Tetsuya, H. | bioRxiv Science

bioRxiv2021

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

Coastal seawater is the habitat of different microbial communities. These communities are affected by seasonal environmental changes and fluctuating nutrient availability, as well as competitive and cooperative interspecific interactions. 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. We performed metabarcoding using ribosomal RNA genes and the Mimiviridae polB gene as marker genes in 43 seawater samples collected during 20 months. Communities characterized by the compositions of amplicon sequence variants (ASVs) showed synchronic seasonal cycles for eukaryotes, Mimiviridae, and prokaryotes. However, the community dynamics showed intriguing differences in several aspects such as the recovery rate after a year. We further show that the differences in the community dynamics can be explained by differences in the recurrence/persistence levels of individual ASVs among eukaryotes, Mimiviridae, and prokaryotes. Mimiviridae ASVs were less persistent than eukaryotic ASVs, and prokaryotic ASVs were the most persistent. We argue that the differences in the specificity of interactions (i.e. virus-eukaryote vs prokaryote-eukaryote) as well as the survival strategies are at the origin of the distinct community dynamics among eukaryotes, Mimiviridae, and prokaryotes. One sentence summaryA one year observation of coastal microbial communities revealed similar but different community dynamics for eukaryotes, a group of large viruses, and prokaryotes.

microbiology↗

bioRxiv2020

Prophages integrating into prophages: a mechanism to accumulate type III secretion effector genes and duplicate Shiga toxin-encoding prophages in Escherichia coli

Bacteriophages (or phages) play major roles in the evolution of bacterial pathogens via horizontal gene transfer. Multiple phages are often integrated in a host chromosome as prophages, not only carrying various novel virulence-related genetic determinants into host bacteria but also providing various possibilities for prophage-prophage interactions in bacterial cells. In particular, Escherichia coli strains such as Shiga toxin (Stx)-producing E. coli (STEC) and enteropathogenic E. coli (EPEC) strains have acquired more than 10 PPs (up to 21 PPs), many of which encode type III secretion system (T3SS) effector gene clusters. In these strains, some prophages are present at a single locus in tandem, which is usually interpreted as the integration of phages that use the same attachment (att) sequence. Here, we present prophages integrating into T3SS effector gene cluster-associated loci in prophages, which are widely distributed in STEC and EPEC. Some of the prophages integrated into prophages are Stx-encoding prophages and have induced the duplication of Stx-encoding phages in a single cell. The identified att sequences in prophage genomes are apparently derived from host chromosomes. In addition, two or three different att sequences are present in some prophages, which results in the generation of prophage clusters in various complex configurations. These "prophages-in-prophages" represent a medically and biologically important type of inter-phage interaction that promotes the accumulation of T3SS effector genes in STEC and EPEC, the duplication of Stx-encoding prophages in STEC, and the conversion of EPEC to STEC and that may be distributed in other types of E. coli strains as well as other prophage-rich bacterial species. Author summaryMultiple prophages are often integrated in a bacterial host chromosome and some are present at a single locus in tandem. The most striking examples are Shiga toxin (Stx)-producing and enteropathogenic Escherichia coli (STEC and EPEC) strains, which usually contain more than 10 prophages (up to 21). Many of them encode a cluster of type III secretion system (T3SS) effector genes, contributing the acquisition of a large number of effectors (>30) by STEC and EPEC. Here, we describe prophages integrating into T3SS effector gene cluster-associated loci in prophages, which are widely distributed in STEC and EPEC. Two or three different attachment sequences derived from host chromosomes are present in some prophages, generating prophage clusters in various complex configurations. Of note, some of such prophages-in-prophages are Stx-encoding prophages and have induced the duplication of Stx-encoding prophages. Thus, these "prophages-in-prophages" represent an important inter-phage interaction as they can promote not only the accumulation of T3SS effectors in STEC and EPEC but also the duplication of Stx-encoding prophages and the conversion of EPEC to STEC.

microbiology↗