Abstract
Rice seed is colonized by endophytic bacterial communities which becomes a source of endophytes and allows for a diverse bacterial community to occur inside the plant host. These endophytes can provide beneficial effects to growth and development of the host plant. Furthermore, the diversity of endophytic bacteria is dynamic within the host plant. Variations as well as density of populations of endophytic bacteria usually decline from the root to the leaf region of the plants. This review gives an overview of the plant growth-promoting mechanisms of endophytes with respect to their intensely studied plant growth-promoting rhizobacteria (PGPR) counterparts. The community dynamics and diversity of bacterial endophytes associated with rice and its microniches including roots, shoots, and the seeds were also discussed. This review also delves into the proposed concept of a potential core microbiota of rice, bacterial endophytes that are highly associated with rice, as well as the interesting abilities of seed endophytes to be transmitted and conserved through generations of rice hosts via the seeds.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Abeles FB, Morgan PW, Saltveit ME Jr (1992) Ethylene in plant biology, 2nd edn. Academic Press, San Diego
Ae N, Shen RF (2002) Root cell-wall properties are proposed to contribute to phosphorus (P) mobilization by groundnut and pigeon pea. Plant Soil 245:95–103
Arkhipova TN, Prinsen E, Veselov SU, Martinenko EV, Melentiev AI, Kudoyarova GR (2007) Cytokinin producing bacteria enhance plant growth in drying soil. Plant Soil 292(1–2):305–315
Bakker PAHM, Pieterse CMJ, van Loon LC (2007) Induced systemic resistance by fluorescent Pseudomonas spp. Phytopathology 97:39–243
Boddey RM, de Oliveira OC, Urquiaga S, Reis VM, de Olivares FL, Baldani VLD, Dobereiner J (1995) Biological nitrogen fixation associated with sugar cane and rice: contributions and prospects for improvement. Plant Soil 174:195–209
Chaintreuil C, Giraud E, Prin Y, Lorquin J, Bâ A, Gillis M, de Lajudie P, Dreyfus B (2000) Photosynthetic Bradyrhizobia are natural endophytes of the African wild rice Oryza breviligulata. Appl Environ Microbiol 66:5437–5447
Chaudhary HJ, Peng G, Hu M, He Y, Yang L, Luo Y, Tan Z (2012) Genetic diversity of endophytic diazotrophs of the wild rice, Oryza alta and identification of the new diazotroph, Acinetobacter oryzae sp. nov. Microb Ecol 63:813–821
Ciardi JA, Tieman DM, Lund ST, Jones JB, Stall RE, Klee HJ (2000) Response to Xanthomonas campestris pv. vesicatoria in tomato involves regulation of ethylene receptor gene expression. Plant Physiol 123:81–92
Compant S, Duffy B, Nowak J, Cle C, Barka E (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
Compant S, Clement C, Sessitsch A (2010) Plant growth-promoting bacteria in the rhizo- and endosphere of plants: their role, colonization, mechanisms involved and prospects of utilization. Soil Biol Biochem 42:669–678
Costa JM, Loper JE (1994) Characterization of siderophore production by the biological control agent Enterobacter cloacae. Mol Plant-Microbe Interac 7(4):440–448
Elbeltagy A, Nishioka K, Sato T, Suzuki H, Ye B, Hamada T, Isawa T, Mitsui H, Minamisawa K (2001) Endophytic colonization and in planta nitrogen fixation by a Herbaspirillum sp. isolated from wild rice species. Appl Environ Microbiol 67:5285–5293
Ferrando L, Manay JF, Scavino AF (2012) Molecular and culture-dependent analyses revealed similarities in the endophytic bacterial community composition of leaves from three rice (Oryza sativa) varieties. FEMS Microbiol Ecol 80:696–708
GarcÃa de Salamone IE, Hynes RK, Nelson LM (2005) Chapter 6: role of cytokinins in plant growth promotion by rhizosphere bacteria. PGPR Biocontrol Biofertil 6:173–195
Glick B, Penrose D, Li J (1998) A model for the lowering of plant ethylene concentrations by plant growth-promoting bacteria. J Theor Biol 190:63–68
