Afzal I, Shinwari Z K, Sikandar S, Shahzad S. 2019. Plant beneficial endophytic bacteria: Mechanisms, diversity, host range and genetic determinants. Microbiological Research, 221, 36–49.
Aulakh M S, Malhi S S. 2005. Interactions of nitrogen with other nutrients and water: Effect on crop yield and quality, nutrient use efficiency, carbon sequestration, and environmental pollution. Advances in Agronomy, 86, 341–409.
Balasjin N M, Maki J S, Schläppi M R, Marshall C W. 2022. Plant growth-promoting activity of bacteria isolated from Asian rice (Oryza sativa L.) depends on rice genotype. Microbiology Spectrum, 10, doi: 10.1128/spectrum.02787-21.
Bashan Y, Kamnev A A, de-Bashan L E. 2013. Tricalcium phosphate is inappropriate as a universal selection factor for isolating and testing phosphate-solubilizing bacteria that enhance plant growth: A proposal for an alternative procedure. Biology and Fertility of Soils, 49, 465–479.
Beckers B, De Beeck M O, Weyens N, Boerjan W, Vangronsveld J. 2017. Structural variability and niche differentiation in the rhizosphere and endosphere bacterial microbiome of field-grown poplar trees. Microbiome, 5, 25.
Becze A, Vincze E B, Varga H M, Gyongyver M. 2021. Effect of plant growth promoting rhizobacteria on Zea mays development and growth under heavy metal and salt stress condition. Environmental Engineering and Management Journal, 20, 547–557.
Bolyen E, Rideout J R, Dillon M R, Bokulich N A, Caporaso J G. 2018. QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science. PeerJ, 6, e27295v1.
Borah M, Das S, Bora S S, Boro R C, Barooah M. 2021. Comparative assessment of multi-trait plant growth-promoting endophytes associated with cultivated and wild Oryza germplasm of Assam, India. Archives of Microbiology, 203, 2007–2028.
Cai H Y, Wang Y A, Xu H C, Yan Z S, Jia B, Maszenan A M, Jiang H L. 2015. Niveispirillum cyanobacteriorum sp. nov., a nitrogen-fixing bacterium isolated from cyanobacterial aggregates in a eutrophic lake. International Journal of Systematic and Evolutionary Microbiology, 65, 2537–2541.
van Campen J C, Yaapar M N, Narawatthana S, Lehmeier C, Wanchana S, Thakur V, Chater C, Kelly S, Rolfe S A, Quick W P, Fleming A J. 2016. Combined chlorophyll fluorescence and transcriptomic analysis identifies the p3/p4 transition as a key stage in rice leaf photosynthetic development. Plant Physiology, 170, 1655–1674.
Chang J J, Tian L, Leite M, Sun Y, Shi S H, Xu S Q, Wang J L, Chen H P, Chen D Z, Zhang J F, Tian C J, Kuramae E E. 2022. Nitrogen, manganese, iron, and carbon resource acquisition are potential functions of the wild rice Oryza rufipogon core rhizomicrobiome. Microbiome, 10, 196.
Cao P, Li C X, Tan K F, Liu C Z, Xu X, Zhang S Y, Wang X J, Zhao J W, Xiang W S. 2020. Characterization, phylogenetic analyses, and pathogenicity of Enterobacter cloacae on rice seedlings in Heilongjiang Province, China. Plant Disease, 104, 1601–1609.
Chaudhry V, Runge P, Sengupta P, Doehlemann G, Parker J E, Kemen E. 2021. Shaping the leaf microbiota: Plant–microbe–microbe interactions. Journal of Experimental Botany, 72, 36–56.
Chu C, Fan M, Song C, Li N, Zhang C, Fu S, Wang W, Yang Z. 2021. Unveiling endophytic bacterial community structures of different rice cultivars grown in a cadmium-contaminated paddy field. Frontiers in Microbiology, 12, 756327.
Douglas G M, Maffei V J, Zaneveld J R, Yurgel S N, Brown J R, Taylor C M, Huttenhower C, Langille M G I. 2020. PICRUSt2: An improved and customizable approach for metagenome inference. Nature Biotechnology, 38, 685–688.
