High-throughput Sequencing Analysis Research Articles

Exosomal circ-0100519 promotes breast cancer progression via inducing M2 macrophage polarisation by USP7/NRF2 axis.

Breast cancer (BC) is one of the most prevalent malignant tumours that threatens women health worldwide. It has been reported that circular RNAs (circRNAs) play an important role in regulating tumour progression and tumour microenvironment (TME) remodelling. Differentially expression characteristics and immune correlations of circRNAs in BC were verified using high-throughput sequencing and bioinformatic analysis. Exosomes were characterised by nanoparticle transmission electron microscopy and tracking analysis. The biological function of circ-0100519 in BC development was demonstrated both in vitro and in vivo. Western blotting, RNA pull-down, RNA immunoprecipitation, flow cytometry, and luciferase reporter were conducted to investigate the underlying mechanism. Circ-0100519 was significant abundant in BC tumour tissues and related to poor prognosis. It can be encapsulated into secreted exosomes, thereby promoting BC cell invasion and metastasis via inducing M2-like macrophages polarisation.Mechanistically, circ-0100519 acted as a scaffold to enhance the interaction between the deubiquitinating enzyme ubiquitin-specific protease 7 (USP7) and nuclear factor-like 2 (NRF2) in macrophages, inducing the USP7-mediated deubiquitination of NRF2. Additionally,HIF-1α could function as an upstream effector to enhance circ-0100519 transcription. Our study revealed that exosomal circ-0100519 is a potential biomarker for BC diagnosis and prognosis, and the HIF-1α inhibitor PX-478 may provide a therapeutic target for BC.

Identification of key genes involved in lignin and flavonoid accumulation during Tilia tuan seed maturation.

Transcriptomics and phenotypic data analysis identified 24 transcription factors (TFs) that play key roles in regulating the competitive accumulation of lignin and flavonoids. Tilia tuan Szyszyl. (T. tuan) is a timber tree species with important ecological and commercial value. However, its highly lignified pericarp results in a low seed germination rate and a long dormancy period. In addition, it is unknown whether there is an interaction between the biosynthesis of flavonoids and lignin as products of the phenylpropanoid pathway during seed development. To explore the molecular regulatory mechanism of lignin and flavonoid biosynthesis, T. tuan seeds were harvested at five stages (30, 60, 90, 120, and 150 days after pollination) for lignin and flavonoid analyses. The results showed that lignin accumulated rapidly in the early and middle stages (S1, S3, and S4), and rapid accumulation of flavonoids during the early and late stages (S1 and S5). High-throughput RNA sequencing analysis of developing seeds identified 50,553 transcripts, including 223 phenylpropanoid biosynthetic pathway genes involved in lignin accumulation grouped into 3 clusters, and 106 flavonoid biosynthetic pathway genes (FBPGs) grouped into 2 clusters. Subsequent WGCNA and time-ordered gene co-expression network (TO-GCN) analysis revealed that 24 TFs (e.g., TtARF2 and TtWRKY15) were involved in flavonoids and lignin biosynthesis regulation. The transcriptome data were validated by qRT-PCR to analyze the expression profiles of key enzyme-coding genes. This study revealed that there existed a competitive relationship between flavonoid and lignin biosynthesis pathway during the development of T. tuan seeds, that provide a foundation for the further exploration of molecular mechanisms underlying lignin and flavonoid accumulation in T. tuan seeds.

BCL6 confers resistance to HDAC inhibitors in DLBCL

Diffuse large B-cell lymphoma (DLBCL) is an aggressive non-Hodgkin lymphoma with limited response to chemotherapy. Histone acetylation is reduced in DLBCL. Chidamide, a histone deacetylase inhibitor, shows promise in lymphomas but needs further investigation for DLBCL. Our study indicated that chidamide effectively suppresses DLBCL both in vitro and in vivo. High-throughput RNA sequencing analysis provided comprehensive evidence that chidamide markedly influences crucial signaling pathways in DLBCL, including the MAPK, MYC and p53 pathway. Additionally, we observed substantial variability in the sensitivity of DLBCL cells to chidamide, and identified that elevated expression of BCL6 might confer resistance to chidamide in DLBCL. Moreover, our investigations revealed that BCL6 inhibited chidamide-induced histone acetylation by recruiting histone deacetylase (HDACs), leading to drug resistance in DLBCL cells. Furthermore, we found that lenalidomide targeted BCL6 degradation through the ubiquitination pathway and restore the sensitivity of drug-resistant DLBCL to chidamide. Collectively, these findings provided valuable insights into the global impact of chidamide on DLBCL and highlight the potential of targeting HDACs as a therapeutic strategy for DLBCL. Identifying BCL6 as a biomarker for predicting the response to chidamide and the combination therapy with BCL6 inhibition has the potential to lead to more personalized and effective treatments for DLBCL patients.

