Computational Analysis of T-Cell Receptor Repertoire Workflow: From T-Cell Isolation to Bioinformatics Analysis.

The T-cell receptor (TCR) is the key molecule involved in the adaptive immune response. It is generated by the V(D)J recombination, responsible of the enormous diversity of the TCR repertoire, a crucial feature determining the individual capability to response to antigens and to build immunological memory. A pivotal role in the recognition of antigen is played by the hypervariable complementarity-determining region 3 (CDR3) of the V-beta chain of TCR. Investigating the CDR3 supports the understanding of the adaptive immune system dynamics in physiological processes, such as immune aging, and in disease, especially autoimmune disorders in which T cells are main actors. High-throughput sequencing (HTS) paved the way for a great progress in the investigation of TCR repertoire, enhancing the read depth in the process of library generation of sequencing and the number of samples that can be analyzed simultaneously. Therefore, the leverage of big datasets stressed the need to develop computational approach, by bioinformatics, to unravel the characteristics of the TCR repertoire.

Insights into cytomegalovirus-associated T cell receptors in recipients following allogeneic hematopoietic stem cell transplantation.

BACKGROUND: Cytomegalovirus (CMV) reactivation is a serious problem in recipients of allogeneic hematopoietic stem cell transplantation. Long-term latency depends on specific T cell immune reconstitution, which identifies various pathogens by T cell receptors (TCRs). However, the mechanisms underlying the selection of CMV-specific TCRs in recipients after transplantation remain unclear. METHODS: Using high-throughput sequencing and bioinformatics analysis, the T cell immune repertoire of seven CMV reactivated recipients (CRRs) were analyzed and compared to those of seven CMV non-activated recipients (CNRs) at an early stage after transplant. RESULTS: The counts of unique complementarity-determining region 3 (CDR3) were significantly higher in CNRs than in CRRs. The CDR3 clones in the CNRs exhibit higher homogeneity compared to the CRRs. With regard to T cell receptor ß-chain variable region (TRBV) and joint region (TRBJ) genotypes, significant differences were observed in the frequencies of TRBV6, BV23, and BV7-8 between the two groups. In addition to TRBV29-1/BJ1-2, TRBV2/BJ2-2, and TRBV12-4/BJ1-5, 11 V-J combinations had significantly different expression levels between CRRs and CNRs. CONCLUSIONS: The differences in TCR diversity, TRBV segments, and TRBV-BJ combinations observed between CNRs and CRRs might be associated with post-transplant CMV reactivation and could serve as a foundation for further research.

Changes in Soil Bacterial and Nematode Communities during Long-term Continuous Cotton Cropping in an Arid Region.

larifying the effects of continuous cotton cropping (CC) on soil biological communities is essential for maintaining agricultural productivity. In this study, high-throughput sequencing was used to study the effects of different CC durations (0-yr, 5-yr, 10-yr, 15-yr, 20-yr, and 25-yr CC treatments) on soil microbial and nematode communities. The results showed that the dominant bacterial phyla were Actinobacteria and Proteobacteria, and the dominant nematode genus was Helicotylenchus in all CC treatments. The richness indexes (ACE and Chao1 index) and diversity index (Shannon index) of bacterial and nematode communities were the highest in the 15-yr and 10-yr CC treatments, respectively. Bacterial community was significantly correlated with soil pH and available potassium (AK), and nematode abundance was significantly correlated with microbial biomass carbon (MBC). Soil bacterial PICRUSt analysis results showed that carbon metabolism and amino acid metabolism were the main metabolic functions of bacteria in the CC treatments. The composition and diversity of soil nematode communities were significantly related to the structure of soil bacterial communities, and the niche breadth of soil bacteria was negatively correlated with that of nematodes. Panagrolaimus and Acrobeles were the main genera of bacterialfeeding nematodes affecting bacterial communities, and their relative abundances were significantly positively correlated with the relative abundance of bacterial communities. Overall, long-term (10-15 years) continuous cotton cropping negatively impacts soil biota and the microecological environment of cotton fields in arid regions.

Metagenomic insights into traditional fermentation of rice-based beverages among ethnic tribes in southern Assam, Northeast India.

