Spatial and temporal variations inSynechococcusmicrodiversity in the Southern California coastal ecosystem

Abstract

Summary The Synechococcus cyanobacterial population at the Scripps Institution of Oceanography pier in La Jolla, CA, shows large increases in abundance, typically in the spring and summer followed, by rapid declines within weeks. Here we used amplicon sequencing of the ribosomal RNA internal transcribed spacer region to examine the microdiversity within this cyanobacterial genus during these blooms as well as further offshore in the Southern California coastal ecosystem (CCE). These analyses revealed numerous Synechococcus amplicon sequence variants (ASVs) and that clade and ASV composition can change over the course of blooms. We also found that a large bloom in August 2016 was highly anomalous both in its overall Synechococcus abundance and in terms of the presence of normally oligotrophic Synechococcus clade II. The dominant ASVs at the pier were found further offshore and in the California Current, but we did observe more oligotrophic ASVs and clades along with depth variation in Synechococcus diversity. We also observed that the dominant sequence variant switched during the peak of multiple Synechococcus blooms, with this switch occurring in multiple clades, but we present initial evidence that this apparent ASV switch is a physiological response rather than a change in the dominant population.

Seasonal and Spatial Variations in Synechococcus Abundance and Diversity Throughout the Gullmar Fjord, Swedish Skagerrak

“…During fall, Syn-223 (clade IV) commonly had a maximum relative abundance around 30 m while Syn-102 (clade I) was proportionally dominant below 50 m depth. This trend between the clades was not as clear in the summer, however, a similar pattern has been previously observed at multiple sites off the coast of southern California attributed to seasonal stratification ( Nagarkar et al, 2021 ). We observed that there was a greater degree of stratification below the shallow surface-mixing layer in fall compared to summer, but the deep-water mass showed similar stratification between the two seasons, only deeper by 5 m in September.…”

“…By August, Syn-223 (clade IV) slightly overcomes Syn-102 (clade I) in abundance. Similar patterns in clades IV and I dynamics have previously been observed in marine systems with clade I starting as the dominant clade during blooms and later shifting to IV ( Tai and Palenik, 2009 ; Nagarkar et al, 2021 ). This suggests there are either environmental factors that facilitate Syn-102 accumulation and dominance in early summer, which change to favor Syn-223 as the season progresses, or that Syn-102 is more of an opportunist and quickly responded to changes in the environment while Syn-223 more slowly grew to dominance.…”

Spatio-Temporal Variation of Synechococcus Assemblages at DNA and cDNA Levels in the Tropical Estuarine and Coastal Waters

“…Synechococcus cell abundance ranged from 10 3 to 10 4 cells/ml at the coastal stations ( Figure 2A ). It is lower than those in temperate or subtropic coastal waters, such as Bohai coastal marine ranch ( Li et al, 2021 ), Hong Kong coastal waters ( Liu et al, 2014 ), coastal western subtropical Pacific ( Tsai et al, 2006 ), and Southern California coast ( Nagarkar et al, 2021 ). However, it is consistent with those in other tropical coastal waters, such as the equatorial eastern Indian Ocean ( Wei et al, 2019 ) and coastal waters of the Philippines (Southeast China Sea) ( Agawin et al, 2003 ).…”

“…Marine Synechococcus exhibits high genetic diversity ( Farrant et al, 2016 ; Xia et al, 2019 ). Gene markers, such as the 16S rRNA gene ( Mackey et al, 2017 ), the 16S–23S internally transcribed spacer (ITS) ( Li et al, 2021 ; Nagarkar et al, 2021 ), the RNA polymerase gene ( rpo C1) ( Kent et al, 2019 ; Wang et al, 2021a ), the nitrate reductase gene ( nar B) ( Robidart et al, 2012 ), the cytochrome b 6 gene ( pet B) ( Mazard et al, 2012 ), and the ribulose–1,5–bisphosphate carboxylase oxygenase gene ( rbc L) ( Paerl et al, 2012 ), have been commonly applied to study the genetic diversity of Synechococcus . Among these gene markers, ITS is the locus with the most sequences available for primer design ( Ahlgren and Rocap, 2012 ).…”

Relating sinking and suspended microbial communities in the California Current Ecosystem: digestion resistance and the contributions of phytoplankton taxa to export

“…Lastly, depth distribution might also be a relevant factor for interpreting the relative associations of Synechococcus clades with export. The mixed‐layer dominance of clades I and IV at all CCE sites is consistent with upwelling regions of the North and South Pacific (Zwirglmaier et al ., 2008; Sohm et al ., 2016; Nagarkar et al ., 2021). In the Sargasso Sea, however, clades II and III dominate the water column, with clade III more strongly associated with export (De Martini et al ., 2018).…”