Unveiling the Microbes of the World’s Largest Flower

Authors

DOI:

https://doi.org/10.33043/7qd65x2knn7

Abstract

The plant family Rafflesiaceae is known for producing the largest flowers in the world. They are solely parasitic to the plant genus Tetrastigma of the grape family. Interestingly, members of Rafflesiaceae are the only plants we know so far that have lost their chloroplast genome. Rafflesiaceae is comprised of three genera: Rafflesia, Sapria, and Rhizanthes. Members of Rafflesiaceae are restricted to the fast-disappearing tropical forests of Southeast Asia and are endangered. It is virtually unknown how Rafflesiaceae infects its hosts. This makes Rafflesiaceae very difficult to conserve and propagate. However, bacterial endophytes have shown to play a major role in promoting the growth of plants. In this study, we characterized and analyzed the associated microbiome of Rafflesiaceae, particularly Rafflesia speciosa and Sapria himalayana to find “microbial markers” of Rafflesiaceae infection. It was hypothesized that Rafflesia and its Tetrastigma host will have similar microbiomes given their intimate connection, however, results across different taxonomic levels demonstrate that Rafflesia buds have a distinct microbial endophyte composition and possessed some unique genera compared to its infected hosts. Its microbiome was also diverse compared to Sapria’s. Non-host Tetrastigma spp. possessed unique bacteria that may be antagonistic to Rafflesia infection. This study unveiled the symbiotic microbes of Rafflesia and Sapria, which may have potential horticultural application in propagating the world’s largest flowers.

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References

Banerjee, S., Palit, R., Sengupta, C., & Standing, D. (2010). Stress Induced Phosphate Solubilization by “Arthrobacter” Sp. And “Bacillus” Sp. Isolated from Tomato Rhizosphere. Australian Journal of Crop Science, 4: 378–383. doi: 10.3316/informit.414789554792811

Beaman, R. S., Decker, P. J., & Beaman, J. H. (1988). Pollination of Rafflesia (Rafflesiaceae). American Journal of Botany, 75: 1148–1162. doi: 10.1002/j.1537-2197.1988.tb08828.x

Boukhatem, Z. F., Merabet, C., & Tsaki, H. (2022). Plant Growth Promoting Actinobacteria, the Most Promising Candidates as Bioinoculants? Frontiers in Agronomy. doi: 10.3389/fagro.2022.849911

Broccanello, C., Ravi, S., Deb, S., Bolton, M., Secor, G., Richards, C., Maretto, L., Lucia, M. C. D., Bertoldo, G., Orsini, E., Ronquillo-López, M. G., Concheri, G., Campagna, G., Squartini, A., & Stevanato, P. (2022). Bacterial endophytes as indicators of susceptibility to Cercospora Leaf Spot (CLS) disease in L. Scientific Reports, 12: 10719. doi: 10.1038/s41598-022-14769-8

Brown, R. (1821). An Account of a new Genus of Plants, named Rafflesia. Transactions of the Linnean Society of London, os-13: 201–234. doi: 10.1111/j.1095-8339.1821.tb00062.x

Cai, L., Arnold, B. J., Xi, Z., Khost, D. E., Patel, N., Hartmann, C. B., Manickam, S., Sasirat, S., Nikolov, L. A., Mathews, S., Sackton, T. B., & Davis, C. C. (2021). Deeply Altered Genome Architecture in the Endoparasitic Flowering Plant Sapria himalayana Griff. (Rafflesiaceae). Current Biology, 31: 1002-1011. doi: 10.1016/j.cub.2020.12.045

Cui, F., Yang, Y., Ye, M., Wei, W., Huang, W., Wu, Y., Jiao, X., Ye, X., Zhou, S., Hu, Z., Zhang, Y., Gui, R., Wu, W., Yrjälä, K., Overmyer, K., Liu, S., Cui, F., Yang, Y., Ye, M., & Liu, S. (2021). Case study of a rhizosphere microbiome assay on a bamboo rhizome with excessive shoots. Forestry Research, doi:10.48130/FR-2021-0010

Dasgupta, M. G., Burragoni, S., Amrutha, S., Muthupandi, M., Parveen, A. B. M., Sivakumar, V., & Ulaganathan, K. (2020). Diversity of bacterial endophyte in Eucalyptus clones and their implications in water stress tolerance. Microbiological Research, 241: 126579. doi: 10.1016/j.micres.2020.126579

