Integrative metabolome and transcriptome analyses reveal the differences in flavonoid and terpenoid synthesis between Glycyrrhiza uralensis (licorice) leaves and roots.

Licorice from Glycyrrhiza uralensis roots is used in foods and medicines. Although we are aware that licorice roots and leaves have distinct material compositions, the specific reasons for these differences remain unknown. Comparison of the metabolomes and transcriptomes between the leaves and roots revealed flavonoids and triterpenoid saponins were significantly different. Isoflavones were enriched in roots because of upregulation of genes encoding chalcone isomerase and flavone synthase, which are involved in isoflavone synthesis. Six triterpenoid saponins were significantly enriched only in the roots. The leaves did not accumulate glycyrrhetinic acid because of low expression levels of genes involved in its synthesis. A gene encoding a UDP glycosyltransferase, which likely catalyzes the key step in the transformation of glycyrrhetinic acid to glycyrrhizin, was screened. Our results provide information about the differences in flavonoid and triterpenoid synthesis between roots and leaves, and highlight targets for genetic engineering. Supplementary Information: The online version contains supplementary material available at 10.1007/s10068-023-01467-y.

Systematic evaluation of the impact of standard storage conditions on plasmid conjugation behavior in wastewater samples.

Filter mating experiment is widely used to study the conjugation behavior of plasmids and associated antibiotic resistance in environmental settings, however, the influence and biases brought by sample storage conditions (temperature and duration) were not yet systematically elaborated. This study systematically investigated the influence of standard storage conditions (4 °C, -20 °C, -80 °C) on plasmid conjugation behavior in influent (Inf) and activated sludge (AS) samples from sewage treatment plants (STP). The findings revealed a significant reduction in conjugation efficiency under all the tested storage conditions except for 1-week storage at 4 °C. Notably, storing at -80 °C maintained conjugation activities in activated sludge more effectively compared to -20 °C. However, the preservation performance was less effective for influent samples, which consist mainly of anaerobe-dominant communities. Systematic loss of IncH-type plasmids was observed in influent samples stored at 4 °C and -20 °C. Correspondingly, the plasmid-carrying resistome genotypes detected in the influent samples showed a clear downward trend with the increase in storage duration when stored at 4 °C and -20 °C. A relatively uniform composition in terms of incompatibility type and resistome profile was observed across activated sludge samples, regardless of the varied storage conditions. This study highlights the critical impact of storage conditions on plasmid conjugation behavior and resistome composition, offering valuable insights for optimal sample handling in resistome research.

Effect of CeO2 Nanoparticles on the Spread of Antibiotic Resistance in a Reclaimed Water-Soil-Radish System - Shenzhen City, Guangdong Province, China, April 2023.

Introduction: The use of reclaimed water (RW) for irrigation in agricultural practices raises concerns regarding the dissemination of antibiotic resistance genes (ARGs) from soils to edible crops. The effectiveness of nanoparticles (NPs) in reducing antibiotic resistance in vegetables irrigated with RW remains largely unexplored. Methods: To investigate the effects, we conducted pot experiments in which radishes were planted in soil amended with CeO2 NPs using various application techniques. The abundance of ARGs was characterized using high-throughput quantitative PCR (HT-qPCR). Concurrently, we utilized 16S ribosomal RNA (rRNA) gene sequencing to evaluate the microbial community structure of both the rhizosphere soil and the endophytic compartment within the radishes. Employing bioinformatics analysis, we probed the potential mechanisms by which NPs influence the resistome within the reclaimed water-soil-radish system. Results: Following the application of CeO2 NPs, there was a noticeable reduction in both the number and concentration of ARG genotypes in the rhizosphere soil, as well as within the radish. Concurrently, CeO2 NPs appeared to mitigate the propagation of ARGs within the reclaimed water-soil-radish system. The ability of CeO2 NPs to modulate the resistome is linked to alterations in microbial community structure. Soil treatment with NPs emerged as the most effective strategy for curbing the spread of ARGs. Discussion: This finding provides a theoretical foundation for the development of nano-agricultural technologies aimed at controlling the proliferation of ARGs.