Introduction: Traditional fermented foods have long been recognized for their numerous health benefits along with their potential to aid in the treatment of gastrointestinal disorders. These fermented foods have been shown to promote gut health and contribute to a longer, healthier life. Methods: The high-throughput sequencing using the Illumina MiSeq platform was employed to investigate the microbiome communities of rice-based fermented beverages consumed by ethnic tribes in Southern Assam, namely Zeme Naga, Dimasa Kachari, Hmar, Karbi and Tea tribes. Results: The fermented rice-based beverages were highly predominated by Firmicutes, Bacteroides, Proteobacteria, and Actinobacteria exhibiting the highest relative abundance across all tribes. At genus level, significant abundance of pediococcus, lactobacillus, bacillus, leuconostoc, acetobacter, staphylococcus, delftia, erwinia, klebsiella and chrysebacterium were found amongst these ethnic tribes. Discussion: Understanding the fermented food microbiome will help to know the relationships between microbial communities and their effect on health of humans amongst the tribes. Furthermore, the use of these fermented products could provide enhanced health benefits to southern Assam region of India.

Composition and diversity of endophytic bacterial communities in the tubers of Pinellia ternata from different regions and their effects on succinate biosynthesis based on high-throughput sequencing.

In this study, high-throughput sequencing (HTS) technology was used to investigate the composition and diversity of endophytic bacteria and their effects on succinic acid biosynthesis in P. ternata tubers from three different geographical locations (MS, SL, and ZT). A total of 1777 amplicon sequence variants (ASVs) were annotated, and the diversity and composition of endophytic bacteria in P. ternata tubers were significantly different among different regions. The ZT samples presented the highest α diversity, and the Shannon diversity, richness, and Pielou evenness index were all ZT > MS > SL. Co-occurrence network analysis revealed that endophytic bacterial groups such as Stenotrophomonas, Pseudomonas, Mycobacterium, and Chryseomicrobium were key groups in the endophytic bacterial interaction network, indicating that they play a role in maintaining community stability. In addition, some endophytic bacteria were associated with the biosynthesis of succinic acid, a key bioactive compound in P. ternata. The succinate content was positively correlated with the genera Brevundimonas, Ensifer, Nocardioides, and Paenibacillus, while it was negatively correlated with the genera Lentimicrobium, Anaerovorax, and Pajaroellobacter. These findings highlight the key role of endophytic bacteria in regulating the efficacy of P. ternata. These findings provide key information for further elucidating the mechanism by which endophytic bacteria affect the synthesis of bioactive compounds.

Microbial diversity and potential functional dynamics within the rhizocompartments of Dendrobium huoshanense.

Introduction: Understanding the microbial diversity and potential functional dynamics within the rhizocompartments of Dendrobium huoshanense is crucial for unraveling the plant-microbe interactions that influence its medicinal properties. Methods: This study is the first to characterize the microbiome associated with the rhizocompartments of D. huoshanense, including its cultivation medium, rhizosphere, rhizoplane, and root endosphere, using high-throughput sequencing and subsequent bioinformatic analysis. Results: Bacterial phylogenetic diversity was significantly higher in the endosphere than in the rhizosphere, while fungal α-diversity significantly decreased from the cultivation medium to the endosphere. Both bacterial and fungal niche widths decreased from the cultivation medium to the endosphere. ß-Diversity analysis revealed distinct spatial patterns in both bacterial and fungal communities across the rhizocompartments, with the most pronounced differences between the cultivation medium and the endosphere. Taxonomically, Proteobacteria and Ascomycota were predominant in the endosphere for bacterial and fungal communities, respectively. Functional predictions showed significant enrichment of pathways related to xenobiotics biodegradation, lipid metabolism, and nitrogen fixation in the endosphere, while functions associated with plant pathogens and saprotrophs were significantly reduced. Discussion: The results indicate a shift from generalist to specialist microbes from the cultivation medium to the endosphere, suggesting that D. huoshanense exerts strong selective pressure for endophytic fungi. Interestingly, a high proportion of fungi with unknown functions were found in the endosphere, highlighting an area for further research regarding the medicinal efficacy of D. huoshanense. Overall, this study provides foundational data for understanding the adaptive evolution of these microbial communities in response to specific microhabitats.

