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

Abstract

Our knowledge of the diversity of RNA viruses infecting microbial algae—the microalgae—is minimal. However, describing the RNA viruses infecting these organisms is of primary importance at both the ecological and economic scales because of the fundamental roles these organisms play in aquatic environments and their growing value across a range of industrial fields.

A removable and cosmopolitan dsRNA Toti-like virus causes latent infection in a model diatom strain

“…The positive strand of the dsRNA genome was shown ( Fig. 1D ) and compared with the sequences found in N. oceanica and T. weissflogii [48]. Our findings strongly suggest that the model diatom strain Pt1 contains a marine Toti-like virus, the hosts of which were diverse and prevalent in marine unicellular microalgae.…”

“…Interestingly, highly similar sequences with 99% identities could be found on NCBI database (Sequence ID: OP191686 and OP191687). These two sequences were detected in Nannochloropsis oceanica ( N. oceanica ) and Thalassiosira weissflogii ( T. weissflogii ) commonly existing in marine environment and predicted to be the genome of a kind of marine Toti-like virus belonging to Totiviridae [48]. The positive strand of the dsRNA genome was shown ( Fig.…”

“…Our findings strongly suggest that the model diatom strain Pt1 contains a marine Toti-like virus, the hosts of which were diverse and prevalent in marine unicellular microalgae. Marine Totiviridae has been reported to be one of the most widespread families in non-vertebrate organisms [47], especially in marine microalgae [48, 49]. Consequently, the discovery of a kind of marine Toti-like virus in model diatom strain Pt1 displayed great importance for deep research on the relationship between the host and marine Totiviridae .…”

“…We also found that the terminals of each strand of dsRNA in P. tricornutum were distinct from the versions in N. oceanica and T. weissflogii named Taphios ghabri-like virus 1 isolate Thaweiss1 (OP191686) and Taphios ghabri-like virus 1 isolate Nanocea1 (OP191687) [48]. However, the coding regions were almost the same (identity > 99.5%), suggesting that the three hosts possessed different strains of the same virus.…”

The RNA virosphere: How big and diverse is it?

“…Despite Sanger sequencing's low throughput, this novel survey approach revealed a diverse array of highly‐divergent ‘picorna‐like’ RNA viruses that were likely infecting marine phytoplankton. A decade later, sequencing technologies had advanced sufficiently to enable the exploration of diverse environments, often via mining RdRp sequences in RNA‐seq data derived from (i) biotic samples (including holobiont, unicellular, and multicellular organisms), such as invertebrates (Li et al, 2015 ; Shi et al, 2016 ; Vieira et al, 2022b ; Wu et al, 2020 ), vertebrates (Shi et al, 2018 ), plants (Roossinck, 2012 ; Vieira et al, 2022a ), protists (Cai et al, 2012 ; Charon et al, 2022 , 2020 , 2021 ; Lachnit et al, 2015 ; Nagasaki et al, 2004 ; Sasai et al, 2018 ; Shirai et al, 2008 ; Tai et al, 2003 ; Tomaru et al 2004 , 2009 , 2012 ), and fungi (Deakin et al, 2017 ; Marzano et al, 2016 ) and (ii) environmental samples, such as faeces (Krishnamurthy et al, 2016 ), sediments (Callanan et al, 2020 ), soils (Hillary et al, 2022 ; Starr et al, 2019 ; Wu et al, 2021 ), rivers (French et al, 2022 ), and seawater from specific sites (Culley et al, 2003 , 2006 , 2014 ; Djikeng et al, 2009 ; Steward et al, 2013 ; Urayama et al, 2018 ; Vlok et al, 2019 ; Wolf et al, 2020 ) and from geographic locations representing the entire global oceans (Dominguez‐Huerta et al, 2022 ; Zayed et al, 2022 ). The environments most explored for RNA viruses during these two decades are aquatic (e.g., marine, sewage, and riverine), providing us with the first insights into their ecology, evolution of their viral inhabitants, and methodological challenges associated with characterizing specific natural ecosystems (Culley, 2018 ; Liao et al, ...…”