Abstract
In our previous work, applying biofertilizer containing Bacillus amyloliquefaciens strain NJN-6 to a banana orchard infected by a serious Fusarium wilt disease over two consecutive years effectively controlled this soil-borne disease. In this study, deep pyrosequencing of 16S ribosomal RNA (rRNA) genes and internal transcribed spacer (ITS) sequences was performed to investigate how the composition of rhizosphere microbial community responded to the application of biofertilizer (BIO), pig manure compost (PM), and chemical fertilizer (CF) and to explore the potential correlation between the microbial community composition and the Fusarium wilt disease. A total of 104,201 bacterial 16S rRNA genes and 154,953 fungal ITS sequence reads were obtained after basic quality control, and Acidobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Ascomycota were the most abundant bacterial and fungal phyla across all samples. Compared with the PM and CF control, the alpha diversity of bacteria significantly (P < 0.05) increased, whereas the value of the fungi was significantly (P < 0.05) reduced following two consecutive years of biofertilizer application. Moreover, the abundance of Acidobacteria (Gp1 and Gp3), Firmicutes, Leptosphaeria, and Phaeosphaeriopsis was significantly (P < 0.05) increased, while the abundance of Proteobacteria and Ascomycota was significantly (P < 0.05) decreased in the BIO treatment. Furthermore, the abundance of Fusarium, a causal pathogen for Fusarium wilt disease, was significantly (P < 0.05) reduced in the BIO treatment compared with the CF control and was slightly reduced (not significant) compared with the PM control. Interestingly, the disease incidence was negatively correlated with the enriched taxa of Acidobacteria (Gp1 and Gp3) and Firmicutes, Leptosphaeria, and Phaeosphaeriopsis but positively correlated with abundance of Proteobacteria, Ascomycota, Fusarium, Cylindrocarpon, Gymnascella, Monographella, Pochonia, and Sakaguchia taxa. The results from this study suggest that 2 years of biofertilizer application manipulated the composition of rhizosphere microbial community and induced the Fusarium suppression by increasing bacterial diversity and potentially stimulating microbial consortia taxa, such as Acidobacteria (Gp1 and Gp3), Firmicutes, Leptosphaeria, and Phaeosphaeriopsis.
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References
Acosta-Martinez V, Dowd S, Sun Y, Allen V (2008) Tag-encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use. Soil Biol Biochem 40:2762–2770
Alguacil MM, Torrecillas E, Caravaca F, Fernández DA, Azcón R, Roldán A (2011) The application of an organic amendment modifies the arbuscular mycorrhizal fungal communities colonizing native seedlings grown in a heavy-metal-polluted soil. Soil Biol Biochem 43:1498–1508
Bais HP, Weir TL, Perry LG, Gilroy S, Vivanco JM (2006) The role of root exudates in rhizosphere interactions with plants and other organisms. Annu Rev Plant Biol 57:233–266
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
Binladen J, Gilbert MTP, Bollback JP, Panitz F, Bendixen C, Nielsen R, Willerslev E (2007) The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PLoS One 2:e197
Butler D (2013) Fungus threatens top banana. Nature 504:195–196
Câmara MP, Ramaley AW, Castlebury LA, Palm ME (2003) Neophaeosphaeria and Phaeosphaeriopsis, segregates of Paraphaeosphaeria. Mycol Res 107:516–522
DeAngelis KM, Brodie EL, DeSantis TZ, Andersen GL, Lindow SE, Firestone MK (2008) Selective progressive response of soil microbial community to wild oat roots. ISME J 3:168–178
El-Hassan S, Gowen S (2006) Formulation and delivery of the bacterial antagonist Bacillus subtilis for management of lentil vascular wilt caused by Fusarium oxysporum f. sp. lentis. J Phytopathol 154:148–155
Etten EV (2005) Multivariate analysis of ecological data using CANOCO. Austral Ecol 30:486–487
Fierer N, Bradford MA, Jackson RB (2007) Toward an ecological classification of soil bacteria. Ecology 88:1354–1364
Filion M, Hamelin R, Bernier L, St-Arnaud M (2004) Molecular profiling of rhizosphere microbial communities associated with healthy and diseased black spruce (Picea mariana) seedlings grown in a nursery. Appl Environ Microbiol 70:3541–3551
Garbeva P, Van Veen J, Van Elsas J (2004) Microbial diversity in soil: selection of microbial populations by plant and soil type and implications for disease suppressiveness. Annu Rev Phytopathol 42:243–270
Grayston SJ, Wang S, Campbell CD, Edwards AC (1998) Selective influence of plant species on microbial diversity in the rhizosphere. Soil Biol Biochem 30:369–378