Eco-environmental responses of Eichhornia crassipes rhizobacteria community to co-stress of per(poly)fluoroalkyl substances and microplastics.

The stabilization of rhizobacteria communities plays a crucial role in sustaining healthy macrophyte growth. In light of increasing evidence of combined pollution from microplastics (MPs) and per- and polyfluoroalkyl substances (PFASs), Selecting typical floating macrophyte as a case, this study explored their impacts using hydroponic simulations and 16S rRNA high-throughput sequencing. A total of 31 phyla, 77 classes, 172 orders, 237 families, 332 genera, and 125 rhizobacteria species were identified. Proteobacteria (16.19% to 57.70%) was the dominant phylum, followed by Bacteroidota (12.34% to 44.48%) and Firmicutes (11.31% to 36.36%). In terms of α-diversity, polystyrene (PS) MPs and PFASs significantly impacted community abundance (ACE and PD-tree) rather than evenness (Shannon and Pielou) compared to the control. ßMNTD and ßNTI analyses revealed that PS MPs enhanced deterministic assembly processes driven by F-53B and GenX, while mitigating those induced by PFOA and PFOS. Contamination treatments narrowed the ecological niche breadths at both the phylum (5% (PS) to 49.91% (PS & PFOA)) and genus levels (8% (PS) to 63.96% (PS & PFOA)). Functionally, MPs and PFASs decreased the anaerobic capacity and ammonia nitrogen utilization of rhizosphere bacteria. This study enhances our understanding of the microecological responses of macrophyte-associated bacteria to combined MP and PFAS contamination and offers insights into ecological restoration strategies and mitigating associated environmental risks.

Green manure (Ophiopogon japonicus) cover promotes tea plant growth by regulating soil carbon cycling.

Introduction: In mountainous tea plantations, which are the primary mode of tea cultivation in China, issues such as soil erosion and declining soil fertility are particularly severe. Although green manure cover is an effective agricultural measure for restoring soil fertility, its application in mountainous tea plantations has been relatively understudied. Methods: This study investigated the effects of continuous green manure cover using the slope-protecting plant Ophiopogon japonicus on tea plant growth and soil microbial community structure. We implemented three treatments: 1 year of green manure coverage, 2 years of coverage, and a control, to study their effects on tea plant growth, soil physicochemical properties, and soil bacterial and fungal communities. Results: Results demonstrate that green manure coverage significantly promote the growth of tea plants, enhanced organic matter and pH levels in soil, and various enzyme activities, including peroxidases and cellulases. Further functional prediction results indicate that green manure coverage markedly promoted several carbon cycling functions in soil microbes, including xylanolysis, cellulolysis, degradation of aromatic compounds, and saprotrophic processes. LEfSe analysis indicated that under green manure cover, the soil tends to enrich more beneficial microbial communities with degradation functions, such as Sphingomonas, Sinomonas, and Haliangium (bacteria), and Penicillium, Apiotrichum, and Talaromyce (fungi). In addition. Random forest and structural equation models indicated that carbon cycling, as a significant differentiating factor, has a significant promoting effect on tea plant growth. Discussion: In the management practices of mountainous tea plantations, further utilizing slope-protecting plants as green manure can significantly influence the soil microbial community structure and function, enriching microbes involved in the degradation of organic matter and aromatic compounds, thereby positively impacting tea tree growth and soil nutrient levels.

Genomic mapping of wastewater bacteriophage may predict potential bacterial pathogens infecting the community.

