Aquatic virus culture collection: an absent (but necessary) safety net for environmental microbiologists

Abstract

Viruses are recognised as the most abundant biological entities on the planet. In addition to their role in disease, they are crucial components of co-evolutionary processes, are instrumental in global biogeochemical pathways such as carbon fluxes and nutrient recycling, and in some cases act regionally on climate processes. Importantly, viruses harbour an enormous, as of yet unexplored genetic and metabolic potential. Some viruses infecting microalgae harbour hundreds of genes, including genes involved in cellular metabolic pathways. Collectively, these attributes have given rise to new fields of research: environmental virology and viral ecology. While traditionally the potential of viruses was recognised by isolating novel viruses into culture and subsequent sequencing of their genomes in the laboratory, advancements in next-generation sequencing technologies now allow for direct sequencing of viral genomes from their natural setting, bypassing the need for culturing. Nevertheless, the lack of associated biological reference material with most of these novel environmental genomes is problematic as there are limitations to what can be achieved with sequence data alone. Where aquatic viruses do exist in culture, they are most often kept privately within research institutes and are not available to the wider research community. Many are thus at risk of being lost because research teams rarely have secure long term resources to ensure continued propagation. Culture collections do exist for medically and agriculturally important viruses causing disease, but collections focusing on viruses infecting aquatic algae and bacteria are non-existent. We therefore highlight here the need for a centralised depository for aquatic viruses and present arguments indicating the benefits such a collection would have for the scientific community of environmental virologists.

Revealing RNA virus diversity and evolution in unicellular algae transcriptomes

“…However, because these studies have been conducted with environmental samples, they cannot identify the specific host taxon with certainty. This illustrates the inference gap between broad metagenomic surveys that identify huge numbers of new viral sequences, creating a large but unassigned depiction of the virosphere, and studies based on virus isolation and detailed particle characterization (including cell culture) that are conducted on a very limited number of viruses and create a highly accurate, but very narrow, vision of the virosphere ( Nissimov et al. 2020 ).…”

Antiviral discovery in toxic cyanobacteria: Low hanging fruit in the age of pandemics

“…Although, the antiviral effects we observed were only in a select few Microcystis aeruginosa strains, our approach is valuable because there are hundreds of cyanobacterial species scattered in culture collections globally (Campbell & Lorenz, 2022), many of which may also prove to be good candidates for antiviral discovery, whether they are axenic or in a consortium with other co-habiting microbes that may, too, produce valuable antivirals. The availability of these in culture collections (and other species, including microalgae), together with the ability to test extracts against other viruses from culture collections such as the National Collection of Pathogenic Viruses (NCPV) in the United Kingdom, the American Type Culture Collection (ATCC) in the United States, and privately held collections (Nissimov et al, 2022), when coupled TA B L E 2 Example outline of the assay for evaluating the antiviral effects of Microcystis aeruginosa NIES 298, CPCC 299, and CPCC 300 late exponential growth phase extracts on CtenDNAV a (V1) and CtenRNAV b (V2) diatom viruses.…”

Microbial dynamics in rapidly transforming Arctic proglacial landscapes

“…NCBI) [145], and allow comparison between different studies. However, as sequencing and molecular techniques continue to advance, it may become increasingly difficult to compare newly generated research with older studies without access to the original source material [143,146]. Microbial domain biological resource centres (mBRCs), also known as culture collections, store and distribute microorganisms and replicable genetic and viral material, with ~790 mBRCs worldwide, holding over three million strains [147].…”