High-throughput Sequencing Techniques Research Articles

Bioaugmentation of halophilic consortium for degradation of 1,4 dioxane (1,4-DE) and treatment of cosmetic industrial wastewater in continuous stirred tank reactor under saline condition

The heterocyclic ether 1,4-Dioxane (1,4-DE) is a toxic by-product used widely in various industrial activities as a solvent or stabilizer. 1,4-DE was classified as a probable human carcinogen according to the United States Environmental Protection Agency (USEPA) due to its chemical and physical properties. Emerging pollutants in industrial wastewater is the major challenge for the operation of effluent treatment plant. The bioremediation of 1,4-DE is an effective approach to treat the industrial wastewater. The bacterial consortium was obtained from industrial sludge samples, Yanbu, Saudi Arabia and enriched in 1,4-DE supported basal salt saline medium. Biodegradation of 1,4-DE was studied at several concentrations ranging from 200 to 1200 mg/L. Complete mineralization of 1,4-DE from 200 to 800 mg/L was achieved in 4 to 8 days at 4% salinity. 1,4-DE utilization was studied at different salinity (4% and 6%), the results exhibited complete mineralization of 1,4-DE at 4 days and 6 days respectively. Increase in salinity to 8% displayed 92% degradation of 1,4-DE. Addition of yeast extract accelerated the biomass production correspondingly reduced the time required for biodegradation under saline condition. The bacterial consortium showed the ability to degrade 1,4-DE completely at various range of concentrations. Lab scale continuous stirred tank reactor (CSTR) was used to evaluate the industrial wastewater treatment efficacy of the bacterial consortium under saline condition. CSTR operated for 36 days displayed chemical oxygen demand (COD) removal and 1,4-DE degradation of 96% under saline condition. THF (Tetrahydrofuran) which accelerated the degradation process of 1,4-DE was completely degraded in 28 days. Bacterial analysis with high throughput sequencing technique confirmed the existence of bacterial strains like Ochrobactrum (45%), Marinobacter (21%), Stenotrophomonas (16%), Pseuodomonas (9%), Sphingomonas (4%), Bacillus (3.5%) and Sedimentibacter (1.5%).

In Silico Identification of tRNA Fragments, Novel Candidates for Cancer Biomarkers, and Therapeutic Targets.

The identification of a wide variety of RNA molecules using high-throughput sequencing techniques in the transcriptome pool of living organisms has revealed hidden regulatory insights in the cell. The class of non-coding RNA fragments produced from transfer RNA, or tRFs, is one such example. They are heterogeneously sized molecules with lengths ranging between 15 and 50nt. They have a history of being dysregulated in human malignancies and other illnesses. The detection of these molecules has been made easier by a variety of bioinformatics techniques. The various types of tRFs and how they relate to cancer are covered in this chapter. It also provides a summary of the biological significance of tRFs reported in human cancer. Additionally, it emphasizes the utilities of databases and computational tools that have been created by different research teams for the investigation of tRFs. This will further aid the exploration and analysis of tRFs in cancer research and will support future advancement and a better comprehension of these molecules.

Climatic factors and fertilization rates co-regulate anaerobic methane oxidation driven by multiple electron acceptors in Chinese paddy fields

Paddy fields constitute a substantial anthropogenic reservoir of methane, with their inundation management fostering an ideal habitat for anaerobic methane oxidation. Within this context, a novel clade of anaerobic methanotrophic (ANME) archaea, known as ANME-2d, has been identified as capable of catalyzing anaerobic methane oxidation in conjunction with nitrate and metal oxide reduction processes within paddy fields. Nevertheless, our comprehension of the mechanisms governing anaerobic methane oxidation and its pivotal role in regulating methane emissions within rice paddies remains limited. This study quantified the rates of nitrate- and iron (III)-driven anaerobic methane oxidation through 13C-labeled stable isotope tracing experiments in Chinese paddy fields spanning diverse climate zones. Additionally, it investigated the ANME-2d archaeal community using quantitative polymerase chain reaction and high-throughput sequencing techniques. The nitrate-driven anaerobic methane oxidation contributed 10.9% to methane emission reduction. This contribution is equal to the previously identified contribution of nitrite-driven anaerobic methane oxidation (11.2%) mediated via NC10 bacteria, but played more important roles than iron-driven one (4.1%). The rates of nitrate- and nitrite-driven anaerobic methane oxidation differed significantly among climate zones and showed positive correlation with the mean annual temperature. Furthermore, their rates were more sensitive to temperature increases at higher and lower latitudes, respectively, under both representative concentration pathways 2.6 and 8.5. The rate of anaerobic methane oxidation driven by nitrate exhibited a positive correlation with nitrogen fertilization rate but displayed a negative correlation with phosphorus fertilization rate. Conversely, the rate of anaerobic methane oxidation driven by iron showed no significant correlation with either nitrogen or phosphorus fertilization rates. This study underscores the great potential of anaerobic methane oxidation in mitigating global warming, particularly under the conditions of future climate change and elevated nitrogen loading. These findings underline the necessity of incorporating anaerobic methane oxidation as a crucial parameter in methane emission prediction models.

