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Core Microbiome


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Nerium indicum Pontibacter Raichand et al. (2011) Fritillaria thunbergii Proteobacteria Acidobacteria Actinobacteria Bacteroidetes Shi et al. (2011) Astragalus membranaceus Geodermatophilus obscurus Zhang et al. (2011) Phytolacca acinose Aspergillus fumigatus Guo et al. (2010) Agathosma betulina Cryptococcus laurentii Cloete et al. (2010) Ocimum sanctum, Coleus forskohlii, Catharanthus roseus, Aloe vera Azospirillum, Azotobacter, Pseudomonas Karthikeyan et al. (2008) Annona squamosa, Eclipta alba, Cassia auriculata Bacillus, Pseudomonas, Enterobacter, Corynebacterium, Micrococcus, Serratia Tamilarasi et al. (2008)

      3.4 Microbe-Mediated Mitigation of Abiotic Stresses

      Crop plants need to manage external environment pressure exerted by edaphic factors with intrinsic biological mechanisms, as a result of which growth, development, and productivity fail. Microorganisms are the natural populations of complex environments that have various metabolic abilities to mitigate abiotic stresses. Plant–microbe interaction comprises a complex mechanism within the plant cellular system that modulates local and systemic mechanisms in plants to offer defense under adverse conditions (Meena et al. 2017). Many microbes have genetic and metabolic abilities to mitigate abiotic stresses in plants (Gopalakrishnan et al. 2015). The most important rhizosphere inhabitants comprise Pseudomonas (Sorty et al. 2016), Azotobacter (Sahoo et al. 2014), Pantoea (Sorty et al. 2016), Enterobacter (Nadeem et al. 2014), Burkholderia (Ait Barka et al. 2006), Trichoderma (Ahmad et al. 2015), and cyanobacteria (Singh et al. 2005), which have been used for plant growth to alleviate multiple abiotic stresses.

      A sequence of plant-protective mechanisms was acquired during evolution to combat adverse environmental situations (Yolcu et al. 2012). These processes cause re-programming in the cells to enable repetitive bio-physico-chemical processes regardless of the external situation. Most of the time, plants tend to decrease the burden of environmental stresses with the help of the microbiome residing in the soil (Ngumbi and Kloepper 2016). The application of phytohormones supplementation has been reported to improve plant growth and development as well as metabolic activity under stressful conditions. Root microbes are very important for managing target metabolism and induced host tolerance against abiotic stress in medicinal plants (Egamberdieva et al. 2017).

      3.5 Plant Root Exudates and the Recruitment of Beneficial Microbes

      Root exudates serve as indicators that start the symbiotic relation between arbuscular mycorrhizal fungi and rhizobia. Root exudates contain ions such as oxygen, water, an inorganic acid, and (H+) but mainly consist of carbon compounds (Bais et al. 2004). Lower-weight organic compounds (amino acid, organic acid, phenols, sugars, secondary metabolites) and high-weight organic compounds (proteins, polysaccharides) are present in the soil (Badri et al. 2009). Microorganisms established a sensory system called chemotaxis, which guides these components secreted from roots to deliver essential nutrition and energy for survival under stressful conditions. Moreover, Gao et al. (2011) observed that plants might enhance the degradation by the exudation of enzymes, such as phenol oxidase, laccase, and peroxidase through the root. As a result, the oxidation of various hydrocarbons degrades them into intermediate products. The combined application of arbuscular mycorrhizal fungi and septate endophyte was studied in 36 medicinal plant species. The level of abundance of arbuscular mycorrhizal fungi in the roots varied from 2.5% (Helianthus tuberosus) to 77.9% (Convallaria majalis) (Zubek and Błaszkowski 2009).

      3.5.1 Multi-omics Approaches Used to Mitigate Abiotic Stresses in Medicinal Plants

      3.5.1.1 Genomics

      An analytical database (http://metnetdb.org/mpmr_public/) regarding transcriptome and metabolic data for 14 medicinal plants are available for gene function. In this way, the possible microbial production of glycyrrhetinic acid was recorded. Yamazaki et al. (2013) reported the differential transcriptome analysis along with metabolic profiling, and identified candidate’s genes involved in the biosynthesis pathway of alkaloids and anthraquinones. Transcriptomics of glandular trichomes,