Highly Diverse Synechococcus Pigment Types in the Eastern Indian Ocean

Abstract

Marine picocyanobacteria Synechococcus exhibit highly diverse pigment types (PTs) and hence possess great advantage to utilize different spectrum of light effectively and to occupy a wide range of light niches. In this study, we explored the diversity of Synechococcus PTs in the eastern Indian Ocean (EIO), surface water of Strait of Malacca (SSM), and coastal waters of Sri Lanka (SSL). All the detected PTs were phycourobilin (PUB) containing PT 3 and showed distinct distribution patterns. Low PUB PT 3a and partial chromatic acclimater PT 3eA dominated in coastal and shallow waters (SSM and SSL). In contrast, high PUB and chromatic acclimaters PT 3dA and PT 3c/3dB were mainly distributed in open ocean (EIO). PT 3dA and PT 3c/3dB occurred at similar depths of the lower euphotic layers but showed distinct distribution pattern that are partially exclusive, indicating that they compete with each other for the same light niche. Interestingly, the newly described PT 3f was detected with high relative abundances at all stations and particularly dominated in the upper euphotic layer in EIO, which was confirmed with PT-specific quantitative polymerase chain reaction (qPCR). The relative abundance of PT 3f was negatively correlated with nutrient level, implying that PT 3f is adapted to oligotrophic waters. Pronounced niche partition of different PTs was observed in the upper and lower layers of euphotic zone in EIO and SSM/SSL. Light, nutrients, and strong stratification may play important roles in the niche partition of different PTs. Further analysis about ecologically significant taxonomic units revealed high diversity within each PT at different locations, which provided insights for understanding specific PT with wide range of niches.

Chromatic Acclimating Synechococcus Dominate in Mesoscale Eddies

“…(2013) later suggested its weak ability of chromatic acclimation as it possessed a CA4‐A gene island and named it as PT 3eA to distinguish it from typical chromatic acclimators. Currently whether PT 3eA (RCC 307) are independent pigment subtype is still an issue worthing further investigation and previous studies described RCC 307 with various names including PT 3b (Six et al., 2007; Xia et al., 2018), PT 3e (Humily et al, 2014), PT 3eA (Grébert, 2017; Humily et al., 2013; Zhang et al., 2022), PT 3dA (Chen et al., 2022; Grébert, 2017; Grébert et al., 2021; Xia et al., 2018), and asterisk‐highlighted PT 3b, 3e or 3dA due to its uniqueness (Sanfilippo, Nguyen, et al., 2019; Xia et al., 2018). However, PT 3eA are most possibly different from typical CA4‐A.…”

“…However, PT 3eA are most possibly different from typical CA4‐A. Clear divergence between RCC 307 and PT 3dA were revealed based on analysis of mpeBA and cpeBA operon (Grébert et al., 2021, 2022; Zhang et al., 2022). Moreover, RCC 307 closely related strains were widely distributed and abundant in Eastern Indian Ocean, SCS and surrounding waters based on previous studies (Chen et al., 2022; Zhang et al., 2022).…”

“…Clear divergence between RCC 307 and PT 3dA were revealed based on analysis of mpeBA and cpeBA operon (Grébert et al., 2021, 2022; Zhang et al., 2022). Moreover, RCC 307 closely related strains were widely distributed and abundant in Eastern Indian Ocean, SCS and surrounding waters based on previous studies (Chen et al., 2022; Zhang et al., 2022). In this study, PT 3eA could be detected in all the samples, with the maximum relative abundance reaching 19.6% and 41.9% in CE and ACE, respectively.…”

“…For classification of phylogenetic clade using rpoC1 gene, the taxonomy of ASVs was assigned using the database of reference sequence provided by Xia et al (2019). To identify PTs using the cpeBA operon, we compiled a database containing sequences from PT 2A, PT 3B, PT 3a, PT 3c, PT 3dA, PT 3dB, PT 3eA, and PT 3f, sourced from both isolated strains and field surveys in previous studies (Xia et al, 2017(Xia et al, , 2018Zhang et al, 2022). Subsequently, a native Bayes classifier was trained using databases of rpoC1 and the cpeBA operon, respectively.…”