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

Effect of seed priming with polyethylene glycol, distilled water, and sorbitol on physical, chemical quality parameters, and nodule microbiota of lentil

The aim of this study was to investigate the effects of different seed priming solutions on physical and chemical quality parameters of lentils as well as nodule bacterial diversity before sowing. Therefore, lentil seeds were treated with polyethylene glycol (PEG 6000) (15%), sorbitol (6%), and distilled water, and none pretreated lentils (Lens culinaris) were used as control. The seeds were kept in these solutions for 24 h, then dried on toweling paper for 24 h, and used for the experiment. For nodule microbiota analysis, the plant root was divided into two equal parts, upper and lower, according to the root length and all nodules were collected from each region. According to the results, it was observed that emergence and flowering started late in the control compared to other seed priming treatments. Sorbitol application was found to provide advantages in terms of germination and seedling development. PEG and distilled water (DW) treatments showed an increase in total phenolic component activity; however, no significant change was observed in DPPH radical scavenging activity. Amplicon-based metagenomic analysis revealed that sorbitol and distilled water were the seed priming solutions altering the species diversity, especially Rhizobium sp. as the genus. In the comparison of samples taken from different parts of the root nodules, more Rhizobium sp. as a genus and Rhizobium leguminosarum as the species were found in the nodules collected from the top of the root. According to the overall results of lentil pod, lentil plant, and microbiota, sorbitol and DW can be considered to be a good priming solutions.

Exploring microbial diversity in the rhizosphere: a comprehensive review of metagenomic approaches and their applications

The rhizosphere, the soil region influenced by plant roots, represents a dynamic microenvironment where intricate interactions between plants and microorganisms shape soil health, nutrient cycling, and plant growth. Soil microorganisms are integral players in the transformation of materials, the dynamics of energy flows, and the intricate cycles of biogeochemistry. Considerable research has been dedicated to investigating the abundance, diversity, and intricacies of interactions among different microbes, as well as the relationships between plants and microbes present in the rhizosphere. Metagenomics, a powerful suite of techniques, has emerged as a transformative tool for dissecting the genetic repertoire of complex microbial communities inhabiting the rhizosphere. The review systematically navigates through various metagenomic approaches, ranging from shotgun metagenomics, enabling unbiased analysis of entire microbial genomes, to targeted sequencing of the 16S rRNA gene for taxonomic profiling. Each approach's strengths and limitations are critically evaluated, providing researchers with a nuanced understanding of their applicability in different research contexts. A central focus of the review lies in the practical applications of rhizosphere metagenomics in various fields including agriculture. By decoding the genomic content of rhizospheric microbes, researchers gain insights into their functional roles in nutrient acquisition, disease suppression, and overall plant health. The review also addresses the broader implications of metagenomic studies in advancing our understanding of microbial diversity and community dynamics in the rhizosphere. It serves as a comprehensive guide for researchers, agronomists, and policymakers, offering a roadmap for harnessing metagenomic approaches to unlock the full potential of the rhizosphere microbiome in promoting sustainable agriculture.

Exploring microbial worlds: a review of whole genome sequencing and its application in characterizing the microbial communities

The classical microbiology techniques have inherent limitations in unraveling the complexity of microbial communities, necessitating the pivotal role of sequencing in studying the diversity of microbial communities. Whole genome sequencing (WGS) enables researchers to uncover the metabolic capabilities of the microbial community, providing valuable insights into the microbiome. Herein, we present an overview of the rapid advancements achieved thus far in the use of WGS in microbiome research. There was an upsurge in publications, particularly in 2021 and 2022 with the United States, China, and India leading the metagenomics research landscape. The Illumina platform has emerged as the widely adopted sequencing technology, whereas a significant focus of metagenomics has been on understanding the relationship between the gut microbiome and human health where distinct bacterial species have been linked to various diseases. Additionally, studies have explored the impact of human activities on microbial communities, including the potential spread of pathogenic bacteria and antimicrobial resistance genes in different ecosystems. Furthermore, WGS is used in investigating the microbiome of various animal species and plant tissues such as the rhizosphere microbiome. Overall, this review reflects the importance of WGS in metagenomics studies and underscores its remarkable power in illuminating the variety and intricacy of the microbiome in different environments.

