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

Gu, Chengxiang; Liang, Yantao; Li, Jiansen; Shao, Hongbing; Jiang, Yong; Zhou, Xinhao; Gao, Chen; Li, Xianrong; Zhang, Wenjing; Guo, Cui; He, Hui; Wang, Hualong; Sung, Yeong Yik; Mok, Wen Jye; Wong, Li Lian; Suttle, Curtis A.; McMinn, Andrew; Tian, Jie; Wang, Min

doi:10.1016/j.isci.2021.103439

Cited by 15 publications

(16 citation statements)

References 130 publications

(187 reference statements)

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“…It is noteworthy that 93 of these 222 vOTUs belong to Caudovirales. Consistent with previous studies, most of these vOTUs were predicted to have narrow host ranges [47,74], with only 15 potentially exhibiting a broader host range across several classes. A total of 71 MAGs were assigned from the eleven samples, of which Gammaproteobacteria, Flavobacteriia and Alphaproteobacteria were highly abundant (Fig.…”

Section: Host Prediction and The Spatiotemporal Dynamics Of Viral Rel...supporting

confidence: 87%

“…To place the vOTUs of ASIWV in a broader context, all vOTUs of more than 10kb were piped into vConTACT 2 (-db 'None' -pcs-mode MCL -vcs-mode ClusterONE) with the 21666 viral reference and high-quality sequences in IMG/VR v3 dataset [44,45], including 164 viral genomes from freshwater ice, 14849 from marine environments, 1781 from non-marine saline and alkaline, and 4872 from terrestrial environments. All open reading frames (ORFs) were predicted by metaProdigal (v 2.6.3) [46], then using all-verses-all DIAMOND (v 0.9.29.130) BLASTP (e-value ≤ 1 10 − 5 , query coverage ≥ 50%, identity ≥ 25%) to compare the proteins [47,48]. The gene-sharing network was visualized by Cytoscape v 3.8.2 and the number of VCs were plotted using EVenn [49,50].…”

Section: Comparisons To Viral Sequences From Other Environmental Viromesmentioning

confidence: 99%

“…In order to detect glycol metabolism-related genes, ORFs were blastp against the Carbohydrate-Active enZYmes (CAZymes) Database using DIAMOND (e value < 1 10 − 5 ; > 60% identity ) [48,60]. In addition, ORFs were piped through KEGG GhostKOALA to detect sulfur, nitrogen and lipid metabolic genes, through PfamScan (e value < 1 10 − 5 and bit score > 40) to identify domains and through eggNOG (v 5.0) to obtain the COG functional categories with default parameters [47,61,62]. Protein modeling and prediction were performed using the Phyre2 web portal and PyMOL was used for further visualization [63,64].…”

Section: Open Reading Frames (Orfs) Prediction and Functional Analysesmentioning

confidence: 99%

“…The vOTUs were searched against the IMG/VR v3 dataset, which is the largest available public viral dataset consisting of over 2,314,329 uncultivated viral genomes viral sequences, and against the Global Ocean Viromes (GOV2.0) dataset with 195,728 viral populations, with the threshold(≥ 95% average nucleotide identity, ≥ 85% alignment fraction, ≤ 1*10 − 5 e-value) to test the distinctiveness of the eleven viromes at a species level [26, 45,47]. The results indicate that 16.80% of the vOTUs were aligned with the IMG/VR v3 dataset, nearly all of which were linked to vOTUs from marine, non-marine saline and alkaline, and Aquatic (sediment) ecosystems (Fig.…”

Section: Comparison Of Viral Community Structure Between Sea Ice and ...mentioning

confidence: 99%

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Diversity and biogeochemical roles of DNA viruses in Antarctic sea ice

