Our aim was to investigate factors that influenced bacterial and fungal community composition in the cucumber rhizosphere with the addition of Bacillus subtilis B068150 in soils.
Using pyrosequencing, we tracked changes in total bacterial and fungal community composition and structures in cucumber rhizosphere planted in clay, loam and sandy soils and inoculated with B. subtilis B068150.
B. subtilis B068150 colonized the rhizosphere of cucumber without altering the indigenous microbial community composition. B068150 strain did not significantly affect microbial diversity in cucumber rhizosphere, but both soils texture and chemistry did, based on principal coordinates analysis (PCoA), hierarchical clustering in UniFrac, and canonical correspondence analysis (CCA). Shannon diversity values (H′) suggest that rhizosphere diversity varied among the three soils with the significant highest diversity observed in loamy soil. Fungi were dominated by Ascomycota, Chytridiomycota, Basidiomycotina, with Ascomycota accounting for 29.1%. Fusarium was found only in cucumber rhizosphere grown in loamy soil; however, this did not affect the health of cucumber in three loamy soils during the three months study.
Bacillus subtilis B068150 could be an environmental compatible plant protective agent in soils depending on the soil type.
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Akiba Y (1986) Microbial ecology of Bacillus thuringiensis VI. Germination of Bacillus thuringiensis spores in the soil. Appl Entomol Zool 21:76–80
Arguelles-Arias A, Ongena M, Halimi B, Lara Y, Brans A, Joris B, Fickers P (2009) Bacillus amyloliquefaciens GA1 as a source of potent antibiotics and other secondary metabolites for biocontrol of plant pathogens. Microb Cell Factories 8:63–68
Backman PA, Brannen PM, Mahaffee WF (1994) Plant response and disease control following seed inoculation with Bacillus subtilis. In: Ryder MH, Stephens PM, Bowen GD (Eds.), Improving Plant Productivity with Rhizosphere Bacteria, CSIRO, Division of Soils, Australia, pp. 3–8
Barret M, Morrissey JP, O’Gara F (2011) Functional genomics analysis of plant growth-promoting rhizobacterial traits involved in rhizosphere competence. Biol Fertil Soils 47:729–743
Benson AK, Kelly SA, Legge R, Ma F, Low SJ, Kim J, Zhang M, Oh PL, Nehrenberg D, Hua K, Kachman SD, Moriyama EN, Walter J, Peterson DA, Pomp D (2010) Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors. PNAS 107:18933–18938
Benson DA, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2015) GenBank. Nucleic Acids Res 43:D30–D35
Bulgarelli D, Schlaeppi K, Spaepen S, van Themaat E, Schulze-Lefert P (2013) Structure and functions of the bacterial microbiota of plants. Ann Rev Plant Biology 64:807–838
Cao Y, Zhang Z, Ling N, Yuan Y, Zhang X, Sun B, Shen Q (2011) Bacillus subtilis SQR9 can control Fusarium wilt in cucumber by colonizing plant roots. Biol Fertil Soils 47:495–506
Cavaglieri LR, Andres L, Ibáñez M, Etcheverry MG (2005) Rhizobacteria and their potential to control Fusarium verticillioides: effect of maize bacterisation and inoculum density. Antonie Van Leeuwenhoek 87:179–187
Choudhary DK, Johri BN (2009) Interactions of Bacillus spp. and plants with special reference to induced systemic resistance (ISR). Microbiol Res 164:493–513
Chowdhury SP, Dietel K, Randler M, Schmid M, Junge H et al (2013) 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
Claesson M, O’Sullivan O, Wang Q, Nikkila J, Marchesi J, Smidt H et al (2009) Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine. PLoS One 4:e6669
Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, Tiedje JM (2009) The ribosomal database project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37:D141–D145
Compant S, Duffy B, Nowak J, Clément C, Barka EA (2005) Use of plant growth-promoting bacteria for biocontrol of plant diseases: principles, mechanisms of action, and future prospects. Appl Environ Microbiol 71:4951–4959
Domsch KH, Jagnow G, Anderson TH (1983) An ecological concept for the assessment of side effects of agrochemicals on soil microorganisms. Residue Rev 86:65–105
Duffy BK, Weller DM (1996) Biological control of take-all of wheat in the Pacific north-west of the USA using hypovirulent Gaeumannomyces graminis var. tritici, fluorescent pseudomonads. J Phytopathol 144(11–12):585–590
Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27:2194–2200
El-Hassan SA, Gowen SR (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
