Metagenomic Insights into Rhizospheric Microbiome Profiling in Lentil Cultivars Unveils Differential Microbial Nitrogen and Phosphorus Metabolism under Rice-Fallow Ecology

Pramanik, Krishnendu; Das, Arpita; Banerjee, Joydeep; Das, Ashish; Chatterjee, Shayree; Sharma, Rishu; Kumar, Shiv; Gupta, Sanjeev

doi:10.3390/ijms21238895

Cited by 18 publications

(12 citation statements)

References 96 publications

(117 reference statements)

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“…(2019) , the plant’s growth may have resulted in a decrease in Chlorobiota in the rhizosphere, indicating healthy soil. The upsurge in Planctomycetota in the lentil rhizosphere is in accordance to earlier finding ( Pramanik et al., 2020 ), implying that specific root exudates are involved ( Qiao et al., 2017 ). The role of the rhizospheric microflora in plant growth is crucial.…”

Section: Discussionsupporting

confidence: 91%

Non-rhizobial nodule endophytes improve nodulation, change root exudation pattern and promote the growth of lentil, for prospective application in fallow soil

et al. 2023

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Non-rhizobial endophytes (NREs) are active colonizers inhabiting the root nodules. Though their active role in the lentil agroecosystem is not well defined, here we observed that these NREs might promote the growth of lentils, modulate rhizospheric community structure and could be used as promising organisms for optimal use of rice fallow soil. NREs from root nodules of lentils were isolated and examined for plant growth-promoting traits, exopolysaccharide (EPS) and biofilm production, root metabolites, and the presence of nifH and nifK elements. The greenhouse experiment with the chosen NREs, i.e., Serratia plymuthica 33GS and Serratia sp. R6 significantly increased the germination rate, vigour index, development of nodules (in non-sterile soil) and fresh weight of nodules (33GS 94%, R6 61% growth) and length of the shoot (33GS 86%, R6 51.16%) as well as chlorophyll levels when compared to the uninoculated control. Scanning Electron Microscopy (SEM) revealed that both isolates could successfully colonize the roots and elicit root hair growth. The inoculation of the NREs resulted in specific changes in root exudation patterns. The plants with 33GS and R6 treatment significantly stimulated the exudation of triterpenes, fatty acids, and their methyl esters in comparison to the uninoculated plants, altering the rhizospheric microbial community structure. Proteobacteria dominated the rhizospheric microbiota in all the treatments. Treatment with 33GS or R6 also enhanced the relative abundance of other favourable microbes, including Rhizobium, Mesorhizobium, and Bradyrhizobium. The correlation network analysis of relative abundances resulted in numerous bacterial taxa, which were in cooperation with each other, having a possible role in plant growth promotion. The results indicate the significant role of NREs as plant growth promoters, which also includes their role in root exudation patterns, enhancement of soil nutrient status and modulation of rhizospheric microbiota, suggesting their prospects in sustainable, and bio-based agriculture.

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Section: Discussionsupporting

confidence: 91%

Non-rhizobial nodule endophytes improve nodulation, change root exudation pattern and promote the growth of lentil, for prospective application in fallow soil

et al. 2023

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“…Bulk and rhizosphere soil contain an array of microbes including bacteria, fungi, algae, protozoa, and archaea (Msimbira and Smith, 2020) with great influence on plant health and nutrient cycling. However, the proper functioning of soil microbial communities depends on many factors including the availability of nutrients, temperature, water, soil structure, pH, and host genotypes and their secreted root exudates (Zgadzaj et al, 2016;Li et al, 2017;Pramanik et al, 2020;Vaidya and Stinchcombe, 2020). An understanding of endophytic or epiphytic soilmicrobe interactions with host roots is of great importance because of their potential to promote plant growth in various ways through enhanced nutrient, mineral and water use efficiency, increased production of phytohormones, induced biotic and abiotic stress tolerance, and minimized toxicity of contaminants (Bacon and White, 2016;Kumar et al, 2017;Harman and Uphoff, 2019;Bhattacharyya and Furtak, 2022).…”

Section: Introductionmentioning

confidence: 99%

Microbiome analysis revealed distinct microbial communities occupying different sized nodules in field-grown peanut

Hossain

DeLaune²,

Gentry

2023

Front. Microbiol.

