Illumina High-throughput Sequencing Technology Research Articles

Sex-Dimorphic Differential Expression Profiles in the Brain of the Adult Chinese Soft-Shelled Turtle, Pelodiscus sinensis

The Chinese soft-shelled turtle (Pelodiscus sinensis) is an economically important species in aquaculture, and its growth pattern is characterized by significant sexual dimorphism. However, the underlying molecular mechanisms of this phenomenon have mostly been investigated in the gonadal tissues of P. sinensis, and there are no articles on sex differentiation from the brain of P. sinensis. Here, we analyzed transcriptomes of the brains of adult male and female P. sinensis using high-throughput Illumina sequencing technology, establishing a set of differential genes and differential transcription factors. The data showed that there were 908 genes with significant differences in expression, of which 357 genes were up-regulated and 551 genes were down-regulated. We annotated using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG), and screened some genes and pathways related to growth. There were 282 growth-related differential genes and 181 sex-related differential genes. We screened the genes’ growth hormone receptor (GHR) and vascular endothelial growth factor A (VEGFA), which may be related to the growth of P. sinensis. The pathways related to the growth and development of P. sinensis are the growth hormone synthesis, secretion, and action pathway; the MAPK (mitogen-activated protein kinase) pathway; and the calcium signaling pathway. In addition, through gene set enrichment analysis (GSEA), we screened out two genes, LIM homeobox protein 1 (LHX1) and fibroblast growth factor 7 (FGF7), which are related to both growth and sex differentiation, and through protein interaction analysis of these genes, we screened out eight genes, including LHX1, FGF7, GHR, fibroblast growth factor 4 (FGF4), EGFR, BMP3, GLI family zinc finger 2 (GLI2), and neuronal differentiation 1 (NEUROD1), and verified the expression levels of these eight genes in the brain of the P. sinensis by real-time quantitative PCR (qRT-PCR), which supported the reliability and accuracy of our transcriptome analysis. Our study provides a solid foundation for analyzing the mechanisms of sexual-dimorphic growth of P. sinensis and even other turtles.

Deciphering differences in microbial community characteristics and main factors between healthy and root rot-infected Carya cathayensis rhizosphere soils.

Fusarium-induced root rot of Carya cathayensis (C. cathayensis) is a typical soil-borne disease that has severely damaged the Carya cathayensis industry in China. Understanding the interaction among soil microbial communities, soil characteristics, and pathogenic bacteria is very important for the ecological prevention and control of Carya cathayensis root rot. We used Miseq Illumina high-throughput sequencing technology to study the microbial community in the rhizosphere soil of healthy and diseased C. cathayensis, quantified the abundance of bacteria, fungi, and pathogenic fungi, and combined these with soil chemistry and enzyme activity indicators to analyze the characteristics of healthy and diseased rhizosphere soils. We found that the pH, soil organic carbon(SOC), available nitrogen (AN), available phosphorus (AP), available potassium (AK),N-acetyl-β-D-glucosaminidase (NAG) β-glucosidase (BG), fungal gene copy number, bacterial community diversity and network complexity of the diseased soil were significantly lower (p < 0.05), while Fusarium graminearum copies number levels increased (p < 0.05). Additionally, the study found that healthy soils were enriched with beneficial bacteria such as Subgroup_7 (0.08%), MND1 (0.29%), SWB02 (0.08%), and Bradyrhizobium (0.09%), as well as potential pathogen-suppressing fungi such as Mortierella (0.13%), Preussia (0.03%), and Humicol (0.37%), were found to be associated with the growth and development of C. cathayensis. In summary, this research comprehensively reveals the differences in environmental and biological factors between healthy and diseased soils, as well as their correlations. It provides a theoretical basis for optimal soil environmental regulation and the construction of healthy microbial communities. This foundation facilitates the development of multifaceted strategies for the prevention and control of C. cathayensis root rot.