Etesami H, Alikhani H A, Hosseini H M. 2015. Indole-3-acetic acid (IAA) production trait, a useful screening to select endophytic and rhizosphere competent bacteria for rice growth promoting agents. Methodsx, 2, 72–78.
Evans P N, Boyd J A, Leu A O, Woodcroft B, Parks D H, Hugenholtz P, Tyson G W. 2019. An evolving view of methane metabolism in the Archaea. Nature Reviews Microbiology, 17, 219–232.
Fariman A B, Abbasiliasi S, Abdullah S N A, Saud H M, Wong M Y. 2022. Stenotrophomonas maltophilia isolate UPMKH2 with the abilities to suppress rice blast disease and increase yield a promising biocontrol agent. Physiological and Molecular Plant Pathology, 121, 101872.
Gamalero E, Glick B R. 2015. Bacterial modulation of plant ethylene levels. Plant Physiology, 169, 13–22.
Given C, Haikio E, Kumar M, Nissinen R. 2020. Tissue-specific dynamics in the endophytic bacterial communities in arctic pioneer plant Oxyria digyna. Frontiers in Plant Science, 11, 561.
Harun-Or-Rashid M, Kim H J, Yeom S I, Yu H A, Manir M M, Moon S S, Kang Y J, Chung Y R. 2018. Bacillus velezensis YC7010 enhances plant defenses against brown planthopper through transcriptomic and metabolic changes in rice. Frontiers in Plant Science, 9, 1904.
Hu F Y, Tao D Y, Sacks E, Fu B Y, Xu P, Li J, Yang Y, Mcnally K, Khush G S, Paterson A H, Li Z K. 2003. Convergent evolution of perenniality in rice and sorghum. Proceedings of the National Academy of Sciences of the United States of America, 100, 4050–4054.
Hu J, Lin X, Wang J, Chu H, Yin R, Zhang J. 2009. Population size and specific potential of P-mineralizing and -solubilizing bacteria under long-term P-deficiency fertilization in a sandy loam soil. Pedobiologia, 53, 49–58.
Huang F, Zhu C Y, Huang M L, Song X B, Peng A T. 2023. The root enrichment of bacteria is consistent across different stress-resistant plant species. PeerJ, 11, e14683.
Huang S Y, Liu M M, Chen G L, Si F F, Fan F F, Guo Y, Yuan L, Yang F, Li S Q. 2022. Favorable QTLs from Oryza longistaminata improve rice drought resistance. BMC Plant Biology, 22, 136.
Jauri P V, Taule C, De Los Santos M C, Fernandez B, Di Paolo A, Sotelo J, Battistoni F. 2020. Interactions between putatively endophytic bacteria and tall fescue (Festuca arundinacea): Plant growth promotion and colonization in host and non-host cultivars. Plant and Soil, 451, 207–220.
Kajiya-Kanegae H, Ohyanagi H, Ebata T, Tanizawa Y, Onogi A, Sawada Y, Hirai M Y, Wang Z X, Han B, Toyoda A, Fujiyama A, Iwata H, Tsuda K, Suzuki T, Nosaka-Takahashi M, Nonomura K, Nakamura Y, Kawamoto S, Kurata N, Sato Y. 2021. Rice, 14, 24.
Kim H, Lee Y H. 2021. Spatiotemporal assembly of bacterial and fungal communities of seed–seedling–adult in rice. Frontiers in Microbiology, 12, 708475.
Kumar J, Babele P K, Singh D, Kumar A. 2016. UV-B radiation stress causes alterations in whole cell protein profile and expression of certain genes in the rice phyllospheric bacterium Enterobacter cloacae. Frontiers in Microbiology, 7, 1440.
Kumar V, Nautiyal C S. 2022. Plant abiotic and biotic stress alleviation: From an endophytic microbial perspective. Current Microbiology, 79, 311.
Lee K E, Adhikari A, Kang S M, You Y H, Joo G J, Kim J H, Kim S J, Lee I J. 2019. Isolation and characterization of the high silicate and phosphate solubilizing novel strain Enterobacter ludwigii GAK2 that promotes growth in rice plants. Agronomy, 9, 144.
Lin G Y, Lin C Y, Chang S J, Lin W Y. 2020. The dynamics of endophytic bacterial community structure in rice roots under different field management systems. Agronomy, 10, 1623.
