Targeted metagenome sequencing reveals the abundance of Planctomycetes and Bacteroidetes in the rhizosphere of pomegranate

Ravinath, Renuka; Das, Anupam; Usha, Talambedu; Ramesh, N.; Middha, Sushil Kumar

doi:10.1007/s00203-022-03100-8

Cited by 10 publications

(10 citation statements)

References 41 publications

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“…The taxonomic profiling results demonstrated that the rhizosphere microbiota of the two grapevine varieties shared the same 10 dominant phyla ( Figure 1D ). All of the identified phyla have been previously reported and are known to predominate grapevine rhizospheres ( Zhang et al, 2019 ), as well as in those of peanut ( Xu et al, 2020 ), pomegranate ( Ravinath et al, 2022 ), barley ( Bulgarelli et al, 2015 ), and Arabidopsis thaliana ( Kielak et al, 2016 ). Nevertheless, the relative abundances of these phyla were distinct between 101-14 and 5BB ( Figures 1E , F ; Supplementary Table 2 ).…”

Section: Discussionmentioning

confidence: 99%

Comparative metagenomic analysis reveals rhizosphere microbial community composition and functions help protect grapevines against salt stress

Wang

et al. 2023

Front. Microbiol.

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IntroductionSoil salinization is a serious abiotic stress for grapevines. The rhizosphere microbiota of plants can help counter the negative effects caused by salt stress, but the distinction between rhizosphere microbes of salt-tolerant and salt-sensitive varieties remains unclear.MethodsThis study employed metagenomic sequencing to explore the rhizosphere microbial community of grapevine rootstocks 101-14 (salt tolerant) and 5BB (salt sensitive) with or without salt stress.Results and DiscussionCompared to the control (treated with ddH2O), salt stress induced greater changes in the rhizosphere microbiota of 101-14 than in that of 5BB. The relative abundances of more plant growth-promoting bacteria, including Planctomycetes, Bacteroidetes, Verrucomicrobia, Cyanobacteria, Gemmatimonadetes, Chloroflexi, and Firmicutes, were increased in 101-14 under salt stress, whereas only the relative abundances of four phyla (Actinobacteria, Gemmatimonadetes, Chloroflexi, and Cyanobacteria) were increased in 5BB under salt stress while those of three phyla (Acidobacteria, Verrucomicrobia, and Firmicutes) were depleted. The differentially enriched functions (KEGG level 2) in 101-14 were mainly associated with pathways related to cell motility; folding, sorting, and degradation functions; glycan biosynthesis and metabolism; xenobiotics biodegradation and metabolism; and metabolism of cofactors and vitamins, whereas only the translation function was differentially enriched in 5BB. Under salt stress, the rhizosphere microbiota functions of 101-14 and 5BB differed greatly, especially pathways related to metabolism. Further analysis revealed that pathways associated with sulfur and glutathione metabolism as well as bacterial chemotaxis were uniquely enriched in 101-14 under salt stress and therefore might play vital roles in the mitigation of salt stress on grapevines. In addition, the abundance of various sulfur cycle-related genes, including genes involved in assimilatory sulfate reduction (cysNC, cysQ, sat, and sir), sulfur reduction (fsr), SOX systems (soxB), sulfur oxidation (sqr), organic sulfur transformation (tpa, mdh, gdh, and betC), increased significantly in 101-14 after treatment with NaCl; these genes might mitigate the harmful effects of salt on grapevine. In short, the study findings indicate that both the composition and functions of the rhizosphere microbial community contribute to the enhanced tolerance of some grapevines to salt stress.

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Section: Discussionmentioning

confidence: 99%

Comparative metagenomic analysis reveals rhizosphere microbial community composition and functions help protect grapevines against salt stress

Wang

et al. 2023

Front. Microbiol.

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“…A limitation to consider here is the amplicon-based prediction being less capable of strain-level identification. In a separate study, the microbiome of the infected soil samples the collection site have been explored extensively using the shotgun metagenomics approach 29 . This method offers improved sensitivity, resolution, and detailed characterization of microbial communities compared to traditional methods 49 , 50 .…”

Section: Resultsmentioning

confidence: 99%

“…As a control HSC, sequence data of a healthy plant sample was used from a separate study (BioProject PRJNA540834; SRR9003394). The sample was collected from the same orchard under identical conditions 29 . Whole metagenome analysis of the samples ISI and ASI has been performed and published in a separate study and the presence of Fusarium oxysporum has been ascertained followed by further assessment of its adaptations 30 .…”

Section: Methodsmentioning

confidence: 99%

Improved species level bacterial characterization from rhizosphere soil of wilt infected Punica granatum