Glick BR, Todorovic B, Czarny J, Cheng Z, Duan J, McConkey B (2007a) Promotion of plant growth by bacterial ACC deaminase. Crit Rev Plant Sci 26:227–242
Glick BR, Cheng Z, Czarny J, Duan J (2007b) Promotion of plant growth by ACC deaminase-producing soil bacteria. Eur J Plant Pathol 119:329–339
Hallmann J, Quadt-Hallmann A, Mahaffee WF, Kloepper JW (1997) Bacterial endophytes in agricultural crops. Can J Microbial 43:895–914
Hardoim PR, van Overbeek LS, van Elsas JD (2008) Properties of bacterial endophytes and their proposed role in plant growth. Trends Microbiol 16:463–471
Hardoim PR, Andreote FD, Reinhold-Hurek B, Sessitsch A, van Overbeek LS, van Elsas JD (2011) Rice root-associated bacteria: insights into community structures across 10 cultivars. FEMS Microbiol Ecol 77:154–164
Hardoim PR, Hardoim CCP, van Overbeek LS, van Elsas JD (2012) Dynamics of seed-borne rice endophytes on early plant growth stages. PLoS One 7(2):e30438
Hardoim PR, van Overbeek LS, Berg G, Pirttila AM, Compant S, Campisanto A, Dorling M, Sessitsch A (2015) The hidden world within plants: ecological and evolutionary considerations for defining functioning of microbial endophytes. Microbiol Mol Biol Rev 79:293–320
Hare PD, Cress WA, Staden JV (1997) The involvement of cytokinins in plant responses to environmental stress. Plant Growth Regul 23:79–103
Hider RC, Kong X (2010) Chemistry and biology of siderophores. Nat Prod Rep 27:637–657
Honma M, Shimomura T (1978) Metabolism of 1-aminocyclopropane-1-carboxylic acid. Agric Biol Chem 42:1825–1831
Idris R, Trifonova R, Puschenreiter M, Wenzel WW, Sessitsch A (2004) Bacterial communities associated with flowering plants of the Ni hyperaccumulator Thlaspigoe singense. Appl Environ Microbiol 70:2667–2677
Indananda C, Thamchaipenet A, Matsumoto A, Inahashi Y, Duangmal K, Takahashi Y (2011) Actinoallomurus oryzae sp. nov., an endophytic actinomycete isolated from roots of a Thai jasmine rice plant. Int J Syst Evol Microbiol 61:737–741
Iniguez AL, Dong Y, Carter HD, Ahmer BMM, Stone JM, Triplett EW (2005) Regulation of enteric endophytic bacterial colonization by plant defenses. Mol Plant-Microbe Interact 18:169–178
James EK (2000) Nitrogen fixation in endophytic and associative symbiosis. Field Crop Res 65:197–209
Johnston-Monje D, Raizada MN (2011) Conservation and diversity of seed associated endophytes in Zea across boundaries of evolution, ethnography and ecology. PLoS One 6(6):e20396
Kaga H, Mano H, Tanaka F, Watanabe A, Kaneko S, Morisaki H (2009) Rice seeds as sources of endophytic bacteria. Microbes Environ 24:154–162
Kamensky M, Ovadis M, Chet I, Chernin L (2003) Soil-borne strain IC14 of Serratia plymuthica with multiple mechanisms of antifungal activity provides biocontrol of Botrytis cinerea and Sclerotinia sclerotiorum diseases. Soil Biol Biochem 35:323–331
Kloepper JW, Ryu C (2006) Bacterial endophytes as elicitors of induced systemic resistance. In: Microbial root endophytes, Soil biology, vol 9. Springer, Berlin, pp 33–52
Kloepper JW, Leong J, Teintze M, Schroth MN (1980) Pseudomonas siderophores: a mechanism explaining disease-suppressive soils. Curr Microbiol 4:317–320
Liu Y, Zuo S, Xu L, Zou Y, Song W (2012) Study on diversity of endophytic bacterial communities in seeds of hybrid maize and their parental lines. Arch Microbiol 194:1001–1012
Loaces I, Ferrando L, Fernandez Scavino A (2011) Dynamics, diversity and function of endophytic siderophore-producing bacteria in rice. Microb Ecol 61:606–618
Lodewyckx C, Vangronsveld J, Porteous F, Moore ERB, Taghavi S, Mezgeay M, van der Lelie D (2002) Endophytic bacteria and their potential applications. Crit Rev Plant Sci 21(6):583–606
Ma Y, Prasad MNV, Rajkuma M, Freitas H (2011) Plant growth promoting rhizobacteria and endophytes accelerate phytoremediation of metalliferous soils. Biotechnol Adv 29:248–258
Mano H, Morisaki H (2008) Endophytic bacteria in the rice plant. Microbes Environ 23(2):109–117
Mano H, Tanaka F, Watanabe A, Kaga H, Okunishi S, Morisaki H (2006) Culturable surface and endophytic bacterial flora of the maturing seeds of rice plants (Oryza sativa) cultivated in a paddy field. Microbes Environ 21:86–100