Liu L H, Yuan T, Zhang J Y, Tang G X, Lu H X, Zhao H M, Li H, Li Y W, Mo C H, Tan Z Y, Cai Q Y. 2022. Diversity of endophytic bacteria in wild rice (Oryza meridionalis) and potential for promoting plant growth and degrading phthalates. Science of the Total Environment, 806, 150310.
Long W X, Dan D, Yuan Z Q, Chen Y P, Jin J, Yang W L, Zhang Z H, Li N W, Li S Q. 2020. Deciphering the genetic basis of lodging resistance in wild rice Oryza longistaminata. Frontiers in Plant Science, 11, 628.
Ma J L, Jiang G B, Jiang B, Jin H, Yao S J. 2013. Determination of four kinds of endogenous hormones in poplar dialyzate by HPLC with microdialysis. Acta Chromatographica, 25, 627–637.
Madhaiyan M, Jin T Y, Roy J J, Kim S J, Weon H Y, Kwon S W, Ji L H. 2013. Pleomorphomonas diazotrophica sp. nov., an endophytic N-fixing bacterium isolated from root tissue of Jatropha curcas L. International Journal of Systematic and Evolutionary Microbiology, 63, 2477–2483.
Marag P S, Suman A. 2018. Growth stage and tissue specific colonization of endophytic bacteria having plant growth promoting traits in hybrid and composite maize (Zea mays L.). Microbiological Research, 214, 101–113.
Mizuno D, Kosaka S. 1950. Studies on the nutritional requirements of bacteria. II. on the nutrition of Shigella dysenteriae. Japanese Medical Journal, 3, 99–105.
Moon Y S, Ali S. 2022. Possible mechanisms for the equilibrium of ACC and role of ACC deaminase-producing bacteria. Applied Microbiology and Biotechnology, 106, 877–887.
Moon Y S, Khan M, Khan M A, Ali S. 2023. Ameliorative symbiosis of Serratia fonticola (S1T1) under salt stress condition enhance growth-promoting attributes of Cucumis sativus L. Symbiosis, 89, 283–297.
Morella N M, Weng F C H, Joubert P M, Metcalf C J E, Lindow S, Koskella B. 2020. Successive passaging of a plant-associated microbiome reveals robust habitat and host genotype-dependent selection. Proceedings of the National Academy of Sciences of the United States of America, 117, 1148–1159.
Mushtaq S, Shafiq M, Tariq M R, Sami A, Nawaz-Ul-Rehman M S, Bhatti M H T, Haider M S, Sadiq S, Abbas M T, Hussain M, Shahid M A. 2023. Interaction between bacterial endophytes and host plants. Frontiers in Plant Science, 13, 1092105.
Olanrewaju O S, Babalola O O. 2022. The rhizosphere microbial complex in plant health: A review of interaction dynamics. Journal of Integrative Agriculture, 21, 2168–2182.
Otlewska A, Migliore M, Dybka-Stepien K, Manfredini A, Struszczyk-Swita K, Napoli R, Bialkowska A, Canfora L, Pinzari F. 2020. When salt meddles between plant, soil, and microorganisms. Frontiers in Plant Science, 11, 553087.
Oyserman B O, Cordovez V, Flores S S, Leite M F A, Nijveen H, Medema M H, Raaijmakers J M. 2021. Extracting the GEMs: Genotype, environment, and microbiome interactions shaping host phenotypes. Frontiers in Microbiology, 11, 574053.
Padda K P, Puri A, Nguyen N K, Philpott T J, Chanway C P. 2022. Evaluating the rhizospheric and endophytic bacterial microbiome of pioneering pines in an aggregate mining ecosystem post-disturbance. Plant and Soil, 474, 213–232.
Patil S V, Salunkhe R B, Patil C D, Patil D M, Salunke B K. 2010. Bioflocculant exopolysaccharide production by azotobacter indicus using flower extract of Madhuca latifolia L. Applied Biochemistry and Biotechnology, 162, 1095–1108.
Pattnaik S, Dash D, Mohapatra S, Pattnaik M, Marandi A K, Das S, Samantaray D P. 2020. Improvement of rice plant productivity by native Cr(VI) reducing and plant growth promoting soil bacteria Enterobacter cloacae. Chemosphere, 240, 124895.
