Dataset Information

Metagenomic analysis of viromes in tissues of wild Qinghai vole from the eastern Tibetan Plateau.

ABSTRACT: Rodents are natural reservoirs of diverse zoonotic viruses and widely distributed on the Tibetan Plateau. A comprehensive understanding of the virome in local rodent species could provide baseline of viral content and assist in efforts to reduce the risk for future emergence of rodent related zoonotic diseases. A total of 205 tissue and fecal samples from 41 wild Qinghai voles were collected. Metagenomic analyses were performed to outline the characteristics of the viromes, and phylogenetic analyses were used to identify the novel viral genomes. The virome distribution among five tissues (liver, lung, spleen, small intestine with content and feces) was also compared. We identified sequences related to 46 viral families. Novel viral genomes from distinct evolutionary lineages with known viruses were characterized for their genomic and evolutionary characteristics, including Hepatovirus, Hepacivirus, Rotavirus, and Picobirnavirus. Further analyses revealed that the core virome harbored by rodent internal tissues were quite different from the virome found in intestine and fecal samples. These findings provide an overview of the viromes in wild Qinghai voles, which are unique and the most common rodent species in the eastern Tibetan Plateau. A high diversity of viruses is likely present in rodent species in this area.

SUBMITTER: He X

PROVIDER: S-EPMC9562062 | biostudies-literature | 2022 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Metagenomic analysis of viromes in tissues of wild Qinghai vole from the eastern Tibetan Plateau.

He Xiaozhou X Wang Xu X Fan Guohao G Li Fan F Wu Weiping W Wang Zhenghuan Z Fu Meihua M Wei Xu X Ma Shuo S Ma Xuejun X

Scientific reports 20221014 1

Rodents are natural reservoirs of diverse zoonotic viruses and widely distributed on the Tibetan Plateau. A comprehensive understanding of the virome in local rodent species could provide baseline of viral content and assist in efforts to reduce the risk for future emergence of rodent related zoonotic diseases. A total of 205 tissue and fecal samples from 41 wild Qinghai voles were collected. Metagenomic analyses were performed to outline the characteristics of the viromes, and phylogenetic anal ...[more]

PMID: 36241909

Similar Datasets

Project description:Background and aimsThere is no knowledge of winter plant phenology and its controlling factors on the Qinghai-Tibetan Plateau (QTP). Thus, we conducted a 4 year winter phenology and growth dynamics study in the alpine meadow on the eastern QTP.MethodsFrom November 2013 to March 2017, the phenology of the 'winter-growth' and 'winter-green' species was recorded every 5 d. In November-February from 2014 to 2015, the above-ground biomass (AGB) in random plots was calculated to distinguish different growth patterns among winter growing species. The percentage of winter abundance relative to the summer population for forbs and the percentage of absolute coverage for grasses (W/S) were calculated to describe the importance of the winter population to the summer population. The soil moisture (SM) and soil temperature (ST) were used to explore the controlling factors on the AGB. Pearson's correlation analysis between winter phenology data and environmental variables, including air temperature (Tair), snow cover fraction (SCF), SM and ST, was used to investigate the factors affecting winter phenology during November-February from 2014 to 2017.Key resultsThere were 107 species in total in the sites, including ten 'winter-growth' species and four 'winter-green' species. Among the 'winter-green' species, Festuca ovina and Deschampsia cespitosa were the dominant species in the sites. The 'winter-growth' species grew new leaves or ramets or transitioned to reproductive growth. Gentiana spathulifolia even flowered in winter. 'Winter-growth' made important contributions to the annual AGB, e.g. winter growth of G. spathulifolia accounted for 23.26 % of its annual AGB, while 14.74 % of the annual AGB of G. crassuloides was from winter growth. In addition, winter warming and snowfall reduction under global climate change on the eastern QTP may decrease the AGB increment of the 'winter-growth' and delay the green-up onset date of 'winter-green' species. Also, winter warming and snowfall reduction may advance the first flowering date of 'winter-growth' species.ConclusionsIn contrast to previous views that plants on the QTP were generally considered to remain dormant in winter, our study revealed that alpine meadow plants had strong winter growth which suggested the importance of re-evaluating the dynamics of ecosystem function of alpine meadow, including its contribution to the global carbon balance. It was also shown that soil moisture availability is more important than warmer temperature in controlling the green-up onset of 'winter-green' species on the eastern QTP, which contrasts with the traditional view that warmer winters could advance green-up. As snowmelt is the only source of soil water in winter, the prediction of the green-up trend may be further complicated by snowfall variation in winter.

