Diversity and temporal dynamics of Southern California coastal marine cyanophage isolates

Abstract

Marine ecosystems contain an immense diversity of phages, many of which infect the cyanobacteria responsible for a portion of oceanic primary productivity. To add to the growing body of research on the dynamics and diversity of these cyanophages, we measured cyanophage abundance, diversity, and community composition monthly for 15 mo at 3 coastal locations in Southern California, USA. We characterized over 900 individual cyanophages, isolated on Synechococcus sp. WH7803, by amplifying and sequencing 2 different genes from each isolate: g20 (the portal protein gene) and psbA (a host-derived gene involved in photosynthesis). The taxonomic composition and diversity of isolated cyanophages were highly variable over time, with little variation across the 3 locations. Particular taxa dominated the community at distinct times of year, with more rapid turnover of dominant types and higher overall abundance and diversity during spring and summer. These temporal patterns as well as taxonomic designations were highly congruent for both genes, based on operational taxonomic units (OTUs) defined at 99% nucleotide similarity, despite a greater level of amino acid conservation within psbA as compared to g20. Overall, this suggests that either gene can serve as a useful marker for cyanophage diversity. However, we detected 1 myovirus taxon (representing about 2.5% of the isolates) of uncertain phylogenetic affiliation that was negative for psbA amplification. Further sampling is necessary to assess whether these temporal dynamics in cyanophage composition, diversity, and abundance are seasonally recurring.

Prevalence of Viral Photosynthetic and Capsid Protein Genes from Cyanophages in Two Large and Deep Perialpine Lakes

“…In fact, we found that 90% of these psbA sequences (56 out of 62) had a GC content below 46% and were thus out of the percentage range (46 to 51%) found in marine Synechococcus phages (36). Our results echo the other freshwater studies (11,41), where low GC content has also been detected in some Synechococcus-virus-like psbA sequences and in the only known characterized freshwater Synechococcus phage, S-CRM01 (44.6%), at the same 729-nt region. Together, these results suggest that freshwater Synechococcus phages might have a lower GC content in psbA sequences than their marine counterparts, and this may be a result of a lower GC content in their Synechococcus hosts.…”

“…This is a common issue of diversity studies through the culture-independent approach by using PCR, since the validity of the primers depends on a limited number of isolates. Recently, Clasen et al (11) employed the isolation-based/ culture-dependent approach to examine marine cyanomyoviruses infecting Synechococcus sp. WH7803 and revealed important cooccurring cyanomyovirus genetic diversity.…”

“…Also, the diversity, abundance, or structure of cyanomyoviruses can vary between stations of the same lake (21) or ocean (15,18,27). When sampled from a single location, it has also been shown that abundance and community structure and/or diversity of these cyanophages can vary with time (11,12,16,20,23,28,29) and depth (13,27). Together, these studies reflect distinct temporal, vertical, and/or geographical distribution patterns of cyanomyoviruses across aquatic environments.…”

“…The genetic diversity of this group has been examined using the T4-like portal protein-encoding gene g20 as a molecular marker in different locations of both marine and freshwater ecosystems (11)(12)(13)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23)(24) and even in paddy soils (25). Distinct cyanomyoviruses could be detected in freshwater (12,18,21,26) and paddy soil (25) ecosystems in comparison to their marine counterpart.…”

Using Signature Genes as Tools To Assess Environmental Viral Ecology and Diversity

“…In this study, psbA was also investigated, but it proved less well suited for species diversity studies, since it was found in phages belonging to only one of the two clades. Using two signature genes, g20 and psbA, a collection of over 900 Synechococcus phages, collected at three different coastal sites over a 15-month period, was investigated (92). No spatial variations were found, but distinct seasonal communities were observed, with higher abundances in summer, consistent with previous studies described above (15)(16)(17)(18)77).…”