Dorji, R., Phuentsho, Dechen, U., Gyeltshen, Samdrup, T., Dorji, K., Powrel, R. B., Dorji, P., Dhimal, K. P., & Long, D. G. (2022). Discovery, Distribution and Conservation of the Rare Parasitic Plant Sapria Himalayana (Rafflesiaceae) in Bhutan. Curtis’s Botanical Magazine, 39: 541–554. doi: 10.1111/curt.12461

Doty, S., Dosher, M. R., Singleton, G. L., Moore, A. L., Van Aken, B., Stettler, R., Strand, S., & Gordon, M. P. (2005). Identification of an endophytic Rhizobium in stems of Populus. Symbiosis, 39: 27–35.

Drake, H. L. (2014). The genus Lactovum. Wiley Online Library. doi: 10.1002/9781118655252.ch27

Fan, D., Subramanian, S., & Smith, D. L. (2020). Plant endophytes promote growth and alleviate salt stress in Arabidopsis thaliana. Scientific Reports, doi: 10.1038/s41598-020-69713-5

Felestrino, É. B., Santiago, I. F., Freitas, L. da S., Rosa, L. H., Ribeiro, S. P., & Moreira, L. M. (2017). Plant Growth Promoting Bacteria Associated with Langsdorffia hypogaea-Rhizosphere-Host Biological Interface: A Neglected Model of Bacterial Prospection. Frontiers in Microbiology, 8: 172. doi: 10.3389/fmicb.2017.00172

Feng, Y., Shen, D., & Song, W. (2006). Rice endophyte Pantoea agglomerans YS19 promotes host plant growth and affects allocations of host photosynthates. Journal of Applied Microbiology, 100: 938–945. doi: 10.1111/j.1365-2672.2006.02843.x

Fitzpatrick, C. R., Lu-Irving, P., Copeland, J., Guttman, D. S., Wang, P. W., Baltrus, D. A., Dlugosch, K. M., & Johnson, M. T. J. (2018). Chloroplast sequence variation and the efficacy of peptide nucleic acids for blocking host amplification in plant microbiome studies. Microbiome, 6: 144. doi: 10.1186/s40168-018-0534-0

Fu, B., Olawole, O., & Beattie, G. A. (2021). Biological Control and Microbial Ecology Draft Genome Sequence Data of Glutamicibacter sp. FBE-19, a Bacterium Antagonistic to the Plant Pathogen Erwinia tracheiphila. Phytopathology, 111: 765–768. https://doi.org/10.1094/PHYTO-09-20-0380-A

Glick, B. R. (2014). Bacteria with ACC deaminase can promote plant growth and help to feed the world. Microbiological Research, 169: 30–39. doi: 10.1016/j.micres.2013.09.009

Guzmán, J. P., Reyes-Prieto, M., & Hart, S. C. (2021). Characterization of Erwinia gerundensis A4, an Almond-Derived Plant Growth-Promoting Endophyte. Frontiers in Microbiology. doi: 10.3389/fmicb.2021.687971

Hashmi, I., Bindschedler, S., & Junier, P. (2020). Chapter 18—Firmicutes. Beneficial Microbes in Agro-Ecology. doi: 10.1016/B978-0-12-823414-3.00018-6

Hazarika, S. N., & Thakur, D. (2020). Chapter 21—Actinobacteria. Beneficial Microbes in Agro-Ecology. doi: 10.1016/B978-0-12-823414-3.00021-6

Hidayati, S. N., Meijer, W., Baskin, J. M., & Walck, J. L. (2000). A Contribution to the Life History of the Rare Indonesian Holoparasite Rafflesia patma (Rafflesiaceae). Biotropica, 32: 408–414. doi: 10.1111/j.1744-7429.2000.tb00487.x

Jha, C., Aeron, A., Patel, B., Maheshwari, D., & Saraf, M. (2011). Enterobacter: Role in Plant Growth Promotion. In Bacteria in Agrobiology: Plant Growth Responses. doi: 10.1007/978-3-642-20332-9_8