Virus impacted community adaptation in oligotrophic groundwater environment revealed by Hi-C coupled metagenomic and viromic study.

Viruses play a crucial role in microbial mortality, diversity and biogeochemical cycles. Groundwater is the largest global freshwater and one of the most oligotrophic aquatic systems on Earth, but how microbial and viral communities are shaped in this special habitat is largely unexplored. In this study, we collected groundwater samples from 23 to 60 m aquifers at Yinchuan Plain, China. In total, 1920 non-reductant viral contigs were retrieved from metagenomes and viromes constructed by Illumina and Nanopore hybrid sequencing. Only 3% of them could be clustered with known viruses, most of which were Caudoviricetes. Coupling 1.2 Tb Hi-C sequencing with CRISPR matching and homology search, we connected 469 viruses with their hosts while some viral clusters presented a broad-host-range trait. Meanwhile, a large proportion of biosynthesis related auxiliary metabolism genes were identified. Those characteristics might benefit viruses for a better survival in this special oligotrophic environment. Additionally, the groundwater virome showed genomic features distinct from those of the open ocean and wastewater treatment facilities in GC distribution and unannotated gene compositions. This paper expands the current knowledge of the global viromic records and serves as a foundation for a more thorough understanding of viruses in groundwater.

Electric-Inducive Microbial Interactions in a Thermophilic Anaerobic Digester Revealed by High-Throughput Sequencing of Micron-Scale Single Flocs.

Although conductive materials have been shown to improve efficiency in anaerobic digestion (AD) by modifying microbial interactions, the interacting network under thermophilic conditions has not been examined. To identify the true taxon-taxon associations within thermophilic anaerobic digestion (TAD) microbiome and reveal the influence of carbon cloth (CC) addition, we sampled micron-scale single flocs (40-70 µm) randomly isolated from lab-scale thermophilic digesters. Results revealed that CC addition not only significantly boosted methane yield by 25.3% but also increased the spatial heterogeneity of the community in the sludge medium. After CC addition, an evident translocation of Pseudomonas from the medium to the biofilm was observed, showing their remarkable capacity for biofilm formation. Additionally, Clostridium and Thermotogaceae tightly aggregated and steadily co-occurred in the medium and biofilm of the TAD microbiome, which might be associated with their unique extracellular sugar metabolizing style. Finally, CC induced syntrophic interaction between Syntrophomonas and denitrifiers of Rhodocyclaceae. The upregulated respiration-associated electron transferring genes (Cyst-c, complex III) on the cellular membranes of these collaborating partners indicated a potential coupling of the denitrification pathway with syntrophic acetate oxidation via direct interspecies electron transfer (DIET). These findings provide an insight into how conductive materials promote thermophilic digestion performance and open the path for improved community monitoring of biotreatment systems.

Transcriptomic analyses reveal dynamic changes of defense response in Glycyrrhiza uralensis leaves under enhanced ultraviolet-B radiation.

The amount of solar ultraviolet-B (UV-B) radiation reaching the Earth's surface is increasing due to stratospheric ozone dynamics and global climate change. Increased UV-B radiation poses a major threat to ecosystems. Although many studies have focused on the potential effects of enhanced UV-B radiation on plants, the dynamic changes of defense response in plants under continuous UV-B radiation remains enigmatic. In this study, we investigated the effect of UV-B radiation at 0.024 W/m2 on the UVR8-and reactive oxygen species (ROS-) signaling pathways, antioxidant system, and wax synthesis of G. uralensis. These parameters were investigated at different UV-B radiation stages (2 h, 6 h, 12 h, 24 h, 48 h, and 96 h). The results revealed that the uvr8 expression level was significantly repressed after 2 h of UV-B radiation, partly because G. uralensis rapidly acclimated to UV-B. Significant H2O2 accumulation occurred after 12 h UV-B radiation, resulting in activation of the ROS signaling pathway and the antioxidant system. After 24 h of UV-B radiation, wax synthesis was enhanced alongside a decrease in the capacity of the main antioxidant system. The dynamic and ordered changes in these pathways reveal how different strategies function in G. uralensis at different times during adaption to enhanced UV-B radiation. This study will help us better understand dynamic changes of defense response in plant under enhanced UV-B radiation, further providing fundamental knowledge to develop plant resistance gene resources.

