Viruses are the most common biological entities in the oceans by an order of magnitude. However, very little is known about their diversity. Here we report a genomic analysis of two uncultured marine viral communities. Over 65% of the sequences were not significantly similar to previously reported sequences, suggesting that much of the diversity is previously uncharacterized. The most common significant hits among the known sequences were to viruses. The viral hits included sequences from all of the major families of dsDNA tailed phages, as well as some algal viruses. Several independent mathematical models based on the observed number of contigs predicted that the most abundant viral genome comprised 2-3% of the total population in both communities, which was estimated to contain between 374 and 7,114 viral types. Overall, diversity of the viral communities was extremely high. The results also showed that it would be possible to sequence the entire genome of an uncultured marine viral community.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC137870 | PMC |
| http://dx.doi.org/10.1073/pnas.202488399 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Earth's most needed uncultivated aquatic prokaryotes.
Water Res
December 2024
Department of Environmental Metagenomics, Research Center One Health Ruhr, University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany; Centre of Water and Environmental Research, University of Duisburg-Essen, Essen, Germany. Electronic address:
Aquatic ecosystems house a significant fraction of Earth's biosphere, yet most prokaryotes inhabiting these environments remain uncultivated. While recently developed genome-resolved metagenomics and single-cell genomics techniques have underscored the immense genetic breadth and metabolic potential residing in uncultivated Bacteria and Archaea, cultivation of these microorganisms is required to study their physiology via genetic systems, confirm predicted biochemical pathways, exploit biotechnological potential, and accurately appraise nutrient turnover. Over the past two decades, the limitations of culture-independent investigations highlighted the importance of cultivation in bridging this vast knowledge gap.
View Article and Find Full Text PDFImproving genome-scale metabolic models of incomplete genomes with deep learning.
iScience
December 2024
Theoretical Biology and Bioinformatics, Utrecht University, 3584 CH Utrecht, the Netherlands.
Deciphering microbial metabolism is essential for understanding ecosystem functions. Genome-scale metabolic models (GSMMs) predict metabolic traits from genomic data, but constructing GSMMs for uncultured bacteria is challenging due to incomplete metagenome-assembled genomes, resulting in many gaps. We introduce the deep neural network guided imputation of reactomes (DNNGIOR), which uses AI to improve gap-filling by learning from the presence and absence of metabolic reactions across diverse bacterial genomes.
View Article and Find Full Text PDFAmmonium removal through anaerobic ammonium oxidation coupled to iron(III) reduction along the Yangtze river-estuary continuum.
J Environ Sci (China)
June 2025
State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; Sino-Danish Centre for Science and Education, University of Chinese Academy of Sciences, Beijing 100039, China; The Fuxianhu Station of Plateau Deep Lake Research, Chinese Academy of Sciences, Yuxi 653100, China. Electronic address:
Anaerobic ammonium oxidation coupled to iron(III) reduction (Feammox) process has recently been recognized as an important pathway for removing ammonium in various natural habitats. However, our understanding for Feammox in river-estuary continuum is limited. In this study, stable isotope tracers and high-throughput amplicon sequencing were employed to determine Feammox rates and identify associated microbial communities in sediments along the Yangtze river-estuary continuum.
View Article and Find Full Text PDFTime Series Data Provide Insights into the Evolution and Abundance of One of the Most Abundant Viruses in the Marine Virosphere: The Uncultured Pelagiphages vSAG 37-F6.
Viruses
October 2024
Department of Physiology, Genetics, and Microbiology, University of Alicante, Carretera San Vicente del Raspeig, San Vicente del Raspeig, 03690 Alicante, Spain.
Article Synopsis
- Viruses significantly influence ecosystems, particularly through their interactions with abundant marine microbes like pelagiphages, which affect carbon cycles via the viral shunt.
- The study focuses on the uncultured lytic pelagiphage vSAG 37-F6, investigating its temporal dynamics, including abundance fluctuations and evolutionary patterns over 7 years through metagenomics.
- Findings reveal a seasonal infection pattern with peaks in winter and fall, negative selection on viral genes, and significant insights into the complex dynamics of this oceanic virus, highlighting its ecological importance.
A novel virus potentially evolved from the N4-like viruses represents a unique viral family: .
Appl Environ Microbiol
December 2024
College of Marine Life Sciences, MoE Key Laboratory of Evolution & Marine Biodiversity, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China.
Unlabelled: are widely distributed in marine extreme habitats and exhibit diverse extracellular protease activity, which is essential for marine biogeochemical cycles. However, our understanding of viruses that infect remains limited. This study isolated a virus infecting from Xiaogang in Qingdao, China.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!