High-throughput sequencing analysis of differential microRNA expression in the process of blocking the progression of chronic atrophic gastritis to gastric cancer by Xianglian Huazhuo formula.

To explore the mechanism of Xianglian Huazhuo formula (, XLHZ) blocking the development of chronic atrophic gastritis (CAG) to gastric cancer (GC) through bioinformatics analysis and in vitro. Pathological morphology of gastric mucosa of rats were observed. High-throughput sequencing was used to analyze the miRNA expression profile of gastric mucosa. The miRanda, miRDB and miRWalk databases were used to predict the differential target genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were performed for differential target genes. Real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) was used to verify the differentially expressed miRNAs and target genes. Western blot, EdU, wound healing and flow cytometry were used to observe the effect of XLHZ on epithelial-mesenchymal transition (EMT) markers, proliferation, migration, apoptosis and cell cycle of CAG cells in vitro. A total of five differentially expressed miRNAs and four differential target genes were screened in this study. GO analysis showed that the target genes were enriched in regulation of neuron development, regulation of transcription factor activity and regulation of RNA polymerase. KEGG pathways database differences in gene enrichment of target genes in the Wnt signaling pathway, Phospholipase D signaling pathway and mitogen-activated protein kinase signaling pathway. qRT-PCR confirmed that miRNAs and its target genes were consistent with the screening results. In vitro, our study revealed that XLHZ could increase the expression of E-cadherin, decrease the expression of transforming growth factor β1, vimentin and β-catenin, inhibite the proliferation and migration of CAG cells, cause cell cycle arrest at G0/G1 and G2/M phase, induce the apoptosis of CAG cells, and prevent the progression of CAG to GC. This study provided a new idea for the mechanism of blocking the progression of CAG to GC by XLHZ, which may be related to the expression of miR-20a-3p, miR-320-3p, miR-34b-5p, miR-483-3p and miR-883-3p and their target genes transferrin receptor, nuclear receptor subfamily 4 member 2, delta like canonical Notch ligand 1 and a kinase anchor protein 12 in CAG. In the future, we will continue to investigate the linkage between the active ingredients of XLHZ and the relevant miRNAs and their target genes, so as to provide more sufficient experimental basis for clinically effective prevention of CAG to GC.

High-throughput single-molecule long-read RNA sequencing analysis of tissue-specific genes and isoforms in lettuce (Lactuca sativa L.)

Lettuce is one of the most widely cultivated and consumed dicotyledonous vegetables globally. Despite the availability of its reference genome sequence, lettuce gene annotation remains incomplete, impeding comprehensive research and the broad application of genomic resources. Long-read RNA isoform sequencing (Iso-Seq) offers substantial advantages for analyzing RNA alternative splicing and aiding gene annotation, yet it faces throughput limitations. We present the HIT-ISOseq method tailored for bulk sample analysis, significantly enhancing RNA sequencing throughput on the PacBio platform by concatenating cDNA. Here we show, HIT-ISOseq generates 3-4 cDNA molecules per CCS read in lettuce, yielding 15.7 million long reads per PacBio Sequel II SMRT Cell 8 M. We validate its effectiveness in analyzing six lettuce tissue samples, including roots, stems, and leaves, revealing tissue-specific gene expression patterns and RNA isoforms. Leveraging diverse tissue long-read RNA sequencing, we refine the transcript annotation of the lettuce reference genome, expanding its GO and KEGG annotation repertoire. Collectively, this study serves as a foundational reference for genome annotation and the analysis of multi-sample isoform expression, utilizing high-throughput long-read transcriptome sequencing.

