Transcriptome modulation by endophyte drives rice seedlings response to Pb stress

The impact of Bisphenol A on the endophytic bacterial community and transcriptome of soybean seedlings

Bisphenol A (BPA) is widely acknowledged as an endocrine disruptor, and its toxicological effects have garnered considerable research interest. In this investigation, a soil pot experiment was conducted to examine the consequences of sustained BPA exposure on the growth of soybean seedlings, the transcriptome, and the endophytic bacterial community. We observed a substantial inhibition in soybean seedling growth. Transcriptome analysis showed that growth-related genes in both leaves and roots were markedly downregulated following BPA treatment. Intriguingly, BPA considerably increased the abundance and diversity of endophytic bacteria in leaves while suppressing beta diversity in roots. A significant association was identified between amplicon sequence variants and differentially expressed genes under BPA treatment in the leaves and roots. These findings illuminate the effects of continuous exposure to BPA on the transcriptome and endophyte of soybean seedlings, which may collectively impair soybean seedling growth, offering valuable insights into BPA toxicity in plants.

Transcriptome analysis unveils the functional effects of ectomycorrhizal fungal colonization on cadmium tolerance of willow saplings

Introduction

Ectomycorrhizal fungus (ECMF) could enhance plant tolerance to heavy metal toxicity by altering metal accumulation and protecting plants from oxidative injury. However, the molecular mechanisms underlying ECMF-mediated detoxification of cadmium (Cd) in willow sapling are not well known. This study aimed to unveil the roles of Cenococcum geophilum (CG) and Suillus luteus (SL) in regulating Cd toxicity tolerance in willow (Salix psammophila 'Huangpi1') saplings.

Methods

This study systematically evaluated physiological and biochemical parameters in the leaf and root tissues of 18 willow saplings, while concurrently conducting transcriptomic analysis of the roots under Cd stress. The specific treatments were labeled as follows: NF (no ECMF inoculation and no Cd addition), CG (CG colonization only), SL (SL colonization only), NF+Cd (no ECMF inoculation with 100 μM Cd addition), CG+Cd (CG colonization with 100 μM Cd addition), and SL+Cd (SL colonization with 100 μM Cd addition).

Results

The results showed the growth, photosynthesis, antioxidant system and transcriptome of 2-month-old willow saplings responded differently to ECMFs colonization under Cd stress. S. luteus markedly increased the aerial parts biomass, while C. geophilum significantly enhanced the root property indices of willow saplings under Cd stress. The highest number of differentially expressed genes (DEGs) was observed in the comparison between CG+Cd (CG colonization with 100 μM Cd addition) and NF+Cd (no ECMF inoculation with 100 μM Cd addition). C. geophilum colonization activated plant hormone signal transduction and carbohydrate metabolism pathways, while S. luteus enhanced the synthesis of secondary metabolites.

Discussion

This study provides a molecular perspective on the mechanism of interaction between ECMFs and willow saplings under Cd stress and supports the application of ECMFs for phytoremediation of Cd-contaminated soil.

Long non-coding RNAs modulate glutathione metabolism gene expression and tolerance to Pb stress in root tissue of endophyte-infected rice seedling

Endophyte can improve plant resistance to Pb stress, and long non-coding RNAs (lncRNAs) have been proved to play a vital role in response to environmental stress. However, there are few studies on the role of lncRNAs induced by endophyte in host plants under Pb stress. Therefore, we conducted high-throughput sequencing on root tissue of endophyte-infected and -uninfected rice seedlings under Pb stress, and analyzed the target genes of differentially expressed lncRNAs (DElncRNAs). The results showed that endophyte infection significantly increased plant height, above-ground fresh weight and dry weight, but significantly decreased root length and under-ground dry weight after 5 d of treatment. A total of 413 DElncRNAs (167 down-regulated and 246 up-regulated) were screened. Their target differentially expressed mRNAs (DEmRNAs) were significantly enriched in glutathione metabolism, plasma membrane and mineral elements transfer etc. DEmRNAs were most significantly enriched in glutathione metabolism, thereinto detected total glutathione, reduced and oxidized glutathione contents, glutathione S-transferase and glutathione reductase activities were significantly increased after 5 d of treatment. DElncRNAs and DEmRNAs were combined with miRNA database to construct ceRNA network. DEmRNAs in ceRNA network were mainly participated in carbohydrate metabolic process, peroxidase activity and phenylpropanoid biosynthesis. This study will help to understand the molecular mechanism elicited by endophytic infection within rice seedlings under Pb stress from the perspective of lncRNA.

