A Comparative Metagenomic Analysis of Rhizospheric Bacterial Communities between Suppressive and Conducive Soil towards Ganoderma boninense Infection in Oil Palm (Elaeis guineensis Jacq.)
Keywords:
edaphic factors, conducive and suppressive soils, community structure, Ganoderma boninenseAbstract
The oil palm (Elaeis guineensis Jacq.) yields high economic value. Indonesia, as one of palm oil's major producers, is inseparable from the threat of basal stem rot disease by Ganoderma boninense. This disease causes severe declines in the plant's productivity. Ganoderma suppressive soil is known to suppress the development of pathogens, as the microbes present can improve the plant's health, modulate the immune system, and compete with pathogens. This study aims to compare the community structure of suppressive and conducive soilforming bacteria at topsoil (0-20 cm) and subsoil (20-40 cm) and their correlation with edaphic factors. Research includes performing a metagenomic analysis using 16S rRNA sequencing data. The research flow includes sequence quality control (FastQC), data analysis (QIIME2), taxonomic classification and gene function prediction (PICRISt2), and a Principal Component Analysis with edaphic factors (XLSTAT). Suppressive soils had highest alpha diversity. Potential suppressivesoil-forming agents include Acidothermus, Burkholderia, Reyranella, Rokubacter, Streptomycetaceae, Bryobacter, Alphaproteobacteria, Rhizobiales, and Bradyrhizobium. Predicted gene functions include the synthesis of antibiotics, antifungals, and plant defense enzymes. pH and clay percentage play a role in increasing the incidence of disease. It was concluded that suppressive-soil-forming bacterial community had higher diversity than conducive soil and was not affected by soil depth.
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References
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J. Ma, A. Ibekwe, C. Yang, and D. Crowley, Bacterial diversity and composition in major fresh produce growing soils affected by physiochemical properties and geographic locations, Sci Total Env., pp. 199–209, 2016, doi: 10.1016/j.scitotenv.2016.04.122.
FAO, Land use for palm oil production, 2020. http://www.fao.org/faostat/en/?#data%5C (accessed Apr. 15, 2020).
P. Turner, Infection of oil palms by Ganoderma in Malaya, Oléagineux, vol. 21, p. 73‐76.
V. Rao, C. Lim, C. Chia, and K. Theo, Studies on Ganoderma spread and control, Planter, vol. 79, pp. 367–368, 2003.
R. Hustarian, N. Yusof, and S. Dutse, Detection and control of Ganoderma boninense: strategies and perspectives, Springerplus, vol. 2, p. 555, 2013, doi: 10.1186/2193-1801-2-555.
R. Cook, Plant Health Management: Patogen Suppressive Soils, Encycl. Agric. Food Syst., pp. 441–455, 2014, doi: 10.1016/b978-0-444-52512-3.00182-0.
M. K. Meghvansi and A. Varma, Organic Amendments and Soil Suppressiveness in Plant Disease Management. Cham: Springer International Publishing, 2015. doi: 10.1007/978-3-319-23075-7.
S. Veresoglou, E. Barto, G. Menexes, and M. Rillig, Fertilization affects the severity of disease caused by fungal plant patogen, Plant Pathol, vol. 62, pp. 961–969, 2013, doi: 10.1111/ppa.12014.
B. Tailliez, The root system of the oil palm on the San Alberto plantation in Colombia, Oléagineux, vol. 26, p. 435‐448, 2017.
N. Eisenhauer et al., Root biomass and exudates link plant diversity with soil bacterial and fungal biomass, Sci. Rep., vol. 7, pp. 1–8, 2017, doi: 10.1038/srep44641.
S. Andrew, FastQC: a quality control tool for high throughput sequence data, 2010.
B. J. Callahan, P. J. McMurdie, M. J. Rosen, A. W. Han, A. J. A. Johnson, and S. P. Holmes, DADA2: High-resolution sample inference from Illumina amplicon data, Nat. Methods, vol. 13, no. 7, pp. 581–583, 2016, doi: 10.1038/nmeth.3869.
C. Quast et al., The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools, Nucleic Acids Res., vol. 41, no. D1, pp. 590–596, 2013, doi: 10.1093/nar/gks1219.
W. M. Tong and Y. Chan, GenePiper, a Graphical User Interface Tool for Microbiome Sequence Data Mining, Microbiol. Resour. Announc., vol. 9, no. 1, pp. 13–15, 2020, doi: 10.1128/mra.01195-19.