Project description:BACKGROUND: GeoChip 3.0, a microbial functional gene array, containing ~28,000 oligonucleotide probes and targeting ~57,000 sequences from 292 functional gene families, provided a powerful tool for researching microbial community structure in natural environments. The alpine meadow is a dominant plant community in the Qinghai-Tibetan plateau, hence it is important to profile the unique geographical flora and assess the response of the microbial communities to environmental variables. In this study, Geochip 3.0 was employed to understand the microbial functional gene diversity and structure, and metabolic potential and the major environmental factors in shaping microbial communities structure of alpine meadow soil in Qinghai-Tibetan Plateau. RESULTS: A total of 6143 microbial functional genes involved in carbon degradation, carbon fixation, methane oxidation and production, nitrogen cycling, phosphorus utilization, sulphur cycling, organic remediation, metal resistance, energy process and other category were detected in six soil samples and high diversity was observed. Interestingly, most of the detected genes associated with carbon degradation were derived from cultivated organisms. To identify major environmental factors in shaping microbial communities, Mantel test and CCA Statistical analyses were performed. The results indicated that altitude, C/N, pH and soil organic carbon were significantly (P < 0.05) correlated with the microbial functional structure and a total of 80.97% of the variation was significantly explained by altitude, C/N and pH. The C/N contributed 38.2% to microbial functional gene variation, which is in accordance with the hierarchical clustering of overall microbial functional genes. CONCLUSIONS: High overall functional genes and phylogenetic diversity of the alpine meadow soil microbial communities existed in the Qinghai-Tibetan Plateau. Most of the genes involved in carbon degradation were derived from characterized microbial groups. Microbial composition and structures variation were significantly impacted by local environmental conditions, and soil C/N is the most important factor to impact the microbial structure in alpine meadow in Qinghai-Tibetan plateau.

Project description:As significant evidence of ice-rich permafrost degradation due to climate warming, thermokarst lake was developing and undergoing substantial changes. Thermokarst lake was an essential ecosystem component, which significantly impacted the global carbon cycle, hydrology process and the stability of the Qinghai-Tibet Engineering Corridor. In this paper, based on Sentinel-2 (2021) and Landsat (1988-2020) images, thermokarst lakes within a 5000 m range along both sides of Qinghai-Tibet Highway were extracted to analyse the spatio-temporal variations. The results showed that the number and area of thermokarst lake in 2021 were 3965 and 4038.6 ha (1 ha = 10,000 m[Formula: see text]), with an average size of 1.0186 ha. Small thermokarst lakes ([Formula: see text]1 ha) accounted for 85.65% of the entire lake count, and large thermokarst lakes ([Formula: see text]10 ha) occupied for 44.92% of the whole lake area. In all sub-regions, the number of small lake far exceeds 75% of the total lake number in each sub-region. R1 sub-region (around Wudaoliang region) had the maximum number density of thermokarst lakes with 0.0071, and R6 sub-region (around Anduo region) had the minimum number density with 0.0032. Thermokarst lakes were mainly distributed within elevation range of 4300 m-5000 m a.s.l. (94.27% and 97.13% of the total number and size), on flat terrain with slopes less than 3[Formula: see text] (99.17% and 98.47% of the total number and surface) and in the north, south, and southeast aspects (51.98% and 50.00% of the total number and area). Thermokarst lakes were significantly developed in warm permafrost region with mean annual ground temperature (MAGT) > - 1.5 [Formula: see text]C, accounting for 47.39% and 54.38% of the total count and coverage, respectively. From 1988 to 2020, in spite of shrinkage or even drain of small portion of thermokarst lake, there was a general expansion trend of thermokarst lake with increase in number of 195 (8.58%) and area of 1160.19 ha (41.36%), which decreased during 1988-1995 (- 702 each year and - 706.27 ha/yr) and then increased during 1995-2020 (184.96-702 each year and 360.82 ha/yr). This significant expansion was attributed to ground ice melting as rising air temperature at a rate of 0.03-0.04 [Formula: see text]C/yr. Followed by the increasing precipitation (1.76-3.07 mm/yr) that accelerated the injection of water into lake.

Dataset Information

Metagenomic analysis of viromes in tissues of wild Qinghai vole from the eastern Tibetan Plateau.

Publications

Metagenomic analysis of viromes in tissues of wild Qinghai vole from the eastern Tibetan Plateau.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets