Year-round dynamics of amplicon sequence variant communities differ among eukaryotes,Imiterviralesand prokaryotes in a coastal ecosystem

Abstract

Coastal microbial communities are affected by seasonal environmental change, biotic interactions, and fluctuating nutrient availability. We investigated the seasonal dynamics of communities of eukaryotes, a major group of double-stranded DNA viruses that infect eukaryotes (order Imitervirales; phylum Nucleocytoviricota), and prokaryotes in the Uranouchi Inlet, Kochi, Japan. We performed metabarcoding using ribosomal RNA genes and viral polB genes as markers in 43 seawater samples collected over 20 months. Eukaryotes, prokaryotes, and Imitervirales communities characterized by the compositions of amplicon sequence variants (ASVs) showed synchronic seasonal cycles. However, the community dynamics showed intriguing differences in several aspects, such as the recovery rate after a year. We also showed that the differences in community dynamics were at least partially explained by differences in recurrence/persistence levels of individual ASVs among eukaryotes, prokaryotes, and Imitervirales. Prokaryotic ASVs were the most persistent, followed by eukaryotic ASVs and Imitervirales ASVs, which were the least persistent. We argue that the differences in the specificity of interactions (virus–eukaryote vs. prokaryote–eukaryote) as well as the niche breadth of community members were at the origin of the distinct community dynamics among eukaryotes, their viruses, and prokaryotes.

Prevalence of Viral Frequency-Dependent Infection in Coastal Marine Prokaryotes Revealed Using Monthly Time Series Virome Analysis

“…1 ). Similar seasonal peaks have been observed in previous studies, such as the San-Pedro Ocean Time (SPOT) series conducted in San Pedro Channel ( 22 , 25 , 26 , 39 – 41 ). However, the lower community similarity observed between opposite seasons in both prokaryotic and viral communities at Osaka Bay than observed at SPOT using a similar methodology ( 26 , 41 ) suggests more pronounced seasonality at Osaka Bay.…”

“…We investigated seasonal dynamics of prokaryotic and viral communities using the Bray-Curtis similarity index between all pairwise combinations of samples (136 pairs, 1- to 17-month intervals), following the previous time series observations in different locations ( 22 , 25 , 26 , 39 , 40 ). Both prokaryotic and viral communities showed clear seasonal patterns, with a peak average similarity at an interval of about 12 months, representing the same seasons, and the bottom of average similarity at an interval of 6 months, representing opposite seasons ( Fig.…”

Global observation of plankton communities from space

“…There have been some attempts to capture zooplankton abundance from satellite data [19, 43], but it is still difficult to capture a global view over the wide taxonomic range. Our network approach can be extended to prokaryotes and viruses (as they are strongly associated with eukaryotic communities [44, 45]), which are also difficult to observe from satellites due to their small size and lack of optical properties.…”