Comparison of the rhizospheric soil bacteriomes of Oryza sativa and Solanum melongena crop cultivars reveals key genes and pathways involved in biosynthesis of ectoine, lysine, and catechol meta-cleavage

Adviento-Borbe MAA, Doran JW, Drijber RA, Dobermann A (2006) Soil Electrical Conductivity and Water Content affect Nitrous Oxide and Carbon Dioxide emissions in intensively managed soils. J Env Qual 35:1999–2010. https://doi.org/10.2134/jeq2006.0109

Article  CAS  Google Scholar 

Aghapour AA, Moussavi G, Yaghmaeian K (2013) Biological degradation of catechol in wastewater using the sequencing continuous-inflow reactor (SCR). J Environ Health Sci Eng 11:3. https://doi.org/10.1186/2052-336X-11-3

Article  PubMed  PubMed Central  CAS  Google Scholar 

Allen White R, Borkum MI, Rivas-Ubach A et al (2017) From data to knowledge: the future of multi-omics data analysis for the rhizosphere. Rhizosphere 3:222–229. https://doi.org/10.1016/j.rhisph.2017.05.001

Article  Google Scholar 

Bado S, Forster BP, Ghanim AMA et al (2016) Protocol for measuring soil salinity. Protocols for Pre-field screening of mutants for Salt Tolerance in Rice, Wheat and Barley. Springer International Publishing, Cham, pp 13–19

Chapter  Google Scholar 

Bao SD (2000) Soil and agricultural chemistry analysis. 3rd Edition, China agriculture press, Beijing, 265–267

Berg G, Smalla K (2009) Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere: plant species, soil type and rhizosphere communities. FEMS Microbiol Ecol 68:1–13. https://doi.org/10.1111/j.1574-6941.2009.00654.x

Article  PubMed  CAS  Google Scholar 

Bugg T, Winfield C (1998) Enzymatic cleavage of aromatic rings: mechanistic aspects of the catechol dioxygenases and later enzymes of bacterial oxidative cleavage pathways. Nat Prod Rep 15:513. https://doi.org/10.1039/a815513y

Article  CAS  Google Scholar 

Calderón MI, Vargas C, Rojo F et al (2004) Complex regulation of the synthesis of the compatible solute ectoine in the halophilic bacterium Chromohalobacter salexigens DSM 3043T. Microbiology 150:3051–3063. https://doi.org/10.1099/mic.0.27122-0

Article  PubMed  CAS  Google Scholar 

Church MJ (2008) Resource control of bacterial dynamics in the sea. In: Microbial Ecology of the Oceans, 2nd Edn, Kirchman DL. Wiley Sons, pp 335–382

Dhondge HV, Barvkar VT, Paul D et al (2022) Exploring the core microbiota in scented rice (Oryza sativa L.) rhizosphere through metagenomics approach. Microbiol Res 263:127157. https://doi.org/10.1016/j.micres.2022.127157

Article  PubMed  CAS  Google Scholar 

Edwards J et al. (2015) Structure, variation, and assembly of the root-associated microbiomes of rice. Proc Natl Acad Sci USA 112: 911–920. https://doi.org/10.1073/pnas.1414592112

Faintuch J, Faintuch S (eds) (2019) Microbiome and metabolome in diagnosis, therapy, and other strategic applications. Academic, London, United Kingdom,, pp 451–472

Book  Google Scholar 

Galili G, Amir R (2013) Fortifying plants with the essential amino acids lysine and methionine to improve nutritional quality. Plant Biotechnol J 11:211–222. https://doi.org/10.1111/pbi.12025

Article  PubMed  CAS  Google Scholar 

GeethaThanuja K, Karthikeyan S, SelvaBabu S et al (2023) Rice Rhizosphere metagenome in association with application of biochar under continuous exposure to elevated carbon dioxide. ACS Agric Sci Technol 3:90–100. https://doi.org/10.1021/acsagscitech.2c00244

Article  CAS  Google Scholar 

Gunde-Cimerman N, Plemenitaš A, Oren A (2018) Strategies of adaptation of microorganisms of the three domains of life to high salt concentrations. FEMS Microbiol Rev 42:353–375. https://doi.org/10.1093/femsre/fuy009

Article  PubMed  CAS  Google Scholar 

Head SR, Komori HK, LaMere SA et al (2014) Library construction for next-generation sequencing: overviews and challenges. Biotechniques 56:61–77. https://doi.org/10.2144/000114133

Article  PubMed  PubMed Central  CAS  Google Scholar 

Houba VJG, Temminghoff EJM, Gaikhorst GA et al (2000) Soil analysis procedures using 0.01 M calcium chloride as extraction reagent. Commun Soil Sci Plant Anal 31:1299–1396. https://doi.org/10.1080/00103620009370514