Jiménez-Gómez, A., Saati-Santamaría, Z., Kostovcik, M., Rivas, R., Velázquez, E., Mateos, P. F., Menéndez, E., & García-Fraile, P. (2020). Selection of the Root Endophyte Pseudomonas brassicacearum CDVBN10 as Plant Growth Promoter for Brassica napus L. Crops. Agronomy, doi: 10.3390/agronomy10111788

Kelly, S. M., Munoz-Munoz, J., & Sinderen, D. (2021). Plant Glycan Metabolism by Bifidobacteria. Frontiers in Microbiology, doi: 10.3389/fmicb.2021.609418

Kolton, M., Erlacher, A., Berg, G., & Cytryn, E. (2016). The Flavobacterium Genus in the Plant Holobiont: Ecological, Physiological, and Applicative Insights. doi: 10.1007/978-981-10-2555-6_9

Kruh, L., Lahav, T., Abu-Nassar, J., Achdari, G., Salami, R., Freilich, S., & Aly, R. (2017). Host-Parasite-Bacteria Triangle: The Microbiome of the Parasitic Weed Phelipanche aegyptiaca and Tomato-Solanum lycopersicum (Mill.) as a Host. Frontiers in Plant Science, 8. doi: 10.3389/fpls.2017.00269

Laurentis, V. L., Bortoli, S., Polanczyk, R., Vacari, A. M., Veiga, A., De Bortoli, S. L., & Volpe, H. (2014). Kluyvera ascorbata: A Plant Growth-Promoting Bacteria (PGPB) to Manage Plutella xylostella (L., 1758) (Lepidoptera: Plutellidae). International Journal of Research in Agricultural Sciences.

Li, C., Gong, T., Bian, B., & Liao, W. (2018). Roles of hydrogen gas in plants: a review. Functional Plant Biology: Functional Plant Biology, 45:, 783–792. doi: 10.1071/FP17301

Lin, L., Wei, C., Chen, M., Wang, H., Li, Y., Li, Y., Yang, L., & An, Q. (2015). Complete genome sequence of endophytic nitrogen-fixing Klebsiella variicola strain DX120E. Standards in Genomic Sciences, 10: 22. doi: 10.1186/s40793-015-0004-2

Maimaiti, J., Zhang, Y., Yang, J., Cen, Y.-P., Layzell, D. B., Peoples, M., & Dong, Z. (2007). Isolation and characterization of hydrogen-oxidizing bacteria induced following exposure of soil to hydrogen gas and their impact on plant growth. Environmental Microbiology, 9: 435–444. doi: 10.1111/j.1462-2920.2006.01155.x

Meena, K. K., Bitla, U. M., Sorty, A. M., Singh, D. P., Gupta, V. K., Wakchaure, G. C., & Kumar, S. (2020). Mitigation of Salinity Stress in Wheat Seedlings Due to the Application of Phytohormone-Rich Culture Filtrate Extract of Methylotrophic Actinobacterium Nocardioides sp. NIMMe6. Frontiers in Microbiology, doi: 10.3389/fmicb.2020.02091

Miyamoto, T., Kawahara, M., & Minamisawa, K. (2004). Novel Endophytic Nitrogen-Fixing Clostridia from the Grass Miscanthus sinensis as Revealed by Terminal Restriction Fragment Length Polymorphism Analysis. Applied and Environmental Microbiology, 70: 6580–6586. doi: 10.1128/AEM.70.11.6580-6586.2004

Molina, J., Hazzouri, K. M., Nickrent, D., Geisler, M., Meyer, R. S., Pentony, M. M., Flowers, J. M., Pelser, P., Barcelona, J., Inovejas, S. A., Uy, I., Yuan, W., Wilkins, O., Michel, C.-I., LockLear, S., Concepcion, G. P., & Purugganan, M. D. (2014). Possible Loss of the Chloroplast Genome in the Parasitic Flowering Plant Rafflesia lagascae (Rafflesiaceae). Molecular Biology and Evolution, 31: 793–803. doi: 10.1093/molbev/msu051

Molina, J., McLaughlin, W., Wallick, K., Pedales, R., Marius, V. M., Tandang, D. N., Damatac, A., Stuhr, N., Pell, S. K., Lim, T. M., & Novy, A. (2017). Ex Situ Propagation of Philippine Rafflesia in the United States: Challenges and Prospects. Sibbaldia: The International Journal of Botanic Garden Horticulture. doi: 10.24823/Sibbaldia.2017.224