Characterization of the Community Structure of Rhizosphere Soil and Root-endophytic Bacteria in Different Shrubs

In the process of ecological restoration, vegetation plays a crucial role in restoring ecosystem functions. Soil microorganisms are essential components of soil ecosystems, driving material cycling processes and enhancing plant productivity and resilience. This study aimed to investigate the community structure characteristics of rhizosphere soil and root-endophytic bacteria in different shrubs. Specifically, the composition of rhizosphere soil and root-endophytic bacteria in Cotoneaster acutifolius Turcz., Lonicera japonica Thunb., and Cornus alba L. in the loess hilly area of northwest Shanxi was determined using Illumina high-throughput sequencing technology. The results revealed that the dominant phyla of rhizosphere soil bacteria and root-endophytic bacteria in different shrubs were Proteobacteria and Actinobacteria. Additionally, the genera of rhizosphere soil and root-endophytic bacteria differed. Furthermore, the species richness and diversity index of rhizosphere soil bacteria were significantly higher than those of root-endophytic bacteria （P &lt; 0.05）. It was also observed that approximately 64% of the root-endophytic bacteria in the shrubs were present in the rhizosphere soil bacteria, indicating similarity in the bacterial community compositions of different niches. Redundancy analysis （RDA） and Pearson correlation analysis revealed that soil dehydrogenase, soil N-acetyl-β-D glucosidase, alkaline protease, pH, and total phosphorus were the main influencing factors on the bacterial community structures in root-endophytic bacteria （P &lt; 0.05）, while alkaline protease, pH, total carbon, and total nitrogen significantly impacted rhizosphere soil community structures （P &lt; 0.05）. Additionally, the partial least squares path model （PLS-PM） indicated that vegetation could directly affect bacterial communities and indirectly affect them by influencing soil physicochemical properties and soil enzyme activity. In conclusion, the findings of this study provide a theoretical foundation for further research on the relationship between endophytic bacteria and resistance in shrubs.

Sex-Dependent Rhizosphere Microbial Dynamics and Function in Idesia polycarpa through Floral and Fruit Development

Male Idesia polycarpa, which display distinct morphological and physiological traits, exhibit greater adaptability to stressful environments than females. However, the connection between this adaptability and rhizosphere processes remains unclear. Here, we investigate the differences in root bacterial community structures between male and female plants at different developmental stages, identifying bacterial strains associated with plant sex through functional predictions. This study aims to inform the optimal allocation of male and female plants during cultivation and provide a theoretical basis for sex identification and breeding. Samples from seven-year-old male and female plants were collected during the flowering (May) and fruit ripening (October) stages. Rhizosphere nutrient content and bacterial diversity were analyzed using Illumina high-throughput sequencing technology. The results demonstrate that total nitrogen (TN), total carbon (TC), and available potassium (AK) varied between sexes at different times. No significant differences between male and female plants were observed in the Shannon, Simpson, and Chao1 indexes during the flowering period. However, the Chao1 and Shannon indexes were significantly higher at fruit maturity in male rather than female plants. The predominant phyla of rhizosphere bacteria were Pseudomonadota, Acidobacteriota, and Actinomycetes. Interestingly, from flowering to fruit ripening, the dominant phyla in both male and female plants shifted from Actinomycetes to Pseudomonadota. A significant correlation was observed between pH and AK and rhizosphere bacteria (p &lt; 0.05), with metabolism being the main functional difference. This study provides preliminary insights into the functional predictions and analyses of bacteria associated with Idesia polycarpa. The above findings lay the groundwork for further investigation into the sex-specific differences in microbial flora across different developmental stages, elucidating the mechanisms underlying flora changes and offering theoretical support for the high-quality management of Idesia polycarpa.

The complete chloroplast genome of Fuchsia standishii J. Harrison, 1840 (Onagraceae) from Yunnan, China

Fuchsia standishii J. Harrison, 1840, a perennial shrub, is renowned for its vividly colored and uniquely shaped blooms, which have an extended flowering season. Commonly cultivated as an ornamental potted plant, it is utilized in traditional Chinese medicine. In this study, we successfully sequenced and assembled the complete chloroplast genome of F. standishii using high-throughput Illumina sequencing technology. The assembled chloroplast genome displays a typical quadripartite structure, with a total length of 156,391 bp. It consists of a pair of inverted repeat regions (IRs), each measuring 25,069 bp, separated by a large single-copy region (LSC) of 87,754 bp and a small single-copy region (SSC) of 18,499 bp. The overall GC content of the genome is 37.60%. The genome includes a total of 129 genes, comprising 84 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis of 17 complete chloroplast genomes revealed that F. standishii forms a monophyletic group with the entire Circaea. This study provides a molecular foundation for future phylogenetic research on Fuchsia.

Gut microbiota dysbiosis and neurological function recovery after intracerebral hemorrhage: an analysis of clinical samples.