Metagenomic Next-Generation Sequencing for Accurate Diagnosis of Pneumocystis jirovecii Pneumonia: A Comparative Study with Traditional Methods.

Metagenomic next-generation sequencing (mNGS) is a high-throughput sequencing technique that identifies a wide array of pathogens directly from clinical specimens. This study evaluates the diagnostic value of mNGS in Pneumocystis jirovecii pneumonia (PJP) and compares its efficacy with traditional detection methods, including Grocott's Methenamine Silver (GMS) staining, serum (1-3)-β-D-Glucan (BDG) testing, and Lactate Dehydrogenase (LDH) testing. Seventy-eight patients hospitalized between January 2022 and March 2023 with suspected pulmonary infections were included. Patients were eligible for mNGS if they exhibited symptoms such as fever, cough, dyspnea, or progressive hypoxemia, and met specific clinical criteria for PJP. Specimens obtained included bronchoalveolar lavage fluid, sputum, and peripheral blood. Positive rates and pathogen distributions detected by mNGS and traditional methods were compared. In the PJP group, 25%, 37.5%, and 9.38% of patients had solid organ tumors, corticosteroid use, and skin diseases, respectively, significantly higher than in the non-PJP group. The sensitivity and specificity of mNGS were both 100%, significantly higher than those of serum BDG (sensitivity 50%, specificity 81.8%) and LDH (sensitivity 9.3%, specificity 91.3%). Significant differences in microbial composition between the PJP and Non-PJP groups were observed. mNGS detected multiple mixed pathogens in 96.88% of PJP cases, with 68.75% exhibiting mixed bacterial and viral infections. Notably, 71% of patients improved following antibacterial treatment based on mNGS results. mNGS technology shows superior sensitivity and specificity in diagnosing PJP and guides precise treatment for complex pulmonary infections.

DNA Sequencing Technologies and DNA Barcoding.

DNA barcodes are short, standardized DNA segments that geneticists can use to identify all living taxa. On the other hand, DNA barcoding identifies species by analyzing these specific regions against a DNA barcode reference library. In its initial years, DNA barcodes sequenced by Sanger's method were extensively used by taxonomists for the characterization and identification of species. But in recent years, DNA barcoding by next-generation sequencing (NGS) has found broader applications, such as quality control, biomonitoring of protected species, and biodiversity assessment. Technological advancements have also paved the way to metabarcoding, which has enabled massive parallel sequ.encing of complex bulk samples using high-throughput sequencing techniques. In future, DNA barcoding along with high-throughput techniques will show stupendous progress in taxonomic classification with reference to available sequence data.

Effects of revegetation on soil nitrogen-fixation and carbon-fixation microbial communities in the Horqin Sandy Land, China