Molina, J., Wicaksono, A., Michael, T. P., Kwak, S.-H., Pedales, R. D., Joly-Lopez, Z., Petrus, S., Mamerto, A., Tomek, B., Ahmed, S., Maddu, V., Yakubova, K., Tandang, D., Morin, J. W., Park, S.-Y., Lee, H.-O., McLaughlin, W., Wallick, K., Adams, J., & Purugganan, M. D. (2023). The seed transcriptome of Rafflesia reveals horizontal gene transfer and convergent evolution: Implications for conserving the world’s largest flower. Plants, People, Planet. doi: 10.1002/ppp3.10370

Nais, J. (2001). Rafflesia of the World. Sabah Parks, Borneo, Malaysia.

Nikolov, L. A., & Davis, C. C. (2017). The big, the bad, and the beautiful: Biology of the world’s largest flowers. Journal of Systematics and Evolution, 55: 516–524. doi: 10.1111/jse.12260

Osathanunkul, M. (2019). EDNA-based monitoring of parasitic plant (Sapria himalayana). Scientific Reports, 9: 9161. doi: 10.1038/s41598-019-45647-5

Padda, K. P., Puri, A., & Chanway, C. (2019). Endophytic nitrogen fixation – a possible ‘hidden’ source of nitrogen for lodgepole pine trees growing at unreclaimed gravel mining sites. FEMS Microbiology Ecology, doi: 10.1093/femsec/fiz172

Pankratov, T. A., Tindall, B. J., Liesack, W., & Dedysh, S. N. (2007). Mucilaginibacter paludis gen. nov., sp. Nov. And Mucilaginibacter gracilis sp. nov., pectin-, xylan- and laminarin-degrading members of the family Sphingobacteriaceae from acidic Sphagnum peat bog. International Journal of Systematic and Evolutionary Microbiology. doi: 10.1099/ijs.0.65100-0

Pelser, P. B., Nickrent, D. L., & Barcelona, J. F. (2016). Untangling a vine and its parasite: Host specificity of Philippine Rafflesia (Rafflesiaceae). Taxon, 65: 739–758. doi: 10.12705/654.4

Pérez, M. L., Collavino, M. M., Sansberro, P. A., Mroginski, L. A., & Galdeano, E. (2016). Diversity of endophytic fungal and bacterial communities in Ilex paraguariensis grown under field conditions. World Journal of Microbiology and Biotechnology, 32: 61. doi: 10.1007/s11274-016-2016-5

Pham, V. T. K., Rediers, H., Ghequire, M. G. K., Nguyen, H. H., De Mot, R., Vanderleyden, J., & Spaepen, S. (2017). The plant growth-promoting effect of the nitrogen-fixing endophyte Pseudomonas stutzeri A15. Archives of Microbiology, 199: 513–517. doi: 10.1007/s00203-016-1332-3

Rafflesiaceae Dumort. Plants of the World Online. Kew Science. http://powo.science.kew.org/taxon/urn:lsid:ipni.org:names:30012988-2

Raman, J., Kim, J.-S., Choi, K. R., Eun, H., Yang, D., Ko, Y.-J., & Kim, S.-J. (2022). Application of Lactic Acid Bacteria (LAB) in Sustainable Agriculture: Advantages and Limitations. International Journal of Molecular Sciences, 23: 7784. doi: 10.3390/ijms23147784

Rangjaroen, C., Sungthong, R., Rerkasem, B., Teaumroong, N., Noisangiam, R., & Lumyong, S. (2017). Untapped Endophytic Colonization and Plant Growth-Promoting Potential of the Genus Novosphingobium to Optimize Rice Cultivation. Microbes and Environments, 32: 84-87. doi: 10.1264/jsme2.ME16112

Sánchez-López, A. S., Thijs, S., Beckers, B., González-Chávez, Ma. C., Weyens, N., Carrillo-González, R., & Vangronsveld, J. (2018). Community structure and diversity of endophytic bacteria in seeds of three consecutive generations of Crotalaria pumila growing on metal mine residues. Plant and Soil, 422: 51–66. doi: 10.1007/s11104-017-3176-2

