Periodic Reporting for period 1 - VISIBLE (Virus-host interactions in the Baltic Sea)
Reporting period: 2022-12-01 to 2024-11-30
Microorganisms are essential to aquatic ecosystems. They are the most numerous and diverse organisms, playing a vital role in maintaining ecosystem health. These tiny organisms support food webs, drive half of the world's primary production, and help clean up pollution.
Viruses kill a large number of aquatic microorganisms daily but this process contributes to ecosystem function. Viral lysis releases organic matter for other microbes to consume and has also been implicated in the termination of toxic algal blooms. During infection, viruses can also alter their hosts' metabolism, contributing to primary production and biogeochemical cycles. Viruses can thus shape the structure and function of aquatic microbial communities.
Bacteria and viruses coexist in aquatic environments in complex ways, which can be studied through metagenomics (DNA sequenced directly from the environment). With this approach, it is possible to recover the genomes of both bacteria and viruses. A key challenge is linking viruses to their specific hosts. Funded by the European Union, the VISIBLE project (VIrus-hoSt Interactions in the BaLtic SeA) examined long-term microbial and viral data from the Baltic Sea to uncover virus-host relationships and their role in the ecosystem.
Viruses kill a large number of aquatic microorganisms daily but this process contributes to ecosystem function. Viral lysis releases organic matter for other microbes to consume and has also been implicated in the termination of toxic algal blooms. During infection, viruses can also alter their hosts' metabolism, contributing to primary production and biogeochemical cycles. Viruses can thus shape the structure and function of aquatic microbial communities.
Bacteria and viruses coexist in aquatic environments in complex ways, which can be studied through metagenomics (DNA sequenced directly from the environment). With this approach, it is possible to recover the genomes of both bacteria and viruses. A key challenge is linking viruses to their specific hosts. Funded by the European Union, the VISIBLE project (VIrus-hoSt Interactions in the BaLtic SeA) examined long-term microbial and viral data from the Baltic Sea to uncover virus-host relationships and their role in the ecosystem.
1) Genomes of uncultivated bacteria and archaea
VISIBLE analysed 150 microbial metagenomes from the Baltic Sea and generated over 4000 microbial metagenome-assembled genomes (MAGs). The samples were collected over 9-years from the Linnaeus Microbial Observatory (LMO), a long-term monitoring station in the Baltic Sea. The MAG dataset includes novel genomes and expands upon the known microbial diversity of the Baltic Sea.
2) Genomes of uncultivated viruses
VISIBLE analysed 76 viral metagenomes (viromes) collected from LMO over the same time period. Over 80,000 uncultivated virus genomes (UViGs) were recovered. The UViG dataset hosts extensive novel diversity, with most genomes having limited similarity to known viruses. The recovered genomes includes both single- and double-stranded DNA viruses predicted to infect all domains of life (bacteria, archaea and eukarya).
3) Linking viruses to their hosts
VISIBLE used multiple approaches to link viruses to their hosts in the Baltic Sea.
a) Spacer-protospacer matching
Virus-host interactions were identified using CRISPR sequences in host genomes. CRISPR-Cas systems act as a form of immune defence against viruses for bacteria and archaea. These systems store snippets of DNA from the viruses they’ve encountered, called spacers. If the same virus attacks again, the system uses this information to recognise the same sequence in the virus’s DNA, called a protospacer, and halt the infection. VISIBLE used this genetic memory to link viruses to their hosts using spacer-protospacer matching.
b) Protein-sharing networks
Not all bacteria and bacteria use CRISPR to defend against viruses. Protein-sharing networks were therefore used to predict hosts based on gene content. This approach also uncovered viruses that infect algae and protists in the Baltic Sea.
c) Viral-host correlation
Combining 9-years of relative abundance data for bacteria and viruses revealed seasonal patterns and long-term interactions.
VISIBLE analysed 150 microbial metagenomes from the Baltic Sea and generated over 4000 microbial metagenome-assembled genomes (MAGs). The samples were collected over 9-years from the Linnaeus Microbial Observatory (LMO), a long-term monitoring station in the Baltic Sea. The MAG dataset includes novel genomes and expands upon the known microbial diversity of the Baltic Sea.
2) Genomes of uncultivated viruses
VISIBLE analysed 76 viral metagenomes (viromes) collected from LMO over the same time period. Over 80,000 uncultivated virus genomes (UViGs) were recovered. The UViG dataset hosts extensive novel diversity, with most genomes having limited similarity to known viruses. The recovered genomes includes both single- and double-stranded DNA viruses predicted to infect all domains of life (bacteria, archaea and eukarya).
3) Linking viruses to their hosts
VISIBLE used multiple approaches to link viruses to their hosts in the Baltic Sea.
a) Spacer-protospacer matching
Virus-host interactions were identified using CRISPR sequences in host genomes. CRISPR-Cas systems act as a form of immune defence against viruses for bacteria and archaea. These systems store snippets of DNA from the viruses they’ve encountered, called spacers. If the same virus attacks again, the system uses this information to recognise the same sequence in the virus’s DNA, called a protospacer, and halt the infection. VISIBLE used this genetic memory to link viruses to their hosts using spacer-protospacer matching.
b) Protein-sharing networks
Not all bacteria and bacteria use CRISPR to defend against viruses. Protein-sharing networks were therefore used to predict hosts based on gene content. This approach also uncovered viruses that infect algae and protists in the Baltic Sea.
c) Viral-host correlation
Combining 9-years of relative abundance data for bacteria and viruses revealed seasonal patterns and long-term interactions.
Recent advances in cultivation-independent meta-omics have made it possible to recover the genomes of uncultivated bacteria, archaea and viruses from the environment. Using new bioinformatic approaches VISIBLE recovered thousands of genomes of viruses and their hosts from the Baltic Sea. The data produced is a valuable biodiversity resource and provides insight into the brackish microbiome. Novel diversity was found within the genomic data which is a publicly available resource. The data is of value to researchers in aquatic ecosystems and more broadly data scientists, bioinformaticians and ecologists.