High-Throughput Sequencing

INTRODUCTION: Bacillus amyloliquefaciens DGL1, isolated from the arid sandy areas in Dagler, Qinghai Province, China, promotes the growth of Avena sativa variety "Qing Yan 1". METHODS: 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...

BACKGROUND: 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. METHODS: The connected-lake heterogeneity of bacterial community composition (BCC) was investigated in Poyang Lake during the flood season in 2020...

Exosome-like nanoparticles (ELNs) are novel naturally occurring plant ultrastructures and contain unique bioactive components. However, the potential applications and biological functions of plant ELNs, especially in the context of health promotion and disease prevention, remain largely unexplored. This study aimed to explore the biological activities and functional mechanisms of Actinidia arguta -derived exosome-like nanoparticles (AAELNs). We reported the development of AAELNs, which possess particle sizes of 157...

OBJECTIVE: This study aims to analyze the molecular characteristics of the novel coronavirus (SARS-CoV-2) Omicron variant BA.2.76 in Jining City, China. METHODS: Whole-genome sequencing was performed on 87 cases of SARS-CoV-2 infection. Evolutionary trees were constructed using bioinformatics software to analyze sequence homology, variant sites, N-glycosylation sites, and phosphorylation sites. RESULTS: All 87 SARS-CoV-2 whole-genome sequences were classified under the evolutionary branch of the Omicron variant BA...

Colorectal cancer (CRC) is the third most common cancer affecting people. The discovery of new, non-invasive, specific, and sensitive molecular biomarkers for CRC may assist in the diagnosis and support therapeutic decision making. Exosomal miRNAs have been demonstrated in carcinogenesis and CRC development, which makes these miRNAs strong biomarkers for CRC. Deep sequencing allows a robust high-throughput informatics investigation of the types and abundance of exosomal miRNAs. Thus, exosomal miRNAs can be efficiently examined as diagnostic biomarkers for disease screening...

The COVID-19 pandemic caused by the coronavirus SARS-CoV-2 has significantly impacted global health, stressing the necessity of basic understanding of the host response to this viral infection. In this study, we investigated how SARS-CoV-2 remodels the landscape of small non-coding RNAs (sncRNA) from a large collection of nasopharyngeal swab samples taken at various time points from patients with distinct symptom severity. High-throughput RNA sequencing analysis revealed a global alteration of the sncRNA landscape, with abundance peaks related to species of 21-23 and 32-33 nucleotides...

Seeking low-cost and eco-friendly electrode catalyst of microbial fuel cell (MFC) reactor has received extensive attention in recent decades. In this study, a sludge MFC was coupled with biochar-modified-anode (BC-300, BC-400, and BC-500) for actual brewery wastewater treatment. The physicochemical properties of biochar largely depended on the pyrolysis temperature, further affecting the removal efficiency of wastewater indicators. BC-400 MFC proved to be efficient for TN and NH4 + -N removal, while the maximum removal efficiencies of COD and TP were achieved by BC-500 MFC, reaching respectively 97...

Biogenic manganese oxides (BioMnOx) have attracted considerable attention as active oxidants, adsorbents, and catalysts. However, characteristics and mechanisms of nitrification-denitrification in biological redox reactions mediated by different concentrations of BioMnOx are still unclear. Fate of nutrients (e.g., NH4 + -N, TP, NO3 - -N) and COD were investigated through different concentrations of BioMnOx produced by Mn(II) in the moving bed biofilm reactor (MBBR). 34% and 89.2%, 37.8% and 89.8%, 57.3% and 88...

Trichoderma can enhance the metabolism of organophosphate pesticides in plants, but the mechanism is unclear. Here, we performed high-throughput transcriptome sequencing of roots upon Trichoderma asperellum (TM) inoculation and phoxim (P) application in tomato (Solanum lycopersicum L.). A total of 4059 differentially expressed genes (DEGs) were obtained, including 2110 up-regulated and 1949 down-regulated DEGs in P vs TM+P. COG and KOG analysis indicated that DEGs were mainly enriched in signal transduction mechanisms...

BACKGROUND: Rice vinegar is a worldwide popular cereal vinegar worldwide and is typically produced in an open environment, and the ecosystem of solid-state fermentation is complicated and robust. This study aimed to reveal the shaping force of the establishment of the ecosystem of Beijing rice vinegar, the core function microbiota, and their correlation with critical environmental factors. RESULTS: The experimental findings revealed the changes in environmental factors, major metabolites, and microbial patterns during Beijing rice vinegar fermentation were obtained...

In recent years, the environmental pollution of microplastics in Poyang Lake has received increasing attention. Baisha Lake of Poyang Lake was selected as the study area, and samples of water and sediments of Baisha Lake and the microplastics therein were collected, and the polymer types of microplastics were identified as polyethylene (PE), polyester (PET), polypropylene (PP), and polystyrene (PS) using Fourier infrared spectroscopy. We also analyzed the structural composition of bacterial communities in water, in sediments, and on microplastic surfaces using 16S high-throughput sequencing...

Soil microbes are key drivers in regulating the phosphorus cycle. Elucidating the microbial mineralization process of soil phosphorus-solubilizing bacteria is of great significance for improving nutrient uptake and yield of crops. This study investigated the mechanism by which citrus cultivation affects the soil microbial acquisition strategy for phosphorus by measuring the abundance of the phoD gene, microbial community diversity and structure, and soil phosphorus fractions in the soils of citrus orchards and adjacent natural forests...

To evaluate the effect of thermal hydrolysis pretreatment time on the sludge anaerobic digestion system of wastewater treatment plants (WWTPs) in Daxing district, Beijing, the structure and diversity of microbial communities in primary sludge and an activated sludge anaerobic digestion system with different thermal hydrolysis pretreatment times (15 min, 30 min, and 45 min) were analyzed using Illumina MiSeq high-throughput sequencing. The results showed that the dominant groups of digested sludge were mainly distributed in Firmicutes, Cloacimonadota, Chloroflexi, and Synergistota, with W5 being the most common genus...

Lake wetlands are extremely important and special ecosystems, which are important for regional water resource storage, environmental protection, and biodiversity maintenance. Sediment bacteria are an important component of lake ecosystems and are a major driver of biogeochemical cycling in lakes. In order to investigate the community structure of bacteria in typical lake sediments in Yinchuan City and their influencing factors, three typical lakes in Yinchuan City (Yuehai Lake, Mingcui Lake, and Xiniu Lake) were selected for the study and surface sediments were collected in January, April, July, and October 2021...

Riparian zones are typical fragile and sensitive ecological areas. Fluctuations in water level are the main factor affecting the soil environment in these zones, and vegetation restoration is considered an important means of soil conservation there. However, the interactive effects of water level fluctuations and vegetation restoration on the soil microbial community structure in the reservoir riparian zone remain unclear. Therefore, we selected abandoned grassland and artificial forestland at different water level elevations as research objects in the riparian zone of the Three Gorges Reservoir...

Biofilms attached to submerged macrophytes play an important role in improving the water quality of the water environment supplemented with reclaimed water. In order to explore the effects of reclaimed water quality and submerged macrophyte species on the characteristics of an epiphytic bacterial community, different types of submerged macrophytes were selected as research objects in this study. 16S rRNA high-throughput sequencing technology was used on the epiphytic bacteria and the surrounding environmental samples to analyze the bacterial community structure and functional genes...

Fish dietary niche is a core focus, and it reflects the diversity of resources, habitats, or environments occupied by a species. However, whether geographic segregation among different populations triggers dietary diversification and concomitant fish niche shift remains unknown. In the present study, we selected the Black Amur bream ( Megalobrama terminalis ) is a migratory fish species that plays an important role in the material transfer and energy cycling of river ecosystems, inhabiting southern China drainage with multiple geographic populations...

Crop roots are colonized by large numbers of microorganisms, collectively known as the root-microbiome, which modulate plant growth, development and contribute to elemental nutrient uptake. In conditions of nitrogen limitation, the over-expressed Calcineurin B-like interacting protein kinase 2 (OsCIPK2) gene with root-specific promoter (RC) has been shown to enhance growth and nitrogen uptake in rice. Analysis of root-associated bacteria through high-throughput sequencing revealed that OsCIPK2 has a significant impact on the diversity of the root microbial community under low nitrogen stress...

Constructed wetlands for wastewater treatment pose challenges related to long-term operational efficiency and greenhouse gas emissions on a global scale. This study investigated the impact of adding peat, humic acid, and biochar into the substrates of constructed wetlands and focused on Cr, and Ni removal, greenhouse gas emissions, and microbial communities in constructed wetlands. Biochar addition treatment achieved the highest removal efficiencies for total Cr (99.96%), Cr (VI) (100%), and total Ni (91.04%)...

Genomic effect variants associated with survival and protection against complex diseases vary between populations due to microevolutionary processes. The aim of this study was to analyse diversity and distribution of effect variants in a context of potential positive selection. In total, 475 individuals of Lithuanian origin were genotyped using high-throughput scanning and/or sequencing technologies. Allele frequency analysis for the pre-selected effect variants was performed using the catalogue of single nucleotide polymorphisms...