Haichar FZ, Marol C, Berge O, Rangel-Castro JI, Prosser JI, Balesdent J, Heulin T, Achouak W (2008) Plant host habitat and root exudates shape soil bacterial community structure. ISME J 2:1221–1230
Hunter PJ, Petch GM, Calvo-Bado LA, Pettitt TR, Parsons NR, Morgan JAW, Whipps JM (2006) Differences in microbial activity and microbial populations of peat associated with suppression of damping-off disease caused by Pythium sylvaticum. Appl Environ Microbiol 72:6452–6460
Jack AL, Rangarajan A, Culman SW, Sooksa-Nguan T, Thies JE (2011) Choice of organic amendments in tomato transplants has lasting effects on bacterial rhizosphere communities and crop performance in the field. Appl Soil Ecol 48:94–101
Katoh K, Misawa K, Ki K, Miyata T (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30(14):3059–3066
Kent AD, Triplett EW (2002) Microbial communities and their interactions in soil and rhizosphere ecosystems. Annu Rev Microbiol 56:211–236
Kõljalg U, Nilsson RH, Abarenko K, Tedersoo L, Taylor AFS, Bahram M, Bates ST, Bruns TD, Bengtsson-Palme J, Callaghan TM, Douglas B, Drenkhan T, Eberhardt U, Dueñas M, Grebenc T, Griffith GW, Hartmann M, Kirk PM, Kohout P, Larsson E, Lindahl BD, Lücking R, Martín MP, Matheny PB, Nguyen NH, Niskanen T, Oja J, Peay KG, Peintner U, Peterson M, Põldmaa K, Saag L, Saar I, Schüßler A, Scott JA, Senés C, Smith ME, Suija A, Taylor DL, Telleria MT, Weiss M, Larsson KH (2013) Towards a unified paradigm for sequence-based identification of fungi. Mol Ecol 22:5271–5277
Lauber CL, Hamady M, Knight R, Fierer N (2009) Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol 75:5111–5120
Li JG, Ren GD, Jia ZJ, Dong YH (2014) Composition and activity of rhizosphere microbial communities associated with healthy and diseased greenhouse tomatoes. Plant Soil 380:337–347
Ling N, Deng KY, Song Y, Wu YC, Zhao J, Raza W, Huang QW, Shen QR (2014) Variation of rhizosphere bacterial community in watermelon continuous mono-cropping soil by long-term application of a novel bioorganic fertilizer. Microbiol Res 169:570–578
Lundberg DS, Lebeis SL, Paredes SH, Yourstone S, Gehring J, Malfatti S, Tremblay J, Engelbrektson A, Kunin V, del Rio TG (2012) Defining the core Arabidopsis thaliana root microbiome. Nature 488:86–90
Luo J, Ran W, Hu J, Yang XM, Xu YC, Shen QR (2010) Application of bio-organic fertilizer significantly affected fungal diversity of soils. Soil Sci Soc Am J 74:2039–2048
Manici L, Caputo F (2009) Fungal community diversity and soil health in intensive potato cropping systems of the east Po valley, northern Italy. Ann Appl Biol 155:245–258
Mazzola M (2004) Assessment and management of soil microbial community structure for disease suppression. Annu Rev Phytopathol 42:35–59
Mendes R, Kruijt M, de Bruijn I, Dekkers E, van der Voort M, Schneider JHM, Piceno YM, DeSantis TZ, Andersen GL, Bakker PAHM, Raaijmakers JM (2011) Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science 332:1097–1100
Pegg K, Moore N, Bentley S (1996) Fusarium wilt of banana in Australia: a review. Aust J Agr Res 47:637–650
Philippot L, Raaijmakers JM, Lemanceau P, van der Putten WH (2013) Going back to the roots: the microbial ecology of the rhizosphere. Nat Rev Microbiol 11:789–799
Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glöckner FO (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35:7188–7196
Qiu MH, Zhang RF, Xue C, Zhang SS, Li SQ, Zhang N, Shen QR (2012) Application of bio-organic fertilizer can control Fusarium wilt of cucumber plants by regulating microbial community of rhizosphere soil. Biol Fertil Soils 48:807–816
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO (2012) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41:D590–D596
Raaijmakers JM, Paulitz TC, Steinberg C, Alabouvette C, Moënne-Loccoz Y (2009) The rhizosphere: a playground and battlefield for soilborne pathogens and beneficial microorganisms. Plant Soil 321:341–361
Racine JS (2012) RStudio: a Platform-Independent IDE for R and Sweave. J Appl Econ 27:167–172
Rosenzweig N, Tiedje JM, Quensen JF III, Meng Q, Hao JJ (2012) Microbial communities associated with potato common scab-suppressive soil determined by pyrosequencing analyses. Plant Dis 96:718–725
Rumberger A, Yao SR, 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
Sanguin H, Sarniguet A, Gazengel K, Moënne-Loccoz Y, Grundmann G (2009) Rhizosphere bacterial communities associated with disease suppressiveness stages of take-all decline in wheat monoculture. New Phytol 184:694–707
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541
Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, Levesque CA, Chen W, Bolchacova E, Voigt K, Crous PW (2012) Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for fungi. Proc Natl Acad Sci U S A 109:6241–6246