G. M. Douglas et al., PICRUSt2 for prediction of metagenome functions, Nat. Biotechnol., vol. 38, no. 6, pp. 685–688, 2020, doi: 10.1038/s41587-020-0548-6.
N. P. Vidal, C. F. Manful, T. H. Pham, P. Stewart, D. Keough, and R. H. Thomas, The use of XLSTAT in conducting principal component analysis (PCA) when evaluating the relationships between sensory and quality attributes in grilled foods, MethodsX, vol. 7, p. 100835, 2020, doi: 10.1016/j.mex.2020.100835.
N. Gotelli and R. Colwell, Quantifying biodiversity: procedures and pitfalls in the measurement and comparison of species richness, Ecol Lett, vol. 4, no. 4, pp. 379–391, 2001, doi: doi: 10.1046/j.1461-0248.2001.00230.x.
L. Jost, Entropy and diversity, Oikos, vol. 113, no. 2, pp. 363–375, 2006, doi: 10.1111/j.2006.0030-1299.14714.x.
R. G. Expósito, I. de Bruijn, J. Postma, and J. M. Raaijmakers, Current insights into the role of Rhizosphere bacteria in disease suppressive soils, Front. Microbiol., vol. 8, no. DEC, pp. 1–12, 2017, doi: 10.3389/fmicb.2017.02529.
J. R. Bray, J. T. Curtis, and J. Roger, This content downloaded from 147.8.31.43 on Mon, Source Ecol. Monogr., vol. 27, no. 4, pp. 325–349, 1957.
J. Chen et al., Associating microbiome composition with environmental covariates using generalized UniFrac distances, Bioinformatics, vol. 28, no. 16, pp. 2106–2113, 2012, doi: 10.1093/bioinformatics/bts342.
M. W. Friedrich, Microbial Communities, Structure, and Function. In: Reitner J., Thiel V. (eds) Encyclopedia of Geobiology., in Encyclopedia of Earth Sciences Series, no. 9781402092114, Dordrecht: Springer, 2011, pp. 81–89. doi: 10.1007/978-1-4020-9212-1_16.
A. Shade and J. Handelsman, Beyond the Venn diagram: The hunt for a core microbiome, Environ. Microbiol., vol. 14, no. 1, pp. 4–12, 2012, doi: 10.1111/j.1462-2920.2011.02585.x.
T. Coenye and P. Vandamme, Diversity and significance of Burkholderia species occupying diverse ecological niches, Environ. Microbiol., vol. 5, no. 9, pp. 719–729, 2003, doi: 10.1046/j.1462-2920.2003.00471.x.
P. Kämpfer, S. Glaeser, L. Parkes, G. Keulen, and P. Dyson, The prokaryotes: Actinobacteria, in The Prokaryotes: Actinobacteria, Berlin: Springer, 2014, pp. 889–1010. doi: 10.1007/978-3-642-30138-4.
S. Gopalakrishnan, V. Srinivas, and S. L. Prasanna, S. Gopalakrishnan, V. Srinivas, S.L. Prasanna, Elsevier, pp. 55–71, 2020.
Z. Wei et al., Initial soil microbiome composition and functioning predetermine future plant health, Sci. Adv., vol. 5, no. 9, pp. 1–12, 2019, doi: 10.1126/sciadv.aaw0759.
Y. K. Goh, M. Z. H. M. Zoqratt, Y. K. Goh, Q. Ayub, and A. S. Y. Ting, Determining soil microbial communities and their influence on ganoderma disease incidences in oil palm (Elaeis guineensis) via high-throughput sequencing, Biology (Basel)., vol. 9, no. 12, pp. 1–21, 2020, doi: 10.3390/biology9120424.
L. Xue, H. Ren, S. Li, X. Leng, and X. Yao, Soil bacterial community structure and co-occurrence pattern during vegetation restoration in karst rocky desertification area, Front. Microbiol., vol. 8, no. DEC, pp. 1–11, 2017, doi: 10.3389/fmicb.2017.02377.
S. Omar and M. Abd-Alla, Biokontrol of fungal root rot diseases of crop plants by the use of rhizobia and bradyrhizobia, Folia Microbiolofica, vol. 43, no. 4, pp. 431 – 437, 1998.
