Abstract
Adaxial, abaxial phylloplane (leaf), and spermoplane (seed) are proximal yet contrasting habitats for a microbiota that needs to be adequately explored. Here, we proposed novel methods to decipher the adaxial/abaxial-phylloplane and spermoplane-microbiomes. Comparison of 22 meta barcoded-NGS datasets (size of total data set-1980.48 Mb) enabled us to fine-map the microbiome of the rice foliar niche, which encompasses the lower, middle, top leaf as well panicle. Here, the total- and the cultivable-microbiome profiling revealed 157 genera representing ten phyla and 87 genera from 4 bacterial phyla, respectively, with a predominance of Proteobacteria and Actinobacteria. Interestingly, more bacterial communities (124-genera) preferred the abaxial than the adaxial phylloplane (104-genera) and spermoplane (67-genera) for colonization. The microbiome profiles were nearly identical on the aromatic (125-genera) and non-aromatic rice (116-genera) with high representation of Pantoea, Methylobacterium, Curtobacterium, Sphingopyxis, and Microbacterium. The culturomics investigation confirmed the abundance of Pantoea, Chryseobacterium, Pseudomonas, Acinetobacter, Sphingobacterium, and Exiguobacterium. One hundred bacterial isolates characterized and identified by polyphasic-taxonomic tools revealed the dominance of Acinetobacter, Chryseobacterium, Enterobacter, Massilia, Pantoea, Pseudomonas, and Stenotrophomonas on adaxial/abaxial-phylloplane and spermoplane. The study culminated in identifying hitherto unexplored bacterial communities on the adaxial/abaxial phylloplane and spermoplane of rice that can be harnessed for microbiome-assisted rice cultivation in the future.
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Data availability
The datasets presented in this study can be found in online repositories (GenBank and MG-RAST). The names of the repository/repositories, GenBank accession numbers/MG-RAST deposition numbers: PVA_ADA_7- SAMN22567189/ mgm4874323.3; PVA_ABX_8- SAMN22567185/ mgm4874344.3; PPA_ADA_9- SAMN22567180/ mgm4874339.3; PPA_ABX_10- SAMN22567176/ mgm4874342.3; PVA_ADA_U_11- SAMN22567192/ mgm4874331.3; PVA_ADA_M_12-SAMN22567191/ mgm4874322.3; PVA_ADA_L_13- SAMN22567190/ mgm4874340.3; PVA_ABX_U_14- SAMN22567188/ mgm4874321.3; PVA_ABX_M_15- SAMN22567187/ mgm4874338.3; PVA_ABX_L_16- SAMN22567186/ mgm4874330.3; PPA_ADA_U_17- SAMN22567183/ mgm4874336.3; PPA_ADA_M_18- SAMN22567182/ mgm4874337.3; PPA_ADA_L_19- SAMN22567181/ mgm4874341.3; PPA_ABX_U_20- SAMN22567179/ mgm4874327.3; PPA_ABX_M_21- SAMN22567178/ mgm4874343.3; PPA_ABX_L_22- SAMN22567177/ mgm4874328.3; SPA-IP-6- SAMN22567194/ mgm4874332.3; SPA-PP-5- SAMN22567195/ mgm4874326.3; SPA-SP-4- SAMN22567196/ mgm4874324.3; SVA-IP-3- SAMN22567197/ mgm4874329.3; SVA-PP-2- SAMN22567198/ mgm4874325.3; SVA-SP-1- SAMN22567199/ mgm4874333.3.
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Acknowledgements
We thank the Director, IARI, and Dean, PG School, Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi for logistic support and encouragement. Charishma K is thankful to PM Fellowship Scheme and the advisory committee members at ICAR-IARI, New Delhi and Rallis India Pvt Ltd, Mumbai for their support and help during the investigation. The authors are grateful to NAHEP-CAAST on ‘Genomics-assisted crop improvement and management for providing research facilities. This work was funded by PG School, ICAR-Indian Agricultural Research Institute, New Delhi.
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The work was supported by the PM Fellowship Scheme of the Government of India.
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Charishma K and Aundy Kumar: Conceptualization, Methodology, Resources, and Validation. Charishma K, Mushineni Ashajyothi, Mukesh Kumar, Kuleshwar Prasad Sahu, Asharani Patel: Carried out the field planting in Almora. Hosahatti Rajashekara, Mushineni Ashajyothi, and Mukesh Kumar: Assisted in procuring rice samples and assisted Charishma K in various lab experiments. Aundy Kumar, Neelam Sheoran, Govindasamy V: Supervised the work on a regular interval; Aundy Kumar, Charishma K, Bhaskar Reddy: Data analysis and Manuscript preparation; All authors read and approved the final manuscript.
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Krishnappa, C., Mushineni, A., Reddy, B. et al. Fine-scale mapping of the microbiome on phylloplane and spermoplane of aromatic and non-aromatic rice genotypes. Folia Microbiol 68, 889–910 (2023). https://doi.org/10.1007/s12223-023-01055-x
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DOI: https://doi.org/10.1007/s12223-023-01055-x