Peng X, Xie J, Li W, Xie H, Cai Y, Ding X. 2021. Comparison of wild rice (Oryza longistaminata) tissues identifies rhizome-specific bacterial and archaeal endophytic microbiomes communities and network structures. PLoS ONE, 16, e0246687.
Pope P B, Denman S E, Jones M, Tringe S G, Barry K, Malfatti S A, Mchardy A C, Cheng J F, Hugenholtz P, Mcsweeney C S, Morrison M. 2010. Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores. Proceedings of the National Academy of Sciences of the United States of America, 107, 14793–14798.
Radhakrishnan R, Park J M, Lee I J. 2016. Enterobacter sp. I-3, a bio-herbicide inhibits gibberellins biosynthetic pathway and regulates abscisic acid and amino acids synthesis to control plant growth. Microbiological Research, 193, 132–139.
Rilling J I, Acuña J A, Nannipieri P, Cassan F, Maruyama F, Jorquera M A. 2019. Current opinion and perspectives on the methods for tracking and monitoring plant growth-promoting bacteria. Soil Biology and Biochemistry, 130, 205–219.
Santoyo G, Moreno-Hagelsieb G, Orozco-Mosqueda M D, Glick B R. 2016. Plant growth-promoting bacterial endophytes. Microbiological Research, 183, 92–99.
Schwyn B, Neilands J B. 1987. Universal chemical-assay for the detection and determination of siderophores. Analytical Biochemistry, 160, 47–56.
Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett W S, Huttenhower C. 2011. Metagenomic biomarker discovery and explanation. Genome Biology, 12, R60.
Sharma A, Johri B N. 2003. Growth promoting influence of siderophore-producing Pseudomonas strains GRP3A and PRS9 in maize (Zea mays L.) under iron limiting conditions. Microbiological Research, 158, 243–248.
Sharma P, Kumar S. 2021. Bioremediation of heavy metals from industrial effluents by endophytes and their metabolic activity: Recent advances. Bioresource Technology, 339, 125589.
Shi S H, Chang J J, Tian L, Nasir F, Ji L, Li X J, Tian C J. 2019. Comparative analysis of the rhizomicrobiome of the wild versus cultivated crop: Insights from rice and soybean. Archives of Microbiology, 201, 879–888.
Si F F, Fan F F, Wei X, He S H, Li S H, Peng X J, Li S Q. 2022. Quantitative trait locus mapping of high photosynthetic efficiency and biomass in Oryza longistaminata. Rice Science, 29, 569–576.
Tao D, Sripichitt P. 2000. Preliminary report on transfer traits of vegetative propagation from wild rice species to Oryza sativa via distant hybridization and embryo rescue. The Kasetsart Journal, 34, 1–11.
Tong S, Ashikari M, Nagai K, Pedersen O. 2023. Can the wild perennial, rhizomatous rice species Oryza longistaminata be a candidate for de novo domestication? Rice, 16, 13.
Trivedi P, Batista B D, Bazany K E, Singh B K. 2022. Plant–microbiome interactions under a changing world: Responses, consequences and perspectives. New Phytologist, 234, 1951–1959.
Trivedi P, Leach J E, Tringe S G, Sa T M, Singh B K. 2020. Plant–microbiome interactions: From community assembly to plant health. Nature Reviews Microbiology, 18, 607–621.
Wagner M R, Lundberg D S, del Rio T G, Tringe S G, Dangl J L, Mitchell-Olds T. 2016. Host genotype and age shape the leaf and root microbiomes of a wild perennial plant. Nature Communications, 7, 12151.
Wan Y X, Zhou L A, Wang S, Liao C M, Li N, Liu W T, Wang X. 2018. Syntrophic growth of Geobacter sulfurreducens accelerates anaerobic denitrification. Frontiers in Microbiology, 9, 1572.
Wang Q, Ma L Y, Zhou Q Y, Chen B, Zhang X C, Wu Y J, Pan F S, Huang L K, Yang X E, Feng Y. 2019. Inoculation of plant growth promoting bacteria from hyperaccumulator facilitated non-host root development and provided promising agents for elevated phytoremediation efficiency. Chemosphere, 234, 769–776.