Drought Stress Increases the Complexity of the Bacterial Network in the Rhizosphere and Endosphere of Rice (Oryza sativa L.)

The root microbiota plays a crucial role in assisting the plant host in combating various biotic and abiotic stresses, notably drought, which poses a significant threat to global food security. Despite extensive efforts to understand the shifts in rhizosphere and endosphere bacteriomes, there remains a gap in comprehending how drought stress influences the co-occurring network patterns within these compartments and their ecological functional potentials. To address this gap, a pot experiment was conducted with two treatments: continuous flooding as a control and drought treatment. Bulk soil, rhizosphere, and endosphere samples were collected and subjected to high-throughput sequencing and bioinformatics analysis. The results revealed that drought stress significantly reduced the rice biomass but increased the Shannon diversity index in both the rhizosphere and endosphere bacterial communities with no observable effect on richness across compartments. Additionally, drought treatment markedly altered the community structure and bacterial assemblages in these compartments, resulting in the specific enrichment of Actinobacteriota, Gemmatimonadetes, and Patescibacteria, while Bacteroidetes and Firmicutes were depleted in the rhizosphere and endosphere. Furthermore, drought heightened the complexity of the co-occurring networks and the proportions of positive links across all sampling compartments; this effect was accompanied by an increase in the number of connectors in the bulk soil and rhizosphere, as well as module hubs in the rhizosphere. Functional potential prediction indicated that drought stress significantly altered multiple potential ecological functions across all sampling compartments, particularly enriching functions related to the oxidation of sulfur, manganese, and hydrogen in the bulk soil, while functions associated with iron oxidation were significantly depleted in the rhizosphere. Overall, our results demonstrate that under drought stress, rice may specifically enrich certain bacterial taxa and enhance their positive interactions within its root system to improve adaptation.

Characteristics of microplastics and their abundance impacts on microbial structure and function in agricultural soils of remote areas in west China

As an emergent pollutant, microplastics (MPs) are becoming prevalent in the soil environment. However, the characteristics of MPs and the response of microbial communities to the abundance of MPs in agricultural soils in West China still need to be elucidated in detail. This study utilized the Agilent 8700 Laser Direct Infrared (LDIR) to analyze the characteristics of small-sized MPs (20–1000 μm) in soils from un-mulched and mulched agricultural fields in West China, and illustrated their correlation with microbial diversity. The results revealed a higher abundance of MPs in mulched soil ((4.12 ± 2.13) × 105 items kg−1) than that in un-mulched soil ((1.04 ± 0.26) × 105 items kg−1). The detected MPs were dominated by fragments, 20–50 μm and Polyamide (PA). High-throughput sequencing analysis indicated that alpha diversity (Chao1 and Shannon indices) in the plastisphere was lower compared to that in soil, and varied significantly with MPs abundance in soil. As the abundance of MPs increased, the proportion of soil about the degradation of organic matte and photoautotrophic taxa increased, which showed enrichment in the plastisphere. Functional predictions further indicated that MPs abundance affected potential soil functions, such as metabolic pathways associated with the C and N cycling. The plastisphere showed higher functional abundance associated with organic matter degradation, indicating higher potential health risks compared to soil environments. Based on the RDA analyses, it was determined that environmental physicochemical properties and MPs abundance had a greater impact on fungal communities than on bacterial communities. In general, the abundance of MPs affected the microbial diversity composition and potentially influenced the overall performance of soil ecosystems. This study offers empirical data on the abundance of MPs in long-term mulched agricultural fields and new insights for exploring the ecological risk issues associated with MPs.

