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

Abstract

Synechococcus is a major contributor to global marine primary production. Here, its spatio-temporal variations in abundance and phylogenetic structure were studied at three stations of the South China Sea at both DNA and cDNA levels. Synechococcus cell abundance was lowest in March, but highest in October at two coastal stations. Its abundance was higher at the estuarine station, which reached a peak value of 1.36 × 105 cells/ml in April, owing to the nitrogen nutrients discharged from the Sanya River. Gene and gene transcript abundances of four Synechococcus lineages, clades II, III, VIII, and S5.3, were studied by quantitative PCR, which showed that clade II was the most abundant lineage at both DNA and cDNA levels. High-throughput sequencing revealed that, at the DNA level, Synechococcus assemblage was dominated by clade SY4 (a novel clade defined in this study), S5.2, and clade II in the coastal waters and was dominated by freshwater/S5.2 Synechococcus, reaching a value up to 88.61% in June, in estuarine waters. Changes in salinity and nutrient concentration caused by seasonal monsoonal forcing and river discharge were the key determinants of the spatio-temporal variation in Synechococcus assemblages at the DNA level. In comparison, high dissimilation among samples at the same stations and in the same seasons leads to the imperceptible spatio-temporal variation pattern of Synechococcus assemblages at the cDNA level. Furthermore, co-occurrence networks disclosed that Synechococcus community had closer and more complex internal interactions at the cDNA level. These discrepancies highlighted the necessity to study Synechococcus assemblages at both DNA and cDNA levels.

Seasonal and spatial variations of Synechococcus in abundance, pigment types, and genetic diversity in a temperate semi-enclosed bay

“…This was the first time three pigment types of Synechococcus were simultaneously distinguished. In the Hong Kong coastal waters and Pearl River Estuary, PC-only (type 1) and PE-rich (type 2 + type 3) Synechococcus were detected, whereas, in the Bohai Sea, Yellow Sea, and the East China Sea, only PE-Synechococcus was detected ( Liu et al, 2014 ; Xia et al, 2017a , 2018 ; Wang et al, 2021 , 2022a , 2022c ).…”

“…To improve the accuracy of flow cytometric detection, it is necessary to enrich Synechococcus abundances collected in winter and spring by filtering before analysis and increasing the acquisition time during analysis. On the other hand, there is a need to use more sensitive and efficient molecular methods, such as qPCR for quantitative analysis of specific groups of Synechococcus , making the results more comparable and accurate ( Wang et al, 2022c ).…”

Spatio-temporal patterns of Synechococcus oligotypes in Moroccan lagoonal environments

“…While the rpoC1 gene is a higher resolution diversity marker 36 , 16S amplicon data can be used for exploring the entire bacterial assemblage including Synechococcus clade designations via oligotyping 35 . The latter has a great advantage in answering unexplained diversity contained in taxa using 16S rRNA gene sequences.…”