Wu Y, Sun J, Yu P, Zhang W, Lin Y, Ma D (2022) The rhizosphere bacterial community contributes to the nutritional competitive advantage of weedy rice over cultivated rice in paddy soil. BMC Microbiol 22(1):232. https://doi.org/10.1186/s12866-022-02648-1
Article CAS PubMed PubMed Central Google Scholar
Islam MM, Jana SK, Sengupta S, Mandal S (2024) Impact of the rhizospheric microbiome on rice cultivation. Curr Microbiol 81(7):188. https://doi.org/10.1007/s00284-024-03703-y
Article CAS PubMed Google Scholar
Kong W, Qiu L, Ishii S, Jia X, Su F, Song Y, Hao M, Shao M, Wei X (2023) Contrasting response of soil microbiomes to long-term fertilization in various highland cropping systems. ISME Commun 3(1):81. https://doi.org/10.1038/s43705-023-00286-w
Article PubMed PubMed Central Google Scholar
Xu Q, Ling N, Chen H, Duan Y, Wang S, Shen Q, Vandenkoornhuyse P (2020) Long-term chemical-only fertilization induces a diversity decline and deep selection on the soil bacteria. msystems. https://doi.org/10.1128/mSystems.00337-20
Article PubMed PubMed Central Google Scholar
Ladha JK, Peoples MB, Reddy PM, Biswas JC, Bennett A, Jat ML, Krupnik TJ (2022) Biological nitrogen fixation and prospects for ecological intensification in cereal-based cropping systems. Field Crops Res 283:108541. https://doi.org/10.1016/j.fcr.2022.108541
Article PubMed PubMed Central Google Scholar
Dondjou DT, Diedhiou AG, Mbodj D, Mofini MT, Pignoly S, Ndiaye C, Diedhiou I, Assigbetse K, Manneh B, Laplaze L, Kane A (2023) Rice developmental stages modulate rhizosphere bacteria and archaea co-occurrence and sensitivity to long-term inorganic fertilization in a West African Sahelian agro-ecosystem. Environ Microbiome 18(1):42. https://doi.org/10.1186/s40793-023-00500-1
Article PubMed PubMed Central Google Scholar
Ladha JK, Tirol-Padre A, Reddy CK, Cassman KG, Verma S, Powlson DS, van Kessel C, Richter DB et al (2016) Global nitrogen budgets in cereals, A 50-year assessment for maize, rice, and wheat production systems. Sci Rep 6:19355. https://doi.org/10.1038/srep19355
Article CAS PubMed PubMed Central Google Scholar
Toju H, Peay KG, Yamamichi M, Narisawa K, Hiruma K, Naito K, Fukuda S, Ushio M et al (2018) Core microbiomes for sustainable agroecosystems. Nature Plants 4(5):247–257. https://doi.org/10.1038/s41477-018-0139-4
Alex S, Dean P, Daniel C, Devin C-D (2024) Improving rice drought tolerance through host-mediated microbiome selection. Elife 13:RP97015. https://doi.org/10.7554/eLife.97015.1
Trivedi P, Leach JE, Tringe SG, Sa T, Singh BK (2020) Plant-microbiome interactions: from community assembly to plant health. Nat Rev Microbiol 18:607–621. https://doi.org/10.1038/s41579-020-0412-1
Article CAS PubMed Google Scholar
Zhang X, Ma YN, Wang X, Liao K, He S, Zhao X, Guo H, Zhao D, Wei HL (2022) Dynamics of rice microbiomes reveal core vertically transmitted seed endophytes. Microbiome 10(1):216. https://doi.org/10.1186/s40168-022-01422-9
Article CAS PubMed PubMed Central Google Scholar
Lemanceau P, Blouin M, Muller D, Moënne-Loccoz Y (2017) Let the core microbiota be functional. Trends Plant Sci 22:583–595. https://doi.org/10.1016/j.tplants.2017.04.008
Article CAS PubMed Google Scholar
Xiong C, Lu Y (2022) Microbiomes in agroecosystem: Diversity, function and assembly mechanisms. Environ Microbiol Rep 14(6):833–849. https://doi.org/10.1111/1758-2229.13126
Article CAS PubMed Google Scholar
Ogg CL (1960) Determination of nitrogen by the Micro-Kjeldahl method. AOAC 43(3):689–693. https://doi.org/10.1093/jaoac/43.3.689
Hedge JE, Hofreiter BT. In: Carbohydrate Chemistry, 17 (Eds. Whistler R.L. and Be Miller, J.N.), Academic Press, New York, 1962.