Utilization of halophytes in saline agriculture and restoration of contaminated salinized soils from genes to ecosystem: Suaeda salsa as an example

Halophytes can be used to screen genes for breeding salt-tolerant crops and are of great value in the restoration of salinized or contaminated soils. However, the potential of halophytes in improving saline soils remains limited. In this paper, based on the latest research progress, we use Suaeda salsa L. as an example to evaluate the value of halophytes in developing saline agriculture including: 1) some defined salt-resistance genes and high-affinity nitrate transporter genes in the species for breeding salt-tolerance and nitrogen efficiency crops; 2) the value of S. salsa and microorganisms from S. salsa in remediation of heavy metal contaminated and organic polluted saline soils; and 3) the capacity to remove salts from soils and the application of the species. In conclusion, S. salsa has high value as a candidate to explore the theoretical base and practical application for utilizing halophytes to improve salinized soils from genes to ecosystem.

Endophytic Bacterium Flexivirga meconopsidis sp. nov. with Plant Growth-Promoting Function, Isolated from the Seeds of Meconopsis integrifolia

Strain Q11T of an irregular coccoid Gram-positive bacterium, aerobic and non-motile, was isolated from Meconopsis integrifolia seeds. Strain Q11T grew optimally in 1% (w/v) NaCl, pH 7, at 30 °C. Strain Q11T is most closely related to Flexivirga, as evidenced by 16S rRNA gene analysis, and shares the highest similarity with Flexivirga aerilata ID2601ST (99.24%). Based on genome sequence analysis, the average nucleotide identity and digital DNA-DNA hybridization values of strains Q11T and D2601ST were 88.82% and 36.20%, respectively. Additionally, strain Q11T showed the abilities of nitrogen fixation and indole acetic acid production and was shown to promote maize growth under laboratory conditions. Its genome contains antibiotic resistance genes (the vanY gene in the vanB cluster and the vanW gene in the vanI cluster) and extreme environment tolerance genes (ectoine biosynthetic gene cluster). Shotgun proteomics also detected antibiotic resistance proteins (class A beta-lactamases, D-alanine ligase family proteins) and proteins that improve plant cold tolerance (multispecies cold shock proteins). Strain Q11T was determined to be a novel species of the genus Flexivirga, for which the name Flexivirga meconopsidis sp. nov. is proposed. The strain type is Q11T (GDMCC 1.3002T = JCM 36020 T).

Plant growth-promoting bacteria modulate gene expression and induce antioxidant tolerance to alleviate synergistic toxicity from combined microplastic and Cd pollution in sorghum

Microplastics (MPs) can act as carriers for environmental pollutants; therefore, MPs combined with heavy metal pollution are attracting increasing attention from researchers. In this study, the potential of the plant growth-promoting bacterium Bacillus sp. SL-413 to mitigate the stress caused by exposure to both MPs and cadmium (Cd) in sorghum plants was investigated. The effects of inoculation on sorghum biomass were investigated using hydroponic experiments, and evaluation of Cd accumulation and enzyme activity changes and transcriptomics approaches were used to analyze its effect on sorghum gene expression. The results showed that combined polyethylene (PE) and Cd pollution reduced the length and the fresh and dry weights of sorghum plants and thus exerted a synergistic toxic effect. However, inoculation with the strains alleviated the stress caused by the combined pollution and significantly increased the biomass. Inoculation increased the dry weights of the aboveground and belowground parts by 11.5-44.6% and 14.9-38.4%, respectively. Plant physiological measurements indicated that inoculation reduced the reactive oxygen species (ROS) content of sorghum by 10.5-27.2% and thereby alleviated oxidative stress. Transcriptome sequencing showed that exposure to combined Cd+MP contamination induced downregulation of gene expression, particularly that of genes related to amino sugar and nucleotide sugar metabolism, starch and sucrose metabolism, and plant hormone signal transduction, in sorghum. However, inoculation with Bacillus sp. SL-413 resulted in an increase in the proportion of upregulated genes involved in signal transduction, antioxidant defense, cell wall biology, and other metabolic pathways, which included the phenylpropanoid biosynthesis, photosynthesis, flavonoid biosynthesis, and MAPK signaling pathways. The upregulation of these genes promoted the tolerance of sorghum under combined Cd+MP pollution stress and alleviated the stress induced by these conditions. This study provides the first demonstration that plant growth-promoting bacteria can alleviate the stress caused by combined pollution with MPs and Cd by regulating plant gene expression. These findings provide a reference for the combined plant-microbial remediation of MPs and Cd.