The root microbiome: techniques for exploration and agricultural applications
Abstract
Standfirst
With an ever-growing global population, the pursuit of sustainable agriculture has become paramount. What if the solution lies right beneath our feet? Enter the root microbiome, the hidden hero poised to revolutionize agriculture and bring us closer to a greener future.
References
- 1. . Crop microbiome and sustainable agriculture. Nat. Rev. Microbiol. 18, 601–602 (2020).
- 2. Reaping economic and environmental benefits from sustainable land management. ELD Initiative Bonn, Germany (2015). https://www.eld-initiative.org/fileadmin/pdf/ELD-pm-report_05_web_300dpi.pdf
- 3. . The root microbiome: community assembly and its contributions to plant fitness. J. Integr. Plant Biol. 64(2), 230–243 (2022).
- 4. . Enhancing micronutrient uptake and yield of wheat through bacterial PGPR consortia. Soil Sci, Plant Nutr. 58(5), 573–582 (2012).
- 5. Microbial consortia: An engineering tool to suppress clubroot of Chinese cabbage by changing the rhizosphere bacterial community composition. Biology (Basel). 11(6), 918 (2022).
- 6. . Microorganisms and climate change: terrestrial feedbacks and mitigation options. Nat. Rev. Microbiol. 8, 779–790 (2010).
- 7. . Plant growth regulators; a sustainable approach to combat pesticide toxicity. 3 Biotech. 10(11), 466 (2020).
- 8. . Phosphate starvation triggers distinct alterations of genome expression in Arabidopsis roots and leaves. Plant Physiol. 132(3), 1260–1271 (2003).
- 9. . Metablic adaptations of phosphate-starved plants. Plant Physiol. 156(3), 1006–1015 (2011).
- 10. . The impact of phosphorus on plant immunity. Plant Cell Physiol. 24(62), 582–589 (2021).
- 11. . Structure and ecological function of the soil microbiome affective plant-soil feedbacks in the presence of soil-borne pathogen. Environ. Microbiol. 22(2), 660–676 (2020).
- 12. The effects of soil phosphorus content on plant microbiota are driven by the plant phosphate starvation response. PLOS Biol. 17(11), e3000534 (2019).
- 13. . The impact of microbes in plant immunity and priming induced inheritance: a sustainable approach for crop protection. Plant Stress 4, 100072 (2022).
- 14. . Plant immunity: danger perception and signaling. Cell 181(5), 978–989 (2020).
- 15. . Effects of abiotic stress on soil microbiome. Int. J. Mol. Sci. 22(16), 93036 (2021).
- 16. . Causes and consequences of a conserved bacterial root microbiome response to drought stress. Curr. Opin. Microbiol. 49, 1–6 (2019).
- 17. . Microbiome-mediated stress resistance in plants. Trends Plant Sci. 25(8), 733–743 (2020).
- 18. . Interactions between plants and soil shaping the root microbiome under abiotic stress. Biochem. J. 476(19), 2705–2724 (2019).
- 19. Prolonged drought imparts lasting compositional changes to the rice root microbiome. Nat Plants. 7(8), 1065–1077 (2021).
- 20. . Effect of a fungus, Hypoxylon spp., on endophytes in the roots of asparagus. FES Microbiol. Lett. 366(16), fnz207 (2019).
- 21. Root-secreted coumarins and the microbiota interact to improve iron nutrition in Arabidopsis. Cell Host Microb. 28(6), 825–837 (2020).
- 22. NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice. Nat. Biotech. 37, 676–684 (2019).
- 23. . Specific modulation of the root immune system by a community of commensal bacteria. Proc. Natl. Acad. Sci. 118(16), e2100678118 (2021).
- 24. . Pathogen resistance may be the principal evolutionary advantage provided by the microbiome. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 375(1808), 20190592 (2020).
- 25. . Targeted plant hologenome editing for plant trait enhancement. New Phytol. 229(2), 1067–1077 (2021).
- 26. . Root-associated microorganisms reprogram plant life history along the growth-stress resistance tradeoff. ISME J. 13, 3093–3101 (2019).
- 27. . Natural soil microbes later flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative. Ecol. Lett. 17(6), 717–726 (2014).
- 28. . Effectiveness of plant beneficial microbes: overview of the methodological approaches for the assessment of root colonization and persistence. Front. Plant. Sci. 11, 6 (2020).
- 29. . The role of synthetic microbial communities (SynCom) in sustainable agriculture. Front. Agron. 4, 896307 (2022).
- 30. . High-resolution phenotyping of sorghum genotypic and phenotypic responses to low nitrogen and synthetic microbial communities. Plant Cell Environ. 44(5), 1611–1626 (2021).
- 31. . Disruption of Firmicutes and Actinobacteria abundance in tomato rhizosphere causes the incidence of bacterial wilt disease. ISME J. 15, 330–347 (2021).
- 32. . Native root-associated bacteria rescue a plant from a sudden-wilt disease that emerged during continuous cropping. Proc. Natl. Acad. Sci. 112(36), E5013–E5020 (2015).
- 33. Functional assembly of root-associated microbial consortia improves nutrient efficiency and yield in soybean. J. Integr. Plant Biol. 63(6), 1021–1035 (2021).
- 34. . Metagenomics: a tool for exploring key microbiome with the potentials for improving sustainable agriculture. Front. Sustain. Food Syst. 6, 886987 (2022).
- 35. . Tool and techniques study to plant microbiome current understanding and future needs: an overview. Commun. Integr. Biol. 15(1), 209–225 (2022).