Das,

Sarangi,

Ravinath

et al. 2023

Sci Rep

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Pomegranate crops are prone to wilt complex disease, which is known to severely hamper the crop yield. There have been limited studies that have explored bacteria–plant–host associations in wilt complex disease affecting pomegranate crops. In the present study, wilt infected rhizosphere soil samples (ISI, ASI) in pomegranate were studied in comparison to a healthy control (HSC). The 16S metagenomics sequencing approach using the MinION platform was employed for screening of bacterial communities and predictive functional pathways. Altered physicochemical properties in the soil samples were recorded showing a comparatively acidic pH in the ISI (6.35) and ASI (6.63) soil samples to the HSC soil (7.66), along with higher electrical conductivity in the ISI (139.5 µS/cm), ASI soil (180 µS/cm), HSC soil sample (123.33 µS/cm). While concentration of micronutrients such as Cl and B were significantly higher in the ISI and ASI soil as compared to the HSC, Cu and Zn were significantly higher in the ASI soil. The effectiveness and accuracy of 16S metagenomics studies in identifying beneficial and pathogenic bacterial communities in multi-pathogen–host systems depend on the completeness and consistency of the available 16S rRNA sequence repositories. Enhancing these repositories could significantly improve the exploratory potential of such studies. Thus, multiple 16S rRNA data repositories (RDP, GTDB, EzBioCloud, SILVA, and GreenGenes) were benchmarked, and the findings indicated that SILVA yields the most reliable matches. Consequently, SILVA was chosen for further analysis at the species level. Relative abundance estimates of bacterial species showed variations of growth promoting bacteria, namely, Staphylococcus epidermidis, Bacillus subtilis, Bacillus megatarium, Pseudomonas aeruginosa, Pseudomonas putida, Pseudomonas stutzeri and Micrococcus luteus. Functional profiling predictions employing PICRUSt2 revealed a number of enriched pathways such as transporter protein families involved in signalling and cellular processes, iron complex transport system substrate binding protein, peptidoglycan biosynthesis II (staphylococci) and TCA cycle VII (acetate-producers). In line with past reports, results suggest that an acidic pH along with the bioavailability of micronutrients such as Fe and Mn could be facilitating the prevalence and virulence of Fusarium oxysporum, a known causative pathogen, against the host and beneficial bacterial communities. This study identifies bacterial communities taking into account the physicochemical and other abiotic soil parameters in wilt-affected pomegranate crops. The insights obtained could be instrumental in developing effective management strategies to enhance crop yield and mitigate the impact of wilt complex disease on pomegranate crops.

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“…Metagenomic data indicated the ubiquity of Planctomycetes in diverse ecosystems (Wiegand et al, 2018), encompassing soil (Stackebrandt et al, 1993; Wang et al, 2002; Buckley et al, 2006; Ivanova et al, 2016;), plant rhizosphere (Lei et al, 2023; Ravinath et al, 2022), seawater (Schlesner, 1994; Wiegand et al, 2020), freshwater (Schlesner, 1994; Wang et al, 2002; Dedysh et al, 2020), chlorinated water (Aghnatios and Drancourt, 2015), the human gastrointestinal tract (Cayrou et al, 2013), and very frequently in association with several algae (Bengtsson and Øvreås, 2010; Lage and Bondoso, 2011, 2012; Wiegand et al, 2020). However, the cultivation of Planctomycetes in pure axenic cultures has proven to be challenging, primarily attributed to their recalcitrance to grow on synthetic media and their inherently slow growth kinetics (Kaboré et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Specificities and commonalities of the Planctomycetes plasmidome

Coronel,

Devos,

Garcillán-Barcia

2024

Preprint

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Although plasmids play a crucial role in antibiotic resistance and contemporary biotechnology, our comprehension of their natural ecological dynamics remains restricted to a few bacterial groups. Planctomycetes is a bacterial phylum with unusual molecular and cellular biology for which little is known about its plasmidome. This study provides the first comprehensive description of the diversity of the endogenous plasmids found in Planctomycetes, which may be used as starting points to generate different genetic tools for research on this phylum. Plasmids from Planctomycetes encode a wide variety of biological functions, although for a large portion of the encoded genes a function cannot be assigned, which is usual in Planctomycetes. They seemed to have largely coevolved with the genome of their hosts, with which they share many homologs. We also detected recent transfer events of insertion sequences between co-habiting chromosomes and plasmids. 60% of the plasmid genes are distantly related to chromosomally-encoded genes and 40% have homologs in plasmids from other bacterial groups, while 36% of the proteins composing the planctomycetal plasmidome are exclusive. Most planctomycetal plasmids encode a replication initiation protein of the RPA family in the proximity of a putative iteron-containing replication origin, as well as active type I partition systems. One conjugative and three mobilizable plasmids were identified, suggesting horizontal gene transfer via conjugation in this phylum.

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Targeted metagenome sequencing reveals the abundance of Planctomycetes and Bacteroidetes in the rhizosphere of pomegranate

Cited by 10 publications

References 41 publications

Comparative metagenomic analysis reveals rhizosphere microbial community composition and functions help protect grapevines against salt stress

Comparative metagenomic analysis reveals rhizosphere microbial community composition and functions help protect grapevines against salt stress

Improved species level bacterial characterization from rhizosphere soil of wilt infected Punica granatum

Specificities and commonalities of the Planctomycetes plasmidome

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