Article  CAS  Google Scholar 

Hugenholtz P, Goebel BM, Pace NR (1998) Impact of Culture-Independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180:4765–4774. https://doi.org/10.1128/JB.180.18.4765-4774.1998

Article  PubMed  PubMed Central  CAS  Google Scholar 

Imchen M, Kumavath R, Vaz ABM et al (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 

Jackson ML (1973) Soil Chemical Analysis. Prentice Hall of India Pvt. Ltd., New Delhi, p 498

Google Scholar 

Jacoby R, Peukert M, Succurro A et al (2017) The role of soil microorganisms in plant mineral nutrition—current knowledge and future directions. Front Plant Sci 8:1617. https://doi.org/10.3389/fpls.2017.01617

Article  PubMed  PubMed Central  Google Scholar 

Kim JM, Roh A-S, Choi S-C et al (2016) Soil pH and electrical conductivity are key edaphic factors shaping bacterial communities of greenhouse soils in Korea. J Microbiol 54:838–845. https://doi.org/10.1007/s12275-016-6526-5

Article  PubMed  CAS  Google Scholar 

,

Knief C, Delmotte N, Chaffron S et al (2012) Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice. ISME J 6:1378–1390. https://doi.org/10.1038/ismej.2011.192

Article  PubMed  CAS  Google Scholar 

Kögel-Knabner I, Amelung W, Cao Z et al (2010) Biogeochemistry of paddy soils. Geoderma 157:1–14. https://doi.org/10.1016/j.geoderma.2010.03.009

Article  CAS  Google Scholar 

Kosuge T, Hoshino T (1998) Lysine is synthesized through the α-aminoadipate pathway in Thermus thermophilus. FEMS Microbiol Lett 169:361–367. https://doi.org/10.1111/j.1574-6968.1998.tb13341.x

Article  PubMed  CAS  Google Scholar 

Kusano M, Yang Z, Okazaki Y et al (2015) Using Metabolomic approaches to explore Chemical Diversity in Rice. Mol Plant 8:58–67. https://doi.org/10.1016/j.molp.2014.11.010

Article  PubMed  CAS  Google Scholar 

Levy-Booth DJ, Fetherolf MM, Stewart GR et al (2019) Catabolism of alkylphenols in Rhodococcus via a meta-cleavage pathway associated with genomic islands. Front Microbiol 10:1862. https://doi.org/10.3389/fmicb.2019.01862

Article  PubMed  PubMed Central  Google Scholar 

Li H, Ding X, Chen C et al (2019) Enrichment of phosphate solubilizing bacteria during late developmental stages of eggplant (Solanum melongena L). FEMS Microbiol Ecol 95. https://doi.org/10.1093/femsec/fiz023

Li P, Ye S, Chen J et al (2023) Combined metagenomic and metabolomic analyses reveal that Bt rice planting alters soil C-N metabolism. ISME Commun 3:4. https://doi.org/10.1038/s43705-023-00217-9

Article  PubMed  PubMed Central  Google Scholar 

Ling N, Wang T, Kuzyakov Y (2022) Rhizosphere bacteriome structure and functions. Nat Commun 13:836. https://doi.org/10.1038/s41467-022-28448-9

Article  PubMed  PubMed Central  CAS  Google Scholar 

Liu J, Sui Y, Yu Z et al (2014) High throughput sequencing analysis of biogeographical distribution of bacterial communities in the black soils of northeast China. Soil Biol Biochem 70:113–122. https://doi.org/10.1016/j.soilbio.2013.12.014

Article  CAS  Google Scholar 

Lu T, Ke M, Peijnenburg WJGM et al (2018) Investigation of Rhizospheric Microbial communities in Wheat, Barley, and two Rice varieties at the Seedling Stage. J Agric Food Chem 66:2645–2653. https://doi.org/10.1021/acs.jafc.7b06155

Article  PubMed  CAS  Google Scholar 

Lundberg DS, Lebeis SL, Paredes SH et al (2012) Defining the core Arabidopsis thaliana root microbiome. Nature 488:86–90. https://doi.org/10.1038/nature11237

Article  PubMed  PubMed Central  CAS  Google Scholar 

Mahanta CL, Kalita D (2020) Eggplant. Nutritional composition and antioxidant properties of fruits and vegetables. Elsevier, pp 273–287

Mallick H, Rahnavard A, McIver LJ (2020) MaAsLin 2: Multivariable Association in Population-scale Meta-omics studies. R/Bioconductor package. ht

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