- 36. . Chemical and biological research of Clematis medicinal resources. In: Medicinal Plants. Hao DCGu XJXiao PG (Eds). Woodhead Publishing, Cambridge, UK, 341–371 (2015).
- 37. . Genomic insights into plant growth promoting rhizobia capable of enhancing soybean germination under drought stress. BMC Microbiol. 19, 159 (2019).
- 38. . Shotgun metagenomic sequencing data of sunflower rhizosphere microbial community in South Africa. Data Br. 31, 105831 (2020).
- 39. Soil pH is the primary factor driving the distribution and function of microorganisms in farmland soils in northeastern China. Ann. Microbiol. 69, 1461–1473 (2019).
- 40. Metagenomics: tools and insights for analyzing next-generation sequencing data derived from biodiversity studies. Bioinform. Biol. Insights 9, 75–88 (2015).
- 41. . Coming of age: ten years of next-generation sequencing technologies. Nat. Rev. Gen. 17, 333–351 (2016).
- 42. . Profiling bacterial communities by MinION sequencing of ribosomal operons. Microbiome 5, 116 (2017).
- 43. Evluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis. Nat. Commun. 6(10), 5029 (2019).
- 44. Targeting the 16S rRNA gene for bacterial identification in complex mixed samples; comparative evaluation of second (Illumina) and third (Oxford Nanopore Technologies) generation sequencing technologies. Int. J. Mol. Sci. 21(1), 298 (2020).
- 45. . Increasing the power of interpretation for soil metaproteomics data. Microbiome 9, 195 (2021).
- 46. Soil metaproteomics – comparative evaluation of protein extraction protocols. Soil. Biol. Biochem. 54, 14–24 (2012).
- 47. A two-step database search method improves sensitivity in peptide sequence matches for metaproteomics and proteogenomics studies. Proteomics. 13(8), 1352–1357 (2013).
- 48. . Metaproteomics to unravel major microbial players in leaf litter and soil environments: challenges and perspectives. Proteomics. 13(18–19), 2895–2909 (2013).
- 49. . Comparative metaproteomic analysis on consecutively Rehmannia glutinosa-monocultured rhizosphere soil. PLOS One 6(5), e20611 (2011).
- 50. Response of microbial communities and their metabolic functions to drying-rewetting stress in a temperature forest soil. Microorganisms. 7(5), 129 (2019).
- 51. Community proteogenomics reveals the systemic impact of phosphorus availability on microbial functions in tropical soil. Nat. Ecol. Evol. 2, 499–509 (2018).
- 52. Metaproteomic analysis of ratoon sugarcane rhizospheric soil. BMC Microbiol. 13, 135 (2013).
- 53. Comparing DNA, RNA and protein levels for measuring microbial dynamics in soil microcosms amended with nitrogen fertilizer. Sci. Rep. 9, 17630 (2019).
- 54. Community proteomics of a natural microbial biofilm. Science 308(5730), 1915–1920 (2005).
- 55. Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes. Nature 521(7551), 208–212 (2015).
- 56. The active microbial diversity drives ecosystem multifunctionality and is physiologically related to carbon availability in Mediterranean semi-arid soil. Mol. Ecol. 25(18), 4660–4673 (2016).
- 57. Comparative metatranscriptomics reveals kingdom level changes in the rhizosphere microbiome of plants. ISME J. 7, 2248–2258 (2013).
- 58. . Metatranscriptomic analysis of artic peat soil microbiota. AEM. 80(18), 5761–5772 (2014).
- 59. . Bias in RNA-seq library preparation: current challenges and solutions. Biomed. Res. Int. 2021, 6647597 (2021).
- 60. Microbial community gene expression in ocean surface waters. Proc. Natl. Acad. Sci. 105(10), 3805–3810 (2008).
- 61. Validation of two ribosomal RNA removal methods for microbial metatranscriptomics. Nat. Methods 7, 807–812 (2010).
- 62. . Development and quantitative analyses of a microbial universal rRNA-subtraction protocol for microbial metatranscriptomics. ISME J. 4(7), 896–907 (2010).
- 63. . Targeted metatranscriptomics of soil microbial communities with stable isotope probing. In: Methods in Molecular Biology. Dumont MGGarcía MH (Eds). Humana, NY, USA, 163–174 (2019).
- 64. . Application of metatranscriptomics to soil environments. J. Microbiol. Methods 91(2), 246–251 (2012).
- 65. . Improved purification and PCR amplification of DNA from environmental samples. FEMS Microbiol. Lett. 272(2), 269–275 (2007).
- 66. . Degradation of RNA in bacteria: comparison of mRNA and stable RNA. Nucleic Acids Res. 34(2), 659–666 (2006).
- 67. . Metatranscriptomics and nitrogen fixation from the rhizoplane of maize plantlets inoculated with a group of PGPRs. Syst. Appl. Microbiol. 42(4), 517–525 (2019).
- 68. . Microbiome applications from lab to field: facing complexity. Trends Plant Sci. 24(3), 194–198 (2019).
- 69. . A synthetic community system for probing microbial interactions driven by exometabolites. mSystems 2(6), e00129–e00117 (2017).
- 70. . Dissection of plant microbiota and plant–microbiome interactions. J. Microbiol. 59, 281–291 (2021).
- 71. . New frontiers in agriculture productivity: optimised microbial inoculants and in situ microbiome engineering. Biotechnol. Adv. 37, 107371 (2019).
- 72. . From microbiome to traits: designing synthetic microbial communities for improved crop resiliency. Front. Plant Sci. 11 (2020).