To determine the diversity of nitrogen-fixing and carbon-fixing microbial groups in aeolian sandy soil and the effects of sand-fixation plantation type on the structures of two microbial groups in the Horqin Sandy Land, we selected six representative sand-fixation vegetations with the same age, including Caragana microphylla, Artemisia halodendron, Salix gordejevii, Hedysarum fruticosum, Populus simonii, and Pinus sylvestris var. mongolica as well as their adjacent natural Ulmus pumila open forest as test objects to investigate the diversities and structures of nifH- and cbbL-carrying microbial communities in soil by high-throughput sequencing technique. The results showed that vegetation type significantly affected soil physical and chemical properties, microbiological activities, diversities and the main compositions of nitrogen-fixing and carbon-fixing microbial communities. The diversity of soil nitrogen-fixing microbial communities under S. gordejevii and P. simonii plantations and that of carbon-fixing microbial communities under P. sylvestris var. mongolica and P. simonii plantations were significantly higher than those of other plantations. Skermanella, Bradyrhizobium, Azospirillum, and Azohydromonas were dominant nitrogen-fixation genera, with the average relative abundance of 22.3%, 21.5%, 20.8%, and 17.8%, respectively. Soil carbon-fixation microbial communities were dominated by Pseudonocardia, Bradyrhizobium, Cupriavidus, and Mesorhizobium, with relative abundance of 22.4%, 18.5%, 10.5%, and 6.0%, respectively. Soil nitrogen-fixing microbial community under C. mirophylla plantation and carbon-fixing communities under S. gordejevii and P. simonii plantations were very close to those of natural U. pumila open forest. Soil organic matter, NH4+-N, and total phosphorus were the direct determining factors for nitrogen-fixing microbial community, while pH, soil moisture, and available phosphorus were main factors influencing carbon-fixing microbial community. These observations potentially provide the scienti-fic foundations for evaluating the ecological benefits of revegetation practice in sandy lands.

Microbial fungicides can positively affect aubergine photosynthetic properties, soil enzyme activity and microbial community structure.

This study examined the effects of microbial agents on the enzyme activity, microbial community construction and potential functions of inter-root soil of aubergine (Fragaria × ananassa Duch.). This study also sought to clarify the adaptability of inter-root microorganisms to environmental factors to provide a theoretical basis for the stability of the microbiology of inter-root soil of aubergine and for the ecological preservation of farmland soil. Eggplant inter-root soils treated with Bacillus subtilis (QZ_T1), Bacillus subtilis (QZ_T2), Bacillus amyloliquefaciens (QZ_T3), Verticillium thuringiensis (QZ_T4) and Verticillium purpureum (QZ_T5) were used to analyse the effects of different microbial agents on the inter-root soils of aubergine compared to the untreated control group (QZ_CK). The effects of different microbial agents on the characteristics and functions of inter-root soil microbial communities were analysed using 16S rRNA and ITS (internal transcribed spacer region) high-throughput sequencing techniques. The bacterial diversity index and fungal diversity index of the aubergine inter-root soil increased significantly with the application of microbial fungicides; gas exchange parameters and soil enzyme activities also increased. The structural and functional composition of the bacterial and fungal communities in the aubergine inter-root soil changed after fungicide treatment compared to the control, with a decrease in the abundance of phytopathogenic fungi and an increase in the abundance of beneficial fungi in the soil. Enhancement of key community functions, reduction of pathogenic fungi, modulation of environmental factors and improved functional stability of microbial communities were important factors contributing to the microbial stability of fungicide-treated aubergine inter-root soils.

A blood-based multi-omic landscape for the molecular characterization of kidney stone disease.

Kidney stone disease (KSD, also named renal calculi, nephrolithiasis, or urolithiasis) is a common urological disease entailing the formation of minerals and salts that form inside the urinary tract, frequently caused by diabetes, high blood pressure, hypertension, and monogenetic components in most patients. 10% of adults worldwide are affected by KSD, which continues to be highly prevalent and with increasing incidence. For the identification of novel therapeutic targets in KSD, we adopted high-throughput sequencing and mass spectrometry (MS) techniques in this study and carried out an integrative analysis of exosome proteomic data and DNA methylation data from blood samples of normal and KSD individuals. Our research delineated the profiling of exosomal proteins and DNA methylation in both healthy individuals and those afflicted with KSD, finding that the overexpressed proteins and the demethylated genes in KSD samples are associated with immune responses. The consistency of the results in proteomics and epigenetics supports the feasibility of the comprehensive strategy. Our insights into the molecular landscape of KSD pave the way for a deeper understanding of its pathogenic mechanism, providing an opportunity for more precise diagnosis and targeted treatment strategies for KSD.