A novel Saclayvirus Acinetobacter baumannii phage genomic analysis and effectiveness in preventing pneumonia

Acinetobacter baumannii, which is resistant to multiple drugs, is an opportunistic pathogen responsible for severe nosocomial infections. With no antibiotics available, phages have obtained clinical attention. However, since immunocompromised patients are often susceptible to infection, the appropriate timing of administration is particularly important. During this research, we obtained a lytic phage vB_AbaM_P1 that specifically targets A. baumannii. We then assessed its potential as a prophylactic treatment for lung infections caused by clinical strains. The virus experiences a period of inactivity lasting 30 min and produces approximately 788 particles during an outbreak. Transmission electron microscopy shows that vB_AbaM_P1 was similar to the Saclayvirus. Based on the analysis of high-throughput sequencing and bioinformatics, vB_AbaM_P1 consists of 107537 bases with a G + C content of 37.68%. It contains a total of 177 open reading frames and 14 tRNAs. No antibiotic genes were detected. In vivo experiments, using a cyclophosphamide-induced neutrophil deficiency model, tested the protective effect of phage on neutrophil-deficient rats by prophylactic application of phage. The use of phages resulted in a decrease in rat mortality caused by A. baumannii and a reduction in the bacterial burden in the lungs. Histologic examination of lung tissue revealed a decrease in the presence of immune cells. The presence of phage vB_AbaM_P1 had a notable impact on preventing A. baumannii infection, as evidenced by the decrease in oxidative stress in lung tissue and cytokine levels in serum. Our research offers more robust evidence for the early utilization of bacteriophages to mitigate A. baumannii infection.Key points•A novel Saclayvirus phage infecting A. baumannii was isolated from sewage.•The whole genome was determined, analyzed, and compared to other phages.•Assaying the effect of phage in preventing infection in neutrophil-deficient models.

Microbial Biodiversity of Cryoconites in Palandöken Mountain and Culturing Cold-Adapted Enzyme Producers

Palandöken Mountain is among the highest and coldest ecosystems of Türkiye, and knowledge on its microbial diversity has not been adequately characterized. The aim of the present study is to expand the current understanding of microbial diversity in Palandöken Mountain. Sampling studies were carried out at in winter an altitude of 2400–2900 m. A next-generation sequencing (NGS) based culture-independent approach was employed for elucidating the community structure in the 8 cryoconite samples using 16S and 23S rRNA gene sequencing. In addition, biotechnologically important cold-adapted enzyme producers were isolated and identified by employing conventional culture-dependent studies. High-throughput sequencing analysis revealed the presence of 36 bacterial and 2 fungal phyla. The bacterial communities of 8 samples were dominated by Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes and Acidobacteria. The fungal communities were dominated by Ascomycota and Basidiomycota. 2900 different taxonomic group for bacterial diversity and 51 for fungal diversity were reported in the present study. Furthermore, 25 cold-adapted enzyme-producers were isolated and identified in the culture-dependent studies. Each selected isolate was capable of producing at least one of the enzymes amylase, protease, lipase, cellulase and xylanase isolates were assigned to Aspergillus, Bacillus, Cladosporium, Dioszegia, Flavobacterium, Fusarium, Holtermanniella, Naganishia, Polaromonas, Protomyces, Pseudomonas Rhodosporidiobolus, Vishniacozyma and Yarrowia genera. Consequently, this is the first geomicrobiological investigation that describes bacterial and fungal diversity of cryoconites from Palandöken Mountain using an NGS-based culture-independent approach. Additionally, cultured cold-adapted enzyme producer isolates of the present study have a valuable potential for the development of new biotechnological tools for various industrial applications.

Interactions of graphene oxide with the microbial community of biologically active filters from a water treatment plant

With widespread occurrence and increasing concern of emerging contaminants (CECs) in source water, biologically active filters (BAF) have been gaining acceptance in water treatment. Both BAFs and graphene oxide (GO) have been shown to be effective in treating CECs. However, studies to date have not addressed interactions between GO and microbial communities in water treatment processes such as BAFs. Therefore, in the present study, we investigated the effect of GO on the properties and microbial growth rate in a BAF system. Synthesized GO was characterized with a number of tools, including scanning electron microscopy (SEM), energy dispersive x-ray spectroscopy (EDX), X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), and Raman spectrometry. GO exhibited the characteristic surface functional groups (i.e., C-OH, C=O, C-O-C, and COOH), crystalline structure, and sheet-like morphology. To address the potential toxicity of GO on the microbial community, reactive oxygen species (ROS) generation was measured using nitro blue tetrazolium (NBT) assay. Results revealed that during the exponential growth phase, ROS generation was not observed in the presence of GO compared to the control batch. In fact, the adenosine triphosphate (ATP) concentrations increased in the presence of GO (25 μg/L - 1000 μg/L) compared to the control without GO. The growth rate in systems with GO exceeded the control by 20 % to 46 %. SEM images showed that GO sheets can form an effective scaffold to promote bacterial adhesion, proliferation, and biofilm formation, demonstrating its biocompatibility. Next-generation sequencing (Illumina MiSeq) was used to characterize the BAF microbial community, and high-throughput sequencing analysis confirmed the greater richness and more diverse microbial communities compared to systems without GO. This study is the first to report the effect of GO on the microbial community of BAF from a water treatment plant, which provides new insights into the potential of utilizing a bio-optimized BAF for advanced and sustainable water treatment or reuse strategies.