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Legume nodulation is the powerhouse of biological nitrogen fixation (BNF) where host-specific rhizobia dominate the nodule microbiome. However, other rhizobial or non-rhizobial inhabitants can also colonize legume nodules, and it is unclear how these bacteria interact, compete, or combinedly function in the nodule microbiome. Under such context, to test this hypothesis, we conducted 16S-rRNA based nodule microbiome sequencing to characterize microbial communities in two distinct sized nodules from field-grown peanuts inoculated with a commercial inoculum. We found that microbial communities diverged drastically in the two types of peanut nodules (big and small). Core microbial analysis revealed that the big nodules were inhabited by Bradyrhizobium, which dominated composition (>99%) throughout the plant life cycle. Surprisingly, we observed that in addition to Bradyrhizobium, the small nodules harbored a diverse set of bacteria (~31%) that were not present in big nodules. Notably, these initially less dominant bacteria gradually dominated in small nodules during the later plant growth phases, which suggested that native microbial communities competed with the commercial inoculum in the small nodules only. Conversely, negligible or no competition was observed in the big nodules. Based on the prediction of KEGG pathway analysis for N and P cycling genes and the presence of diverse genera in the small nodules, we foresee great potential of future studies of these microbial communities which may be crucial for peanut growth and development and/or protecting host plants from various biotic and abiotic stresses.

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“…And (3) Identify the abundance of microbes 1.Bowtie 2 v2.2.7 2.MEGAHIT v1.1.3 3.Prodigal v2.6.3 4.MMseqs2 Linclust kaiju v1.7.3 Novel microbial species with zinc mobilizing potential were identified as Massilia and Pseudomonas species, which may have a functional module to accelerate soil zinc mobilization. Around 30 novel bacteria were isolated using high throughput targeted culturomics Involved in zinc mobilization in the given environment and their role in altering the concentration of grain zinc among the cultivars eggNOG-Mapper v2.0.1 These isolates having strong potential to increase the availability of Zn in soil could be used as a synthetic community to improve the nutrition and growth of cereal plants 2 [ 107 ] Legumes To analyze the rhizospheric microbiota assembly of two lentil cultivars under the effect of rice fallow ecology to identify the diversity of the microbial population 1.WINRHIZO software package 2.MeV tool 3.Parallel-metatool The two cultivars Farmer-2 and Moitree show cased insignificant differences in the diversity and role of microbiomes concerning Nitrogen metabolism in their rhizosphere 3 [ 108 ] Legumes To determine the effect of strigolactones on the recruitment of microbes to the rhizosphere 1.LefSe software 2. Mothur software Altering the strigolactone signaling and biosynthesis pathway alters the rhizosphere bacteria community 4 [ 109 ] Wheat and chickpea To understand the microbiome, present in the detritus sphere and the effects it shows due to agricultural management that involves soil tillage and crop rotations 1.…”

Section: Introductionmentioning

confidence: 99%

Analysis and Interpretation of metagenomics data: an approach

et al. 2022

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Advances in next-generation sequencing technologies have accelerated the momentum of metagenomic studies, which is increasing yearly. The metagenomics field is one of the versatile applications in microbiology, where any interaction in the environment involving microorganisms can be the topic of study. Due to this versatility, the number of applications of this omics technology reached its horizons. Agriculture is a crucial sector involving crop plants and microorganisms interacting together. Hence, studying these interactions through the lenses of metagenomics would completely disclose a new meaning to crop health and development. The rhizosphere is an essential reservoir of the microbial community for agricultural soil. Hence, we focus on the R&D of metagenomic studies on the rhizosphere of crops such as rice, wheat, legumes, chickpea, and sorghum. These recent developments are impossible without the continuous advancement seen in the next-generation sequencing platforms; thus, a brief introduction and analysis of the available sequencing platforms are presented here to have a clear picture of the workflow. Concluding the topic is the discussion about different pipelines applied to analyze data produced by sequencing techniques and have a significant role in interpreting the outcome of a particular experiment. A plethora of different software and tools are incorporated in the automated pipelines or individually available to perform manual metagenomic analysis. Here we describe 8–10 advanced, efficient pipelines used for analysis that explain their respective workflows to simplify the whole analysis process.

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Metagenomic Insights into Rhizospheric Microbiome Profiling in Lentil Cultivars Unveils Differential Microbial Nitrogen and Phosphorus Metabolism under Rice-Fallow Ecology

Cited by 18 publications

References 96 publications

Non-rhizobial nodule endophytes improve nodulation, change root exudation pattern and promote the growth of lentil, for prospective application in fallow soil

Non-rhizobial nodule endophytes improve nodulation, change root exudation pattern and promote the growth of lentil, for prospective application in fallow soil

Microbiome analysis revealed distinct microbial communities occupying different sized nodules in field-grown peanut

Analysis and Interpretation of metagenomics data: an approach

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