Toxicity factors to assess the ecological risk for soil microbial communities

The toxicity factor (TF), a critical parameter within the potential ecological risk index (RI), is determined without accounting for microbial factors. It is considerable uncertainty exists concerning its validity for quantitatively assessing the influence of metal(loid)s on microorganisms. To evaluate the suitability of TF, we constructed microcosm experiments with varying RI levels (RI = 100, 200, 300, 500, and 700) by externally adding zinc (Zn), chromium (Cr), copper (Cu), lead (Pb), nickel (Ni), cadmium (Cd), and mercury (Hg) to uncontaminated soil (CK). Quantitative real-time PCR (qPCR) and high-throughput sequencing techniques were employed to measure the abundance and community of bacteria and fungi, and high-throughput qPCR was utilised to quantify functional genes associated with CNPS cycles. The results demonstrated that microbial diversity and function exhibited significant alterations (p < 0.05) in response to increasing RI levels, and the influences on microbial community structure, enzyme activity, and functional gene abundances were different due to the types of metal(loid)s treatments. At the same RI level, significant differences (p < 0.05) were discerned in microbial diversity and function across metal(loid) treatments, and these differences became more pronounced (p < 0.001) at higher levels. These findings suggest that TF may not be suitable for the quantitative assessment of microbial ecological risk. Therefore, we adjusted the TF by following three steps (1) determining the adjustment criteria, (2) deriving the initial TF, and (3) adjusting and optimizing the TF. Ultimately, the optimal adjusted TF was established as Zn = 1.5, Cr = 4.5, Cu = 6, Pb = 4.5, Ni = 5, Cd = 22, and Hg = 34. Our results provide a new reference for quantitatively assessing the ecological risks caused by metal(loid)s to microorganisms.

Research advances in genetic polymorphisms in Kawasaki disease

Kawasaki disease (KD) is a systemic inflammatory vascular disorder that predominantly affects children and is the leading cause of acquired heart disease in children. Although the etiology of this disease remains unclear, genome-wide association and genome-wide linkage studies have shown that some susceptible genes and chromosomal regions are associated with the development and progression of KD. With the advancement of high-throughput DNA sequencing techniques, more and more genomic information related to KD is being discovered. Understanding the genes involved in the pathogenesis of KD may provide novel insights into the diagnosis and treatment of KD. By analyzing related articles and summarizing related research advances, this article mainly discusses the T cell activation-enhancing genes that have been confirmed to be closely associated with the development and progression of KD and reveals their association with the pathogenesis of KD and coronary artery lesions.

The coupled effect of sediment resuspension and microbiota on phosphorus release and transformation in a simulated aquatic ecosystem

Plant microbial involvement in phosphorus (P) release and transformation during resuspension events in bottom aquatic systems remains poorly understood. Laboratory experiments were used in this study to explore the release and transformation of P from sediments and the microbiota involved. Dissolved and labile P were obtained by high-resolution dialysis and the diffusive gradients in thin films (DGT) technique, respectively. The bacterial community was investigated using a scanning electron microscope and 16S rRNA high throughput sequencing technique. Finally, the diffusion fluxes dynamics of phosphorus were calculated using the DGT-induced fluxes in sediments and soils (DIFS) model. These results showed that sustained disturbance can balance dissolved P concentrations in the resuspension layer (overlying water) and enhance the stability of P transformation and release processes. Notably, the bacterial community within the deeper sediment layer (Below 10 mm sediment depth) significantly influences P interception. Acidobacteria and Neobacteria were identified as the key bacterial genera responsible for phosphorus adsorption of plant roots at speeds of 150 rad/min (R150). In addition, as the sediment depths increased, a slower decrease in R curves fitted with the DIFS model, which indicated a continuous resupply process from solid phase to pore water, especially below R150. This study provides theoretical references for managing shallow lakes with frequent sediment resuspension.