Wani Z A, Ashraf N, Mohiuddin T, Riyaz-Ul-Hassan S. 2015. Plant-endophyte symbiosis, an ecological perspective. Applied Microbiology and Biotechnology, 99, 2955–2965.
White J F, Kingsley K L, Zhang Q, Verma R, Obi N, Dvinskikh S, Elmore M T, Verma S K, Gond S K, Kowalski K P. 2019. Review: Endophytic microbes and their potential applications in crop management. Pest Management Science, 75, 2558–2565.
Xie J, Wang X Q, Xu J W, Xie H W, Cai Y H, Liu Y Z, Ding X. 2021. Strategies and structure feature of the aboveground and belowground microbial community respond to drought in wild rice (Oryza longistaminata). Rice, 14, 79.
Xu P, Dong L Y, Zhou J W, Li J, Zhang Y, Hu F Y, Liu S F, Wang Q, Deng W, Deng X N, Tharreau D, Yang Q Z, Tao D Y. 2015. Identification and mapping of a novel blast resistance gene Pi57(t) in Oryza longistaminata. Euphytica, 205, 95–102.
Xu S Q, Chang J J, Chang C L, Tian L, Li X J, Tian C J. 2022. Rhizospheric microbiomes help Dongxiang common wild rice (Oryza rufipogon Griff.) rather than Leersia hexandra Swartz survive under cold stress. Archives of Agronomy and Soil Science, 68, 76–88.
Yang H J, Ye W W, Yu Z, Shen W L, Li S Z, Wang X, Chen J J, Wang Y C, Zheng X B. 2023. Host niche, genotype, and field location shape the diversity and composition of the soybean microbiome. Journal of Integrative Agriculture, 22, 2412–2425.
Yang S F, Liu Y, Su L, Peiser G D, Hoffman N E, Mckeon T. 1985. 2-Metabolism of 1-aminocyclopropane-1-carboxylic acid. In: Roberts J A, Tucker G A, eds., Ethylene and Plant Development. Butterworth-Heinemann, UK. pp. 9–21.
Yang Z Y, Xu Z J, Yang Q W, Qiao W H. 2022. Conservation and utilization of genetic resources of wild rice in China. Rice Science, 29, 216–224.
Yin Y, Wang Y F, Cui H L, Zhou R, Li L, Duan G L, Zhu Y G. 2023. Distinctive structure and assembly of phyllosphere microbial communities between wild and cultivated rice. Microbiology Spectrum, 11, doi: 10.1128/spectrum.04371-22.
Yu P, Hochholdinger F. 2018. The role of host genetic signatures on root-microbe interactions in the rhizosphere and endosphere. Frontiers in Plant Science, 9, 1896.
Yuan L, Zhang L C, Wei X, Wang R H, Li N N, Chen G L, Fan F F, Huang S Y, Li J X, Li S Q. 2022. Quantitative trait locus mapping of salt tolerance in wild rice Oryza longistaminata. International Journal of Molecular Sciences, 23, 2379.
Yvon-Durocher G, Allen A P, Bastviken D, Conrad R, Gudasz C, St-Pierre A, Thanh-Duc N, del Giorgio P A. 2014. Methane fluxes show consistent temperature dependence across microbial to ecosystem scales. Nature, 507, 488–491.
Zhan H L, Wan Q, Wang Y, Cheng J F, Yu X Y, Ge J. 2021. An endophytic bacterial strain, Enterobacter cloacae TMX-6, enhances the degradation of thiamethoxam in rice plants. Chemosphere, 269, 128751.
Zhang S L, Huang G F, Zhang Y J, Lv X T, Wan K J, Liang J, Feng Y P, Dao J R, Wu S K, Zhang L, Yang X, Lian X P, Huang L Y, Shao L, Zhang J, Qin S W, Tao D Y, Crews T E, Sacks E J, Lyu J, et al. 2022. Sustained productivity and agronomic potential of perennial rice. Nature Sustainability, 6, 28–38.
Zhang Z, Liu T, Zhang X, Xie J, Wang Y, Yan R, Jiang Y, Zhu D. 2021. Cultivable endophytic bacteria in seeds of dongxiang wild rice and their role in plant-growth promotion. Diversity, 13, 665.
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