Methane-Driven Perchlorate Reduction by a Microbial Consortium.

The phenomenon of methane oxidation linked to perchlorate reduction has been reported in multiple studies; yet, the underlying microbial mechanisms remain unclear. Here, we enriched suspended cultures by performing methane-driven perchlorate reduction under oxygen-limiting conditions in a membrane bioreactor (MBR). Batch test results proved that perchlorate reduction was coupled to methane oxidation, in which acetate was predicted as the potential intermediate and oxygen played an essential role in activating methane. By combining DNA-based stable isotope probing incubation and high-throughput sequencing analyses of 16S rRNA gene and functional genes (pmoA, pcrA, and narG), we found that synergistic interactions between aerobic methanotrophs (Methylococcus and Methylocystis) and perchlorate-reducing bacteria (PRB; Denitratisoma and Dechloromonas) played active roles in mediating methane-driven perchlorate reduction. This partnership was further demonstrated by coculture experiments in which the aerobic methanotroph could produce acetate to support PRB to complete perchlorate reduction. Our findings advance the understanding of the methane-driven perchlorate reduction process and have implications for similar microbial consortia linking methane and chlorine biogeochemical cycles in natural environments.

Exosomes from Hypoxia Preconditioned Muscle-Derived Stem Cells Enhance Cell-Free Corpus Cavernosa Angiogenesis and Reproductive Function Recovery.

Tissue engineering for penile corpora cavernosa defects requires microvascular system reconstruction.GelMA hydrogels show promise for tissue regeneration. However, using stem cells faces challenges such as immune rejection, limited proliferation and differentiation, and biosafety concerns. Therefore, acellular tissue regeneration may avoid these issues. Exosomes are used from muscle-derived stem cells (MDSCs) to modify 3D-printed hydrogel scaffolds for acellular tissue regeneration. Hypoxia-preconditioned MDSC-derived exosomes are obtained to enhance the therapeutic effect. In contrast to normoxic exosomes (N-Exos), hypoxic exosomes (H-Exos) are found to markedly enhance the proliferation, migration, and capillary-like tube formation of human umbilical vein endothelial cells (HUVECs). High-throughput sequencing analysis of miRNAs isolated from both N-Exos and H-Exos revealed a significant upregulation of miR-21-5p in H-Exos following hypoxic preconditioning. Further validation demonstrated that the miR-21-5p/PDCD4 pathway promoted the proliferation of HUVECs. Epigallocatechin gallate (EGCG) is introduced to improve the mechanical properties and biocompatibility of GelMA hydrogels. EGCG-GelMA scaffolds loaded with different types of Exos are transplanted to repair rabbit penile corpora cavernosa defects, observed the blood flow and repair status of the defect site through color Doppler ultrasound and magnetic resonance imaging, and ultimately restored the rabbit penile erection function and successfully bred offspring. Thus, acellular hydrogel scaffolds offer an effective treatment for penile corpora cavernosa defects.

Characterization of Caulimovirid-like Sequences from Upland Cotton (Gossypium hirsutum L.) Exhibiting Terminal Abortion in Georgia, USA.

In this study, we investigated the potential involvement of endogenous viral elements (EVEs) in the development of apical tissue necrosis, resulting in the terminal abortion of upland cotton (Gossypium hirsutum L.) in Georgia. The high-throughput sequence analysis of symptomatic and asymptomatic plant tissue samples revealed near-complete EVE-Georgia (EVE-GA) sequences closely related to caulimoviruses. The analysis of EVE-GA's putative open reading frames (ORFs) compared to cotton virus A and endogenous cotton pararetroviral elements (eCPRVE) revealed their similarity in putative ORFs 1-4. However, in the ORF 5 and ORF 6 encoding putative coat protein and reverse transcriptase, respectively, the sequences from EVE-GA have stop codons similar to eCPRVE sequences from Mississippi. In silico mining of the cotton genome database using EVE-GA as a query uncovered near-complete viral sequence insertions in the genomes of G. hirsutum species (~7 kb) but partial in G. tomentosum (~5.3 kb) and G. mustelinum (~5.1 kb) species. Furthermore, cotton EVEs' episomal forms and messenger RNA (mRNA) transcripts were detected in both symptomatic and asymptomatic plants collected from cotton fields. No significant yield difference was observed between symptomatic and asymptomatic plants of the two varieties evaluated in the experimental plot. Additionally, EVEs were also detected in cotton seeds and seedlings. This study emphasizes the need for future research on EVE sequences, their coding capacity, and any potential role in host immunity or pathogenicity.

The correlation between TRIM28 expression and immune checkpoints in CRPC.

This study delves into the unexplored realm of castration-resistant prostate cancer (CRPC) by investigating the role of TRIM28 and its intricate molecular mechanisms using high-throughput single-cell transcriptome sequencing and advanced bioinformatics analysis. Our comprehensive examination unveiled dynamic TRIM28 expression changes, particularly in immune cells such as macrophages and CD8+ T cells within CRPC. Correlation analyses with TCGA data highlighted the connection between TRIM28 and immune checkpoint expression and emphasized its pivotal influence on the quantity and functionality of immune cells. Using TRIM28 knockout mouse models, we identified differentially expressed genes and enriched pathways, unraveling the potential regulatory involvement of TRIM28 in the cGAS-STING pathway. Invitro, experiments further illuminated that TRIM28 knockout in prostate cancer cells induced a notable anti-tumor immune effect by inhibiting M2 macrophage polarization and enhancing CD8+ T cell activity. This impactful discovery was validated in an insitu transplant tumor model, where TRIM28 knockout exhibited a deceleration in tumor growth, reduced proportions of M2 macrophages, and enhanced infiltration of CD8+ T cells. In summary, this study elucidates the hitherto unknown anti-tumor immune role of TRIM28 in CRPC and unravels its potential regulatory mechanism via the cGAS-STING signaling pathway. These findings provide novel insights into the immune landscape of CRPC, offering promising directions for developing innovative therapeutic strategies.

Liraglutide reduces bone marrow adipogenesis by miR-150-5p/ GDF11 axis in diabetic rats

In recent years, a common-used antidiabetic drug, liraglutide, was identified with extra effects on lipid metabolism. Its effects against excessive lipid deposition in bone marrow were gained much attention but not well established. Our aim in the present study is to explore the interaction of miRNAs-mRNAs altered by liraglutide administration during bone marrow adipogenesis in diabetes. To establish the diabetic animal model, rats were treated with high fat diet (HFD) and STZ injection. We then identified the lowering effect of liraglutide on lipids metabolism in the diabetes. During this process, high-throughput sequencing and bioinformatics analyses on miRNAs extracted from bone marrow mesenchymal stem cells (BMSCs) were conducted after liraglutide administration. We then identified five differentially expressed miRNAs (miRNA-150-5p, miRNA-129-5p, miRNA-201-3p, miRNA-201-5p, and miRNA-214-5p). The expressions of the DE miRNAs were verified as temporal specific expression patterns in Day 3 and in Day 7. Among them, miRNA-150-5p expression was more stable and consistent with the sequencing data. Of interest, miR-150-5p overexpression facilitated adipogenesis of BMSCs. But this promotion was alleviated by liraglutide. The predicted target gene of miR-150-5p, GDF11, was validated to be involved in liraglutide alleviated BMSCs’ lipid accumulation in diabetes. In vitro, liraglutide increased the GDF11 expression, rescued its down-expression by siGDF11 and inhibit the adipogenesis of BMSCs cultured in high glucose medium. In vivo, liraglutide reversed the HFD-STZ induced excessive lipid droplets by up-regulation of GDF11 expression, which was discounted by agomiR-150-5p injection. Above all, liraglutide might alleviate bone marrow fat accumulation via inactivating miR-150-5p/GDF11 axis in diabetes.

Comparative High-Throughput Sequencing Analysis of the Bacterial Community Associated with the Rhizosphere of Date Palm (Phoenix dactyllifera L.) Irrigated with Treated Wastewater and Groundwater

Water scarcity is a major agricultural issue in most arid and semi-arid regions of the world. Alternative water supplies, such as the reuse of wastewater for agricultural irrigation, have been introduced. However, little is known about their impact on the soil and rhizosphere microbiomes that receive irrigation. Therefore, this work evaluates the impact of treated wastewater (TWW) irrigation on the soil and rhizosphere bacterial communities of date palms in Al Madinah, Saudi Arabia. In this study, metagenomic DNA from the rhizosphere of the date palm was sequenced using Illumina high-throughput sequencing. According to the observed OTUs, Chao1 richness estimations, and Shannon diversity values, soils from groundwater-irrigated date palms showed higher microbial diversity than did soils from TWW-irrigated date palms. A total of 569 OTUs were generated; most of them (97.3%) were assigned into 15 different phyla, whereas 2.7% were marked as unclassified. DNA sequence analysis of the WWT-irrigated rhizosphere showed that the most abundant phyla were Firmicutes (43.6%), Bacteroidetes (17.3%), Proteobacteria (15.2%), and Actinobacteria (14.6%), representing more than 90.7% of the total community, while the soil of the rhizosphere irrigated with GW was dominated by Actinobacteria (44.1%), Proteobacteria (23.4%), Firmicutes (15.5%), and Gemmatimonadetes (4.9%). The most frequently observed species in the two soils were also different. The dominant species in TWW-irrigated soil was Planococcus plakortidis, which is prevalent in saline and moderately saline habitats and can play an important ecological role. The GW-irrigated rhizosphere exhibited higher levels of biocontrol bacteria, particularly Nocardioides mesophilus. These results provide a comprehensive understanding and insights into the population dynamics and microbiome of date palm rhizosphere. The findings show that the irrigation water quality has a significant impact on the microbiome composition. Identifying the microbial diversity is the first step toward determining the best way to use TWW in irrigation.

Enhancement of cadmium uptake in Sedum alfredii through interactions between salicylic acid/jasmonic acid and rhizosphere microbial communities

The focus on phytoremediation in soil cadmium (Cd) remediation is driven by its cost-effectiveness and eco-friendliness. Selecting suitable hyperaccumulators and optimizing their growth conditions are key to enhance the efficiency of heavy metal absorption and accumulation. Our research has concentrated on the role of salicylic acid (SA) and jasmonic acid (JA) in facilitating Cd phytoextraction by “Sedum alfredii (S. alfredii)” through improved soil-microbe interactions. Results showed that SA or JA significantly boosted the growth, stress resistance, and Cd extraction efficiency in S. alfredii. Moreover, these phytohormones enhanced the chemical and biochemical attributes of the rhizosphere soil, such as pH and enzyme activity, affecting soil-root interactions. High-throughput sequencing analysis has shown that Patescibacteria and Umbelopsis enhanced S. alfredii's growth and Cd extraction by modifying the bioavailability and the chemical conditions of Cd in soil. Structural Equation Model analysis further verified that phytohormones significantly enhanced the interaction between S. alfredii, soil, and microbes, leading to a marked increase in Cd accumulation in the plant. These discoveries emphasized the pivotal role of phytohormones in modulating the hyperaccumulators' response to environmental stress and offered significant scientific support for further enhancing the potential of hyperaccumulators in ecological restoration technologies using phytohormones.