Arbuscular mycorrhizal fungi communities vary between poplar species in the same habitat

The species diversity of AMF is influenced by the cultivar of the host plant. For this study, six species of poplar (Populus spp.) were selected from the poplar germplasm conservation experimental forest in Tongzhou, Beijing, China. The aim of the study was to compare the chemical characteristics of the poplar stand soils, including total carbon, total nitrogen, total phosphorus, and available phosphorus. The composition of the AMF community was also analyzed using high-throughput sequencing techniques. Significant differences in soil nutrient content (total phosphorus, available phosphorus, carbon/nitrogen, carbon/phosphorus) were found between different species of Populus spp. (p < 0.05), although the total carbon, total nitrogen, and nitrogen/phosphorus of the soil did not differ significantly (p > 0.05). Notably, the Simpson index and Pielou index of the AMF community exhibited the most significant differences among the various poplar cultivars, with the highest mean values for P. × euramericana cl. ‘J6’ (0.98 and 0.77, respectively). Furthermore, significant correlations were observed between the relative abundance of AMF communities at each taxonomic level and soil nutrient content. At the generic level, the relative abundance of Glomus has the highest correlation with C/N and C/P (r = −0.79). Overall, the findings of this study highlight the impact of poplar species on the composition and structure of the soil AMF community, which is closely related to soil nutrient content. These results contribute to our understanding of the plant–AMF–soil interaction mechanisms and provide a solid basis for future research in this field.

Effect of runx2b deficiency in intermuscular bones on the regulatory network of lncRNA-miRNA-mRNA

Intermuscular bones (IBs) are mineralized spicules that negatively impact the quality and value of fish products. Runx2b is a crucial modulator in promoting bone formation through regulating osteoblast differentiation. Previous studies suggested that loss of runx2b gene completely inhibited IBs formation in zebrafish. However, how the whole transcriptome, including mRNA and non-coding RNA (ncRNA), affects the IBs development in runx2b−/− zebrafish are not known. The aim of this study was to identify the regulatory networks of differentially expressed (DE) lncRNAs, miRNAs, and mRNAs in zebrafish with and without IBs (runx2b+/+ fish and runx2b−/− fish) utilizing high-throughput sequencing techniques. All together there are 1051 mRNAs, 456 lncRNAs, and 18 miRNAs differentially expressed were found between these two strains. The analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG) has highlighted significant pathways linked to the development of IBs, specifically the TGF-beta and Wnt signaling pathways, and a number of genes concentrated on these two signaling pathways related to the formation of IBs. Further, 1989 competing endogenous RNA (ceRNA) networks were created according to the correlation among mRNAs, miRNAs and lncRNAs. The ceRNA networks results revealed 52 ceRNA pairs related to the IBs formation, consisting of 52 mRNAs, 37 lncRNAs, and 6 miRNAs. Of these, we found that dre-miR-2189 was the key element of ceRNA pairs, interacting with 19 mRNAs and 11 lncRNAs, and MSTRG.13175.1 could regulate sp7 expression by interacting with dre-miR-2189 to function in osteogenic differentiation. Subsequent experiments at the cellular level also revealed the interaction mechanism. The outcomes indicated a crucial role of miRNAs and lncRNAs in the development of fish IBs, which offer new views into the functions of ncRNAs involved in IBs formation.

Changes in the structure and function of soil prokaryotic communities in subalpine Picea asperata plantations

The structural and functional characteristics of soil prokaryotic community are important for maintaining ecosystem functions. In this study, we examined the diversity and compositions, the key drivers, as well as functional characteristics of prokaryotic communities in the rhizosphere and non-rhizosphere soils of Picea asperata with different stand ages using high-throughput sequencing technique and bioinformatics methods. The results showed that β-diversity of soil prokaryotic communities in both rhizosphere and non-rhizosphere showed significant differences among different stand ages, but no significant difference between rhizosphere and non-rhizosphere in the same stand age. In terms of community composition at the phylum level, the relative abundances of Proteobacteria and Rokubacteria showed an increasing trend with the increases of stand age, while the relative abundance of Actinobacteria showed a decreasing trend, but no significant difference was observed between 75 year-old planted forests (PF75) and natural forests (NF). The relative abundances of Firmicutes and Thaumarchaeota in the soil of the 25 year-old planted forests (PF25) were significantly higher than in other planted forests and NF. At the genus level, the relative abundances of RB41, Terrimonas and Acidibacter showed an increasing trend with the increases of stand age, and RB41 and Terrimonas in rhizosphere soil of PF75 were significantly higher than those in NF. Soil properties and vegetation characteristics jointly influenced the structure of soil prokaryotic communities, with herb layer coverage, soil pH, total phosphorus, and total nitrogen as major drivers. The functional characteristics of soil prokaryotic communities were significantly different among different stand ages. The relative abundances of functions involved in carbon and nitrogen cycle, e.g., cellulolysis and nitrification, decreased with the increases of stand age, whereas that of sulfate respiration involved in the sulfur cycle increased. We proposed that the structure and functional characteristics of soil prokaryotic communities could serve as important indicators of the development stages of P. asperata forests. In the later stages of plantation forest development, soil nutrient availability could be improved by mediating phosphorus-dissolving and nitrogen-enhancing microorganisms to maintain the stability of the plantation ecosystem.