Liu

Han

Liang

et al. 2022

Preprint

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Background Polar sea ice is one of the largest ecosystems on Earth, harboring a vast and unexplored microbial diversity, which sustains the polar ecosystems during the long dark winters. Viruses are the most abundant “life forms” in the sea and are considered the main manipulators of microorganisms. However, little is known about the viral assemblages inhabiting Antarctic sea ice and under ice seawater or their biogeochemical roles. Results Here we establish an Antarctic sea ice and water DNA virome (ASIWV) dataset by analyzing 11 viral metagenomes derived from sea ice and seawater from below the melting ice in spring. A total of 28,169 viral contigs were identified and classified into 17,284 nonredundant viral Operational Taxonomic Units (vOTUs). Most of vOTUs could not be classified and so are considered probably endemic to Antarctic marine environments. Compared with those from sea water, viruses from within the sea ice preferentially adopted a lysogenic infection strategy, comprising more than 20% of viruses in multiple sea ice samples. The vOTUs in sea ice and sea water were quite similar, but there was still a distinction between their relative abundances. Potential hosts of 222 vOTUs were predicted, mainly linked to the dominant bacterial classes Gammaproteobacteria and Flavobacteriia. Notably, 220 virus-encoded auxiliary metabolic genes from 28 categories were identified, suggesting that viruses mediate microbial metabolism of carbon, sulfur, nitrogen, lipids and cold adaption. Conclusions This study is the first to reveal the unique taxonomic characteristics of viruses from polar sea ice and the under ice seawater, provides a baseline for sea ice DNA viral assemblages, highlights an unexplored hotspot of viral diversity and enhances our understanding of the viral contribution to the regulation microbial ecology and biogeochemistry.

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Section: Host Prediction and The Spatiotemporal Dynamics Of Viral Rel...supporting

confidence: 87%

Section: Comparisons To Viral Sequences From Other Environmental Viromesmentioning

confidence: 99%

Section: Open Reading Frames (Orfs) Prediction and Functional Analysesmentioning

confidence: 99%

Section: Comparison Of Viral Community Structure Between Sea Ice and ...mentioning

confidence: 99%

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Diversity and biogeochemical roles of DNA viruses in Antarctic sea ice

Liu

Han

Liang

et al. 2022

Preprint

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“…However, genome analysis has shown that this population also infects free-living hosts ( 21 ). Members of the Bullavirinae subfamily generally infect Enterobacteria ( 20 , 22 ). In recent years, Microviridae phages infecting other bacterial groups have also been discovered, suggesting that ssDNA bacteriophages should be more diverse than previously thought ( 23 – 28 ).…”

Section: Resultsmentioning

confidence: 99%

Characterization and Genomic Analysis of ssDNA Vibriophage vB_VpaM_PG19 within Microviridae , Representing a Novel Viral Genus

et al. 2022

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Salinity as a key factor affecting viral activity and life strategies in alpine lakes

Zang,

Liu,

Jiao

et al. 2024

Limnology & Oceanography

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Viruses are major players in the biosphere, yet little is known about their dynamics and life strategies in alpine lakes, particularly those on the Tibetan Plateau. We investigated microbial abundance, viral dynamics, and viral life strategies in 10 high‐altitude Tibetan lakes and found that they harbor high levels of active viruses. Salinity was identified as a crucial factor influencing viral abundance, dynamics, as well as viral life strategies. Lytic and lysogenic viral productions in moderate‐ and high‐salinity lakes were significantly higher than those in freshwater lakes. A trade‐off between viral life strategies resulted in a switch from lysis to lysogeny in high‐salinity lakes. Virus‐mediated cell lysis and virus decay in sampled Tibetan lakes could release about 162.72 and 2.84 μg C L−1 d−1, respectively. These findings revealed the crucial role of viruses in the carbon cycle of Tibetan lakes, and a switch in viral life strategies may impact their contribution to the carbon cycle. The potential impact of salinity changes triggered by climate change on the carbon cycle in alpine lakes worldwide is highlighted.

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

Abstract: HighlightsOf all, 4,560 viral populations were identified Many virus-encoded auxiliary metabolic genes were predicted Qinghai-Tibet plateau and bathypelagic ocean might represent a viral habitat

Cited by 15 publications

References 130 publications

Diversity and biogeochemical roles of DNA viruses in Antarctic sea ice

Diversity and biogeochemical roles of DNA viruses in Antarctic sea ice

Characterization and Genomic Analysis of ssDNA Vibriophage vB_VpaM_PG19 within Microviridae , Representing a Novel Viral Genus

Salinity as a key factor affecting viral activity and life strategies in alpine lakes

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