Disease spectrum and its molecular characterisation in the lentil production system of lower-Indo Gangetic plains

Lentil is a food legume grown in the Indo-Gangetic plains including lower Gangetic Bengal (LGB). Lentil productivity in this zone is severely impeded because of the prevalence of several biotic cues. Plausible reports regarding the status of disease scenario and the associated risk factors are missing. Therefore, judicious crop management strategies are lacking. An intensive survey of 267 farmers' fields was conducted over 3 years in major lentil-growing districts of LGB to evaluate the disease incidence and prevalence. Additional insights were generated, apprehending isolation and characterisation of associated pathogens through spore morphology and molecular markers as well as elucidating the role of biophysical factors in influencing disease development. Climate change has shifted the disease dimension of lentil and precipitated new disease complexes of great risk, which was reflected through geospatial mapping results in the present study. The prevalence of three major diseases, namely collar rot (Sclerotium rolfsii), lentil blight complex (LBC) incited by both Alternaria and Stemphylium, and lentil rust (Uromyces viciae-fabae), was ascertained through cultural and molecular studies and contextualised through pathogenicity appraisal. This study is the first to investigate the complex mixed infection of Alternaria alternata and Stemphylium botryosum, successfully isolating S. botyrosum in India, and confirming the pathogens through sequencing by using internal transcribed spacer (ITS) primers and Stemphylium-specific Glycerol-3-phosphate dehydrogenase 1 (gpd1) and gpd2 primers. Unlike late planting, early planting promoted collar rot infestation. LBC and rust incidence were magnified in late planting. Soil texture resulted in the spatial distribution of collar rot disease. The surveyed data also highlighted the potential role of resistant cultivars and cropping pattern intervention to ensure associational resistance towards addressing the disease bottleneck in lentil.

The 'microbiome counterattack': Insights on the soil and root-associated microbiome in diverse chickpea and lentil genotypes after an erratic rainfall event

Legumes maintain soil fertility thanks to their associated microbiota but are threatened by climate change that causes soil microbial community structural and functional modifications. The core microbiome associated with different chickpea and lentil genotypes was described after an unexpected climatic event. Results showed that chickpea and lentil bulk soil microbiomes varied significantly between two sampling time points, the first immediately after the rainfall and the second 2 weeks later. Rhizobia were associated with the soil of the more productive chickpea genotypes in terms of flower and fruit number. The root-associated bacteria and fungi were surveyed in lentil genotypes, considering that several parcels showed disease symptoms. The metabarcoding analysis revealed that reads related to fungal pathogens were significantly associated with one lentil genotype. A lentil core prokaryotic community common to all genotypes was identified as well as a genotype-specific one. A higher number of specific bacterial taxa and an enhanced tolerance to fungal diseases characterized a lentil landrace compared to the commercial varieties. This outcome supported the hypothesis that locally adapted landraces might have a high recruiting efficiency of beneficial soil microbes.

The Composition and Function of the Rhizosphere Bacterial Community of Paeonia lactiflora Varies with the Cultivar

The composition and diversity of the rhizosphere microbial community maintain the stability of the root microclimate, and several studies have focused on this aspect of rhizosphere microorganisms. However, how these communities vary with cultivars of a species is not completely understood. Paeonia lactiflora-a perennial herb species of the family Paeoniaceae-includes a wide variety of cultivars, with rich rhizosphere microbial resources. Hence, we studied the differences in rhizosphere bacterial communities associated with eight P. lactiflora cultivars. We noted that Actinobacteria, Proteobacteria, Acidobacteria, Bacteroidetes, Firmicutes, Verrucomicrobia, Planctomycetes and Chloroflexi were the dominant phyla associated with the cultivars. The composition of rhizosphere bacterial community of different cultivars was highly similar at taxonomic levels, but there were slightly differences in the relative abundance. LEfSe analysis showed that the cultivars "Sheng Tao Hua" and "Zi Lou Xian Jin" exhibited the most biomarkers. Differential ASV analysis revealed the maximum difference in ASV abundance between "Lian Tai" and "Zi Hong Zheng Hui", as well as between "Sheng Tao Hua" and "Tao Hua Fei Xue", and the maximum similarity between "Duo Ye Zi" and "Xue Feng". Co-occurrence network analysis revealed that rhizosphere bacteria in most cultivars maintain homeostasis by cooperation, wherein Actinobacteria and Proteobacteria played a vital role. In addition, microbial resources related to cultivars like bioremediation, organic degradation and resistance to diseases are found. This study revealed the structures of the rhizosphere bacterial communities associated with different cultivars of P. lactiflora and explored their stress resistance potential, which can be used to guide future agricultural practices.

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

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.

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

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.

Analysis and Interpretation of metagenomics data: an approach

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.

Treatment with atypical rhizobia, Pararhizobium giardinii and Ochrobactrum sp. modulate the rhizospheric bacterial community, and enhances Lens culinaris growth in fallow-soil

