Browse
Submit Data
Databases
API
Help

Dataset Information

24 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Saline lakes on the Qinghai-Tibet Plateau harbor unique viral assemblages mediating microbial environmental adaption.

ABSTRACT: The highest plateau on Earth, Qinghai-Tibet Plateau, contains thousands of lakes with broad salinity and diverse and unique microbial communities. However, little is known about their co-occurring viruses. Herein, we identify 4,560 viral Operational Taxonomic Units (vOTUs) from six viromes of three saline lakes on Qinghai-Tibet Plateau, with less than 1% that could be classified. Most of the predicted vOTUs were associated with the dominant bacterial and archaeal phyla. Virus-encoded auxiliary metabolic genes suggest that viruses influence microbial metabolisms of carbon, nitrogen, sulfur, and lipid; the antibiotic resistance mediation; and their salinity adaption. The six viromes clustered together with the ice core viromes and bathypelagic ocean viromes and might represent a new viral habitat. This study has revealed the unique characteristics and potential ecological roles of DNA viromes in the lakes of the highest plateau and established a foundation for the recognition of the viral roles in plateau lake ecosystems.

SUBMITTER: Gu C

PROVIDER: S-EPMC8710556 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Qinghai-Tibet Plateau soil

Project description:Qinghai-Tibet Plateau soil

| PRJNA658924 | ENA

Bacterial and Microeukaryotic Community Compositions and Their Assembly Processes in Lakes on the Eastern Qinghai-Tibet Plateau.

Project description:Bacterial and microeukaryotic community compositions and their assembly processes have remained challenging and remained unclear in lake ecosystems on the Qinghai-Tibet Plateau (QTP). We revealed the diversity and community compositions, driving factors, ecological assembly processes, and co-occurrence networks of bacterial and microeukaryotic communities in water bodies of the eight lake ecosystems across the Eastern QTP. The results demonstrated that the predominant bacteria in most samples were Proteobacteria, with an average relative abundance of 41.78%, whereas the most abundant of microeukaryotes differed among the sample sites. The redundancy analysis revealed that latitude and pH were the most important driving factors in shaping the bacterial and microeukaryotic community compositions. Homogeneous selection (56.40%) was the dominant process in assembling the bacterial communities, whereas dispersal limitation (67.24%) was the major process in governing the microeukaryotic communities. Furthermore, dissolved organic carbon and salinity were the major factors mediating the balance of deterministic and stochastic assembly processes in the bacterial and microeukaryotic communities. Both the bacterial and microeukaryotic community co-occurrence networks exhibited topological features of modularity and non-random topological features. The results offer insights into the mechanisms underpinning bacterial and microeukaryotic diversities and communities in the lake ecosystems on the QTP.

| S-EPMC10821157 | biostudies-literature

Expansion of Cyclophyllidea Biodiversity in Rodents of Qinghai-Tibet Plateau and the "Out of Qinghai-Tibet Plateau" Hypothesis of Cyclophyllideans.

Project description:The Cyclophyllidea comprises the most species-rich order of tapeworms (Platyhelminthes, Cestoda) and includes species with some of the most severe health impact on wildlife, livestock, and humans. We collected seven Cyclophyllidea specimens from rodents in Qinghai-Tibet Plateau (QTP) and its surrounding mountain systems, of which four specimens in QTP were unsequenced, representing "putative new species." Their complete mitochondrial (mt) genomes were sequenced and annotated. Phylogenetic reconstruction of partial 28S rDNA, cox1 and nad1 datasets provided high bootstrap frequency support for the categorization of three "putative new species," assigning each, respectively, to the genera Mesocestoides, Paranoplocephala, and Mosgovoyia, and revealing that some species and families in these three datasets, which contain 291 species from nine families, may require taxonomic revision. The partial 18S rDNA phylogeny of 29 species from Taeniidae provided high bootstrap frequency support for the categorization of the "putative new species" in the genus Hydatigera. Combined with the current investigation, the other three known Taeniidae species found in this study were Taenia caixuepengi, T. crassiceps, and Versteria mustelae and may be widely distributed in western China. Estimates of divergence time based on cox1 + nad1 fragment and mt protein-coding genes (PCGs) showed that the differentiation rate of Cyclophyllidea species was strongly associated with the rate of change in the biogeographic scenarios, likely caused by the uplift of the QTP; i.e., species differentiation of Cyclophyllidea might be driven by host-parasite co-evolution caused by the uplift of QTP. We propose an "out of QTP" hypothesis for the radiation of these cyclophyllidean tapeworms.

| S-EPMC8861457 | biostudies-literature

The microbial community structure and nitrogen cycle of high-altitude pristine saline lakes on the Qinghai-Tibetan plateau.