Shen ZZ, Zhong ST, Wang YG, Wang BB, Mei XL, Li R, Ruan YZ, Shen QR (2013) Induced soil microbial suppression of banana Fusarium wilt disease using compost and biofertilizers to improve yield and quality. Eur J Soil Biol 57:1–8
Shen ZZ, Wang BB, Lv NN, Sun YF, Jiang XY, Li R, Ruan YZ, Shen QR (2015) Effect of the combination of bio-organic fertilizer with Bacillus amyloliquefaciens NJN-6 on the control of banana Fusarium wilt disease, crop production and banana rhizosphere microflora. Biocontrol Sci Tech. doi:10.1080/09583157.2015.1010482
Sprague SJ, Watt M, Kirkegaard JA, Howlett BJ (2007) Pathways of infection of Brassica napus roots by Leptosphaeria maculans. New Phytol 176:211–222
Teixeira LC, Peixoto RS, Cury JC, Sul WJ, Pellizari VH, Tiedje J, Rosado AS (2010) Bacterial diversity in rhizosphere soil from Antarctic vascular plants of Admiralty Bay, maritime Antarctica. ISME J 4:989–1001
Wang BB, Yuan J, Zhang J, Shen ZZ, Zhang MX, Li R, Ruan YX, Shen QR (2013) Effects of novel bioorganic fertilizer produced by Bacillus amyloliquefaciens W19 on antagonism of Fusarium wilt of banana. Biol Fertil Soils 49:435–446
Xu L, Huang BZ, Wu YL, Huang YH, Dong T (2011) The cost-benefit analysis for bananas diversity production in China Foc. zones. Am J Plant Sci 2:561–568
Yin C, Hulbert SH, Schroeder KL, Mavrodi O, Mavrodi D, Dhingra A, Schillinger WF, Paulitz TC (2013) Role of bacterial communities in the natural suppression of Rhizoctonia solani bare patch of wheat (Triticum aestivum L.). Appl Environ Microbiol 79:7428–7438
Yu L, Nicolaisen M, Larsen J, Ravnskov S (2012) Molecular characterization of root-associated fungal communities in relation to health status of Pisum sativum using barcoded pyrosequencing. Plant Soil 357:395–405
Yu L, Nicolaisen M, Larsen J, Ravnskov S (2013) Organic fertilization alters the community composition of root associated fungi in Pisum sativum. Soil Biol Biochem 58:36–41
Yuan SF, Wang LL, Wu K, Shi JX, Wang MS, Yang XM, Shen QR, Shen B (2014) Evaluation of Bacillus-fortified organic fertilizer for controlling tobacco bacterial wilt in greenhouse and field experiments. Appl Soil Ecol 75:86–94
Zhang FG, Zhu Z, Yang XM, Ran W, Shen QR (2013) Trichoderma harzianum T-E5 significantly affects cucumber root exudates and fungal community in the cucumber rhizosphere. Appl Soil Ecol 72:41–48
Zhang M, Li R, Cao LL, Shi JJ, Liu HJ, Huang Y, Shen QR (2014a) Algal sludge from Taihu Lake can be utilized to create novel PGPR-containing bio-organic fertilizers. J Environ Manag 132:230–236
Zhang N, He X, Zhang J, Raza W, Yang XM, Ruan YZ, Shen QR, Huang QW (2014b) Suppression of Fusarium wilt of banana with application of bio-organic fertilizers. Pedosphere 24:613–624
Zhao QY, Dong CX, Yang XM, Mei XL, Ran W, Shen QR, Xu YC (2011) Biocontrol of Fusarium wilt disease for Cucumis melo melon using bio-organic fertilizer. Appl Soil Ecol 47:67–75
Zhao S, Liu DY, Ling N, Chen FD, Fang WM, Shen QR (2014) Bio-organic fertilizer application significantly reduces the Fusarium oxysporum population and alters the composition of fungi communities of watermelon Fusarium wilt rhizosphere soil. Biol Fertil Soils 50:765–774
Acknowledgments
We are very grateful to Shanghai Tongji-SCBIT Biotechnology Co. Ltd and Shanghai Personal Biotechnology Co., Ltd for deep 16S rRNA gene and ITS sequence barcode pyrosequencing, respectively. We thank the banana orchard owner Yusheng Li for providing access to the experimental field and facilities. In addition, we thank all staff members in the Hainan Wanzhong Agriculture Company for their considerable help with banana planting and management.
This research was supported by the National Key Basic Research Program of China (2015CB150506), the National Natural Science Foundation of China (41101231 and 31372142), the Department of Science and Technology of Hainan Province (ZDZX2013023), the Priority Academic Program Development of the Jiangsu Higher Education Institutions (PAPD), the 111 project (B12009), the Agricultural Ministry of China (201103004), and the Innovative Research Team Development Plan of the Ministry of Education of China (IRT1256).
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Z. Shen and Y. Ruan contributed equally to this article.
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Shen, Z., Ruan, Y., Chao, X. et al. Rhizosphere microbial community manipulated by 2 years of consecutive biofertilizer application associated with banana Fusarium wilt disease suppression. Biol Fertil Soils 51, 553–562 (2015). https://doi.org/10.1007/s00374-015-1002-7
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DOI: https://doi.org/10.1007/s00374-015-1002-7