Abstract
Earlier plant growth promoting rhizo-bacteria (PGPRs) were isolated from the plants, by cultivation based techniques and the interaction was mostly thought to be bilateral. The routine bilateral study, with no information on the associated microbiome, could be one of the reasons for the limited success of PGPRs in the field conditions. Keeping in view the role of PGPRs in rhizo-bacteriome on the growth and production of plant, the present study was aimed at studying the diversity of the rhizo-bacteriome of saffron grown across three geographical locations namely Kashmir, Kishtwar and Bengaluru. Variation in the rhizo-bacteriome of saffron growing across 10 different sites from 3 geographical locations was studied using 16S rDNA amplicon metagenomic sequencing. 16 bacterial phyla, 261 genera and 73 bacterial species were cataloged from all the rhizosphere samples. Proteobacteria was a dominant phylum in all the rhizosphere samples. Rhizo-bacteriome of saffron grown in Kishtwar was found to be significantly different from the rhizo-bacteriome of saffron grown in Kashmir and Bengaluru. Interestingly, the rhizo-bacteriome of saffron grown in Bengaluru was very similar to the saffron grown in Kashmir, thereby indicating that the rhizo-bacteriome in saffron is “plant driven” as the corm sown in Bengaluru were from Kashmir. Despite variation in rhizo-bacteriome, core rhizo-bacteriome in saffron was identified that was represented by 53 genera and eight bacterial species belonging to 11 phyla irrespective of their geographical distribution. In addition, 21 PGPRs were reported for the first time from the saffron rhizosphere. The high yielding saffron field Wuyan was found to have the highest number of PGPRs; this indicates that the presence of PGPR is important for yield enhancement than diversity. The two PGPR Rhizobium leguminosarum and Luteibacter rhizovicinus were reported from all the locations except Kishtwar that had escaped isolation in our previous attempts using cultivation based techniques. It is being proposed instead of going for random isolation and screening for PGPRs from plant rhizosphere, an alternate strategy using metagenomic cataloging of the rhizo-bacteriome community and cultivation of the dominant PGPR should be undertaken. This strategy will help in the selection of dominant PGPRs, specific to the plant in question.
Highlights
IntroductionMicrobiomics is a fast-growing field in which collective genomes of microorganisms, of a given community (a microbiota) are investigated
Microbiomics is a fast-growing field in which collective genomes of microorganisms, of a given community are investigated
Ten rhizosphere samples were collected from 8 different saffron fields from Kashmir and 1 from Kishtwar (Jammu and Kashmir); and 1 from corms grown in pots at TransDisciplinary University, Bengaluru (Karnataka)
Summary
Microbiomics is a fast-growing field in which collective genomes of microorganisms, of a given community (a microbiota) are investigated. Earlier microbiome associated with different plants would be studied mostly using cultivation based techniques. It is a fact that not more than 1% of bacteria can be cultivated by routine cultivation and 99% remained uncultivated (Steen et al, 2019). In order to study microbiomes associated with any niche, cultivation independent technique metagenomics, complements the cultivation based techniques. Metagenomics has revolutionized the study of complex microbial communities, as it overcomes the limitation of cultivation based methods, as far as cataloging of bacteria present and functions performed by them, in any niche is concerned (Boughner and Singh, 2016; Alteio et al, 2020; Tas et al, 2021). Plant growth promotion by Plant growth promoting bacteria (PGPBs) has been reported in various plants such as in rice (Chauhan et al, 2019), wheat (Çakmakçı et al, 2017), maize (Zerrouk et al, 2019), tomato (Cordero et al, 2018), soya bean (De Gregorio et al, 2017) and saffron (Ambardar and Vakhlu, 2013; Ambardar, 2014; Ambardar et al, 2014, 2016; Kour et al, 2018; Magotra et al, 2021)
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