We aimed to investigate the microbial community composition in patients with intracerebral hemorrhage (ICH) and its effect on prognosis. We designed two clinical cohort studies to explore the gut dysbiosis after ICH and their relationship with neurological function prognosis. First, fecal samples from patients with ICH at three time points: T1 (within 24 h of admission), T2 (3 days after surgery), and T3 (7 days after surgery), and healthy volunteers were subjected to 16S rRNA sequencing using Illumina high-throughput sequencing technology. When differential gut microbiota was identified, the correlation between clinical indicators and microbiotas was analyzed. Subsequently, the patients with ICH were categorized into GOOD and POOR groups based on their Glasgow Outcome Scale Extended (GOS-E) score, and the disparities in gut microbiota between the two groups were assessed. Univariate and multivariate logistic regression analyses were performed to identify independent risk factors. The composition and diversity of the gut microbiota in patients with ICH were different from those in the control group and changed dynamically with the extension of the course of cerebral hemorrhage. The abundances of Enterococcaceae, Clostridiales incertae sedis XI, and Peptoniphilaceae were significantly increased in patients with ICH, whereas Bacteroidaceae, Ruminococcaceae, Lachnospiraceae, and Veillonellaceae were significantly reduced. The relative abundance of Enterococcus gradually increased with the extension of the duration of ICH after surgery, and the abundance of Bacteroides gradually decreased. The abundance of Enterococcus before surgery was found to be negatively associated with patient neurological function prognosis. The original ICH score and Lachnospiraceae status were independent risk factors for predicting the prognosis of neurological function in patients with ICH (P < 0.05). Changes in the gut microbiota diversity in patients with ICH were related to prognosis. Lachnospiraceae may have a protective effect on prognosis.IMPORTANCEAcute central nervous system injuries like hemorrhagic stroke are major global health issues. While surgical hematoma removal can alleviate brain damage, severe cases still have a high 1-month mortality rate of up to 40%. Gut microbiota significantly impacts health, and treatments like fecal microbiota transplantation (FMT) and probiotics can improve brain damage by correcting gut microbiota imbalances caused by ischemic stroke. However, few clinical studies have explored this relationship in hemorrhagic stroke. This study investigated the impact of cerebral hemorrhage on the composition of gut microbiota, and we found that Lachnospiraceae were the independent risk factors for poor prognosis in intracerebral hemorrhage (ICH). The findings offer potential insights for the application of FMT in patients with ICH, and it may improve the prognosis of patients.

Microbial Community Structure and Metabolic Function in the Venom Glands of the Predatory Stink Bug, Picromerus lewisi (Hemiptera: Pentatomidae).

The predatory stink bug, Picromerus lewisi (Hemiptera: Pentatomidae), is an important and valuable natural enemy of insect pests in their ecosystems. While insects are known to harbor symbiotic microorganisms, and these microbial symbionts play a crucial role in various aspects of the host's biology, there is a paucity of knowledge regarding the microbiota present in the venom glands of P. lewisi. This study investigated the venom glands of adult bugs using both traditional in vitro isolation and cultural methods, as well as Illumina high-throughput sequencing technology. Additionally, the carbon metabolism of the venom gland's microorganisms was analyzed using Biolog ECO metabolic phenotyping technology. The results showed 10 different culturable bacteria where the dominant ones were Enterococcus spp. and Lactococcus lactis. With high-throughput sequencing, the main bacterial phyla in the microbial community of the venom glands of P. lewisi were Proteobacteria (78.1%) and Firmicutes (20.3%), with the dominant bacterial genera being Wolbachia, Enterococcus, Serratia, and Lactococcus. At the fungal community level, Ascomycota accounted for the largest proportion (64.1%), followed by Basidiomycota (27.6%), with Vishniacozyma, Cladosporium, Papiliotrema, Penicillium, Fusarium, and Aspergillus as the most highly represented fungal genera. The bacterial and fungal community structure of the venom glands of P. lewisi exhibited high species richness and diversity, along with a strong metabolism of 22 carbon sources. Functional prediction indicated that the primary dominant function of P. lewisi venom-gland bacteria was metabolism. The dominant eco-functional groups of the fungal community included undefined saprotroph, fungal parasite-undefined saprotroph, unassigned, endophyte-plant pathogen, plant pathogen-soil saprotroph-wood saprotroph, animal pathogen-endophyte-plant pathogen-wood saprotroph, plant pathogen, and animal pathogen-endophyte-epiphyte-plant pathogen-undefined saprotroph. These results provide a comprehensive characterization of the venom-gland microbiota of P. lewisi and demonstrate the stability (over one week) of the microbial community within the venom glands. This study represents the first report on the characterization of microbial composition from the venom glands of captive-reared P. lewisi individuals. The insights gained from this study are invaluable for future investigations into P. lewisi's development and the possible interactions between P. lewisi's microbiota and some Lepidopteran pests.