Santoyo, G., Moreno-Hagelsieb, G., Orozco-Mosqueda, M. del C., & Glick, B. R. (2016). Plant growth-promoting bacterial endophytes. Microbiological Research, 183: 92–99. doi: 10.1016/j.micres.2015.11.008

Shen, G., Zhang, S., Liu, X., Jiang, Q., & Ding, W. (2018). Soil acidification amendments change the rhizosphere bacterial community of tobacco in a bacterial wilt affected field. Applied Microbiology and Biotechnology, 102:, 9781–9791. doi: 10.1007/s00253-018-9347-0

Taulé, C., Castillo, A., Villar, S., Olivares, F., & Battistoni, F. (2016). Endophytic colonization of sugarcane (Saccharum officinarum) by the novel diazotrophs Shinella sp. UYSO24 and Enterobacter sp. UYSO10. Plant and Soil, 403: 403–418. doi: 10.1007/s11104-016-2813-5

Taulé, C., Luizzi, H., Beracochea, M., Mareque, C., Platero, R., & Battistoni, F. (2019). The Mo- and Fe-nitrogenases of the endophyte Kosakonia sp. UYSO10 are necessary for growth promotion of sugarcane. Annals of Microbiology, 69: 741-750. doi: 10.1007/s13213-019-01466-7

Taulé, C., Mareque, C., Barlocco, C., Hackembruch, F., Reis, V. M., Sicardi, M., & Battistoni, F. (2012). The contribution of nitrogen fixation to sugarcane (Saccharum officinarum L.), and the identification and characterization of part of the associated diazotrophic bacterial community. Plant and Soil, 356: 35–49. doi: 10.1007/s11104-011-1023-4

Thomas, P., & Sahu, P. K. (2021). Vertical Transmission of Diverse Cultivation-Recalcitrant Endophytic Bacteria Elucidated Using Watermelon Seed Embryos. Frontiers in Microbiology. doi: 10.3389/fmicb.2021.635810

Wicaksono, A., Cristy, G. P., Raihandhany, R., Mursidawati, S., Teixeira da Silva, J. A., & Susatya, A. (2022). Rhizanthes, the Forgotten Relative of Rafflesia in the Rafflesiaceae. The Botanical Review, 88: 130–143. doi: 10.1007/s12229-021-09261-3

Wicaksono, A., Mursidawati, S., & Molina, J. (2021). A Plant within a Plant: Insights on the Development of the Rafflesia Endophyte within its Host. The Botanical Review, 87: 233–242. doi: 10.1007/s12229-020-09236-w

Wicaksono, A., Mursidawati, S., Sukamto, L. A., & Teixeira da Silva, J. A. (2016). Rafflesia spp.: Propagation and conservation. Planta, 244: 289–296. doi: 10.1007/s00425-016-2512-8

Wu, K., Luo, J., Li, J., An, Q., Yang, X., Liang, Y., & Li, T. (2018). Endophytic bacterium Buttiauxella sp. SaSR13 improves plant growth and cadmium accumulation of hyperaccumulator Sedum alfredii. Environmental Science and Pollution Research, 25: 21844–21854. doi: 10.1007/s11356-018-2322-6

Yu, X., Yang, J., Wang, E., Li, B., & Yuan, H. (2015). Effects of growth stage and fulvic acid on the diversity and dynamics of endophytic bacterial community in Stevia rebaudiana Bertoni leaves. Frontiers in Microbiology, doi: 10.3389/fmicb.2015.00867

Zahran, H. H. (1999). Rhizobium-Legume Symbiosis and Nitrogen Fixation under Severe Conditions and in an Arid Climate. Microbiology and Molecular Biology Reviews. doi: 10.1128/MMBR.63.4.968-989.1999

Zhang, S., Liu, X., Jiang, Q., Shen, G., & Ding, W. (2017). Legacy effects of continuous chloropicrin-fumigation for 3-years on soil microbial community composition and metabolic activity. AMB Express, 7: 178. doi: 10.1186/s13568-017-0475-

Published

2026-10-27

How to Cite

Denia Diaz, & Molina, J. (2026). Unveiling the Microbes of the World’s Largest Flower. Fine Focus, 12(1), 4–20. https://doi.org/10.33043/7qd65x2knn7

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