van Elsas JD, Dijkstra AF, Govaert JM, van Veen JA (1986) Survival of Pseudomonas fluorescens and Bacillus subtilis introduced into two soils of different texture in field micro plots. FEMS Microbiol Ecol 38:151–160
Gamalero E, Lingua G, Capr FG, Fusconi A, Berta G, Lemanceau P (2004) Colonization pattern of primary tomato roots by Pseudomonas fluorescens A6RI characterized by dilution plating, flow cytometry, fluorescence, confocal and scanning electron microscopy. FEMS Microbiol Ecol 48:79–87
Gardes M, Bruns T (1993) ITS primers with enhanced specificity for basidiomycetes – application to the identification of mycorrhizae and rusts. Mol Ecol 2:113–118
Haas BJ, Gevers D, Earl AM, Feldgarden M, War DV, Giannoukos G et al (2011) Chimeric 16S rRNA sequence formation and detection in sanger and 454-pyrosequenced PCR amplicons. Genome Res 21:494–504
Hamady M, Lozupone C, Knight R (2010) Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME J 4:17–27
Hervás A, Landa B, Datnoff LE, Jiménez-Díaz RM (1998) Effects of commercial and indigenous microorganisms on Fusarium wilt development in chickpea. Biol Control 13:166–176
Huse SM, Welch DM, Morrison HG, Sogin M (2010) Ironing out the wrinkles in the rabiosphere through improved OTU clustering. Environ Microbiol 12:1889–1898
Janssen PH (2006) Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl Environ Microbiol 72:1719–1728
Johnson M, Zaretskaya I, Raytselis Y, Merezhuk Y, Mcginnis S, Madden TL (2008) NCBI BLAST: a better web interface. Nucleic Acids Res 36:W5–W9
Kautz S, Rubin BE, Russell JA, Moreau CS (2013) Surveying the microbiome of ants: comparing 454 pyrosequencing with traditional methods to uncover bacterial diversity. Appl Environ Microbiol 79:525–534
Klute A (1986) Methods of soil analysis. Part 1: physical and mineralogical methods 9(1). American Society of Agronomy 1188 pp.
Kokalis-Burelle N, Vavrina CS, Rosskopf EN, Shelby RA (2002) Field evaluation of plant growth-promoting rhizobacteria amended transplant mixes and soil solarization for tomato and pepper production in Florida. Plant Soil 238:257–266
Kröber M, Wibberg D, Grosch R, Eikmeyer FG, Verwaaijen B, Chowdhury SP, Hartmann A, Pühler A, Schlüter A (2014) Effect of the strain Bacillus amyloliquefaciens FZB42 on the microbial community in the rhizosphere of lettuce under field conditions analyzed by whole metagenome sequencing. Front Microbiol 5:252. https://doi.org/10.3389/fmicb.2014.00252
Li W, Godzik A (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22:1658–1659
Li C, Li X, Kong W, Kong W, Wu Y, Wang J (2010) Effect of monoculture soybean on soil microbial community in the Northeast China. Plant Soil 330:423–433
Li L, Ma J, Yan L, Wang Z, Gao T, Wang Q (2012) Screening and partial characterization of Bacillus with potential applications in biocontrol of cucumber Fusarium wilt. Crop Prot 35:29–35
Li X, Ding C, Zhang T, Wang X (2014a) Fungal pathogen accumulation at the expense of plant-beneficial fungi as a consequence of consecutive peanut monoculturing. Soil Biol Biochem 72:11–18
Li P, Jiang D, Li B, Dai X, Wang Y, Jiang Z, Wang Y (2014b) Comparative survey of bacterial and archaeal communities in high arsenic shallow aquifers using 454 pyrosequencing and traditional methods. Ecotoxicology 23:1878–1889
Li L, Ma J, Ibekwe AM, Wang Q, Yang C-H (2016) Cucumber rhizosphere microbial community response to biocontrol agent Bacillus subtilis B068150. Agricul 6:2. https://doi.org/10.3390/agriculture6010002
Liang BC, MacKenzie AF, Schnitzer M, Monreal CM, Voroney PR et al (1998) Management-induced change in labile soil organic matter under continuous corn in eastern Canadian soils. Biol Fertil Soils 26:88–94
Liu X, Zhao H, Chen S (2006) Colonization of maize and rice plants by strain Bacillus megaterium C4. Curr Microbiol 52:186–190
Liu QF, Xiong GR, Mao ZC, Wu YX, He YQ (2012) Analyses for the colonization ability of Bacillus subtilis XF-1 in the rhizosphere. Acta Phytophylacica Sinica 39:425–430
Liu X, Zhang J, Gu T, Zhang W, Shen Q, Yin S, Qiu H (2014) Microbial community diversities and taxa abundances in soils along a seven-year gradient of potato monoculture using high throughput pyrosequencing approach. PLoS One 9:e86610
Lottmann J, Heuer H, de Vries J, Mahn A, Du ring K et al (2000) Establishment of introduced antagonistic bacteria in the rhizosphere of transgenic potatoes and their effect on the bacterial community. FEMS Microbiol Ecol 33:41–49