Microbial community diversity analysis of kiwifruit pollen and identification of potential pathogens.

The kiwifruit industry typically uses commercial pollen for artificial pollination. However, during the collection of male flowers and pollen production, pollen can be easily contaminated by pathogenic bacteria that cause diseases such as canker and flower rot. Consequently, it is crucial to understand the structure of the pollen microbial community. This study employed Illumina high-throughput sequencing technology to analyze the fungal and bacterial composition in pollen samples from various regions in Shaanxi Province. Concurrently, potential pathogenic strains were isolated using traditional microbial isolation and cultivation techniques, and their molecular identification was performed through 16S rDNA sequence analysis. A tieback test was conducted on healthy branches to verify the pathogenicity of the strains. The results revealed a rich diversity of fungi and bacteria in kiwifruit pollen. At the phylum level, pollen fungi were mainly distributed in Ascomycota, and bacteria were mainly distributed in Proteobacteria and Firmicutes. The dominant fungal genera were Mycosphaerella, Aspergillus, and Cladosporium; the dominant bacterial genera were Weissella, Pantoea, Enterobacter, and Pseudomonas, respectively. Additionally, both Erwinia persicina and Pseudomonas fluorescens, isolated from pollen, exhibited high pathogenicity toward healthy kiwifruit branches. These findings contribute to a deeper understanding of the microbial diversity in commercial kiwifruit pollen used for mass pollination.

Complete chloroplast genome sequence and phylogenetic analysis of Populus maximowiczii Henry 1913 (Salicaceae Mirb.)

The classification and identification of species in Populus has remained a formidable challenge due to widespread interspecies hybridization. The complete chloroplast genome of Populus maximowiczii was obtained by Illumina high-throughput sequencing technology, with a typical quadripartite structure and 37.0% GC content. The chloroplast genome of P. maximowiczii was 156,892 in length, including a large single-copy region (LSC: 84,988 bp), a small single-copy region (SSC: 16,630 bp), and a pair of inverted repeats (IRs: each 27,637 bp in length). A total of 131 genes were annotated, including 86 protein-coding genes, 37 tRNAs, and 8 rRNAs. The phylogenetic analysis indicated that 43 species belonging to Populus were classified into monophyly, with P. cathayana being the closest relatives to P. maximowiczii. In conclusion, this study provides valuable insights into understanding the phylogeny of Populus.

Structure and Diversity of Endophytic Bacteria in Maize Seeds and Germinating Roots.

Seed endophytes in maize, which facilitate the transmission of microorganisms from one plant generation to the next, may play a crucial role in plant protection and growth promotion. This study aimed to investigate the effects of various maize varieties on the communities of endophytic bacteria in seeds and germinating roots. This study utilized Illumina high-throughput sequencing technology to examine the structural and diversity differences of endophytic bacterial communities within seed maize (BY1507), silage maize (QQ446), and wild maize (Teosinte) in both seeds and germinating roots. The results showed that 416 bacterial genera were detected, with Pantoea, Lachnospiraceae, Pararhizobium, Enterobacteriaceae, Stenotrophomonas, and Pseudonocardia being the most prevalent (relative abundance > 10%) at the genus level. No significant difference was observed in diversity indices (Chao1, ACE, Shannon, and Simpson) of seed endophytes among BY1507, QQ446, and Teosinte. The Shannon and Simpson indices for the germinating root endophyte from the wild variety (Teosinte) were significantly higher than the domesticated varieties (BY1507 and QQ446). PCoA revealed a notable overlap in the endophytic bacterial communities from the seeds of BY1507, QQ446, and Teosinte. Yet, clustering patterns were found. Co-occurrence network analysis showed that BY1507, QQ446, and Teosinte share a notable proportion of shared endophytic bacteria (>30%) between the seeds and germinating roots. This investigation elucidates the characteristics of endophytic microbial communities of seeds and germinating roots with seed maize, silage maize, and wild maize, offering data for future research on the physiological ecological adaptation of these endophytic microbial communities.

Analyzing the quality differences between healthy and moldy cigar tobacco leaves during the air-curing process through fungal communities and physicochemical components.