Diazotrophic nodule isolates are acknowledged promoters of plant growth and rhizospheric community. Consequently, in the lentil agroecosystem, inoculation of atypical rhizobial isolates could be a viable alternative to chemical fertilizers for fallow land usage optimization. The aim of this study is to evaluate and select the rhizobial isolates of lentil nodules with plant-growth-promoting (PGP) attributes and to elucidate their application in rice-fallow soil for determining the growth of lentils and its impact on the rhizospheric bacterial community. Lentil's nodule isolates were identified and screened for their PGP attributes, biofilm, exopolysaccharide (EPS) formation, and early plant growth promotion. The pot experiment with the selected atypical rhizobial isolates Pararhizobium giardinii (P1) and Ochrobactrum sp. (42S) significantly enhanced germination, vigour index, nodule formation (P1 60%, 42S 42% increase), nodule fresh weight, shoot length (65% P1 & 35% 42S), and chlorophyll content as compared to the uninoculated control treatment. The genes for nitrogen fixation nifH and nifK were detected in both isolates. Scanning Electron Microscopy (SEM) revealed successful root and nodule colonization by both isolates, while Transmission Electron Microscopy (TEM) displayed nitrogen-fixing zones within root nodules. Proteobacteria predominated in the lentil rhizosphere of all the treatments. Whereas, application of either P1 or 42S increased Rhizobium, Mesorhizobium, and Bradyrhizobium genra, thus positively modulating rhizospheric community structure. The correlation network analysis revealed an abundance of some interdependent bacterial genera with a possible role in overall plant growth. Functional genes for siderophore biosynthesis and ABC transporter were positively modulated by application of either P1 or 42S. This study showed the significant effect of P. giardinii P1 and Ochrobactrum sp. 42S of L. culinaris on lentil growth, improving fallowsoil health for optimum usage, and modulated rhizospheric community structure which strongly manifest prospects of low-cost, eco-friendly and sustainable biofertilizers.

Rhizospheric microorganisms: The gateway to a sustainable plant health

Plant health is essential for food security, and constitutes a major predictor to safe and sustainable food systems. Over 40% of the global crops' productions are lost to pests, insects, diseases, and weeds, while the routinely used chemical-based pesticides to manage the menace also have detrimental effects on the microbial communities and ecosystem functioning. The rhizosphere serves as the microbial seed bank where microorganisms transform organic and inorganic substances in the rhizosphere into accessible plant nutrients as plants harbor diverse microorganisms such as fungi, bacteria, nematodes, viruses, and protists among others. Although, the pathogenic microbes initiate diseases by infiltrating the protective microbial barrier and plants' natural defense systems in the rhizosphere. Whereas, the process is often circumvented by the beneficial microorganisms which antagonize the pathogens to instill disease resistance. The management of plant health through approaches focused on disease prevention is instrumental to attaining sustainable food security, and safety. Therefore, an in-depth understanding of the evolving and succession of root microbiomes in response to crop development as discussed in this review opens up new-fangled possibilities for reaping the profit of beneficial root–microbiomes' interactions toward attaining sustainable plant health.

Management of abiotic stresses by microbiome-based engineering of the rhizosphere

Abiotic stresses detrimentally affect both plant and soil health, threatening food security in an ever-increasing world population. Sustainable agriculture is necessary to augment crop yield with simultaneous management of stresses. Limitations of conventional bioinoculants has shifted the focus on more effective alternatives. With the realisation of the potential of rhizospheric microbiome engineering in enhancing plant's fitness under stresses, efforts have accelerated in this direction. Though still in its infancy, microbiome-based engineering has gained popularity because of its advantages over microbe-based approach. This review briefly presents major abiotic stresses afflicting arable land, followed by introduction to the conventional approach of microbe-based enhancement of plant attributes and stress mitigation with its inherent limitations. It then focusses on the significance of rhizospheric microbiome, and harnessing its potential by its strategic engineering for stress management. Further, success stories related to two major approaches of microbiome engineering (generation of synthetic microbial community/consortium, and host-mediated artificial selection) pertaining to stress management have been critically presented. Together with bringing forth the challenges associated with wide application of rhizospheric microbiome engineering in agriculture, the review proposes the adoption of combinatorial scheme for the same, bringing together ecological and reductionist approaches for improvised sustainable agricultural practices.

Assembly and potential transmission of the lens culinaris seed microbiome

Soil is an important source of bacteria and fungi for the plant, but seeds can also provide microbial inocula through heritable or stochastic assembly. Seed-associated microbial communities can potentially interact with the host plant through multiple generations. Here, we assessed the impact of two different soil types on the seed microbiome assembly of seven lentil (Lens culinaris) genotypes under environmentally controlled conditions and examined the vertical transmission of bacterial communities from seed to seed across two generations. Bulk soil microbiomes and seed microbiomes were characterized using high-throughput amplicon sequencing of the bacterial 16S rRNA gene. Our results revealed that bacterial communities in the two soils differed significantly and that bacterial communities associated with seeds were significantly impacted by genotype (15%) in one of the soils. Co-occurrence of amplicon sequence variants (ASVs) between generations suggests members of the genera Cutibacterium, Methylobacterium, Sphingomonas, Streptococcus, and Tepidimonas are transmitted and preserved in lentil genotypes irrespective of the soil in which they were grown. Increasing our knowledge of how microbial communities carried by seeds are assembled, transmitted, and preserved offers a promising way for future breeding programs to consider microbial communities when selecting for more resilient and productive cultivars.