Mano H, Tanaka F, Nakamura C, Kaga H, Morisaki H (2007) Culturable endophytic bacterial flora of the maturing leaves and roots of rice plants (Oryza sativa) cultivated in a paddy field. Microbes Environ 22:175–185
Mastretta C, Taghavi S, Lelie DVD (2010) Endophytic bacteria from seeds of Nicotiana tabacum can reduce cadmium phytotoxicity. Int J Phytoremediation 11(3):37–41
Mathesius U, Mulders S, Gao M, Teplitski M, Caetano-Anolles G, Rolfe BG, Bauer WD (2003) Extensive and specific responses of a eukaryote to bacterial quorum-sensing signals. Proc Natl Acad Sci U S A 100:1444–1449
McInroy JA, Kloepper JW (1995) Population dynamics of endophytic bacteria in field-grown sweet corn and cotton. Can J Microbiol 41:895–901
Minamisawa K, Nishioka K, Miyaki T, Ye B, Miyamoto T, You M, Saito A, Saito M, Barraquio WL, Teaumroong N, Sein T, Sato T (2004) Anaerobic nitrogen-fixing consortia consisting of clostridia isolated from gramineous plants. Appl Environ Microbiol 70:3096–3102
Morgan PW, Drew MC (1997) Ethylene and plant responses to stress. Physiol Plant 100:620–630
Mukhopadhyay K, Garrison NK, Hinton DM, Bacon CW, Khush GS, Peck HD, Datta N (1996) Identification and characterization of bacterial endophytes of rice. Mycopathologia 134:151–159
Mundt JO, Hinkle NF (1976) Bacteria within ovules and seeds. Appl Environ Microbiol 32(5):694
Neilands JB (1995) Siderophores: structure and function of microbial iron transport compounds. J Biol Chem 270:26723–26726
Ordentlich A, Elad Y, Chet I (1988) The role of chitinase of Serratia marcescens in biocontrol of Sclerotium rolfsii. Phytopathology 78:84–88
Peng G, Yuan Q, Li H, Zhang W, Tan Z (2008) Rhizobium oryzae sp. nov., isolated from the wild rice Oryza alta. Int J Syst Evol Microbiol 58:2158–2163
Puente ME, Li CY, Bashan Y (2009) Rock-degrading endophytic bacteria in cacti. Environ Exp Bot 66:389–401
Reinhold-Hurek B, Hurek T (1998) Life in grasses: diazotrophic endophytes. Trends Microbiol 6(4):139–143
Reinhold-Hurek B, Hurek T (2011) Living inside plants: bacterial endophytes. Curr Opin Plant Biol 14:435–443
RodrÃguez H, Fraga R (1999) Phosphate solubilizing bacteria and their role in plant growth promotion. Biotechnol Adv 17:319–339
Rodriguez H, Gonzalez T, Goire I, Bashan Y (2004) Gluconic acid production and phosphate solubilization by the plant growth-promoting bacterium Azospirillum sp. Naturwissenschaften 91:552–555
Rosenblueth M, MartÃnez-Romero E (2006) Bacterial endophytes and their interactions with hosts. Mol Plant-Microbe Interact 19(8):827–837
Ruiza D, Agaras B, de Werrab P, Wall LG, Valverde C (2011) Characterization and screening of plant probiotic traits of bacteria isolated from rice seeds cultivated in Argentina. J Microbiol 49:902–912
Salisbury FB (1994) The role of plant hormones. In: Wilkinson RE (ed) Plant-environment interactions. Marcel Dekker, New York, pp 39–81
Schachtman DP, Reid RJ, Ayling SM (1998) Phosphorus uptake by plants: from soil to cell. Plant Physiol 116:447–453
Sharma A, Johri BN (2003) Growth promoting influence of siderophore-producing Pseudomonas strains GRP3A and PRS9 in maize (Zea mays L.) under iron limiting conditions. Microbiol Res 158:243–248
Sharma SB, Sayyed RZ, Trivedi MH, Gobi TA (2013) Phosphate solubilizing microbes: sustainable approach for managing phosphorus deficiency in agricultural soils. Springerplus 2:587
Sheng XF, Xia JJ, Jiang CY, He LY, Qian M (2008) Characterization of heavy metal-resistant endophytic bacteria from rape (Brassica napus) roots and their potential in promoting the growth and lead accumulation of rape. Environ Pollut 156:1164–1170
Singh RK, Mishra RP, Jaiswal HK, Kumar V, Pandey SP, Rao SB, Annapurna K (2006) Isolation and identification of natural endophytic rhizobia from rice (Oryza sativa L.) through rDNA PCR-RFLP and sequence analysis. Curr Microbiol 52:117–122
