Illumina High-throughput Sequencing Research Articles

The characteristics of intestinal microflora in infants with rotavirus enteritis, changes in microflora before and after treatment and their clinical values

Rotavirus (RV) is a leading pathogen causing diarrhea in children. In this study, a total of 51 fecal samples from children with RV enteritis, 29 post-treatment fecal samples, and 38 fecal samples from age-matched healthy controls were collected. Microbial DNA was isolated from the samples followed by high throughput Illumina sequencing targeting 16 S rRNA gene. Compared to the healthy group, the RV-infected group exhibited reduced microbial diversity. Both groups shared Firmicutes as the dominant phylum. Additionally, the abundance of Proteobacteria increased significantly in the RV-infected group. At the genus level, among the top 50 most abundant genera, 34 showed significant differences, with these differential genera correlating with certain clinical indicators such as dehydration levels and C-reactive protein (CRP). Notably, there were no significant differences in the microbiota before and after treatment in RV-infected children. Only 8.82% (3/34) of the differential genera in the post-treatment group showed a recovery trend towards the healthy state. This study enhances the understanding of how RV infection alters the gut microbiota structure in children and provides a scientific basis for improving clinical diagnosis and treatment strategies.

The complete mitochondrial genome sequence of Pseudomphala latericea (Littorinimorpha: Truncatelloidea: Assimineidae)

In this study, the complete mitochondrial genome of Pseudomphala latericea was sequenced by Illumina high-throughput sequencing and its characteristics were analyzed. The mitogenome of P. latericea is 16,635 bp long, and it encodes the standard set of 13 PCGs, 22 tRNA genes, and two rRNA genes. The mitogenome has a GC content of 29.3% and a very high AT content of 70.7%. The maximum-likelihood and Bayesian inference phylogenetic trees clearly demonstrated the relationships among the four genera (Pseudomphala, Assiminea, Sculptassiminea, and Optediceros) within the Assimineidae.

The complete chloroplast genome of Solanum melongena ‘Yunqie 9’

Solanum melongena ‘Yunqie 9’ was selected by the Horticultural Research Institute of Yunnan Academy of Agricultural Sciences based on the local environment of Yunnan Province. It is excellent in fruit quality and yield, but it is relatively weak in disease resistance. No information on complete chloroplast genome and position in the phylogeny of Solanum to restrict its genetic improvement. In this study, the chloroplast genome of ‘Yunqie 9’ was sequenced using Illumina high-throughput sequencing technology. The size of the complete chloroplast genome was 155,579 bp in length with an GC content of 37.70%, composed of a large single-copy region (86,189 bp), a small single-copy region (18,504 bp), and a pair of inverted repeat regions (25,443 bp). A total of 134 coding genes were annotated in the entire chloroplast genome, including 89 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. Phylogenetic analysis based on chloroplast genome sequences of 20 species in the Solanaceae family indicated that except for the cultivated Solanum, ’Yunqie 9’ was closely related to Solanum melongena×Solanum torvum and Solanum insanum.

The neurodevelopmental regulatory role and clinical value of hsa-circ-CORO1C–hsa-miR-708-3p–JARID2 + LNPEP axis in early-onset schizophrenia