Ma J, Ibekwe AM, Yi X, Wang H, Yamazaki A, Crowley DE, Yang C-H (2011) Persistence of Escherichia coli O157:H7 and its mutants in soils. PLoS One 6(8):e23191
Ma J, Ibekwe AM, Wang H, Xu J, Leddy M, Yang C-H, Crowley DE (2012) Assimilable organic carbon (AOC) in soil water extracts using Vibrio harveyi BB721 and its implication for microbial biomass. PLoS One 7:e28519
Ma A, Zhuang X, Wu J, Cui, M, Di LV, Liu, C., et al. (2013) Ascomycota members dominate fungal communities during straw residue decomposition in arable soil. PLoS One 8:e66146. https://doi.org/10.1371/journal.pone.0066146
McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A et al (2012) An improved greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 6:610–618
Pedersen JC, Damgaard PH, Eilenberg J, Hansen BM (1995) Dispersal of Bacillus thuringiensis var. kurstaki in an experimental cabbage field. Can J Microbiol 41:118–125
Prıńcipe A, Alvarez F, Castro MG, Zachi L, Fischer SE, Mori GB, Jofre´ E (2007) Biocontrol and PGPR features in native strains isolated from saline soils of Argentina. Curr Microbiol 55:314–322
Roeselers G, Mittge EK, Stephens WZ, Parichy DM, Cavanaugh CM, Guillemin K, Rawls JF (2011) Evidence for a core gut microbiota in the zebrafish. ISME J 5:1595–1608
Schloss PD, Handelsman J (2006) Introducing treeclimber, a test to compare microbial community structures. Appl Environ Microbiol 72:2379–2384
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541
Sheneman L, Evans J, Foster JA (2006) Clearcut: a fast implementation of relaxed neighbor joining. Bioinformatics 22:2823–2824
Solankia MK, Kumara S, Pandeyb AK, Srivastavaa S, Singha RK, Kashyapa PL, Srivastavaa AK Arora DK (2012) Diversity and antagonistic potential of Bacillus spp. associated to the rhizosphere of tomato for the management of Rhizoctonia solani. Biocontrol Sci Tech 22:203–217
Tedersoo L, Nilsson RH, Abarenkov K, Jairus T, Sadam A, Saar I, Bahram M, Bechem E, Chuyong G, Kõljalg U (2010) 454 pyrosequencing and sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases. New Phytol 188:291–301
Vance ED, Brookes PC, Jenkinson DS (1987) An extraction method for measuring soil microbial biomass C. Soil Biol Biochem 19:703–707
White T, Brans T, Lee S, Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky J, White TJ (eds) PCR Protocols: A Guide to Methods and Applications. Academic Press, San Diego, pp 315–322
Winding A, Binnerup SJ, Pritchard H (2004) Non-target effects of bacterial biological control agents suppressing root pathogenic fungi. FEMS Microbiol Ecol 47:129–141
Wubet T, Christ S, Schoning I, Boch S, Gawlich M, Schnabel B et al (2012) Differences in soil fungal communities between European beech (Fagus sylvatica L.) dominated forests are related to soil and understory vegetation. PLoS One 7:e47500
Xu Z, Zhang R, Wang D, Qiu M, Feng H, Zhang N, Shen Q (2014) Enhanced control of cucumber wilt disease by Bacillus amyloliquefaciens SQR9 by altering the regulation of its DegU phosphorylation. Appl Environ Microbiol 80:2941–2950
Zhou X, Wu F (2012) Dynamics of the diversity of fungal and fusarium communities during continuous cropping of cucumber in the greenhouse. FEMS Microbiol Ecol 80:469–478
Zhou J, Xue K, Xie J, Deng Y, Wu L, Cheng X, Fei S, Deng S, He Z, Van Nostrand JD, Luo Y (2012) Microbial mediation of carbon-cycle feedbacks to climate warming. Nat Clim Chang 2:106–110
This research was supported by the 214 Manure and Byproduct Utilization Project of the USDA-ARS. We thank Damon Baptista for technical assistance. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. The U.S. Department of Agriculture (USDA) prohibits discrimination in all its programs and activities on the basis of race, color, national origin, age, disability, and where applicable, sex, marital status, familial status, parental status, religion, sexual orientation, genetic information, political beliefs, reprisal, or because all or part of an individual’s income is derived from any public assistance program.
This work was also supported by Program for Excellent Talents of Modem Agriculture of China, the innovation team of grape diseases and insect pests biocontrol.
Responsible Editor: Stéphane Compant.
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Li, L., Ma, J., Mark Ibekwe, A. et al. Influence of Bacillus subtilis B068150 on cucumber rhizosphere microbial composition as a plant protective agent. Plant Soil 429, 519–531 (2018). https://doi.org/10.1007/s11104-018-3709-3