Most existing wastewater surveillance studies that focus on viruses have identified a large fraction of bacteriophages. Identifying bacteria by considering bacteriophage-host interactions is a novel method for detecting bacterial pathogens circulating in a community, using wastewater surveillance. This study aims to identify human-related bacterial pathogens in municipal wastewater collected in metro Detroit, using high-throughput sequencing and bioinformatics. Untreated municipal wastewater samples were collected on August 11, 2020, and bacteriophages were concentrated using the VIRus ADsorption-ELution (VIRADEL) method. Bacteriophage-related contigs in samples ranged from 15.53 % to 18.91 %, with 2477 classified and 8853 unclassified contigs. Most identified bacteriophages were from Caudoviricetes and Malgrandaviricetes classes belonging to 19 families. Hosts of bacteriophages were predicted with the PhaBOX (CHERRY) tool. The results indicated that out of the 2477 classified phages, 2373 were associated with known bacterial hosts. Also, out of 8853 unclassified bacteriophages, 8421 were associated with known bacterial hosts, and the remaining 432 were with unknown bacterial hosts. Among all bacteriophage-associated hosts, 399 were identified as pathogenic bacteria at the species level. Approximately, 85 % of the identified pathogenic bacteria are reported to be associated with human diseases. Genome quality assessments showed that 15 bacteriophages had nearly complete genomes, which were further analyzed to understand bacteriophage-bacteria interactions in wastewater. Identified hosts of these complete-genome phages included human pathogens such as Salmonella enterica, Bacillus cereus, Achromobacter xylosoxidans, and Escherichia coli. The S. enterica bacteriophage (k141_1005294) genomic map was annotated, and responsible open reading frames (ORFs) were characterized to illustrate bacteriophage behavior during infection of pathogenic bacteria in untreated wastewater. To the best of our knowledge, this is the first attempt to characterize human bacterial pathogens in wastewater through bacteriophage-pathogen interactions. Novel bioinformatic approaches enhance pathogen detection and improve the understanding of community wastewater microbiomes.

Intestinal microbiota composition in broilers fed protein-free or casein-based diets.

Growing broiler chickens of the Cobb500 strain were used to determine the effects on intestinal microbiota composition of a protein-free (PF) diet as compared to a diet based in casein (CAS) as the only protein source. CAS was formulated to contain the same amount of protein (190 g kg-1) as a commercial Maize-soy diet which was used as a practical reference. The ileal AA flow (g kg-1 dry matter intake) was significantly higher (P < 0.001) than PF in birds fed protein containing diets (CAS or Maize-soy). Taken as a whole (discriminant and ANOSIM analysis), the intestinal (ileal and caecal contents and ileal tissue) microbiota composition of PF and CAS were significantly (P < 0.001) different from Maize-soy and not different from each other in some cases. RT-qPCR and sequencing analysis of the ileal and caecal microbiota revealed significant (P < 0.05) differences in a number of bacterial groups between broilers fed PF, CAS or Maize-soy diets. The main result was that the lack of protein in the intestinal medium of PF birds resulted in a drop of Lactobacillus spp. counts (on average, 43 in PF vs 1,734 in the Maize-soy diet) and increased Enterobacteriaceae (on average, 419 in PF vs 172 in the Maize-soy diet) and other potentially pathogenic bacterial groups (in both intestinal contents and tissue). Thus, the lack of protein in the intestinal medium of PF birds resulted in a microbiota composition compatible with a pro-inflammatory state, and this effect was somewhat less marked in birds fed CAS. The results reported here suggest that the adverse effects on microbiota composition in broilers fed CAS were less marked than in those fed PF, which would be in line with a preferential use of a highly digestible protein containing diet to determine endogenous AA excretion instead of a PF diet.

The inoculation of Bacillus paralicheniformis and Streptomyces thermoviolaceus enhances the lignocellulose degradation and microbial communities during spent mushroom substrate composting.

The burgeoning global mushroom industry has precipitated challenges related to the efficient and sustainable utilization of spent mushroom substrate (SMS). Composting is regarded as an efficient way for the ecological utilization of SMS. The addition of microbial inoculants can promote the composting process and improve the quality of compost products. This study introduced two bacterial inoculants, Bacillus paralicheniformis HL-05 (BP) and Streptomyces thermoviolaceus LC-10 (ST), into the composting process of SMS. The impact of these inoculants was evaluated through analyses of physicochemical properties, lignocellulose degradation, and high-throughput sequencing to elucidate their ecological roles and optimize the composting process. The results suggest that inoculation with BP and ST significantly prolonged the thermophilic stage by 2-3 days, representing an increase of 22.22-33.33%. Moreover, it boosted the degradation rates of cellulose, hemicellulose, and lignin by 18.37-29.77%, 35.74-50.43%, and 40.32-40.83%, respectively, compared to the control. Furthermore, inoculation rapidly altered the microbial community structure during the rapid temperature-rising stage and strengthened interconnections among composting microorganisms. The microbial inoculation substantially enhanced the proliferation of thermophilic lignocellulose-degrading microorganisms during the thermophilic stage, thereby facilitating the utilization of lignocellulose. This study proposes a novel and effective strategy for SMS composting using microbial inoculants.