The air-curing process of cigar tobacco, as a key step in enhancing the quality of cigars, is often susceptible to contamination by mold spores, which severely constrains the quality of cigar tobacco. This study employed high-throughput Illumina sequencing technology and a continuous flow analysis system to analyze the differences between the microbial communities and physicochemical components of moldy and healthy cigar tobacco leaves. Furthermore, correlation analysis was performed to reveal the impact of mold on the quality of cigar tobacco. The differences between the microbial flora and physicochemical compositions of moldy (MC) and healthy (HC) tobacco leaves were analyzed, revealing significant disparities between the two groups. Aspergillus spp. represented the dominant mold in MC, with nine out of twelve isolated molds showing higher quantities on MC than on HC. Mold contamination notably decreased the total nitrogen (TN), total phosphorus (TP), total alkaloids (TA), starch, protein, and flavor constituents while increasing the total fatty acid esters (TFAA), which was accompanied by a shift towards weakly acidic pH in the leaves. Fungal community analysis indicated a significant reduction in the fungal operational taxonomic unit (OUT) numbers and diversity indices in MC, contrasting with the bacterial trends. Aspergillus exhibited significantly higher relative abundance in MC, with LEfSe analysis pinpointing it as the primary driver of differentiation. Furthermore, significant negative correlations were observed between Aspergillus and TP, starch, TA, and protein, while a significant positive association was evident with TFAA. Network analysis underscored the pivotal role of Aspergillus as the species influencing disparities between HC and MC, with its abundance serving as a critical determinant during the air-curing process. This study elucidated substantial quality distinctions between MC and HC during air-curing, with Aspergillus emerging as the key species contributing to leaf mold.

Transcriptome analysis and development of EST-SSR markers in the mushroom Auricularia heimuer

Auricularia heimuer, the third most frequently cultivated edible mushroom species worldwide, has high medicinal value. However, a shortage of molecular marker hinders the efficiency and accuracy of genetic breeding efforts for A. heimuer. High-throughput transcriptome sequencing data are essential for gene discovery and molecular markers development. This study aimed to clarify the distribution of SSR loci across the A. heimuer transcriptome and to develop highly informative EST-SSR markers. These tools can be used for phylogenetic analysis, functional gene mining, and molecular marker-assisted breeding of A. heimuer. This study used Illumina high-throughput sequencing technology to obtain A. heimuer transcriptome data. The results revealed 37,538 unigenes in the A. heimuer transcriptome. Of these unigenes, 24,777 (66.01%) were annotated via comparison with the COG, Pfam, and NR databases. Overall, 2510 SSRs were identified from the unigenes, including 6 types of SSRs. The most abundant type of repeats were trinucleotides (1425, 56.77%), followed by mononucleotides (391, 15.58%) and dinucleotides (456, 18.17%). Primer pairs for 102 SSR loci were randomly designed for validity confirmation and polymorphism identification; this process yielded 53 polymorphic EST-SSR markers. Finally, 13 pairs of highly polymorphic EST-SSR primers were used to analyze the genetic diversity and population structure of 52 wild A. heimuer germplasms, revealing that the 52 germplasms could be divided into three categories. These results indicated that SSR loci were abundant in types, numbers, and frequencies, providing a potential basis for germplasm resource identification, genetic diversity analysis, and molecular marker-assisted breeding of A. heimuer.

Response of the microbial community structure to the environmental factors during the extreme flood season in Poyang Lake, the largest freshwater lake in China.

Poyang Lake is the largest freshwater lake in China, and there are several studies on the composition and diversity of bacteria in Poyang Lake, while few quantitative studies were carried out on the response of the bacterial community to environmental factors during the extreme flood season in Poyang Lake. The connected-lake heterogeneity of bacterial community composition (BCC) was investigated in Poyang Lake during the flood season in 2020. Illumina high-throughput sequencing technology was used in this study. The bacterial community structure in the water was different from that in the sediment of Poyang Lake during extreme flood seasons. The bacterial diversity in water was much lower than that in sediment. In the water column, the dominant phyla were Actinobacteriota, while the composition of bacteria in sediment was more complex than that in water, and the dominant phyla in sediment were Proteobacteria, Chloroflexi, Acidobacteriota, and Actinobacteriota. The bacterial diversity in the water of Poyang Lake showed seasonal dynamics, while no seasonal variation of bacterial communities in sediment was observed. The bacterial community structure in the sediment from the two bays and channel areas of Poyang Lake can be distinguished from each other. The microbial diversity in sediment gradually increased from the Sancha Bay to the Zhouxi Bay and then to the channel, but the total nitrogen (TN) concentration in sediment (STN) and the total phosphorus (TP) concentration in sediment (STP) showed opposite trends. This might be due to the anthropogenic disturbances from the extreme flood. The bacterial community structure in, water column was significantly correlated with WT, NH4-N, STP, SOM, Chl a, DO, TP, and Eh, while the bacterial community structure in sediment was significantly correlated with SOM and STP. The bacterial community structure in water was greatly different from that in sediment in Poyang Lake during extreme flood seasons. The bacterial community structure in the water column was not only sensitive to the geochemical characteristics of the water but also affected by some nutrient concentrations in the sediment. During the wet seasons, bacterial diversity was only affected by SOM and STP.