Genes discovered by previous epigenetic studies of schizophrenia have focused solely on diagnostics or pathology, potentially leading to a disconnection between them. Using these molecules to identify the disease is considered insufficient. MicroRNAs (miRNAs) binding to messenger RNAs (mRNAs) can lead to mRNA degradation, while circular RNAs (circRNAs), by binding to miRNAs as sponge, can reduce the inhibitory effect of miRNAs on mRNAs. CircRNAs, miRNAs, and mRNAs form the multi-molecular axis that can bind and regulate expression between each other, thereby affecting biological function. This study focused on early-onset schizophrenia (EOS), aiming to identify the multi-molecular axis consisting of circRNAs, miRNAs, and mRNAs with both neurobiological function and diagnostic value to assist in disease identification. In the discovery cohort of 10 drug-naïve, first-episode patients with EOS and 10 matched healthy controls (HCs), differentially expressed (DE) circRNAs and miRNAs were identified via Illumina high-throughput sequencing. In the validation cohort-1 (40 EOS v.s. 50 HCs), the candidate circRNAs and miRNAs were further screened using Real-time polymerase chain reaction, Sanger sequencing, and RNase R assay. Combining dual-luciferase reporter assay with overexpression/knockdown experiments, the axis consisting of circRNAs–miRNAs-mRNAs with binding and regulatory relationships has been established. Subsequently, the functions of genes on the axis were explored through zebrafish embryo manipulation and neural differentiation. The clinical value of the entire axis was assessed in the validation cohort-2 (84 EOS v.s. 67 HCs). Patients with EOS exhibited expression profiles of 487 DE circRNAs and 101 DE miRNAs compared to HCs. The binding relationships and regulatory effects of hsa-circ-CORO1C on hsa-miR-708-3p, hsa-miR-708-3p on target JARID2 and LNPEP were elucidated. Among them, hsa-miR-708-3p caused aberrant phenotypes including significant craniocerebral malformation and impaired neuron axon growth. JARID2 and LNPEP could facilitate neuronal differentiation and augment synaptic formation. In addition to their neurobiological functions, the combined diagnostic efficacy of the whole axis, where hsa-circ-CORO1C could serve as a sponge for hsa-miR-708-3p to alleviate its suppressive effects on JARID2 and LNPEP, surpassed any individual gene we found in EOS. Our study demonstrated a multi-molecular axis, hsa-circ-CORO1C–hsa-miR-708-3p–JARID2 + LNPEP, in EOS for the first time. By integrating evidence from genetic, neurophenotypic, and clinical perspectives, we have expanded the comprehension of the pathological mechanism and provided the reference for identifying reliable objective diagnostic biomarkers for EOS.

Dynamic Impact of One-Year Integrated Rice-Crayfish Farming on Bacterioplankton Communities in Paddy Water.

As global food security issues become increasingly severe, an important innovation in agricultural production patterns, namely integrated rice-fish farming, has been widely implemented around the world, especially in Asia. To assess the impact of integrated rice-crayfish (Procambarus clarkii) farming (IRCF) on agricultural ecosystems, we used Illumina high-throughput 16S rRNA gene sequencing to analyze differences in diversity, composition, co-occurrence network, and assembly process of planktonic bacterial communities in paddy water between traditional rice farming (TRM) and IRCF. Environmental factors and planktonic bacterial communities were evaluated during the tillering, jointing, flowering, and grain-filling stages on August 24, September 5, September 24, and October 16, respectively. Our findings revealed that, throughout the entire cultivation period, IRCF had no notable impacts on bacterioplankton community diversity in paddy water, but it changed the composition and relative abundance of the dominant bacterioplankton. Specifically, IRCF promoted the Chloroflexota during the tillering stage but reduced its presence during the grain-filling stage. It also significantly decreased the Bacillota during the jointing stage while notably enhancing Actinomycetota during the flowering stage. Furthermore, IRCF markedly improved the robustness and negative/positive cohesion within bacterioplankton co-occurrence networks during jointing and grain-filling stages. IRCF altered the assembly processes shaping planktonic bacterial communities, promoting a greater dominance of stochastic processes during the tillering, jointing, and flowering stages and a diminished dominance during the grain-filling stage. IRCF dramatically changed aquatic environmental factors, particularly during the jointing stage, by substantially increasing the TN, ammonium, nitrate, and phosphate levels in paddy water. These nutrient levels were closely correlated with the dynamics of the planktonic bacterial communities. Our findings underscore the considerable potential of IRCF in enhancing the stability of bacterioplankton communities and promoting rice growth while also providing valuable data and theoretical insights into the microbiological ecological impacts of IRCF on the agroecosystem.

Higher frequency of interstate over international transmission chains of SARS-CoV-2 virus at the Rio Grande do Sul - Brazil state borders.

Brazil's COVID-19 response has faced challenges due to the continuous emergence of variants of concern (VOCs), emphasizing the need for ongoing genomic surveillance and retrospective analyses of past epidemic waves to reassess and fine tune containment protocols. Rio Grande do Sul (RS), Brazil's southernmost state, has international borders and trades with Argentina and Uruguay, along with significant domestic connections within Brazil. The identification of source and sink transmission chains at national and international scales can identify main hubs and pathways to target future interventions. In this study we investigated the RS state role in the national and international SARS-CoV-2 transmission chains, which has not been fully explored. Nasopharyngeal samples from various municipalities in RS were collected between June 2020 and July 2022. SARS-CoV-2 whole genome amplification and sequencing were performed using high-throughput Illumina sequencing. Bioinformatics analysis encompassed the development of scripts and tools to perform subsampling taking into account epidemiological information to reduce sequencing disparities bias among the regions/countries, genome assembly, and large-scale alignment and phylogenetic reconstruction. We sequenced a total of 1,480 SARS-CoV-2 genomes from RS, covering all major regions. Sequences predominantly represented Gamma (April-June 2021) and Omicron (January-July 2022) lineages. Phylogenetic analysis revealed a regional pattern for transmission dynamics, particularly with Southeast Brazil for Gamma, and a range of inter-regional connections for Delta and Omicron within the country. On the other hand, international and cross-border transmission with Argentina and Uruguay was rather limited. We evaluated the three VOCs circulation over two years in RS using a new subsampling strategy based on the number of cases in each state during the circulation of each VOC. In summary, the retrospective analysis of genomic surveillance data demonstrated that virus transmission was less intense between country borders than within the country. These findings suggest that while non-pharmacological interventions were effective to mitigate transmission across international RS land borders, while they were insufficient to contain transmission at the domestic level.