Hammer O, Harper D, Ryan P (2001) PAST: paleontological statistics software package for education and data analysis. Palaeontol Electron 4:1–9
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13(11):2498–2504. https://doi.org/10.1101/gr.1239303
Article CAS PubMed PubMed Central Google Scholar
van der Laken PA (2020) Create a publication-ready correlation matrix, with significance levels, in R. paulvanderlaken.com. https://paulvanderlaken.com/2020/07/28/publication-ready-correlation-matrix-significance-r/comment-page-1/#comment-27232
Imchen M, Kumavath R, Vaz ABM, Góes-Neto A, Barh D, Ghosh P, Kozyrovska N, Podolich O, Azevedo V (2019) 16S rRNA Gene amplicon based metagenomic signatures of rhizobiome community in rice field during various growth stages. Front Microbiol 10:2103. https://doi.org/10.3389/fmicb.2019.02103
Article PubMed PubMed Central Google Scholar
Shenton M, Iwamoto C, Kurata N, Ikeo K (2016) Effect of wild and cultivated rice genotypes on rhizosphere bacterial community composition. Rice 9:42. https://doi.org/10.1186/s12284-016-0111-8
Article PubMed PubMed Central Google Scholar
White JR, Nagarajan N, Pop M (2009) Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comput Biol 5(4):e1000352. https://doi.org/10.1371/journal.pcbi.1000352
Article CAS PubMed PubMed Central Google Scholar
Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet C, Al-Ghalith GA et al (2018) QIIME 2: reproducible, interactive, scalable, and extensible microbiome data science. PeerJ Preprints 6:e27295v2. https://doi.org/10.7287/peerj.preprints.27295v2
Estrada-De Los Santos P, Bustillos-Cristales R, Caballero-Mellado J (2001) Burkholderia, a genus rich in plant-associated nitrogen fixers with wide environmental and geographic distribution. Appl Environ Microbiol 67(6):2790–2798. https://doi.org/10.1128/AEM.67.6.2790-2798.2001
Article CAS PubMed PubMed Central Google Scholar
Dixon R, Kahn D (2004) Genetic regulation of biological nitrogen fixation. Nat Rev Microbiol 2(8):621–631. https://doi.org/10.1038/nrmicro954
Article CAS PubMed Google Scholar
Coutinho BG, Passos da Silva D, Previato JO, Mendonça-Previato L, Venturi V (2013) Draft genome sequence of the rice endophyte Burkholderia kururiensis M130. Genome Announc 1(2):e00225-e312. https://doi.org/10.1128/genomeA.00225-12
Article PubMed PubMed Central Google Scholar
Dias GM, de Sousa PA, Grilo VS, Castro MR, de Figueiredo VL, Neves BC (2019) Comparative genomics of Paraburkholderia kururiensis and its potential in bioremediation, biofertilization, and biocontrol of plant pathogens. MicrobiologyOpen 8(8):e00801. https://doi.org/10.1002/mbo3.801
Article CAS PubMed PubMed Central Google Scholar
Estrada-de Los Santos P, Palmer M, Chávez-Ramírez B et al (2018) Whole genome analyses suggest that Burkholderia sensu lato contains two additional novel genera (Mycetohabitans gen. nov., and Trinickia gen nov.): implications for the evolution of diazotrophy and nodulation in the Burkholderiaceae. Genes (Basel) 9(8):389. https://doi.org/10.3390/genes9080389
Article CAS PubMed Google Scholar
Mosley OE, Gios E, Close M, Weaver L, Daughney C, Handley KM (2022) Nitrogen cycling and microbial cooperation in the terrestrial subsurface. ISME J 16(11):2561–2573. https://doi.org/10.1038/s41396-022-01300-0
Article CAS PubMed PubMed Central Google Scholar
Dove NC, Veach AM, Muchero W, Wahl T, Stegen JC, Schadt CW, Cregger MA (2021) Assembly of the populus microbiome is temporally dynamic and determined by selective and stochastic factors. msphere. 6(3):0131620. https://doi.org/10.1128/mSphere.01316-20
Dibner RR, Weaver AM, Brock MT, CusterGF MHG, Maignien L, Weinig C (2021) Time outweighs the effect of host developmental stage on microbial community composition. FEMS Microbiol Ecol.
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