Paeonol attenuates nonalcoholic steatohepatitis by regulating intestinal flora and AhR/NLRP3/Caspase-1 metabolic pathway

Ethnopharmacological relevanceNon-alcoholic steatohepatitis (NASH) is a common metabolic liver injury disease that is closely associated with obesity and metabolic disorders. Paeonol, an active ingredient found in Moutan Cortex, a traditional Chinese medicine which exhibits significant therapeutic effect on liver protection, has shown promising effects in treating liver diseases, particularly NASH. However, the specific intervention mechanism of paeonol on NASH is still unknown. Aim of the studyOur objective is to elucidate the pharmacological mechanism of paeonol in intervening NASH at the in vivo level, focusing on the impact on intestinal flora, tryptophan-related targeted metabolome, and related Aryl hydrocarbon receptor (AhR) pathways. Materials and methodsHere, we explored the intervention effect of paeonol on NASH by utilizing the NASH mouse model. The Illumina highthroughput sequencing technology was preformed to determine the differences of gut microbiota of model and paeonol treatment group. The concentration of Indoleacetic acid is determined by ELISA. The intervention effect of NASH mouse and AhR/NLRP3/Caspase-1 metabolic pathway is analyzed by HE staining, oil red O staining, Immunohistochemistry, Immunofluorescence, Western blot and qRT-PCR assays. Fecal microbiota transplantation experiment also was performed to verify the intervention effect of paeonol on NASH by affecting gut microbiota. ResultsFirstly, we discovered that paeonol effectively reduced liver pathology and blood lipid levels in NASH mice, thereby intervening in the progression of NASH. Subsequently, through 16S meta-analysis, we identified that paeonol can effectively regulate the composition of intestinal flora in NASH mice, transforming it to resemble that of normal mice. Specifically, paeonol decreased the abundance of certain Gram-negative tryptophan-metabolizing bacteria. Moreover, we discovered that paeonol significantly increased the levels of metabolites Indoleacetic acid, subsequently enhancing the expression of AhR-related pathway proteins. This led to the inhibition of the NOD-like receptor protein 3 (NLRP3) inflammasome production and inflammation generation in NASH. Lastly, we verified the efficacy of paeonol in intervening NASH by conducting fecal microbiota transplantation experiments, which confirmed its role in promoting the AhR/NLRP3/cysteinyl aspartate specific proteinase (Caspase-1) pathway. ConclusionsOur findings suggest that paeonol can increase the production of Indoleacetic acid by regulating the gut flora, and promote the AhR/NLRP3/Caspase-1 metabolic pathway to intervene NASH.

Transcriptomic analysis of the response of Avena sativa to Bacillus amyloliquefaciens DGL1.

Bacillus amyloliquefaciens DGL1, isolated from the arid sandy areas in Dagler, Qinghai Province, China, promotes the growth of Avena sativa variety "Qing Yan 1". To elucidate the transcriptomic changes in the oat root system following interaction with DGL1 and to reveal the molecular mechanism by which DGL1 promotes oat growth, treatment and control groups of oat roots at 2, 4, 8, and 12 h after inoculation with a suspension of strain DGL1 were analyzed using Illumina high-throughput transcriptome sequencing technology. The differentially expressed genes were determined through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses, and the metabolic pathways and key genes were analyzed. The results showed that 7874, 13,392, 13,169, and 19,026 differentially expressed genes were significantly enriched in the glycolysis/gluconeogenesis pathway, amino acid metabolism, nitrogen metabolism, plant hormone signal transduction, and other related metabolic pathways in the oat roots at 2, 4, 8, and 12 h after inoculation with a DGL1 suspension. The GO and KEGG enrichment analyses revealed that the genes encoding plasma membrane ATPase, phosphoglycerate kinase gene PGK, ammonium transporter protein gene AMT, cellulose synthase gene CSLF6, and growth hormone response family gene IAA18 were significantly upregulated. It is hypothesized that the pro-growth mechanism of strain DGL1 in oats is the result of the coordination of multiple pathways through the promotion of oat energy metabolism, phytohormone signaling, secondary metabolite synthesis, and amino acid metabolism.