Enhancement of exopolysaccharides production and reactive oxygen species level of Nostoc flagelliforme in response to dehydration.

Nostoc flagelliforme is a remarkable drought-resistant terrestrial cyanobacterium whose exopolysaccharides (EPS) have been found to exert important physiological and ecological functions, and the EPS are known to improve soil physicochemical properties. In this study, we used physiological and molecular methods to investigate the influences of three moisture loss levels on EPS production and the antioxidant system in N. flagelliforme. The aim was to reveal the EPS production mechanism involved in the gene differential expression and antioxidant system of N. flagelliforme in response to drought. Our results showed that EPS contents increased by 13% and 22% after 6-h and 48-h dehydration (6HAD and 48HAD) compared with 4-h rehydration (4HAR), respectively. The same trends were also detected for most EPS synthesis genes, especially glycosyltransferases. Furthermore, the intracellular reactive oxygen species (ROS) levels in N. flagelliforme were generally higher at 6HAD and 48HAD than at 4HAR. Superoxide dismutase (SOD) and peroxidase (POD) activities were restricted in N. flagelliforme under 6HAD and 48HAD compared with 4HAR, but the opposite result was found in catalase (CAT) activity. These results provide a new foundation for understanding the mechanism of EPS accumulation in N. flagelliforme in response to drought.

A Rise in ROS and EPS Production: New Insights into the Trichodesmium erythraeum Response to Ocean Acidification.

The diazotrophic cyanobacterium Trichodesmium is thought to be a major contributor to the new N in parts of the oligotrophic, subtropical, and tropical oceans. In this study, physiological and biochemical methods and transcriptome sequencing were used to investigate the influences of ocean acidification (OA) on Trichodesmium erythraeum (T. erythraeum). We presented evidence that OA caused by CO2 slowed the growth rate and physiological activity of T. erythraeum. OA led to reduced development of proportion of the vegetative cells into diazocytes which included up-regulated genes of nitrogen fixation. Reactive oxygen species (ROS) accumulation was increased due to the disruption of photosynthetic electron transport and decrease in antioxidant enzyme activities under acidified conditions. This study showed that OA increased the amounts of (exopolysaccharides) EPS in T. erythraeum, and the key genes of ribose-5-phosphate (R5P) and glycosyltransferases (Tery_3818) were up-regulated. These results provide new insight into how ROS and EPS of T. erythraeum increase in an acidified future ocean to cope with OA-imposed stress.

CeO2 Nanoparticles Regulate the Propagation of Antibiotic Resistance Genes by Altering Cellular Contact and Plasmid Transfer.

The dissemination and propagation of antibiotic resistance genes (ARGs) via plasmid-mediated conjugation pose a major threat to global public health. The potential effects of nanomaterials on ARGs fates have drawn much attention recently. In this study, CeO2 nanoparticles (NPs), one of the typical nanomaterials proposed for increasing crop production, were applied at the concentration range of 1-50 mg/L to investigate their effects on ARGs transfer between Escherichia coli. Our results revealed that the conjugative transfer of RP4 plasmid was enhanced by 118-123% at relatively high concentrations (25 and 50 mg/L) of CeO2 NPs, however, CeO2 NPs at low concentrations (1 and 5 mg/L) inhibited the transfer by 22-26%. The opposite effect at low concentrations is mainly attributed to (i) the reduced ROS level, (ii) the weakened intercellular contact via inhibiting the synthesis of polysaccharides in extracellular polymeric substances, and (iii) the down-regulated expression of plasmid transfer genes due to the shortage of ATP supply. Our findings highlight the distinct dose-dependent responses of ARGs conjugative transfer, providing evidence for selecting appropriate NPs dose to reduce the spread of ARGs while applying nanoagrotechnology.

Cleavage and transformation inhibition of extracellular antibiotic resistance genes by graphene oxides with different lateral sizes.