Unveiling the bacterial diversity and potential of the Avicennia marina ecosystem for enhancing plant resilience to saline conditions

BackgroundAvicennia marina ecosystems are critical for coastal protection, water quality enhancement, and biodiversity support. These unique ecosystems thrive in extreme saline conditions and host a diverse microbiome that significantly contributes to plant resilience and growth. Global food security is increasingly threatened by crop yield losses due to abiotic stresses, including saline soils. Traditional plant breeding for salt tolerance is both costly and time-consuming. This study explores the potential of bacteria from A. marina to enhance plant growth under saline conditions, emphasizing their ecological significance.ResultsWe analyzed the microbiome of A. marina from the Red Sea coast using high-throughput Illumina sequencing and culture-dependent methods across various compartments (bulk soil, rhizosphere, rhizoplane, roots, and leaves). Our findings revealed distinct compartment-specific microbial communities, with Proteobacteria being the dominant phylum. Functional predictions indicated diverse microbial roles in metal uptake and plant growth promotion (PGP). Remarkably, our culture-dependent methods allowed us to recover 56% of the bacterial diversity present in the microbiome, resulting in the isolation and characterization of 256 bacterial strains. These isolates were screened for PGP traits, including salt and heat tolerance, siderophore production, and pectinase activity. Out of the 77 bacterial isolates tested, 11 demonstrated a significant ability to enhance Arabidopsis growth under salt stress.ConclusionsOur study highlights the ecological significance of mangrove microbiomes and the potential of culture collections in offering innovative solutions for ecological restoration and crop production in saline conditions. The unique collection of mangrove bacteria, particularly from the rhizosphere and endophytes, showcases significant PGP traits and stress tolerance capabilities. These findings emphasize the importance of functional traits, such as salt tolerance, in the recruitment of endophytic bacteria by plants over taxonomic affiliation. The identified bacterial strains hold potential not only for developing biofertilizers to improve crop productivity but also for ecological restoration projects aimed at rehabilitating saline-degraded lands, thereby contributing to overall ecosystem health and sustainability.

Knockdown of the ZcVgR Gene Alters the Expression of Genes Related to Reproduction and Lifespan in Zeugodacus cucurbitae (Coquillett) Under Extreme Heat Conditions.

Zeugodacus cucurbitae (Coquillett) is an important migratory vegetable pest. Previous research has demonstrated that short-term high temperatures induce differential expression of the vitellogenin receptor (ZcVgR) gene, reducing the number of eggs laid and the lifespan of female Z. cucurbitae. In this paper, we used Tandem Mass Tags (TMT) quantitative proteomics and Illumina high-throughput sequencing to determine the proteomic and transcriptomic information of female Z. cucurbitae after siRNA-mediated silencing of the target gene (ZcVgR) to gain a comprehensive understanding of the molecular mechanism of this gene in the regulation of reproduction and lifespan. The findings demonstrated that following the target gene's silencing, the ZcVgR gene's transcriptional expression was significantly downregulated, and there was no significant difference in protein level. The transcriptome and proteome had a low correlation; when the ZcVgR gene was silenced, vitellogenin-1 (ZcVg1), juvenile hormone epoxide hydrolase (JHEH), troponin C (TnC), heat shock protein 70 (HSP70), and other related genes were downregulated at the transcriptional level. By silencing the ZcVgR gene, transcriptionally level immune-related pathways were activated and energy metabolism-related pathways were inhibited; protein-level glycometabolism and phagosome pathways were activated, while phototransduction-fly and autophagy-animal pathways were inhibited. The findings of this study might offer a theoretical foundation for integrated management of Z. cucurbitae in the summertime.