Dothistroma septosporum and Dothistroma pini, the causal agents of Dothistroma needle blight, are infected by multiple viruses.

Dothistroma septosporum and Dothistroma pini are severe foliar pathogens of conifers. They infect a broad spectrum of hosts (mainly Pinus spp.), causing chlorosis, defoliation of needles, and eventually the death of pine trees in extreme cases. Mycoviruses represent a novel and innovative avenue for controlling pathogens. To search for possible viruses hosted by Dothistroma spp. we screened a subset of isolates (20 strains of D. septosporum and one D. pini) originating from the Czech Republic, Slovenia, Italy, Austria and Ireland for viral dsRNA segments. Only five of them showed the presence of dsRNA segments. A total of 21 fungal isolates were prepared for total RNA extractions. RNA samples were pooled, and two separate RNA libraries were constructed for stranded total RNA sequencing. RNA-Seq data processing, pairwise sequence comparisons (PASC) and phylogenetic analyses revealed the presence of thirteen novel putative viruses with varying genome types: seven negative-sense single-stranded RNA viruses, including six bunya-like viruses and one new member of the order Mononegavirales; three positive-sense single-stranded RNA viruses, two of which are similar to those of the family Narnaviridae, while the genome of the third correspond to those of the family Gammaflexiviridae; and three double-stranded RNA viruses, comprising two novel members of the family Chrysoviridae and a potentially new species of gammapartitivirus. The results were confirmed with RT-PCR screening that the fungal pathogens hosted all the viruses and showed that particular fungal strains harbour multiple virus infections and that they are transmitted vertically. In this study, we described the narnavirus infecting D. pini. To our knowledge, this is the first virus discovered in D. pini.

Identification of Black Cumin (Nigella sativa) MicroRNAs by Next-Generation Sequencing and Their Implications in Secondary Metabolite Biosynthesis.

Secondary metabolites are bioactive compounds believed to contribute to the pharmacological properties of plants. MicroRNAs (miRNAs) are small non-coding RNA molecules involved in post-transcriptional regulation and are thought to play an important role in regulating secondary metabolism biosynthesis. Nevertheless, the extent of miRNA involvement in secondary metabolism remains minimal. Nigella sativa (black cumin/black seed) is a popular medicinal and culinary plant known for its pharmaceutical properties; however, its genomic information is scarce. In this study, next-generation sequencing (NGS) technology was employed to obtain the miRNA profile of N. sativa, and their involvement in secondary metabolite biosynthesis was explored. A total of 25,139,003 unique reads ranging from 16 to 40 nucleotides were attained, out of which 240 conserved and 34 novel miRNAs were identified. Moreover, 6083 potential target genes were recognized in this study. Several conserved and novel black cumin miRNAs were found to target enzymes involved in the terpenoid, diterpenoid, phenylpropanoid, carotenoid, flavonoid, steroid, and ubiquinone biosynthetic pathways, among others, for example, beta-carotene 3-hydroxylase, gibberellin 3 beta-dioxygenase, trimethyltridecatetraene synthase, carboxylic ester hydrolases, acetyl-CoA C-acetyltransferase, isoprene synthase, peroxidase, shikimate O-hydroxycinnamoyltransferase, etc. Furthermore, sequencing data were validated through qPCR by checking the relative expression of eleven randomly selected conserved and novel miRNAs (nsa-miR164d, nsa-miR166a, nsa-miR167b, nsa-miR171a, nsa-miR390b, nsa-miR396, nsa-miR159a, nsa-miRN1, nsa-miRN29, nsa-miRN32, and nsa-miRN34) and their expression patterns were found to be corroborated with the sequencing data. We anticipate that this work will assist in clarifying the implications of miRNAs in plant secondary metabolism and aid in the generation of artificial miRNA-based strategies to overproduce highly valuable secondary metabolites from N. sativa.

A deployable film method to enable replicable sampling of low-abundance environmental microbiomes.

