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

Abstract

Coastal seawater is the habitat of diverse microbial communities. These communities are affected by seasonal environmental changes and fluctuating nutrient availability, as well as competitive and cooperative interspecific interactions. The complex interplay of these factors affects elemental cycles and therefore, the environment, which in turn affects microbial communities. In this work, we investigated the seasonal dynamics of communities of eukaryotes, a major group of double-stranded DNA viruses infecting eukaryotes (i.e., Mimiviridae), as well as prokaryotes in the Uranouchi Inlet, Kochi, Japan. This inlet harbors several microalgae that recurrently form blooms throughout the year. We performed metabarcoding using ribosomal RNA genes and a Mimiviridae DNA polymerase gene as marker genes and counted cells of major algal species in 43 seawater samples collected during 20 months. Communities of eukaryotes, Mimiviridae, and prokaryotes characterized at the amplicon sequence variant (ASV) level showed similar seasonal cycles but differences in several aspects such as the recovery rate after a year. The ASV persistence level differed among eukaryote, Mimiviridae, and prokaryote communities. Mimiviridae ASVs were less persistent than were eukaryotic ASVs, and prokaryotic ASVs were the most persistent. These observations are discussed in the context of survival strategies of the major microbes in these three communities.

The Eco-Evo Mandala: Simplifying Bacterioplankton Complexity into Ecohealth Signatures

“…For instance, recently, Zhang et al [73] considered sampled microbiomes in the Pearl River Delta and found associations with algal blooms and salinity gradients. Prodinger et al [74] recently observed during diverse eukaryotic species blooms the Megavirus occurrence in the Uranouchi Inlet (JP), confirming the importance of viruses in the bacterioplankton dynamics. Debates still exist about the causal pathways between eukaryotes, prokaryotes, and viruses, and so further research is needed.…”

Tight association between microbial eukaryote and giant virus communities in the Arctic Ocean

“…For the Imitervirales sequences, MAPS2 ( Mimiviridae Amplicon Processing System) was used for the sequence analysis (Prodinger et al 2022). DADA2 was used to check and remove megaprimer sequences, merging, quality control, dereplication, chimera check, and non‐singleton ASV output.…”

“…Imitervirales ASVs were then assigned to the reference tree. The 662 Imitervirales leaves in the tree were classified into 13 Imitervirales clades that were manually defined in a previous publication (Prodinger et al 2022). The phylogenetic tree was edited and produced by iTOL v5.7 (https://itol.embl.de/).…”

“…Investigating such virus‐host associations at smaller geographic and time scales can provide further insights into the possible regulatory role of viruses on the host community structure. However, such local studies are currently scarce for Imitervirales (or NCLDVs) (Sandaa et al 2018; Prodinger et al 2022), and to the best of our knowledge, no study has investigated both Imitervirales and eukaryotic communities in the Arctic Ocean. We reasoned that examining whether the two communities are associated with each other in geographically close locations with similar environmental conditions and in the same period would lead to a better understanding of the interactions between Imitervirales and microbial eukaryotes.…”

“…S6 . Non‐metric multidimensional scaling (NMDS) plot with Imitervirales amplicon sequence variant (ASV) composition of Arctic samples (this study), hotspring samples, subtropical coastal sea water samples (Li et al 2019; Prodinger et al 2020, 2022). ASVs were firstly subsampled by the minimum number of each sample, and relative abundance was calculated by percentage of ASVs in each sample.…”