Multi‐year dynamics of fine‐scale marine cyanobacterial populations are more strongly explained by phage interactions than abiotic, bottom‐up factors

Abstract

Summary Currently defined ecotypes in marine cyanobacteria Prochlorococcus and Synechococcus likely contain subpopulations that themselves are ecologically distinct. We developed and applied high‐throughput sequencing for the 16S‐23S rRNA internally transcribed spacer (ITS) to examine ecotype and fine‐scale genotypic community dynamics for monthly surface water samples spanning 5 years at the San Pedro Ocean Time‐series site. Ecotype‐level structure displayed regular seasonal patterns including succession, consistent with strong forcing by seasonally varying abiotic parameters (e.g. temperature, nutrients, light). We identified tens to thousands of amplicon sequence variants (ASVs) within ecotypes, many of which exhibited distinct patterns over time, suggesting ecologically distinct populations within ecotypes. Community structure within some ecotypes exhibited regular, seasonal patterns, but not for others, indicating other more irregular processes such as phage interactions are important. Network analysis including T4‐like phage genotypic data revealed distinct viral variants correlated with different groups of cyanobacterial ASVs including time‐lagged predator–prey relationships. Variation partitioning analysis indicated that phage community structure more strongly explains cyanobacterial community structure at the ASV level than the abiotic environmental factors. These results support a hierarchical model whereby abiotic environmental factors more strongly shape niche partitioning at the broader ecotype level while phage interactions are more important in shaping community structure of fine‐scale variants within ecotypes.

Genomic mosaicism underlies the adaptation of marine Synechococcus ecotypes to distinct oceanic iron niches

“…Here we highlight how Fe‐related genes can be combined in different ways to arrive at distinct approaches to living in similar niches, and genomic mosaicism is an important theme more broadly in metal acquisition and tolerance in marine bacteria (Stuart et al ., ; Stuart et al ., ; Hogle et al ., ). On‐going work must take into consideration that currently‐defined ecotypes appear to contain multiple ecologically distinct populations (Kashtan et al ., ; Farrant et al ., ; Kent et al ., ; Ahlgren et al ., ), with significant physiological and genomic variation (Kashtan et al ., ; Pittera et al ., ). In particular, it will be interesting to examine genomic and physiologically diversity among CRD1 subpopulations as more genomes and isolates become available.…”

Investigating the Diversity of Marine Bacteriophage in Contrasting Water Masses Associated with the East Australian Current (EAC) System

“…Due to the reliance of bacteriophage on their hosts for replication, their abundance is usually tightly coupled to the presence and regional distribution of their specific hosts. Moreover, bacteriophage have been strongly correlated with the succession of their specific host ecotypes [57]. Previous work [25] and concurrent genomic ( Figure 5) data showed that cyanobacteria are highly abundant in the EAC; not surprisingly phage thought to infect cyanobacteria predominated in the warm water of the samples collected in the EAC (EAC, EAC_2).…”

Differential Activity of Coexisting Prochlorococcus Ecotypes

“…Prochlorococcus ecotype identity was determined by sequencing the cyanobacterial 16S-23S rRNA intergenic transcribed (ITS) region as described previously (Ahlgren et al, 2019). For sorted cells, DNA template in PCR was 5 ng of diluted MDA product.…”

“…Sequencing of PCR products was by Illumina MiSeq (2 × 250 bp paired end reads). Due to read lengths too short for robust overlap of 16S-23S rRNA ITS fragments, only reverse reads were used for calling OTUs as previously (Ahlgren et al, 2019). QIIME 1 (Caporaso et al, 2010) was used to quality filter sequence reads and call OTUs de novo at 97% similarity using Uclust in the pick_de_novo_otus.py script.…”