Genome-resolved viral and cellular metagenomes revealed potential key virus-host interactions in a deep freshwater lake

SummaryMetagenomics has dramatically expanded the known virosphere, but freshwater viral diversity and their ecological interaction with hosts remain poorly understood. Here, we conducted a metagenomic exploration of planktonic dsDNA prokaryotic viruses by sequencing both virion (<0.22 μm) and cellular (0.22–5.0 μm) fractions collected spatiotemporally from a deep freshwater lake (Lake Biwa, Japan). This simultaneously reconstructed 183 complete (i.e., circular) viral genomes and 57 bacterioplankton metagenome-assembled genomes. Analysis of metagenomic read coverage revealed vertical partitioning of the viral community analogous to the vertically stratified bacterioplankton community. The hypolimnetic community was generally stable during stratification, but occasionally shifted abruptly, presumably due to lysogenic induction. Genes involved in assimilatory sulfate reduction were encoded in 20 (10.9%) viral genomes, including those of dominant viruses, and may aid viral propagation in sulfur-limited freshwater systems. Hosts were predicted for 40 (21.9%) viral genomes, encompassing 10 phyla (or classes of Proteobacteria) including ubiquitous freshwater bacterioplankton lineages (e.g., Ca. Fonsibacter and Ca. Nitrosoarchaeum). Comparison with viral genomes derived from published metagenomes revealed viral phylogeographic connectivity in geographically isolated habitats. Notably, analogous to their hosts, actinobacterial viruses were among the most diverse, ubiquitous, and abundant viral groups in freshwater systems, with potential high lytic activity in surface waters.

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Contribution of large bacteria to bacterial biomass in a deep freshwater lake (Lake Biwa, Japan)

Aquatic Microbial Ecology ◽

10.3354/ame01949 ◽

2020 ◽

Vol 85 ◽

pp. 131-139

Author(s):

S Shen ◽

Y Shimizu

Keyword(s):

Cell Volume ◽

Bacterial Cell ◽

Lake Biwa ◽

Bacterial Biomass ◽

Spatial Variations ◽

Freshwater Lake ◽

Heterotrophic Nanoflagellates ◽

Bacterial Productivity ◽

Transmission Electron ◽

Seasonal And Spatial Variations

Despite the importance of bacterial cell volume in microbial ecology in aquatic environments, literature regarding the effects of seasonal and spatial variations on bacterial cell volume remains scarce. We used transmission electron microscopy to examine seasonal and spatial variations in bacterial cell size for 18 mo in 2 layers (epilimnion 0.5 m and hypolimnion 60 m) of Lake Biwa, Japan, a large and deep freshwater lake. During the stratified period, we found that the bacterial cell volume in the hypolimnion ranged from 0.017 to 0.12 µm3 (median), whereas that in the epilimnion was less variable (0.016 to 0.033 µm3, median) and much lower than that in the hypolimnion. Additionally, in the hypolimnion, cell volume during the stratified period was greater than that during the mixing period (up to 5.7-fold). These differences in cell volume resulted in comparable bacterial biomass in the hypolimnion and epilimnion, despite the fact that there was lower bacterial abundance in the hypolimnion than in the epilimnion. We also found that the biomass of larger bacteria, which are not likely to be grazed by heterotrophic nanoflagellates, increased in the hypolimnion during the stratified period. Our data suggest that estimation of carbon flux (e.g. bacterial productivity) needs to be interpreted cautiously when cell volume is used as a constant parametric value. In deep freshwater lakes, a difference in cell volume with seasonal and spatial variation may largely affect estimations.

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Current and Emerging Themes in the Structural Analysis of Viral RNA Genomes: Applications for the Development of Novel Therapeutic Drugs

Genomics and Computational Biology ◽

10.18547/gcb.2015.vol1.iss1.e15 ◽

2015 ◽

Vol 1 (1) ◽

pp. 15 ◽

Cited By ~ 2

Author(s):

Cristina Romero-López ◽

Alfredo Berzal-Herranz

Keyword(s):

Rna Folding ◽

Viral Infections ◽

Genome Structure ◽

Rna Molecules ◽

Molecular Virology ◽

Viral Genomes ◽

Viral Propagation ◽

Bioinformatic Tools ◽

Rna Domains ◽

Functional Rna

RNA molecules assume different roles in many different biological processes. This functional diversity is intimately related to RNA folding. In recent years, advances in the field of structure analysis by high-throughput methodologies and the development of novel potent bioinformatic tools have enabled the first structural maps of the eukaryotic transcriptome and the further establishment of novel function-structure relationships. This important progress has been of special relevance in the field of molecular virology. Viral genomes are compact entities that require overlapping coding levels to bear all the genetic information required for viral propagation. This is achieved by the acquisition of functional RNA domains, structurally conserved encoding units that perform essential roles for the consecution of the viral cycle. Interfering with the activity of these structural elements offers a potential means of treating viral infections, such as that caused by the hepatitis C virus, HCV. This review summarizes major achievements in the development of emerging methodologies for the analysis of RNA folding and their application to the study of the HCV genome structure. It will also examine the progress toward the design of novel antiviral compounds based in nucleic acids able to interfere with the folding of functional RNA domains.