Urbanizing global populations spend over 90% of their time indoors where microbiome abundance and diversity are low. Chronic exposure to microbiomes with low abundance and diversity have demonstrated negative long-term impacts on human health. Sequencing-based analyses of environmental nucleic acids are critical to understanding the impact of the indoor microbiome on human health, however low DNA yields indoors, alongside sample collection and processing inconsistencies, currently challenge study replicability. This study presents a comparative assessment of a novel, passive, easily replicable sampling strategy using polydimethylsiloxane (PDMS) sheets alongside a representative swab-based collection protocol. Deployable, customizable PDMS films designed for whole-sample insertion into standardized extraction kits demonstrated 43% higher DNA yields per sample, and 76% higher yields per cm2 of sampler over swab-based protocols. These results indicate that this accessible, scalable method enables sufficient DNA collection to comprehensively evaluate indoor microbiome exposures and potential human health impacts using smaller, more space efficient samplers, representing an attractive alternative to swab-based collection. In addition, this process reduces the manual steps required for microbiome sampling which could address inter-study variability, transform the current microbiome sampling paradigm, and ultimately benefit the replicability and accessibility of microbiome exposure studies.

Immune repertoire profiling in myasthenia gravis.

Myasthenia gravis (MG) is the most frequent immune-mediated neurological disorder, characterized by fluctuating muscle weakness. Specific recognition of self-antigens by T-cell receptors (TCRs) and B-cell receptors (BCRs), coupled with T-B cell interactions, activates B cells to produce autoantibodies, which are critical for the initiation and perpetuation of MG. The immune repertoire comprises all functionally diverse T and B cells at a specific time point in an individual, reflecting the essence of immune selectivity. By sequencing the nucleotide sequences of TCRs and BCRs, it is possible to track individual T- and B-cell clones. This review delves into the generation of autoreactive TCRs and BCRs in MG and comprehensively examines the applications of immune repertoire sequencing in understanding disease pathogenesis, developing diagnostic and prognostic markers and informing targeted therapies. We also discuss the current limitations and future potential of this approach.

M6A Modification and Transcription Analysis of LncRNA in Cerebral Ischemia/Reperfusion Injury.

LncRNA is a major factor in the occurrence and development of many diseases. However, its mechanism in cerebral ischemia/reperfusion injury (CIRI) is yet unknown. In this study, the transcriptional level and methylation modification level of LncRNAs before and after mechanical thrombectomy were compared by high-throughput sequencing. Venn diagram, Spearman correlation analysis, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, TargetScan, and miRanda were used to analyze the experimental data. The results showed that four key LncRNAs changed at both transcription and methylation levels. Specifically, LncRNA FAR2, LINC02431, and AL357060.1 were downregulated and hypomethylated, while LncRNA FOXD2-AS1 was upregulated and hypomethylated. Moreover, positive regulation of angiogenesis, protein domain-specific binding, autophagy pathway, PPAR signaling pathway, and MAPK signaling pathway were co-enriched between LncRNAs with different expression levels and different methylation levels. Finally, a LncRNA-miRNA-mRNA network was constructed. Therefore, this study explored the potential key LncRNAs and regulatory mechanisms of CIRI.

Progress in the study of the correlation between sepsis and intestinal microecology.

Sepsis, a disease with high incidence, mortality, and treatment costs, has a complex interaction with the gut microbiota. With advances in high-throughput sequencing technology, the relationship between sepsis and intestinal dysbiosis has become a new research focus. However, owing to the intricate interplay between critical illness and clinical interventions, it is challenging to establish a causal relationship between sepsis and intestinal microbiota imbalance. In this review, the correlation between intestinal microecology and sepsis was summarized, and new therapies for sepsis intervention based on microecological target therapy were proposed, and the shortcomings of bacterial selection and application timing in clinical practice were addressed. In conclusion, current studies on metabolomics, genomics and other aspects aimed at continuously discovering potential probiotics are all providing theoretical basis for restoring intestinal flora homeostasis for subsequent treatment of sepsis.

Effect of temperature on the quality and microbial community during Daocai fermentation.

