A High Rate Algal Pond Hosting a Dynamic Community of RNA Viruses

Abstract

Despite a surge of RNA virome sequencing in recent years, there are still many RNA viruses to uncover—as indicated by the relevance of viral dark matter to RNA virome studies (i.e., putative viruses that do not match to taxonomically identified viruses). This study explores a unique site, a high-rate algal pond (HRAP), for culturing industrially microalgae, to elucidate new RNA viruses. The importance of viral-host interactions in aquatic systems are well documented, and the ever-expanding microalgae industry is no exception. As the industry becomes a more important source of sustainable plastic manufacturing, a producer of cosmetic pigments and alternative protein sources, and a means of CO2 remediation in the face of climate change, studying microalgal viruses becomes a vital practice for proactive management of microalgae cultures at the industrial level. This study provides evidence of RNA microalgal viruses persisting in a CO2 remediation pilot project HRAP and uncovers the diversity of the RNA virosphere contained within it. Evidence shows that family Marnaviridae is cultured in the basin, alongside other potential microalgal infecting viruses (e.g., family Narnaviridae, family Totitiviridae, and family Yueviridae). Finally, we demonstrate that the RNA viral diversity of the HRAP is temporally dynamic across two successive culturing seasons.

Diverse RNA Viruses Associated with Diatom, Eustigmatophyte, Dinoflagellate, and Rhodophyte Microalgae Cultures

“…), the metagenomic era has multiplied the number of RNA viruses described by many thousands ( 10 – 13 ). This is evident in the field of “phycovirology” (the study of algal viruses), for which recent studies investigating RNA viruses using metagenomic approaches have revealed a high diversity and prevalence of RNA viruses in several microalgae lineages ( 11 , 14 – 21 ). While the positive-sense single-strand (ss+) picorna-like Marnaviridae are the best described family of microalgae-infecting viruses ( 11 , 22 , 23 ), metagenomic studies continue to expand the diversity of microalgal viruses, including identification of the double-strand RNA (dsRNA) viruses from the orders Ghabrivirales (Totiviridae-like), Durnavirales (Partitiviridae-like), and Martellivirales (Endornaviridae-like) ( 19 , 20 , 24 – 26 ), as well as ss+ RNA viruses from the Sobelivirales (Alvernaviridae), Nodamuvirales (Nodaviridae), Wolframvirales (Narnaviridae) , and Cryppavirales (Mitoviridae) phyla ( 19 , 20 , 24 , 27 , 28 ).…”

“Quasigenus” amongPhycodnaviridae: A diversity of chlorophyte-infecting viruses in response to a dense algal culture in a high-rate algal pond

“…Water sampling and HRAP characteristics are as described in a previous publication (Chase et al, 2021). Samples were processed ( e .…”

“…The number of isolated particles (events) per population ranged between 89 000 and 500 000. Lysis was carried out as detailed in (Chase et al, 2021), and nucleic acid was extracted using EZ1 Advanced XL extraction with a Virus Card (QIAGEN). Six of the 20 FACS populations did not generate sufficient DNA and were not subsequently sequenced.…”

“…The selection of putative viruses for targeting, processing of raw water samples for qPCR, and the qPCR reaction setup were conducted in the same way as described in previous work (Chase et al, 2021) without the need for cDNA construction. Briefly, Primer3 (Untergasser et al, 2012) and PerlPrimer v.1.2.3 (Marshall, 2004) were used to produce efficient primers in silico before in vitro testing.…”

“…Six of the 20 FACS populations did not generate sufficient DNA and were not subsequently sequenced. Library preparation and paired-end 2 × 250 bp Illumina MiSeq sequencing of the UVs were done as described in a previous publication (Chase et al, 2021). FACS population were amplified using Ready-To-Go Genomiphi V3 kit (GE Healthcare), followed by purification and Illumina HiSeq sequencing (paired-end 2 × 151 bp) performed by DOE Joint Genome Institute (JGI).…”