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Application of CRISPR/Cas9 in Understanding Avian Viruses and Developing Poultry Vaccines

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2020.581504 ◽

2020 ◽

Vol 10 ◽

Author(s):

Julianne Vilela ◽

Mohammed A. Rohaim ◽

Muhammad Munir

Keyword(s):

Genome Editing ◽

Genome Instability ◽

Viral Gene ◽

Recombinant Vaccines ◽

Viral Genomes ◽

Host Interactions ◽

Avian Diseases ◽

Host Virus Interactions ◽

Virus Interactions ◽

User Friendly

Clustered regularly interspaced short palindromic repeats associated protein nuclease 9 (CRISPR-Cas9) technology offers novel approaches to precisely, cost-effectively, and user-friendly edit genomes for a wide array of applications and across multiple disciplines. This methodology can be leveraged to underpin host-virus interactions, elucidate viral gene functions, and to develop recombinant vaccines. The successful utilization of CRISPR/Cas9 in editing viral genomes has paved the way of developing novel and multiplex viral vectored poultry vaccines. Furthermore, CRISPR/Cas9 can be exploited to rectify major limitations of conventional approaches including reversion to virulent form, recombination with field viruses and transgene, and genome instability. This review provides comprehensive analysis of the potential of CRISPR/Cas9 genome editing technique in understanding avian virus-host interactions and developing novel poultry vaccines. Finally, we discuss the simplest and practical aspects of genome editing approaches in generating multivalent recombinant poultry vaccines that conform simultaneous protection against major avian diseases.

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Draft Genome Sequences of Tersicoccus phoenicis DSM 30849T, Isolated from a Cleanroom for Spacecraft Assembly, and Tersicoccus sp. Strain Bi-70, Isolated from a Freshwater Lake

Genome Announcements ◽

10.1128/genomea.00079-17 ◽

2017 ◽

Vol 5 (13) ◽

Author(s):

Yu Nakajima ◽

Susumu Yoshizawa ◽

Keiji Nakamura ◽

Yoshitoshi Ogura ◽

Tetsuya Hayashi ◽

...

Keyword(s):

Lake Biwa ◽

Draft Genome ◽

Freshwater Lake ◽

Genome Sequences ◽

Content Type ◽

Spacecraft Assembly

ABSTRACT Here, we report the draft genome sequences of Tersicoccus phoenicis DSM 30849T, isolated from a spacecraft assembly cleanroom at the National Aeronautics and Space Administration (NASA), and Tersicoccus sp. strain Bi-70, isolated from Lake Biwa, the largest lake in Japan. These genome sequences facilitate our understanding of the adaptation of these closely related strains to different habitats.

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Growth and mortality rates of prokaryotes in the hypolimnion of a deep freshwater lake (Lake Biwa, Japan)

Inland Waters ◽

10.1080/20442041.2017.1298222 ◽

2017 ◽

Vol 7 (2) ◽

pp. 164-170 ◽

Cited By ~ 1

Author(s):

Hiroyuki Takasu ◽

Shin-ichi Nakano

Keyword(s):

Lake Biwa ◽

Mortality Rates ◽

Freshwater Lake

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Isolated history of the coastal plant Lathyrus japonicus (Leguminosae) in Lake Biwa, an ancient freshwater lake

AoB Plants ◽

10.1093/aobpla/plr021 ◽

2011 ◽

Vol 2011 ◽

Cited By ~ 8

Author(s):

Tatsuo Ohtsuki ◽

Yuko Kaneko ◽

Hiroaki Setoguchi

Keyword(s):

Lake Biwa ◽

Freshwater Lake ◽

History Of ◽

Coastal Plant

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Genome binning of viral entities from bulk metagenomics data

10.1101/2021.07.07.451412 ◽

2021 ◽

Author(s):

Joachim Johansen ◽

Damian R Plichta ◽

Jakob Nybo Nissen ◽

Marie Louise Jespersen ◽

Shiraz A Shah ◽

...

Keyword(s):

Deep Learning ◽

Human Microbiome ◽

Human Microbiome Project ◽

Gastrointestinal Diseases ◽

Human Gut ◽

Viral Genomes ◽

Host Interactions ◽

Metagenomics Data ◽

Health And Disease ◽

Viral Host Interactions

Despite the accelerating number of uncultivated virus sequences discovered in metagenomics and their apparent importance for health and disease, the human gut virome and its interactions with bacteria in the gastrointestinal are not well understood. In addition, a paucity of whole-virome datasets from subjects with gastrointestinal diseases is preventing a deeper understanding of the virome role in disease and in gastrointestinal ecology as a whole. By combining a deep-learning based metagenomics binning algorithm with paired metagenome and metavirome datasets we developed the Phages from Metagenomics Binning (PHAMB) approach for binning thousands of viral genomes directly from bulk metagenomics data. Simultaneously our methodology enables clustering of viral genomes into accurate taxonomic viral populations. We applied this methodology on the Human Microbiome Project 2 (HMP2) cohort and recovered 6,077 HQ genomes from 1,024 viral populations and explored viral-host interactions. We show that binning can be advantageously applied to existing and future metagenomes to illuminate viral ecological dynamics with other microbiome constituents.

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