Effects of Four-Year Oilseed Flax Rotations on the Soil Bacterial Community in a Semi-Arid Agroecosystem

Crop rotation aims to improve the sustainability and production efficiency of agricultural ecosystems, especially as demands for food and energy continue to increase. However, the regulation of soil microbial communities using crop rotation with oilseed flax and its relationship with key soil physicochemical driving factors are still not clear. In order to investigate this matter, we carried out a field study lasting four years involving various crop rotation sequences including FWPF, FPFW, PFWF, FWFP, ContF, and ContF1. In addition to evaluating soil physicochemical parameters, we employed Illumina high-throughput sequencing technology to explore the structure and variety of soil microbial communities. The findings indicated a notable rise in pH value with the FPFW treatment in contrast to other treatments, along with significant increases in AP, MBC, MBN, and qSMBC compared to ContF. The number of OTUs in the FPFW, WFPF, FPFW, and PFWF treatments was significantly increased by 4.10–11.11% compared to ContF (p &lt; 0.05). The presence of Actinobacteria and Acidobacteria was greatly impacted by the FPFW treatment, whereas the presence of Actinobacteria and Chloroflexi was notably influenced by the ContF treatment. The soil bacterial community was primarily influenced by TC, pH, and NO3−-N according to correlation analysis. Specifically, the FPFW therapy notably raised the soil pH level while lowering the TC level. Furthermore, the FPFW therapy led to a notable rise in the proportion of Acidobacteria and a significant decline in the proportion of Actinobacteria. These findings provide important theoretical support for using FPFW rotation to regulate soil microbial communities and solve the problems of continuous cropping.

Helicobacter pylori causes gastric dysbacteriosis in chronic gastritis patients.

Gastric mucosal samples were procured and underwent the sequencing of 16S ribosomal RNA (16S rRNA) via Illumina high-throughput sequencing technology to explore the impact of Helicobacter pylori (H. pylori) infection on the composition of gastric flora in chronic gastritis (CG) patients. In the results, the operational taxonomic unit (OTU) analysis revealed an overlap of 5706 OTUs shared between the two groups. The top 5 abundance ranking (TOP5) phyla comprised Bacteroidetes, Proteobacteria, Firmicutes, Actinobacteria, and Epsilonbacteraeota, while the TOP5 genus was Lachnospiraceae_NK4A136_group, Helicobacter, Bacteroides, Klebsiella, and Pseudomonas. In the metabolic pathways at the Kyoto Encyclopedia of Genes and Genomes (KEGG)_L3 level, conspicuous variations across seven functions were observed between the H. pylori-positive (HP_Pos) and H. pylori-negative (HP_Neg) groups. Subsequently, functional gene enrichment in KEGG pathways was further validated through animal experimentation. In contrast to the mice in the HP_Neg group, those infected with H. pylori manifested an infiltration of inflammatory cells, an augmentation in gastric acid secretion, and conspicuously elevated scores regarding gastric activity, along with heightened levels of malondialdehyde. In conclusion, CG patients infected with H. pylori displayed a disorder in gastric flora, furnishing a theoretical basis for the prophylaxis of H. pylori infection and its associated pathogenic ramifications.

Molecular Characterization and Phylogenetic Analysis of Centipedegrass [Eremochloa ophiuroides (Munro) Hack.] Based on the Complete Chloroplast Genome Sequence.

