil nutrient levels, enzyme activities, microbial community function, and structure during apple orchard maturation. Appl Soil Ecol 77: 18-25.
23. Jia T, Chao S, Mingyan Y, Xiaoqi Z (2012) Studies on the activities of three kinds of soil enzyme, organic matters, microbes and the yields and quality of apple in different tree-aged apple orchards in Loess plateau. Journal of Agricultural Science and Technology (Beijing) 14: 115-122.
24. Zhang Q, Sun J, Liu S, Wei Q (2013) Manure Refinement Affects Apple Rhizosphere Bacterial Community Structure: A Study in Sandy Soil. PloS one 8: e76937.
25. Sun J, Zhang Q, Zhou J, Wei Q (2014) Pyrosequencing technology reveals the impact of different manure doses on the bacterial community in apple rhizosphere soil. Appl Soil Ecol 78: 28-36.
26. Dullahide SR, Stirling GR, Nikulin A, Stirling AM (1994) The role of nematodes, fungi, bacteria, and abiotic factors in the etiology of apple replant problems in the Granite Belt of Queensland. Animal Production Science 34: 1177-1182.
27. St. Laurent A, Merwin I, Fazio G, Thies J, Brown M (2010) Rootstock genotype succession influences apple replant disease and root-zone microbial community composition in an orchard soil. Plant Soil 337: 259-272.
28. Atucha A, Emmett B, Bauerle T (2014) Growth rate of fine root systems influences rootstock tolerance to replant disease. Plant Soil 376: 337-346.
29. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, et al. (2010) QIIME allows analysis of high-throughput community sequencing data. Nature methods 7: 335-336.
30. Magoč T, Salzberg SL (2011) FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27: 2957-2963.
31. Wang Q, Garrity MG, Tiedje MJ, James RC (2007) Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy. Applied and Environmental Microbiology 73: 5261-5267.
32. Edgar RC (2013) UPARSE: highly accurate OTU sequences from microbial amplicon reads. 10: 996-998.
33. Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, et al. (2011) Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci U S A 108 Suppl 1: 4516-4522.
34. Kämpfer P, Dreyer U, Neef A, Dott W, Busse H (2003) Chryseobacterium defluvii sp. nov., isolated from wastewater. Int J Syst Evol Micr 53: 93-97.
35. Gauthier MJ, Lafay B, Christen R, Fernandez L, Acquaviva M, et al. (1992) Marinobacter hydrocarbonoclasticus gen. nov., sp. nov., a new, extremely halotolerant, hydrocarbon-degrading marine bacterium. International Journal of Systematic Bacteriology 42: 568-576.
36. Sewell G (1981) Effects of Pythium species on the growth of apple and their possible causal role in apple replant disease. Ann Appl Biol 97: 31-42.
37. Sun J, Zhang Q, Liu S, Wang X, Liu J, et al. (2013) Comparison of soil microbe community structure between organic and conventional apple orchards. Journal of Fruit Science 30: 230-234.
38. García Salamanca A, Molina Henares MA, Dillewijn P, Solano J, Pizarro Tobías P, et al. (2013) Bacterial diversity in the rhizosphere of maize and the surrounding carbonate-rich bulk soil. Microbial biotechnology 6: 36-44.
39. Mao Y, Li X, Smyth EM, Yannarell AC, Mackie RI (2014) Enrichment of specific bacterial and eukaryotic microbes in the rhizosphere of switchgrass (Panicum virgatum L.) through root exudates. Environmental Microbiology Reports.
40. Hou S, Makarova KS, Saw JH, Senin P, Ly BV, et al. (2008) Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia. Biol Direct 3: 11.
41. Dunfield PF, Yuryev A, Senin P, Smirnova AV, Stott MB, et al. (2007) Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia. Nature 450: 879-882.
42. Sato T, Kuwahara H, Fujita K, Noda S, Kihara K, et al. (2013) Intranuclear verrucomicrobial symbionts and evidence of lateral gene transfer to the host protist in the termite gut. The ISME journal.
43. Kanso S, Patel BK (2004) Phenylobacterium lituiforme sp. nov., a moderately thermophilic bacterium from a subsurface aquifer, and emended description of the genus Phenylobacterium. Int J Syst Evol Micr 54: 2141-2146.
44. Xu Z, Xu Q, Zheng Z, Huang Y (2012) Kribbella amoyensis sp. nov., isolated from rhizosphere soil of a pharmaceutical plant, Typhonium giganteum Engl. Int J Syst Evol Micr 62: 1081-1085.
45. Kaewkla O, Franco CM (2013) Kribbella endophytica sp. nov., an endophytic actinobacterium isolated from the surface-sterilized leaf of a native apricot tree. Int J Syst Evol Micr 63: 1249-1253.
46. Trujillo ME, Kroppenstedt RM, Schumann P, Martínez-Molina E (2006) Kribbella lupini sp. nov., isolated from the roots of Lupinus angustifolius. Int J Syst Evol Micr 56: 407-411.
47. Wang D, Zhang Y, Jiang Y, Wu W, Jiang C (2003) A study on polyphasic taxonomy of one antifungal actinomycete strain YIM31530∼(T). Journal of Yunnan University (Natural Sciences) 26: 265-269.
48. Kausar J, Ohyama Y, Terato H, Ide H, Yamamoto O (1997) 16S rRNA gene sequence of Rubrobacter radiotolerans and its phylogenetic alignment with members of the genus Arthrobacter, gram-positive bacteria, and members of the family Deinococcaceae. International journal of systematic bacteriology 47: 684-686.
49. Asgarani E, Terato H, Asagoshi K, Shahmohammadi HR, Ohyama Y, et al. (2000) Purification and characterization of a novel DNA repair enzyme from the extremely radioresistant bacterium Rubrobacter radiotolerans. J Radiat Res 41: 19-34.
50. Yang J, Ruegger PM, McKenry MV, Becker JO, Borneman J (2012) Correlations between root-associated microorganisms and peach replant disease symptoms in a California soil. PloS one 7: e46420.
51. Rumberger A, Merwin IA, Thies JE (2007) Microbial community development in the rhizosphere of apple trees at a replant disease site. Soil Biology and Biochemistry 39: 1645-1654.
52. Himani S, Mohinder K, Prakash VP, Sheetal R (2011) Phenotypic and genotypic characterization of plant beneficial fluorescent Pseudomonas species associated with apple to overcome replant problem. Plant Disease Research 26.
53. Santoyo G, Orozco-Mosqueda MDC, Govindappa M (2012) Mechanisms of biocontrol and plant growth-promoting activity in soil bacterial species of Bacillus and Pseudomonas : a review. Biocontrol Sci Techn 22: 855-872.
54. Xie Y, Wright S, Shen Y, Du L (2012) Bioactive natural products from Lysobacter. Nat Prod Rep 29: 1277-1287.
55. Lee KC, Dunfield PF, Morgan XC, Crowe MA, Houghton KM, et al. (2011) Chthonomonas calidirosea gen. nov., sp. nov., an aerobic, pigmented, thermophilic micro-organism of a novel bacterial class, Chthonomonadetes classis nov., of the newly described phylum Armatimonadetes originally designated candidate division OP10. Int J Syst Evol Micr 61: 2482-2490.
56. Yoon M, Im W (2007) Flavisolibacter ginsengiterrae gen. nov., sp. nov. and Flavisolibacter ginsengisoli sp. nov., isolated from ginseng cultivating soil. Int J Syst Evol Micr 57: 1834-1839.