Loss of Mir-221/222 Cluster Expression Results in Short-Term Disease Progression and Poor Post-Treatment Outcome in Multiple Myeloma

Despite the notable progress that has been achieved in the realm of MM treatment, the persistence of elevated relapse rates and therapy resistance remain a substantial hindrance to effective management of the patients. Therefore, the development of modern tools to ameliorate patients' prognosis and predict treatment outcome is of first clinical priority. MicroRNAs (miRNAs) have emerged as powerful post-transcriptional regulators of gene expression, while recent advances in high-throughput sequencing techniques have unveiled their prognostic utility in numerous pathologies. Herein, using a miRNA-seq we have investigated miRNA profiles in association with Revised International Staging System (R-ISS), aiming to reveal potential MM-related miRNAs able to improve patients' risk stratification. Bone marrow (BM) aspiration samples were collected from 120 MM patients at diagnosis (screening cohort). Mononuclear cells were isolated using Ficoll-Paque, while CD138 + plasma cells were positively selected using anti-CD138 mAbs magnetic beads. miRNA-seq was performed in CD138 + cells from 8 R-ISS I, 8 R-ISS II and 8 R-ISS III MM patients. Following 3‘-end polyadenylation of total RNA, miR-221/222 levels were quantified in our screening cohort by RT-qPCR. Disease progression (relapse and/or death) and patients’ mortality were assessed as clinical endpoint events, while internal validation was accomplished by bootstrap Cox proportional regression analysis. Aash et al. 2023 (n=86) and Kruykov et al. 2016 (n=149) served as external validation cohorts. miRNA-seq revealed miR-221/222 to be concurrently downregulated in R-ISS III versus R-ISS I/II MM patients (miR-221: FC=0.356; miR-222: FC=0.357; Fig.1B,C). The analysis of our screening cohort documented that CD138 + miR-221/222 loss is significantly associated with higher risk for short-term disease progression ( p=0.010; Fig.1D) and poor survival ( p=0.001; Fig.1E) of MM patients. Furthermore, the analysis of the two independent validation cohorts (Aass et al. cohort A, p=0.019; and Kryukov et al. cohort B, p=0.013) clearly confirmed the worse treatment outcome of the patients with miR-221/222 loss (Fig.1F,G). Moreover, miR-221/222-fitted multivariate models demonstrated the ability of miR-221/222 cluster to ameliorate the clinical routine of the established MM prognostic markers, including “R-ISS stage”, “high-risk cytogenetics” [+1q21, t (4;14) del(17p13), t(14;16), t(11;14), del(13q)] and “response to 1 st line therapy” (IMWG guidelines). In this context, the evaluation of CD138 + miR-221/222 levels significantly improved the risk-stratification of MM patients, resulting in the advanced positive prediction of patients' poor treatment outcome within R-ISS III (PFS: p=0.006, OS: p=0.019; Fig.2A,B) and high-risk cytogenetics groups (PFS: p=0.025, OS: p=0.022; Fig.2C,D). Finally, focusing on patients' response to 1 st line therapy stratification, loss of miR-221/222 could efficiently define optimal (sCR/CR/VGPR) and poor (PR/SD/PD) responders' subgroups (PFS: p&amp;lt;0.001, OS: p&amp;lt;0.001; Fig.2E,F). In conclusion, we identified miR-221/222 loss in CD138 + plasma cells as a powerful independent predictor of patients' risk for disease progression and poor treatment outcome, while miR-221/222-fitted multivariate prognostic models resulted to improved patients' risk-stratification and prediction of MM treatment outcome.