Centipedegrass (Eremochloa ophiuroides) is an important warm-season grass plant used as a turfgrass as well as pasture grass in tropical and subtropical regions, with wide application in land surface greening and soil conservation in South China and southern United States. In this study, the complete cp genome of E. ophiuroides was assembled using high-throughput Illumina sequencing technology. The circle pseudomolecule for E. ophiuroides cp genome is 139,107 bp in length, with a quadripartite structure consisting of a large single copyregion of 82,081 bp and a small single copy region of 12,566 bp separated by a pair of inverted repeat regions of 22,230 bp each. The overall A + T content of the whole genome is 61.60%, showing an asymmetric nucleotide composition. The genome encodes a total of 131 gene species, composed of 20 duplicated genes within the IR regions and 111 unique genes comprising 77 protein-coding genes, 30 transfer RNA genes, and 4 ribosome RNA genes. The complete cp genome sequence contains 51 long repeats and 197 simple sequence repeats, and a high degree of collinearity among E. ophiuroide and other Gramineae plants was disclosed. Phylogenetic analysis showed E. ophiuroides, together with the other two Eremochloa species, is closely related to Mnesithea helferi within the subtribe Rottboelliinae. These findings will be beneficial for the classification and identification of the Eremochloa taxa, phylogenetic resolution, novel gene discovery, and functional genomic studies for the genus Eremochloa.

Impact of artisanal refining activities on bacterial diversity in a Niger Delta fallow land

Hydrocarbon pollution is a major ecological problem facing oil-producing countries, especially in the Niger Delta region of Nigeria. In this study, a site that had been previously polluted by artisanal refining activity was investigated using 16S rRNA Illumina high-throughput sequencing technology and bioinformatics tools. These were used to investigate the bacterial diversity in soil with varying degrees of contamination, determined with a gas chromatography-flame ionization detector (GC-FID). Soil samples were collected from a heavily polluted (HP), mildly polluted (MP), and unpolluted (control sample, CS) portion of the study site. DNA was extracted using the Zymo Research (ZR) Fungi/Bacteria DNA MiniPrep kit, followed by PCR amplification and agarose gel electrophoresis. The microbiome was characterized based on the V3 and V4 hypervariable regions of the 16S rRNA gene. QIIME (Quantitative Insights Into Microbial Ecology) 2 software was used to analyse the sequence data. The final data set covered 20,640 demultiplexed high-quality reads and a total of 160 filtered bacterial OTUs. Proteobacteria dominated samples HP and CS, while Actinobacteria dominated sample MP. Denitratisoma, Pseudorhodoplanes, and Spirilospora were the leading genera in samples HP, CS, and MP respectively. Diversity analysis indicated that CS [with 25.98 ppm of total petroleum hydrocarbon (TPH)] is more diverse than HP (with 490,630 ppm of TPH) and MP (with 5398 ppm of TPH). A functional prediction study revealed that six functional modules dominated the dataset, with metabolism covering up to 70%, and 11 metabolic pathways. This study demonstrates that a higher hydrocarbon concentration in soil adversely impacts microbial diversity, creating a narrow bacterial diversity dominated by hydrocarbon-degrading species, in addition to the obvious land and ecosystem degradation caused by artisanal refining activities. Overall, the artisanal refining business is significantly driving ecosystem services losses in the Niger Delta, which calls for urgent intervention, with focus on bioremediation.

Paddy-Lilium Crop Rotation Improves Potential Beneficial Soil Fungi and Alleviates Soil Acidification in Lilium Cropping Soil

Lilium growth is severely impeded by continuous cropping, and crop rotation is essential to reducing the detrimental effects of monocultures. Soil (0–20 cm) was collected in three Lilium cropping patterns in Longshan County, Hunan Province, including continuous Lilium cropping (Lilium), corn upland rotation with Lilium (Corn), and paddy rotation with Lilium (Rice). Using Illumina high-throughput sequencing technology, the fungal ribosomal DNA internal-transcribed spacer 1 (ITS1) was examined to evaluate the features of soil fungi communities among three cropping patterns. Crop rotation has an impact on soil properties and the microbial community. Rice soil has a significantly higher pH than Lilium and corn soil, while corn and rice soil have a greater total nitrogen and total phosphorus content than Lilium soil. Rotation cropping clearly shifted the fungi community diversity based on the results of principal coordinate analysis (PCoA) and nonmetric multidimensional scaling (NMDS). Ascomycota was the most prevalent phylum, with the highest levels in Lilium soil. Genetic analysis revealed that paddy rotation led to a clear reduction in or non-detection of eight potentially pathogenic fungal genera and a noticeable accumulation of eight beneficial fungal genera compared to Lilium continuous cropping. Fungi communities and their abundant taxa were correlated with soil pH and nutrients. Altogether, we propose that rice rotation, with its ability to mitigate soil acidification, reducing pathogenic and accumulating beneficial communities, may be an effective strategy for alleviating the continuous cropping barrier.