Due to excessive consumption of antibiotics, antibiotic resistance genes (ARGs) become a ubiquitous pollutant in aquatic environments. Graphene oxide (GO), an emerging 2D nanomaterial, was used for potential control of ARG contamination in the present work. We systematically investigated the interaction of GOs with Kanamycin resistance gene (aphA)-containing plasmid DNA, and related the inhibition of ARG transformation by GOs. Four GOs with different lateral sizes (1.0, 0.60, 0.17, and 0.08 µm2) were prepared, and defined as GO1.0, GO0.60, GO0.17 and GO0.08. It is found that all the four GOs could effectively intercalate into plasmid DNA, and the intercalation abilities followed the order: GO0.08 > GO0.17 > GO0.60 > GO1.0. Based on circular dichroism (CD) spectrum analysis, all GOs disturbed the base stacking mode and double helix structure of DNA, which is positively related to the intercalation activities of GOs. For GO0.08 at 25 µg/mL, the supercoiled plasmid DNA was partially cleaved, and the nicked and linear structures were observed based on agarose gel electrophoresis analysis. Moreover, the amplification and transformation of aphA gene were both inhibited due to GO-plasmid DNA interactions, and the inhibition was stronger with increasing GO concentrations and smaller lateral sizes. The inhibition of aphA transformation after GO0.08 (25 µg/mL) exposure achieved 50%. The size-dependent interaction of GOs with ARGs-containing plasmid DNA will be useful for guiding the environmental applications of GOs in reducing extracellular ARG transformation.

Early development of apoplastic barriers and molecular mechanisms in juvenile maize roots in response to La2O3 nanoparticles.

The increasing occurrence of engineered nanoparticles (NPs) in soils may decrease water uptake in crops, followed by lower crop yield and quality. As one of the most common rare earth oxide NPs, lanthanum oxide (La2O3) NPs may inhibit the relative expressions of aquaporin genes, thus reduce water uptake. In the present study, maize plants were exposed to different La2O3 NPs concentrations (0, 5, 50 mg L-1) for 72 h and 144 h right after the first leaf extended completely. Our results revealed that water uptake was reduced by La2O3 NPs through accelerating the development of apoplastic barriers in maize roots. The level of abscisic acid, determined by using ultra high performance liquid chromatography-tandem mass spectrometry, was increased upon La2O3 NPs exposure. Furthermore, ZmPAL, ZmCCR2 and ZmCAD6, the core genes specific for biosynthesis of lignin, were up-regulated by 3-13 fold in roots exposed to 50 mg L-1 La2O3 NPs. However, ZmF5H was suppressed, indicating that lignin with S units could be excluded for the formed lignin in apoplastic barriers upon La2O3 NPs exposure. The level of essential component of apoplastic barriers - lignin was increased by 1.5-fold. The early development of apoplastic barriers was observed, and stomatal conductance and transpiration rate of La2O3 NPs-treated plants were significantly decreased by 63%-83% and 42%-86%, respectively, as compared to the control. The lignin enriched apoplastic barriers in juvenile maize thus led to the reduction of water uptake, subsequently causing significant growth inhibition. This is the first study to show early development of root apoplastic barriers upon La2O3 NPs exposure. This study will help us better understand the function of apoplastic barriers in roots in response to NPs, further providing fundamental knowledge to develop safer and more efficient agricultural nanotechnology.

[Terahertz Spectrum Modulation with Liquid Crystal Spatial Light Modulator].

Terahertz wave with modulation spectrum is valuable in many fields. Terahertz spectrum has been modulated with a pure-phase liquid crystal spatial light modulator by shaping the femtosecond laser beam profile. In the experiment, terahertz wave is generated by femtosecond laser pulses in mode of Optical Rectification and then its signals are detected by a terahertz time-domain spectroscopy system. Phase maps obtained with the GS algorithm are loaded to get the shaped beam profile. Therefore, Terahertz spectrum has been successfully modulated by changing the detection range and beam profile parameters. Simultaneously, the simulations have been performed with the Fresnel diffraction, and they agree with the experimental results well. The results show that the modulation of the THz spectrum with this method is feasible.