Genomic insights into the adaptation of Synechococcus to the coastal environment on Xiamen

Abstract

Synechococcus are widely distributed in the global ocean, from the pelagic zone to coastal waters. However, little is known about Synechococcus in coastal seawater due to limitations in isolation and culture conditions. In this study, a combination of metagenomic sequencing technology, flow cytometry sorting, and multiple displacement amplification was used to investigate Synechococcus in the coastal seawater of Xiamen Island. The results revealed 18 clades of Synechococcus and diverse metabolic genes that appear to contribute to their adaptation to the coastal environment. Intriguingly, some metabolic genes related to the metabolism of carbohydrates, energy, nucleotides, and amino acids were found in 89 prophage regions that were detected in 16,258 Synechococcus sequences. The detected metabolic genes can enable prophages to contribute to the adaptation of Synechococcus hosts to the coastal marine environment. The detection of prophages also suggests that the cyanophages have infected Synechococcus. On the other hand, the identification of 773 genes associated with antiviral defense systems indicates that Synechococcus in Xiamen have evolved genetic traits in response to cyanophage infection. Studying the community diversity and functional genes of Synechococcus provides insights into their role in environmental adaptation and marine ecosystems.

Keywords: Synechococcus; Xiamen coast; cyanophages; metagenomics; mini-metagenomics.

Figure 1

Phylogenetic tree of Synechococcus, based on the ITS sequence alignment of 1,388 positions, including tRNAs, showing the phylogenetic relationships among Synechococcus genotypes. The two clades identified in this study are depicted in purple. The unclassified representative sequences from our study are indicated in boldface, while some sequences obtained in this study are not shown (represented by triangles). The numbers at the nodes of the tree represent the bootstrap values for maximum likelihood (ML) analyses, posterior probabilities for Bayesian inference (BI), and bootstrap values for the neighbor-joining (NJ) method, respectively.

Figure 2

Distribution of the species of Synechococcus in Xiamen coastal waters. Map of the sampling station (A). Venn diagram of the species number of Synechococcus (B). Community composition of Synechococcus in Xiamen coastal waters (C).

Figure 3

Top 20 metabolic pathways of Synechococcus.

Figure 4

Representatives of putative prophages in Synechococcus genomes.

Figure 5

Count of antiviral defense-related genes in Synechococcus genomes (A) and antiviral defense systems in Synechococcus genomes (B).