Daocai is a traditional salted pickle in the southeastern region of Guizhou with a unique aroma, color, and taste. The quality of Daocai is greatly influenced by the fermentation temperature. In this study, high-throughput sequencing and headspace-gas chromatography-ion mobility spectrometry were used to investigate the changes in microbial community succession and volatile flavor compounds during Daocai fermentation under temperature-controlled (D group) and non-temperature-controlled (C group).We found that the predominant genera in the C group samples were Latilactobacillus(40.57 %), Leuconostoc(21.25 %), Cystofilobasidium(22.12 %), Vishniacozyma(23.89 %), and Leucosporidium(24.95 %), whereas Weissella(29.39 %), Lactiplantibacillus(45.61 %), Mucor(68.26 %), and Saccharomyces(23.94 %) were the predominant genera in the D group. A total of 92 VFCs were detected in Daocai samples, including 5 isothiocyanates, 16 esters, 14 alcohols, 24 aldehydes, 17 ketones, 3 acids, 2 pyrazines, 1 pyridines, 1 thiazoles, 3 furans, 4 alkenes, and 2 nitriles. Further analysis revealed Latilactobacillus, Leuconostoc, Lactococcus, Cystofilobasidium, Leucosporidium, Holtermanniella, and Dioszegia as key bacteria involved in flavor formation. They are closely related to the formation of flavors such as aldehydes, furans, pyridines, and alkenes. This study contributes to our understanding of the relationship between bacterial communities and the flavor formation during Daocai fermentation.

High-Throughput Sequencing Identified Multiple Fig Viruses and Viroids Associated with Fig Mosaic Disease in Iraq.

Mosaic is the most common viral disease affecting fig plants. Although the Fig mosaic virus is the leading cause of mosaic disease, other viruses are also involved. High-throughput sequencing was used to assess viral infections in fig plants with mosaic. The genomic DNA and total RNAseq of mosaic-symptomatic fig leaves were sequenced using the Illumina platform. The analysis revealed the presence of fig badnavirus 1 (FBV-1), grapevine badnavirus 1 (GBV-1), citrus exocortis viroid (CEVd), and apple dimple fruit viroid (ADFVd). The FBV-1 and GBV-1 sequences were 7,140 bp and 7,239 bp long, respectively. The two genomes encode one open reading frame containing five major protein domains. The viroids, CEVd and ADFVd, were 397 bp and 305 bp long. Phylogenetic analyses revealed a close relationship between FBV-1 and Iranian isolates of the same species, while GBV-1 was closely related to Russian grapevine badnavirus isolates (Tem64, Blu17, KDH48, and Pal9). CEVd was closely related to other Iraqi isolates, while ADFVd was strongly related to a Spanish isolate. A registered endogenous pararetrovirus, caulimovirus-Fca1, with a size of 7,556 bp, was found in the RNA transcripts with a low expression level. This integrant was also detected in the genomes of the two lines 'Horaishi' (a female line) and 'Caprifig 6085' (a male line). Phylogenetic analyses revealed that caulimovirus-Fca1 was distinct from two other clades of different endogenous virus genera.

Soil microbial community composition and diversity in the rhizosphere of Alsophila spinulosa growing in different habitats within the Chishui Alsophila National Nature Reserve in Guizhou Province, China.

The rhizosphere is considered a highly complex and dynamic ecosystem. Rhizosphere soil microorganisms influence the growth and development of plants by mediating the transformation and absorption of nutrients. In order to explore the microbial community composition and diversity of Alsophila spinulosa growing in different habitats. Rhizosphere samples were collected from four different habitats within the Chishui Alsophila National Nature Reserve in Guizhou Province, China. According to the high-throughput sequencing results of 16 s rDNA and ITS, Proteobacteria and Ascomycota were the most abundant bacterial and fungal phyla in the rhizosphere soil of all four habitats. The alpha diversity analysis indicated that two particular habitats, Buddha Rock and Botanical Garden, harbored the highest microbial richness and diversity. LEfSe analysis revealed that Buddha Rock contained the highest relative abundance of Bacteroidetes compared to the other three study areas. Meanwhile, Tiantang Gou contained the highest relative abundance of Basidiomycota. Bacterial community composition and diversity were greatly influenced by soil pH, while fungal community composition and diversity were greatly influenced by available phosphorus, organic carbon, sucrase, and urease. The results of this study provide a scientific basis for the habitat restoration of A. spinulosa, and the improvement of the structure of the A. spinulosa rhizosphere soil microbial community. Laying a theoretical foundation for the next screening of inter-root functional flora.