Stevenson FJ, Cole MA (1999) Cycles of soil: carbon, nitrogen, phosphorus, sulfur, micronutrients. Wiley, New York
Sugawara M, Okasaki S, Nukui N, Ezura H, Mitsui H, Minamisawa K (2006) Rhizobitoxine modulates plant-microbe interactions by ethylene inhibition. Biotechnol Adv 24:382–388
Spaepen S, Vanderleyden J (2011) Auxin and plant-microbe interactions. Cold Spring Harb Perspect Biol 3(4):a001438
Sun L, Qiu F, Zhang X, Dai X, Dong X, Song W (2008) Endophytic bacterial diversity in rice (Oryza sativa L.) roots estimated by 16S rDNA sequence analysis. Microb Ecol 55:415–424
Taghavi S, Garafola C, Moncy S, Newman L, Hoffman A, Weyens N, Barac T, Vangronsveld J, van der Lelie D (2009) Genome survey and characterization of endophytic bacteria exhibiting a beneficial effect on growth and development of poplar trees. Appl Environ Microbiol 75:748–757
Tan Z, Hurek T, Gyaneshwar P, Ladha JK, Reinhold-Hurek B (2001) Novel endophytes of rice form a taxonomically distinct subgroup of Serratia marcescens. System Appl Microbiol 24(2):245–251
Tanimoto E (2005) Regulation of root growth by plant hormones—roles for auxin and gibberellin. Crit Rev Plant Sci 24:249–265
Tian X, Cao L, Tan H, Han W, Chen M, Liu Y, Zhou S (2007) Diversity of cultivated and uncultivated actinobacterial endophytes in the stems and roots of rice. Microb Ecol 53:700–707
Truyens S, Weyens N, Cuypers A, Vangronsveld J (2015) Bacterial seed endophytes: genera, vertical transmission and interaction with plants. Environ Microbiol 7:40–50
Verhagen BWM, Glzebrook J, Zhu T, Chang HS, van Loon LC, Pieterse CMJ (2004) The transcriptome of rhizobacteria-induced systemic resistance in Arabidopsis. Mol Plant-Microbe Interact 17:895–908
Vessey JK (2003) Plant growth promoting rhizobacteria as biofertilizers. Plant Soil 255:571–586
Walitang DI, Kim K, Madhaiyan M, Kim YK, Kang Y, Sa T (2017) Characterizing endophytic competence and plant growth promotion of bacterial endophytes inhabiting the seed endosphere of rice. BMC Microbiol 17:209. https://doi.org/10.1186/s12866-017-1117-0
Walitang DI, Kim K, Kim Y, Kang YK, Kim ST (2018a) The influence of host genotype and salt stress on the seed endophytic community of salt-sensitive and salt-tolerant rice cultivars. BMC Plant Biol 18(1):51. https://doi.org/10.1186/s12870-018-1261-1
Walitang DI, Kim CG, Jeon S, Kang Y, Sa T (2018b) Conservation and transmission of seed bacterial endophytes across generations following crossbreeding and repeated inbreeding of rice at different geographic locations. Microbiol Open:e662. https://doi.org/10.1002/mbo3.662
Weyens N, van der Lelie D, Taghavi S, Vangronsveld J (2009) Phytoremediation: plant-endophyte partnerships take the challenge. Curr Opin Biotechnol 20:248–254
Yang JH, Liu HX, Zhu GM, Pan YL, Xu LP, Guo JH (2008) Diversity analysis of antagonists from rice-associated bacteria and their application in biocontrol of rice diseases. J Appl Microbiol 104:91–104
Zhang XX, Gao JS, Cao YH, Ma XT, He JZ (2013) Long-term rice and green manure rotation alters the endophytic bacterial communities of the rice root. Microb Ecol 66:917–926
Acknowledgments
This work was supported by the Strategic Initiative for Microbiomes in Agriculture and Food, Ministry of Agriculture (914004-4), Food and Rural Affairs, Republic of Korea.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2019 Springer Nature Singapore Pte Ltd.
About this chapter
Cite this chapter
Walitang, D., Samaddar, S., Roy Choudhury, A., Chatterjee, P., Ahmed, S., Sa, T. (2019). Diversity and Plant Growth-Promoting Potential of Bacterial Endophytes in Rice. In: Sayyed, R., Reddy, M., Antonius, S. (eds) Plant Growth Promoting Rhizobacteria (PGPR): Prospects for Sustainable Agriculture. Springer, Singapore. https://doi.org/10.1007/978-981-13-6790-8_1
Download citation
DOI: https://doi.org/10.1007/978-981-13-6790-8_1
Published:
Publisher Name: Springer, Singapore
Print ISBN: 978-981-13-6789-2
Online ISBN: 978-981-13-6790-8
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)