Screening and Identification of Excellent Strains of Endophytic Bacteria Promoting Rice Iron Absorption from Wild Rice

doi:10.13560/j.cnki.biotech.bull.1985.2024-0178

Abstract

Abstract:

【Objective】To identify siderophilic endophytic bacteria that efficiently promote iron absorption in rice, and to investigate the siderophore-producing capacity and iron absorption promoting effect of different genera of endophytic bacteria from four wild rice.【Method】This study analyzed the siderophore contents of 198 endophytic bacteria isolated from four types of wild rice including Oryza longistaminata, O. rufipogon, O. officinalis, and O. minuta. The 82 strains with highly efficient siderophore-producing ability were screened from 128 strains with siderophore-producing ability. Analysis of the 16S rRNA gene sequences revealed that these 82 strains belonged to 18 different genera or species. Based on their siderophore production abilities, 18 candidate strains were selected to assess their abilities of promoting iron absorption in rice.【Result】The results demonstrated that different genera had varying effects on promoting rice iron absorption, with Bacillus（class）, Pseudomonas, and Saccharomycetes showing significant effects. Five high-efficient siderophore producing strains were selected from 18 strains and further confirmed that endophytic bacteria partially restored the iron deficiency phenotype of a rice iron-absorption-deficient mutant（osbhlh156）.【Conclusion】This study elucidates that siderophore produced by plant-interacting microorganisms can be utilized by rice, thereby enriching the microbial resources associated with iron absorption in rice. Additionally, it provides valuable bacterial resources and a theoretical basis for promoting iron absorption in rice through rice-microbial interactions.

Key words: rice, endophytic bacteria, siderophores, plant - microbial interaction, iron absorption

LI Qing-mao, PENG Cong-gui, QI Xiao-han, LIU Xing-lei, LI Zhen-yuan, LI Qin-yan, HUANG Li-yu. Screening and Identification of Excellent Strains of Endophytic Bacteria Promoting Rice Iron Absorption from Wild Rice[J]. Biotechnology Bulletin, 2024, 40(8): 255-263.

Figures/Tables 5

Fig. 1 Siderophore-producing ability analysis of isolated endophytic bacteria A: Plate schematic diagram of strains with the strongest siderophore-producing function from four wild rices. B: mp values of siderophore contents of endophytic bacteria among four wild rices. C: PCA diagram of siderophore contents produced by 128 endophytic bacteria. OL refers to Oryza longistaminata, OR to O. rufipogon, OO to O. officinalis, and OM to O. minuta

Fig. 2 Diversity classification of 82 endophytic bacteria (A)and siderophore-producing ability of 18 candidate strains of different genera/species (B)

Fig. 3 Phenotyping of rice treated by different endophytic bacteria with siderophore-producing ability Morphological phenotype（A）and statistical analysis of plant height（B）, root length（C）, chlorophyll（D）, and iron content（E）after treated with different endophytic bacteria. Scale bar: 10 cm; * indicates significant difference compared with the control（P < 0.05）

Table 1 Effect of 18 siderophore-producing strains on the plant height, root length, chlorophyll and iron content of ZH11

接种菌株 Inoculated strain	生长和生理指标Growth and physiological indicators
接种菌株 Inoculated strain	株高 Plant height/cm	根长 Root length/cm	叶绿素含量（SPAD）Chlorophyll content （SPAD）	铁含量 Total iron content/（mg·kg^-1）
OML3-3	-	+	+	+
OMR1-7	+	+	+	+
OOS1-3	-	+	+	+
OOS2-3	-	-	+	+
ORL1-5	-	-	+	-
OML3-6	+	+	+	+
ORL1-9	-	-	+	+
ORR1-18	+	-	+	-
OLL1-12	-	-	-	-
OML2-8	-	-	+	-
ORR3-11	-	-	-	+
OOR2-3	-	-	-	-
OMS2-7	-	+	-	+
OMR2-7	+	-	+	+
OOL1-5	+	-	-	+
ORR3-14	-	-	-	+
OLL1-10	-	+	-	+
OLL2-1	+	+	-	-

Fig. 4 Phenotype of osbhlh156 mutants recovered by highly efficient candidate strains Morphological phenotype（A）and iron content（B）and chlorophyll content（C）of osbhlh156 plants before and after treated with endophytic bacteria. Scale bar: 5 cm. * indicates significant difference compared with the control（P < 0.05）