Changes in bacterial communities induced by integrated production systems and the phenological stages of soybean

Plant development and productivity depend on interactions with soil microorganisms for nutrient availability, promotion of growth and protection against phytopathogens. Although the influence of the phenological stages of soybean crops and their environmental conditions on the soil bacterial communities have already been reported, no studies have focused on the influence of integrated agrosilvopastoral systems on bacterial consortia. In this study, we evaluated the influence of the phenological stages of soybean cultivated under conventional full sunlight (CFS) and integrated crop-livestock-forestry (ICLF) systems on bacterial communities in the rhizosphere and in bulk soil using high-throughput sequencing techniques. Proteobacteria, Actinobacteriota and Acidobacteriota were the most abundant phyla in both the rhizosphere and the bulk soil at all growth stages. The results support our hypotheses that the richness and diversity of soil bacterial communities are influenced by different cultivation systems, and that the structure of the bacterial communities in the rhizosphere and the bulk soil are modulated by the phenological stages of the soybean crop.

Soil prokaryotic characterization in response to natural moisture gradient in the temperate grassland ecosystems

Abstract Soil moisture, which is an important factor affecting ecosystem function, can maintain microbial activity and ultimately change the microbial community by altering vegetation diversity and controlling the diffusion and transport of soil nutrients. To explore the effects of soil water content (SWC) on soil prokaryotic community, we established a study area covering a natural soil moisture gradient and subdivided it into high (HW, 4.80 ± 1.18%), medium (MW, 2.17 ± 0.09%) and low water contents (LW, 1.85 ± 0.14%) in the grassland ecosystem along the south shore of Hulun Lake in Inner Mongolia, China. Environmental factors were determined by field surveys and laboratory analyses. Soil prokaryotes were determined by high-throughput sequencing techniques. Vegetation characteristics and soil physicochemical properties had a significant effect on prokaryotic richness diversity, and SWC was the most important factor influencing prokaryotic richness diversity. In the MW, the number of differential prokaryotes was lowest, and prokaryotic microorganisms had the highest diversity and relative abundance at the phylum level, which may reflect less intrinsic variation and higher overall activity of the prokaryotic community in the MW. In addition, HW and LW had lower prokaryotic diversity and relative abundance at the phylum level, and phenotypic predictions for both groups indicated a more tolerant prokaryotic community. In summary, the prokaryotic community responded significantly to the natural moisture gradients in grassland ecosystems along the south shore of Hulun Lake, and both too high and too low soil moisture increased prokaryotic stress resistance.

Astragalus polysaccharide promotes autophagy and alleviates diabetic nephropathy by targeting the lncRNA Gm41268/PRLR pathway

Background Astragalus polysaccharide (APS) is a major bioactive component of the Chinese herb astragalus, with well-established protective effects on the kidney. However, the effect of APS on diabetic nephropathy (DN) is unclear. Methods Long non-coding RNA (lncRNA) expression profiles in kidney samples from control, db/db, and APS-treated db/db mice were evaluated using RNA high-throughput sequencing techniques. Additionally, rat renal tubular epithelial (NRK-52E) cells were cultured in high glucose (HG) media. We inhibited the expression of Gm41268 and prolactin receptor (PRLR) by transfecting NRK-52E cells with Gm41268-targeting antisense oligonucleotides and PRLR siRNA. Results We found that APS treatment reduced 24-h urinary protein levels and fasting blood glucose and improved glucose intolerance and pathological renal damage in db/db mice. Furthermore, APS treatment enhanced autophagy and alleviated fibrosis in the db/db mice. We identified a novel lncRNA, Gm41268, which was differentially expressed in the three groups, and the cis-regulatory target gene PRLR. APS treatment induced autophagy by reducing p62 and p-mammalian target of rapamycin (mTOR) protein levels and increasing the LC3 II/I ratio. Furthermore, APS alleviated fibrosis by downregulating fibronectin (FN), transforming growth factor-β (TGF-β), and collagen IV levels. In addition, APS reversed the HG-induced overexpression of Gm41268 and PRLR. Reduction of Gm41268 decreased PRLR expression, restored autophagy, and ameliorated renal fibrosis in vitro. Inhibition of PRLR could enhance the protective effect of APS. Conclusions In summary, we demonstrated that the therapeutic effect of APS on DN is mediated via the Gm41268/PRLR pathway. This information contributes to the exploration of bioactive constituents in Chinese herbs as potential treatments for DN.