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.

Diversity and Function Patterns of Soil Microbial Communities in Native and Invasive Plants Along an Altitudinal Gradient in the Qinling Mountains

Soil microbial communities are essential drivers of ecosystem functions, yet the factors shaping their structure and function, particularly at different altitudes and between invasive and native plants, remain insufficiently understood. Using high-throughput Illumina sequencing, we assessed the composition, diversity, impact factors, and functional potential of the microbial communities associated with Galinsoga quadriradiata (an invasive species) and Artemisia lavandulifolia (a native species) across an altitudinal gradient ranging from 896 m to 1889 m in the Qinling Mountains. The results revealed that both plant species and altitude significantly influenced soil bacterial diversity and community structure. Actinobacteriota, Proteobacteria, and Acidobacteriota accounted for higher proportions in the soils of G. quadriradiata and A. lavandulifolia. A linear discriminant analysis showed that the two species hosted distinct microbial communities, with variations driven by species-specific traits and environmental factors. Compared with plant parameters, environmental factors had a greater impact on plant soil bacterial abundance. Functional analysis indicated that A. lavandulifolia soils were more associated with nitrogen cycling processes, while G. quadriradiata soils contributed more to organic matter decomposition. Therefore, invasive and native plants harbored microbial flora with different nutritional preferences and metabolic characteristics. These findings advance our understanding of plant–microbe interactions along altitudinal gradients, and they have practical implications for managing invasive species and supporting ecosystem resilience.

Comparative Transcriptome Analysis of Sexual Differentiation in Male and Female Gonads of Nao-Zhou Stock Large Yellow Croaker (Larimichthys crocea).

The Nao-zhou stock large yellow croaker (Larimichthys crocea) is a unique economic seawater fish species in China and exhibits significant dimorphism in both male and female phenotypes. Cultivating all-female seedlings can significantly improve breeding efficiency. To accelerate the cultivation process of all female seedlings of this species, it is necessary to deeply understand the regulatory mechanisms of sexual differentiation and gonadal development. This study used Illumina high-throughput sequencing to sequence the transcriptome of the testes and ovaries of Nao-zhou stock large yellow croaker to identify genes and molecular functions related to sex determination. A total of 10,536 differentially expressed genes were identified between males and females, including 5682 upregulated and 4854 downregulated genes. Functional annotation screened out 70 important candidate genes related to sex, including 34 genes highly expressed in the testis (including dmrt1, foxm1, and amh) and 36 genes highly expressed in the ovary (including gdf9, hsd3b1, and sox19b). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis found that differentially expressed genes were significantly enriched in nine signaling pathways related to sex determination and gonadal development, including steroid hormone biosynthesis, MAPK signaling pathway, and the TGF-beta signaling pathway. By screening sex-related differentially expressed genes and mapping protein-protein interaction networks, hub genes such as dmrt1, amh, and cyp19a1a were found to be highly connected. The expression levels of 15 sex-related genes, including amh, dmrt1, dmrt2a, foxl1, and zp3b, were determined by qRT-PCR and RNA sequencing. This study screened for differentially expressed genes related to sex determination and differentiation of Nao-zhou stock large yellow croaker and revealed the signaling pathways involved in gonad development of male and female individuals. The results provide important data for future research on sex determination and differentiation mechanisms, thereby providing a scientific basis for the cultivation of all-female seedlings.

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.

Flue-cured tobacco intercropping with insectary floral plants improves rhizosphere soil microbial communities and chemical properties of flue-cured tobacco