References 37

[1]	刘金涛, 姚凡, 李臻园, 等. 植物铁素吸收机制研究进展[J]. 热带农业科学, 2022, 42(5): 26-33.
	Liu JT, Yao F, Li ZY, et al. Advances on the mechanism of iron absorption in plants[J]. Chin J Trop Agric, 2022, 42(5): 26-33.
[2]	李利敏, 吴良欢, 马国瑞. 植物吸收铁机理及其相关基因研究进展[J]. 土壤通报, 2010, 41(4): 994-999.
	Li LM, Wu LH, Ma GR. The progress on iron-absorbing mechanism and related gene in plant[J]. Chin J Soil Sci, 2010, 41(4): 994-999.
[3]	张进, 吴良欢, 孔向军, 等. 铁锌混合肥喷施对豌豆子粒铁、锌、可溶性糖和维生素C含量的影响[J]. 植物营养与肥料学报, 2006, 12(2): 2245-2249.
	Zhang J, Wu LH, Kong XJ, et al. Effect of foliar application of iron, zinc mixed fertilizers on the content of iron, zinc, soluble sugar and Vitamin C in green pea seeds[J]. Plant Nutr Fertil Sci, 2006, 12(2): 2245-2249.
[4]	Gupta A, Rico-Medina A, Caño-Delgado AI. The physiology of plant responses to drought[J]. Science, 2020, 368(6488): 266-269. doi: 10.1126/science.aaz7614 pmid: 32299946
[5]	Yuan X, Wang YM, Ji P, et al. A global transition to flash droughts under climate change[J]. Science, 2023, 380(6641): 187-191. doi: 10.1126/science.abn6301 pmid: 37053316
[6]	Barbosa Filho MP, Yamada T. Upland rice production in Brazil[J]. Better Crops International, 2002, 16: 43-46.
[7]	Guerinot ML, Yi Y. Iron: nutritious, noxious, and not readily available[J]. Plant Physiol, 1994, 104(3): 815-820. doi: 10.1104/pp.104.3.815 pmid: 12232127
[8]	章艺, 刘鹏, 宋金敏, 等. 水稻根尖铁的积累及附着形态研究[J]. 中国生态农业学报, 2009, 17(5): 929-932.
	Zhang Y, Liu P, Song JM, et al. Forms and accumulation ofiron at rice root tip[J]. Chin J Eco Agric, 2009, 17(5): 929-932.
[9]	Staiger D. Chemical strategies for iron acquisition in plants[J]. Angew Chem Int Ed Engl, 2002, 41(13): 2259-2264.
[10]	Nozoye T, Nagasaka S, Kobayashi T, et al. Phytosiderophore efflux transporters are crucial for iron acquisition in graminaceous plants[J]. J Biol Chem, 2011, 286(7): 5446-5454. doi: 10.1074/jbc.M110.180026 pmid: 21156806
[11]	Takahashi K, Hayashi KI, Kinoshita T. Auxin activates the plasma membrane H⁺-ATPase by phosphorylation during hypocotyl elongation in Arabidopsis[J]. Plant Physiol, 2012, 159(2): 632-641. doi: 10.1104/pp.112.196428 pmid: 22492846
[12]	Lee S, Chiecko JC, Kim SA, et al. Disruption of OsYSL15 leads to iron inefficiency in rice plants[J]. Plant Physiol, 2009, 150(2): 786-800. doi: 10.1104/pp.109.135418 pmid: 19376836
[13]	张妮娜, 上官周平, 陈娟. 植物应答缺铁胁迫的分子生理机制及其调控[J]. 植物营养与肥料学报, 2018, 24(5): 1365-1377.
	Zhang NN, Shangguan ZP, Chen J. Molecular physiological mechanism and regulation of plant responses to iron deficiency stress[J]. J Plant Nutr Fertil, 2018, 24(5): 1365-1377.
[14]	Gu SH, Wei Z, Shao ZY, et al. Competition for iron drives phytopathogen control by natural rhizosphere microbiomes[J]. Nat Microbiol, 2020, 5(8): 1002-1010. doi: 10.1038/s41564-020-0719-8 pmid: 32393858
[15]	Wang NQ, Wang TQ, Chen Y, et al. Microbiome convergence enables siderophore-secreting-rhizobacteria to improve iron nutrition and yield of peanut intercropped with maize[J]. Nat Commun, 2024, 15(1): 839. doi: 10.1038/s41467-024-45207-0 pmid: 38287073
[16]	Ahmed E, Holmström SJM. Siderophores in environmental research: roles and applications[J]. Microb Biotechnol, 2014, 7(3): 196-208. doi: 10.1111/1751-7915.12117 pmid: 24576157
[17]	董子阳, 胡佳杰, 胡宝兰. 微生物铁载体转运调控机制及其在环境污染修复中的应用[J]. 生物工程学报, 2019, 35(11): 2189-2200.
	Dong ZY, Hu JJ, Hu BL. Regulation of microbial siderophore transport and its application in environmental remediation[J]. Chin J Biotechnol, 2019, 35(11): 2189-2200.
[18]	Baakza A, Vala AK, Dave BP, et al. A comparative study of siderophore production by fungi from marine and terrestrial habitats[J]. J Exp Mar Biol Ecol, 2004, 311(1): 1-9.
[19]	Wilson BR, Bogdan AR, Miyazawa M, et al. Siderophores in iron metabolism: from mechanism to therapy potential[J]. Trends Mol Med, 2016, 22(12): 1077-1090. doi: S1471-4914(16)30147-2 pmid: 27825668