W. Y. Yu et al., Microbial community associated with ectomycorrhizal Russula symbiosis and dominated nature areas in southern China, FEMS Microbiol. Lett., vol. 368, no. 6, pp. 1–11, 2021, doi: 10.1093/femsle/fnab028.
J. Loh, E. Pierson, L. Pierson, G. Stacey, and A. Chatterjee, Quorum sensing in plant-associated bacteria, Curr Opin Plant Biol, vol. 5, no. 4, pp. 285–290, 2002, doi: 10.1016/s1369-5266(02)00274-1.
K. Pal and B. Gardener, Biological control of plant patogens, Plant Heal. Instr., 2006, doi: 10.1094/PHI-A-2006-1117-02.
P. Eckburg et al., Safety, Tolerability, Pharmacokinetics, and Drug Interaction Potential of SPR741, an Intravenous Potentiator, after Single and Multiple Ascending Doses and When Combined with β-Lactam Antibiotics in Healthy Subjects, Antimicrob Agents Chemother, vol. 63, no. 9, 2019, doi: 10.1128/AAC.00892-19. PMID: 31262767.
M. Hashmi, V. Kumar, and A. Varma, Xenobiotics in the Soil Environment: Monitoring: Toxicity and Management. Springer International Publishing, 2017. doi: 10.1007/978-3-319-47744-2.
N. Govender, M. Mahmood, I. Seman, and M.-Y. Wong, The phenylpropanoid pathway and lignin in defense against Ganoderma boninense colonized root tissues in oil palm (Elaeis guineensis Jacq.), Front Plant Sci, vol. 8, 2017, doi: 10.3389/fpls.2017.01395.
M. Reitz, P. Oger, and A. Meyer, Importance of the O-antigen, core-region and lipid A of rhizobial lipopolysaccharides for the induction of systemic resistance in potato to Globodera pallida, Nematology, vol. 4, pp. 73–79, 2002, doi: 10.1163/156854102760082221.
S. Kordali, A. Cakir, A. Mavi, H. Kilic, and A. Yildirim, Screening of chemical composition and antifungal and antioxidant activities of the essential oils from three Turkish artemisia species, J Agric Food Chem, vol. 53, no. 5, pp. 1408–16, 2005, doi: 10.1021/jf048429n. PMID: 15740015.
T. Fouché, S. Claassens, and M. Maboeta, Aflatoxins in the soil ecosystem: an overview of its occurrence, fate, effects and future perspectives, Mycotoxin Res, vol. 36, no. 3, pp. 303–309, 2020, doi: 10.1007/s12550-020-00393-w.
N. Kondo and A. N. N. Azmi, Temporal Changes Analysis of Soil Properties Associated with Ganoderma boninense Pat. Infection in Oil Palm Seedlings in a Controlled Environment, 2021.
R. H. V Corley and P. B. Tinker, The Oil Palm, 5th ed. UK: Blackwell Publishing, 2015.
A. Surendran, Y. Siddiqui, H. Saud, and N. Ali, Inhibition and kinetic studies of lignin degrading enzymes of Ganoderma boninense by naturally occurring phenolic compounds, J Appl Microbiol, vol. 125, pp. 876–887, doi: 10.1111/jam.13922.
A. Surendran, Y. Siddiqui, N. Ali, and S. Manickam, Inhibition and kenetic studies of cellulose- and hemicellulose-degrading enzymes of Ganoderma boninense by naturally occurring phenolic compounds, J Appl Microbiol, p. 124, doi: 10.1111/jam.13717.
J. Ma, A. Ibekwe, C. Yang, and D. Crowley, Bacterial diversity and composition in major fresh produce growing soils affected by physiochemical properties and geographic locations, Sci Total Env., pp. 199–209, 2016, doi: 10.1016/j.scitotenv.2016.04.122.
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Published
2022-10-24
How to Cite
Verdiani, H., Syafira, D., Loebis, S. A., & Pancoro, A. (2022). A Comparative Metagenomic Analysis of Rhizospheric Bacterial Communities between Suppressive and Conducive Soil towards Ganoderma boninense Infection in Oil Palm (Elaeis guineensis Jacq.). ITB Graduate School Conference, 1(1), 743–757. Retrieved from https://gcs.itb.ac.id/proceeding-igsc/index.php/igsc/article/view/63
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