BackgroundContinuous cropping of the same crop leads to land degradation. This is also called the continuous-cropping obstacle. Currently, intercropping tobacco with other crops can serve as an effective strategy to alleviate continuous cropping obstacles.ResultsIn this study, tobacco K326 and insectary floral plants were used as materials, and seven treatments of tobacco monoculture (CK), tobacco intercropped with Tagetes erecta, Vicia villosa, Fagopyrum esculentum, Lobularia maritima, Trifolium repens, and Argyranthemum frutescens respectively, were set up to study their effects on rhizosphere soil chemical properties and composition and structure of rhizosphere soil microbial community of tobacco. The 16 S rRNA gene and ITS amplicons were sequenced using Illumina high-throughput sequencing. tobacco/insectary floral plants intercropping can influence rhizosphere soil chemical properties, which also change rhizosphere microbial communities. The CK and treatment groups tobacco rhizosphere soil microorganisms had significantly different genera, such as tobacco intercropping with T. repens and A. frutescens significantly increased the number of Fusarium and intercropping T. erecta, V. villosa, L. maritima, T. repens, and A. frutescens significantly increased the number of Sphingomonas and unknown Gemmatimonadaceae. Additionally, intercropping T. erecta, V. villosa and L. maritima changed the rhizosphere fungal and bacteria community and composition of tobacco and the positive correlation between tobacco rhizosphere the genera of fungi and bacterial were greater than CK. The pathway of the carbohydrate metabolism, amino acid metabolism, and energy metabolism in rhizosphere bacteria were significantly decreased after continuous cropping. Fungal symbiotic trophic and saprophytic trophic were significantly increased after intercropping V. villosa, L. maritima and plant pathogen and animal pathogen were increased after intercropping T. repens and A. frutescens. Additionally, bacterial and fungal communities significantly correlated with soil chemical properties, respectively.ConclusionThis study reveals that intercropping tobacco with insectary floral plants, particularly T. erecta, V. villosa, L. maritima and A. frutescens significantly affects soil chemical properties and alters rhizosphere microbial communities, increasing the abundance of certain microbial genera. Additionally, intercropping enhances pathways related to carbohydrate, amino acid, and energy metabolism in rhizosphere bacteria. These findings suggest that intercropping could provide a promising strategy to overcome challenges associated with continuous tobacco cropping by regulating the rhizosphere environment.

Fungal Footprints: Soil Fungal Communities in Black Walnut and Red Oak Forests.

Soil fungal communities are critical for forest ecosystem functions in the Central Hardwood Region (CHR) of the USA. This evaluation, which took place in 2022-2023, investigates the influence of Juglans nigra (BW, black walnut) and Quercus rubra (NRO, Northern red oak) on soil properties and fungal community structures across three CHR sites. The objectives of this study are to investigate how the fungal communities identified beneath J. nigra and Q. rubra serve to influence biodiversity and soil health within hardwood plantations. Soils from two locations in Indiana and one in Michigan were examined and assessed for variations in fungal composition and diversity. Soil fungal communities were characterized using Illumina high-throughput sequencing while multivariate analysis was applied to analyze patterns in these fungal communities. These data provided insights into how environment, location, and tree species affect fungal community structure. Results indicate that J. nigra soils exhibited higher carbon (0.36%, 1.02%, 0.72%), nitrogen (25%, 29%, 56%), and pH (0.46, 1.08, 1.54) levels than Q. rubra soils across all three sites and foster greater fungal diversity. Specifically, J. nigra was associated with increased Ascomycota diversity, whereas Q. rubra supported a higher prevalence of Basidiomycota. Basidiomycota were negatively correlated with carbon and pH, while Ascomycota showed positive correlations with these variables. These findings highlight how crucial it is to understand how different tree species influence fungal communities and, consequently, how they influence forest soil health. Our findings serve to improve forest management practices by emphasizing the importance of fungal communities in maintaining the function and resilience of an ecosystem. Our study underscores that grasping these specific interactions is essential for effective forest management, especially when considering how to use fungal communities to boost plant growth. This work focuses on hardwood plantations rather than either agricultural ecosystems, monocultures, or native forests, thus filling a gap in the current literature where many studies are limited to specific fungal groups such as mycorrhizae. In future research, it is important to examine a wider range of tree species. This will deepen our understanding of fungal community dynamics and their impact on maintaining healthy forest ecosystems. Our hardwood plantation focus also notes the potential for adaptive forest management as environmental conditions change.

Spatiotemporal Distribution of nirS-Type Denitrifiers in Cascade Reservoir Sediments of the Qinghai Plateau