Project description:The nitrogen (N) cycle is the foundation of the biogeochemistry on Earth and plays a crucial role in global climate stability. It is one of the most important nutrient cycles in high-altitude lakes. The biogeochemistry of nitrogen is almost entirely dependent on redox reactions mediated by microorganisms. However, the nitrogen cycling of microbial communities in the high-altitude saline lakes of the Qinghai-Tibet Plateau (QTP), the world's "third pole" has not been investigated extensively. In this study, we used a metagenomic approach to investigate the microbial communities in four high-altitude pristine saline lakes in the Altun mountain on the QTP. We observed that Proteobacteria, Bacteroidota, and Actinobacteriota were dominant in these lakes. We reconstructed 1,593 bacterial MAGs and 8 archaeal MAGs, 1,060 of which were found to contain nitrogen cycle related genes. Our analysis revealed that nitrite reduction, nitrogen fixation, and assimilatory nitrate reduction processes might be active in the lakes. Denitrification might be a major mechanism driving the potential nitrogen loss, while nitrification might be inactive. A wide variety of microorganisms in the lake, dominated by Proteobacteria, participate together in the nitrogen cycle. The prevalence of the dominant taxon Yoonia in these lakes may be attributed to its well-established nitrogen functions and the coupled proton dynamics. This study is the first to systematically investigate the structure and nitrogen function of the microbial community in the high-altitude pristine saline lakes in the Altun mountain on the QTP. As such, it contributes to a better comprehension of biogeochemistry of high-altitude saline lakes.

| S-EPMC11312105 | biostudies-literature

Diversity of prokaryotic microorganisms in alkaline saline soil of the Qarhan Salt Lake area in the Qinghai-Tibet Plateau.

Project description:The composition of microbial communities varies considerably across ecological environments, particularly in extreme environments, where unique microorganisms are typically used as the indicators of environmental conditions. However, the ecological reasons for the differences in microbial communities remain largely unknown. Herein, we analyzed taxonomic and functional community profiles via high-throughput sequencing to determine the alkaline saline soil bacterial and archaeal communities in the Qarhan Salt Lake area in the Qinghai-Tibet Plateau. The results showed that Betaproteobacteria (Proteobacteria) and Halobacteria (Euryarchaeota) were the most abundant in the soils of this area, which are common in high salinity environments. Accordingly, microbes that can adapt to local extremes typically have unique metabolic pathways and functions, such as chemoheterotrophy, aerobic chemoheterotrophy, nitrogen fixation, ureolysis, nitrate reduction, fermentation, dark hydrogen oxidation, and methanogenesis. Methanogenesis pathways include hydrogenotrophic methanogenesis, CO2 reduction with H2, and formate methanogenesis. Thus, prokaryotic microorganisms in high salinity environments are indispensable in nitrogen and carbon cycling via particular metabolic pathways.

| S-EPMC8888737 | biostudies-literature

Mosquitoes and mosquito-borne arboviruses in the Qinghai-Tibet Plateau--focused on the Qinghai area, China.

Project description:An investigation was conducted to identify the distribution of mosquitoes and mosquito-borne arboviruses in the Qinghai-Tibet Plateau, China from July to August in 2007. A total of 8,147 mosquitoes representing six species from three genera (Aedes, Culex, and Anopheles) were collected in three locations (Geermu city, altitude of 2,780 m; Xining city, 2,200 m; Minhe county, 1,700 m). Six virus isolates were obtained including Tahyna virus (TAHV), Liaoning virus, and Culex pipiens pallens Densovirus. A serosurvey showed immunoglobulin G antibodies by immunofluorescence assay (IFA) against TAHV in residents of all three locations. The IFA-positive human samples were confirmed by 90% plaque-reduction neutralization tests (PRNT(90)) against TAHV with titers ranging from 1:20 to 1:10,240. In addition, TAHV seropositive cows, sheep, and swine were found in these locations. This investigation represents the first isolation of TAHV from Ae. (Och.) detritus and the first evidence of TAHV infection in residents and livestock in the Qinghai-Tibet Plateau.

| S-EPMC2844569 | biostudies-literature

Rare bacterial biosphere is more environmental controlled and deterministically governed than abundant one in sediment of thermokarst lakes across the Qinghai-Tibet Plateau.