Transcriptomic responses of ‘Huping jujube’ (Zizyphus jujuba mill. cv. Huping) fruit to combined treatment of acidic electrolyzed water and high-voltage electrostatic field

The molecular mechanism underlying the preserving superior quality attributes of postharvest Huping jujube fruit by combining acidic electrolyzed water and high-voltage electrostatic field (AH) treatment remained unclear. The high-throughput sequencing analysis revealed a total of 3590 common differentially expressed genes (DEGs) in the T-W-CK0 vs T-W-CK75 and T-W-CK75 vs T-W-AH75 groups. AH treatment down-regulated most genes associated with respiratory metabolism, as well as lignin and anthocyanin biosynthesis, thereby maintaining lower physiological activities, improving taste and color quality of mature-white jujube. Additionally, AH treatment downregulated the genes involved in reactive oxygen species (ROS) generation and disease resistance, while simultaneously upregulating the genes associated with ROS elimination. This suggested that AH treatment could inhibit pathogen infection to prevent the activation of plants’ active defense and reduce the ROS-induced damage. In sum, the present study provided a comprehension explanation that AH treatment improved the storage quality attributes of jujube fruit at the genetic level.

Telomere length as a predictor of therapy response and survival in patients diagnosed with ovarian carcinoma

Impaired telomere length (TL) maintenance in ovarian tissue may play a pivotal role in the onset of epithelial ovarian cancer (OvC). TL in either target or surrogate tissue (blood) is currently being investigated for use as a predictor in anti-OvC therapy or as a biomarker of the disease progression, respectively. There is currently an urgent need for an appropriate approach to chemotherapy response prediction.We performed a monochrome multiplex qPCR measurement of TL in peripheral blood leukocytes (PBL) and tumor tissues of 209 OvC patients. The methylation status and gene expression of the shelterin complex and telomerase catalytic subunit (hTERT) were determined within tumor tissues by High-Throughput DNA methylation profiling and RNA sequencing (RNA-Seq) analysis, respectively. The patients sensitive to cancer treatment (n = 46) had shorter telomeres in PBL compared to treatment-resistant patients (n = 93; P = 0.037). In the patients with a different therapy response, transcriptomic analysis showed alterations in the peroxisome proliferator-activated receptor (PPAR) signaling pathway (q = 0.001). Moreover, tumor TL shorter than the median corresponded to better overall survival (OS) (P = 0.006). TPP1 gene expression was positively associated with TL in tumor tissue (P = 0.026).TL measured in PBL could serve as a marker of platinum therapy response in OvC patients. Additionally, TL determined in tumor tissue provides information on OvC patients' OS.

Microbial community structure in an uranium-rich acid mine drainage site: implication for the biogeochemical release of uranium.

The generation of acid mine drainage (AMD) characterized by high acidity and elevated levels of toxic metals primarily results from the oxidation and dissolution of sulfide minerals facilitated by microbial catalysis. Although there has been significant research on microbial diversity and community composition in AMD, as well as the relationship between microbes and heavy metals, there remains a gap in understanding the microbial community structure in uranium-enriched AMD sites. In this paper, water samples with varying levels of uranium pollution were collected from an abandoned stone coal mine in Jiangxi Province, China during summer and winter, respectively. Geochemical and high-throughput sequencing analyses were conducted to characterize spatiotemporal variations in bacterial diversity and community composition along pollution groups. The results indicated that uranium was predominantly concentrated in the AMD of new pits with strong acid production capacity, reaching a peak concentration of 9,370 μg/L. This was accompanied by elevated acidity and concentrations of iron and total phosphorus, which were identified as significant drivers shaping the composition of bacterial communities, rather than fluctuations in seasonal conditions. In an extremely polluted environment (pH < 3), bacterial diversity was lowest, with a predominant presence of acidophilic iron-oxidizing bacteria (such as Ferrovum), and a portion of acidophilic heterotrophic bacteria synergistically coexisting. As pollution levels decreased, the microbial community gradually evolved to cohabitation of various pH-neutral heterotrophic species, ultimately reverting back to background level. The pH was the dominant factor determining biogeochemical release of uranium in AMD. Acidophilic and uranium-tolerant bacteria, including Ferrovum, Leptospirillum, Acidiphilium, and Metallibacterium, were identified as playing key roles in this process through mechanisms such as enhancing acid production rate and facilitating organic matter biodegradation.