[20]	Oberegger H, Schoeser M, Zadra I, et al. SREA is involved in regulation of siderophore biosynthesis, utilization and uptake in Aspergillus nidulans[J]. Mol Microbiol, 2001, 41(5): 1077-1089. pmid: 11555288
[21]	雷平, 黄军, 黄彬彬, 等. 1株产铁载体辣椒内生细菌的分离鉴定及其促生长作用[J]. 激光生物学报, 2020, 29(4): 379-384.
	Lei P, Huang J, Huang BB, et al. Isolation, identification and growth promoting effect of a siderophore-producing endophytic bacterium from capscium[J]. Acta Laser Biol Sin, 2020, 29(4): 379-384.
[22]	Wang YH, Zhang GY, Huang Y, et al. A potential biofertilizer-siderophilic bacteria isolated from the rhizosphere of Paris polyphylla var. yunnanensis[J]. Front Microbiol, 2022, 13: 870413.
[23]	Qi B, Han M. Microbial siderophore enterobactin promotes mitochondrial iron uptake and development of the host via interaction with ATP synthase[J]. Cell, 2018, 175(2): 571-582.e11. doi: S0092-8674(18)30959-0 pmid: 30146159
[24]	Priyanka, Agrawal T, Kotasthane AS, et al. Crop specific plant growth promoting effects of ACCd enzyme and siderophore producing and cynogenic fluorescent Pseudomonas[J]. 3 Biotech, 2017, 7(1): 27. doi: 10.1007/s13205-017-0602-3 pmid: 28401463
[25]	Liu Q, Cheng L, Nian H, et al. Linking plant functional genes to rhizosphere microbes: a review[J]. Plant Biotechnol J, 2023, 21(5): 902-917.
[26]	Vannier N, Mesny F, Getzke F, et al. Genome-resolved metatranscriptomics reveals conserved root colonization determinants in a synthetic microbiota[J]. Nat Commun, 2023, 14(1): 8274. doi: 10.1038/s41467-023-43688-z pmid: 38092730
[27]	杨立凡, 田青霖, 龚禹瑞, 等. 小粒野生稻内生细菌的分离鉴定和促生功能分析[J]. 中国稻米, 2023, 29(4): 78-83. doi: 10.3969/j.issn.1006-8082.2023.04.014
	Yang LF, Tian QL, Gong YR, et al. Screening and identification of endophytic bacteria from Oryza minuta and their plant growth-promoting activities[J]. China Rice, 2023, 29(4): 78-83.
[28]	马永海, 田青霖, 龚禹瑞, 等. 普通野生稻内生细菌的分离鉴定及其对多年生稻的促生效果[J]. 云南大学学报: 自然科学版, 2023, 45(3): 768-778.
	Ma YH, Tian QL, Gong YR, et al. Screening and identification of endophytic bacteria from Oryza rufipogon and their effect on perennial rice growth[J]. J Yunnan Univ Nat Sci Ed, 2023, 45(3): 768-778.
[29]	Tian QL, Gong YR, Liu S, et al. Endophytic bacterial communities in wild rice(Oryza officinalis)and their plant growth-promoting effects on perennial rice[J]. Front Plant Sci, 2023, 14: 1184489.
[30]	Rungin S, Indananda C, Suttiviriya P, et al. Plant growth enhancing effects by a siderophore-producing endophytic streptomycete isolated from a Thai jasmine rice plant(Oryza sativa L. cv. KDML105)[J]. Antonie Van Leeuwenhoek, 2012, 102(3): 463-472.
[31]	Wein T, Romero Picazo D, Blow F, et al. Currency, exchange, and inheritance in the evolution of symbiosis[J]. Trends Microbiol, 2019, 27(10): 836-849. doi: S0966-842X(19)30151-9 pmid: 31257129
[32]	Bai B, Liu WD, Qiu XY, et al. The root microbiome: community assembly and its contributions to plant fitness[J]. J Integr Plant Biol, 2022, 64(2): 230-243. doi: 10.1111/jipb.13226
[33]	崔冬明, 单晨, 史利桦, 等. 生物源新型铁螯合剂研究进展及其应用[J]. 华中农业大学学报, 2023, 42(6): 59-72.
	Cui DM, Shan C, Shi LH, et al. Progress and application of novel iron biochelates[J]. J Huazhong Agric Univ, 2023, 42(6): 59-72.
[34]	Sah S, Singh N, Singh R. Iron acquisition in maize(Zea mays L.)using Pseudomonas siderophore[J]. 3 Biotech, 2017, 7(2): 121.
[35]	da Silva JF, da Silva TR, Escobar IEC, et al. Screening of plant growth promotion ability among bacteria isolated from field-grown sorghum under different managements in Brazilian drylands[J]. World J Microbiol Biotechnol, 2018, 34(12): 186.
[36]	Finazzi G, Petroutsos D, Tomizioli M, et al. Ions channels/transporters and chloroplast regulation[J]. Cell Calcium, 2015, 58(1): 86-97. doi: 10.1016/j.ceca.2014.10.002 pmid: 25454594
[37]	Liang G, Zhang HM, Li Y, et al. Oryza sativa fer-like fe deficiency-induced transcription factor(Osfit/Osbhlh156)interacts with Osiro2 to regulate iron homeostasis[J]. J Integr Plant Biol, 2020, 62(5): 668-689.