Project description:Thermokarst lakes are widely distributed in cold regions as a result of ice-rich permafrost thaw. Disentangling the biogeography of abundant and rare microbes is essential to understanding the environmental influences, assembly mechanisms, and responses to climate change of bacterial communities in thermokarst lakes. In light of this, we assessed the abundant and rare bacterial subcommunities in sediments from thermokarst lakes across the Qinghai-Tibet Plateau (QTP). The operational taxonomic unit (OTU) richness was more strongly associated with location and climate factors for abundant subcommunities, while more strongly associated with physicochemical variables for rare subcommunities. The relative abundance of abundant and rare taxa showed opposite patterns with abundant taxa having greater relative abundance at higher latitude and pH, but at lower mean annual precipitation and nutrients. Both the abundant and rare subcommunities had a clear distribution pattern along the gradient of latitude and mean annual precipitation. Abundant subcommunities were dominantly shaped by dispersal limitation processes (80.9%), while rare subcommunities were shaped almost equally by deterministic (47.3%) and stochastic (52.7%) processes. The balance between stochastic and deterministic processes was strongly environmentally adjusted for rare subcommunities, while not associated with environmental changes for abundant subcommunities. The results shed light on biogeography patterns and structuring mechanisms of bacterial communities in thermokarst lakes, improving our ability to predict the influences of future climate change on these lakes.

| S-EPMC9358708 | biostudies-literature

Plant Resource Availability of Medicinal Fritillaria Species in Traditional Producing Regions in Qinghai-Tibet Plateau.

Project description:The genus Fritillaria (Liliaceae) comprises of ~140 species of bulbous perennials, which are distributed in the temperate zone of the Northern Hemisphere. Fritillaria species have attracted much attention because of their commercial value, partly as ornamental plants but principally as a source of material for use in traditional medicine. The use of Fritillaria extracts is well established in some countries in Eastern Europe (e.g., Turkey), and Asia (e.g., China, Japan). In traditional Chinese medicine, the medicinal Fritillaria species is called Bulbus Fritillariae Cirrhosae (BFC), which has been used as a traditional medicine for thousands of years. However, to the best of our knowledge, there are no reports on resource investigation of plants of BFC in the last ten years. In this study, we chose 32 traditional producing regions in Qinghai-Tibet Plateau to perform an investigation on resource availability of BFC. In five sites we did not find any plants of BFC. Results show that the average number of the plants of BFC per quadrat in 26 sites was less than 7, and the average resource density was <22 mg/m2. Habitat types and plant morphology of BFC plants were recorded. Our investigation shows that the area for artificial cultivation of BFC is larger than 400 hm2 and productivity was higher than 180 t. In addition, the total alkaloid contents of samples from cultivated bases and plantations are higher than that from wild fields. This study suggests that the wild populations of BFC are still at the risk of depletion. Artificial cultivation of BFC might be an important way to resolve the current contradiction between resource protection and resource utilization. In addition, identifying the closest European relatives of the Fritillaria species used in traditional medicine may resolve this contradiction.

| S-EPMC5545572 | biostudies-other

Flower color polymorphism of a wild Iris on the Qinghai-Tibet plateau.

Project description:BackgroundFlower color plays a crucial role in attracting pollinators and facilitating environmental adaptation. Investigating the causes of flower color polymorphism and understanding their potential effects on both ecology and genetics can enhance our understanding of flower color polymorphism in wild plant.ResultsIn this study, we examined the differences of potential male and female fitness between purple- and yellow- flower individuals in Iris potaninii on the Qinghai-Tibet Plateau, and screened key genes and positively selective genes involved in flower color change. Our results showed that yellow flower exhibited a higher pollen-to-ovule ratio. Yellow flowers were derived from purple flowers due to the loss of anthocyanins, and F3H could be an essential gene affecting flower color variation though expression regulation and sequence polymorphism in this species. Furthermore, our findings suggest that genes positively selected in yellow-flowered I. potaninii might be involved in nucleotide excision repair and plant-pathogen interactions.ConclusionsThese results suggest that F3H induces the flower color variation of Iris potaninii, and the subsequent ecological and additive positive selection on yellow flowers may further enhance plant adaptations to alpine environments.

| S-EPMC10709947 | biostudies-literature

Ptilagrostis contracta (Stipeae, Poaceae), a New Species Endemic to Qinghai-Tibet Plateau.

Project description:A new species, Ptilagrostis contracta, endemic to Qinghai-Tibet Plateau is described and illustrated. It is distinguished from other species in Ptilagrostis by having contracted panicles, 1-geniculate awns with hairy columns and scabrous bristles and evenly pubescent lemmas. Evidence from lemma epidermal pattern, cytology and molecular phylogenetic analyses based on the nuclear ITS sequence data confirm its systematic position in Ptilagrostis.

| S-EPMC5218392 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data