Compared to single damming, the impact of cascade damming on nitrogen-related microorganisms in river ecosystems exhibits greater complexity. However, there is still a lack of research on the response of denitrifiers to the construction of cascade reservoirs. A study was conducted on 10 cascade reservoirs in the upper reaches of the Yellow River to investigate the impact of cascade reservoir construction on nirS-type denitrifying bacteria in sediments. Sediment samples were collected in May (dry season) and August (wet season) of 2023. The spatiotemporal characteristics of the nirS-type denitrifying bacterial community and gene abundance were analyzed using Illumina high-throughput sequencing and real-time fluorescence quantification PCR (qPCR). Redundancy analysis (RDA) and variation partitioning (VP) were utilized to assess the impact of environmental factors on these communities. The results showed the following: (1) Proteobacteria was the predominant phylum of nirS-type denitrifying bacteria in cascade reservoir sediments. At the genus level, unclassified Proteobacteria (69.51–95.64%) showed the highest relative abundance, followed by Paracoccus, Rhodanobacter, and Pseudomonas, indicating that unclassified Proteobacteria may dominate denitrification in these reservoir sediments. (2) The α and β diversity indices of nirS-type denitrifying bacteria were higher in the dry season than in the wet season, and also higher in young reservoirs compared to old reservoirs (p &lt; 0.05). (3) Temporally, the abundance of the nirS gene was significantly higher in the wet season (12.71 × 107 copies/g dry sediment) compared to the dry season (66.35 × 105 copies/g dry sediment). Spatially, the abundance of the nirS gene was higher in the central region, while relatively lower at both ends. (4) RDA and VP analysis indicated that the community structure and abundance of nirS-type denitrifying bacteria were significantly influenced by the total nitrogen in sediments (19.31%) and water temperature (14.13%). Spearman correlation analysis showed that organic carbon significantly affected the diversity of nirS-type denitrifying bacteria (p &lt; 0.05). The results contribute to a better understanding of the nitrogen-related microbial community in cascade reservoir sediments of the Yellow River, providing a scientific basis for reservoir management.

Shift in potential pathogenic bacteria during permafrost degradation on the Qinghai-Tibet Plateau

Permafrost acts as a potential pathogen reservoir. With accelerating climate change and intensifying permafrost degradation, the release of these pathogens poses significant threats to ecosystems and public health. However, the changes in pathogenic communities during permafrost degradation remain unclear. This study utilized quantitative PCR and Illumina high-throughput sequencing to analyze the composition and quantities of potential pathogenic bacteria in four types of permafrost soil on the northeast edge of the Qinghai-Tibet Plateau (QTP): sub-stable permafrost (SSP), transition permafrost (TP), unstable permafrost (UP), and extremely unstable permafrost (EUP). The results showed that during permafrost degradation, the quantity of potential pathogenic bacteria decreased from 7.8 × 106 to 3.1 × 106 copies/g. Both the Richness and Shannon indices initially declined from SSP, to TP, UP, and then began to rise when permafrost degraded to EUP. A total of 216 potential pathogenic bacterial species were identified, including 166 animal pathogens, 28 zoonotic pathogens, and 22 plant pathogens. The pathogenic community intergroup differences (ANOSIM), unique taxa, and dominant pathogen analysis indicated the significant changes in pathogenic communities during permafrost degradation. The potential pathogenic community was significantly influenced by non-pathogenic bacterial communities (Procrustes analysis), with soil moisture being the primary environmental factor, followed by TDS, soil organic carbon, and total nitrogen. SourceTracker2 analysis indicated that the majority of potential pathogenic bacteria in the soil originated from external sources, only a small portion coming from the permafrost itself. These findings suggest that a large number of pathogens were released into the environment while also preserving amount from external sources. It elucidates that each stage of permafrost degradation presents unique biosecurity risks. This study highlights the release and redistribution of pathogenic bacteria associated with the potential public health risks. It provides the crucial insights into the ecological dynamics of permafrost degradation, emphasizing the need for ongoing monitoring and proactive management strategies.

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.

Impact of mixed groups on the gut bacterial structure of herring gull (Larus argentatus) and common shelduck (Tadorna tadorna) on Binzhou Seashell Island in Wudi, China

Abstract The cross-species transmission of intestinal bacteria caused by mixed-group contact in animals is currently an issue of concern. Herring gulls (Larus argentatus) and common shelducks (Tadorna tadorna) often forage in mixed groups, a process which is known as sympatric mixed foraging. This study sought to explore how mixed foraging affects the gut bacteria structure in herring gulls and common shelducks on Binzhou Seashell Island, China. Illumina high-throughput sequencing was employed to analyze the intestinal bacteria of these birds during their wintering period, with the goal of understanding the impact of mixed-species interactions on gut microbiota diversity. The results showed that alpha diversity of intestinal flora in common shelducks was higher than that in herring gulls, and there was no significant difference in beta diversity between the two species. The similarity ratio of the top five abundances of bacteria at the phylum classification level reached 42.86%. Judging from the results, there is resemblance in the structure of the intestinal flora between the two species. The study not only enhances our understanding of the adaptive strategies and interactions of these two avian species within the ecosystem, but also establishes a crucial foundation for bird resource management and disease prevention and control in this region. It holds significant scientific and practical implications for fields such as ecological conservation and biodiversity.