Composition, interaction networks, and nitrogen metabolism patterns of bacterioplankton communities in a grassland type Lake: a case of Hulun Lake, China

The composition of bacterial communities in freshwater ecosystems is influenced by numerous factors including environmental conditions and biological interactions. In grassland inland closed lakes, factors affecting lake ecosystems are either exogenous or endogenous, contributing to the formation of distinct habitats in the surface and bottom waters of the bacterial communities. However, the extent to which environmental factors selectively shape the bacterial communities in aquatic systems remains unclear. Therefore, we sampled the surface, middle, and bottom waters at 13 sampling points in each layer. High-throughput sequencing techniques were employed to examine the spatial heterogeneity of the bacterial community structure during summer in Hulun Lake, the largest grassland-type lake in Inner Mongolia, China, to determine the microbial community dynamics and symbiosis patterns under different habitat conditions. Our results revealed a decrease in the diversity and heterogeneity of the bacterioplankton community, influenced by changes in the environment from exogenous inputs to endogenous releases. Furthermore, this alteration in community structure was concomitant with enhanced co-occurrences among microorganisms in the bottom water layers. This finding suggests that endogenous release promotes heightened symbiotic interactions, thereby facilitating the development of more complex modular structures. Symbiotic networks in different layers were differentiated by key species, with the ecological clustering modules of these species demonstrating dissimilar environmental preferences. The microbial communities were highly habitat-specific, mimicking responses to total nitrogen (TN) in the surface layer, pH in the middle layer, and chemical oxygen demand (COD) in the bottom layer. Bacterioplankton functions were assessed using Tax4Fun, indicating exogenous inputs and endogenous release increased the relative abundance of genes with nitrogen-fixing and nitrification potential nitrogen metabolism functions in surface and bottom waters, respectively. With Planctomycetota and Proteobacteria phyla as potential key groups for regulating nitrogen metabolic processes, Proteobacteria may facilitate the depletion of nitrate in surface and bottom waters, while the close contact of surface waters with the atmosphere accelerated Planctomycetota-dominated nitrogen fixation into the lake. Our findings contribute to the understanding of vertical microbial diversity and its network patterns in grassland type lakes, underscoring the potential role of environmental factors (exogenous inputs and endogenous releases) in bacterioplankton community formation.

Leaf, root, and soil microbiomes of an invasive plant, Ardisia crenata, differ between its native and exotic ranges

IntroductionEcological underpinnings of the invasion success of exotic plants may be found in their interactions with microbes, either through the enemy release hypothesis and the enhanced mutualism hypothesis. Whereas recent high-throughput sequencing techniques have significantly expanded our understanding of plant-associated microbiomes and their functional guilds, few studies to date have used these techniques to compare the microbiome associated with invasive plants between their native and exotic ranges.MethodsWe extracted fungal and bacterial DNA within leaf endosphere, root endosphere and soil of an invasive plant, Ardisia crenata, sampled from their native range Japan and exotic range Florida, USA. Using Illumina sequencing data, we compared microbial community compositions and diversity between the native and exotic ranges, and tested whether abundance of pathogenic or mutualistic microbes differ between the native or exotic ranges in accordance to the enemy release hypothesis or the enhanced mutualism hypothesis.ResultsFungal and bacterial community compositions differed among leaves, roots and soil, and between the native and exotic ranges. Despite a higher microbial diversity in the soil in the exotic range than in the native range, the microbial diversity within leaf and root was lower in the exotic range compared to the native range. In addition, leaves in the native range harbored a greater number of plant pathogenic fungi compared to those in the exotic range.DiscussionThese patterns suggest plant controls over what microbes become associated with leaves and roots. The higher abundance of leaf pathogenic fungi, including the pathogen which is known to cause specific disease in A. crenata in the exotic range than in the native range, support the enemy release hypothesis and highlighted potential importance of examining microbial communities both above- and below-ground.