Pseudo-nitzschia Challenged with Co-occurring Viral Communities Display Diverse Infection Phenotypes

Abstract

Viruses are catalysts of biogeochemical cycling, architects of microbial community structure, and terminators of phytoplankton blooms. Viral lysis of diatoms, a key group of eukaryotic phytoplankton, has the potential to impact carbon export and marine food webs. However, the impact of viruses on diatom abundance and community composition is unknown. Diatom-virus dynamics were explored by sampling every month at two coastal and estuarine locations in Washington state, USA resulting in 41 new isolates of the pennate diatom Pseudo-nitzschia and 20 environmental virus samples. We conducted a total of 820 pair-wise crosses of the Pseudo-nitzschia isolates and viral communities. Viral communities infected Pseudo-nitzschia isolates in 8% of the crosses overall and 16% of crosses when the host and viral communities were isolated from the same sample. Isolates ranged in their permissivity to infection with some isolates not infected by any viral samples and others infected by up to 10 viral communities. Isolates that were infected by the most viral communities also had the highest maximum observed viral titers (as high as 16000 infectious units ml-1). Titers of the viral communities were host dependent, as titers for one viral sample on eight different hosts spanned four orders of magnitude. Sequencing of the Pseudo-nitzschia Internal Transcribed Spacer 1 (ITS1) of the revealed multiple subgroups of hosts with 100% ITS1 identities that were infected by different viral communities. Indeed, we repeatedly isolated groups of isolates with identical ITS1 sequences from the same water sample that displayed different viral infection phenotypes. The interactions between Pseudo-nitzschia and the viral communities highlight the diversity of diatoms and emphasize the complexity and variability of diatom-virus dynamics in the ocean.

Evaluation of the rbcL marker for metabarcoding of marine diatoms and inference of population structure of selected genera

“…For example, it has been shown that virus infection can drive haplotypic differentiation of phytoplankton and that host ASV variation is relevant for protection against the virus (Needham et al, 2017). The existence of Pseudo-nitzschia viruses has been demonstrated (Carlson et al, 2016) and also recently isolated from the GoT (unpublished data), while strain specificity for viral infections has also been demonstrated and is common in diatom viruses (Nagasaki et al, 2004). Another commonly observed pattern in metabarcoding data is that more common taxa tend to be more microdiverse (Needham et al, 2017;Ruggiero et al, 2022).…”

Reduced representation sequencing accurately quantifies relative abundance and reveals population-level variation in Pseudo-nitzschia spp.

“…4). Ten were associated with species previously reported along the US Pacific Coast based on reference sequences available in GenBank and prior studies using ARISA (Carlson et al, 2016; Hubbard et al, 2014, 2008; Smith et al, 2018b). Half were putatively identified based on prior observations as P. australis/P.…”

“…Globally sampled populations of P. pungens were found to exhibit strong isolation by distance, however, time-series samples were pooled by region (Casteleyn et al, 2010), potentially masking relevant temporal shifts which have been repeatedly identified in other marine diatoms (Godhe and Härnström, 2010; Rynearson et al, 2006; Whittaker and Rynearson, 2017). Interestingly, morphologically and genetically distinct P. pungens varieties have been identified along the US West Coast (Carlson et al, 2016; Hubbard et al, 2014, 2008; Villac and Fryxell, 1998). Here we show that not only do allele frequencies show temporal shifts, in some instances these shifts correlate to some extent with the presence of DA (Fig.…”

Reduced representation sequencing accurately quantifies relative abundance and reveals population-level variation in Pseudo-nitzschia spp.

“…Globally sampled populations of P. pungens were found to exhibit strong isolation by distance, however, time-series samples were pooled by region (Casteleyn et al, 2010), potentially masking relevant temporal shifts which have been repeatedly identified in other marine diatoms (Godhe and Härnström, 2010;Rynearson et al, 2006;Whittaker and Rynearson, 2017). Interestingly, morphologically and genetically distinct P. pungens varieties have been identified along the US West Coast (Carlson et al, 2016;Hubbard et al, 2014Hubbard et al, , 2008Villac and Fryxell, 1998). Here we show that not only do allele frequencies show temporal shifts, in some instances these shifts correlate to some extent with the presence of DA (Fig.…”

“…blooms using ARISA Seventeen distinctly-sized amplicons were observed with ARISA (Fig.4). Ten were associated with species previously reported along the US Pacific Coast based on reference sequences available in GenBank and prior studies using ARISA(Carlson et al, 2016;Hubbard et al, 2014Hubbard et al, , 2008Smith et al, 2018b). Half were putatively identified based on prior observations as P. australis/P.…”