Abstract
Fonsibacter (LD12 subclade) is among the most abundant bacterioplankton in freshwater ecosystems. These bacteria belong to the order Pelagibacterales (SAR11) and are related to Pelagibacter (marine SAR11), which dominates many marine habitats. Although a few Pelagibacter phage (Pelagiphage) have been described, no phage that infect Fonsibacter have been reported. In this study, we describe two groups of Podoviridae phage that infect Fonsibacter A complete Fonsibacter genome containing a prophage was reconstructed from metagenomic data. A circularized and complete genome related to the prophage, referred to as uv-Fonsiphage-EPL (lysogenic strategy), shows high similarity to marine Pelagiphage HTVC025P. Additionally, we reconstructed three complete genomes and one draft genome of phage related to marine Pelagiphage HTVC010P and predicted a lytic strategy. The similarity in codon usage and cooccurrence patterns of HTVC010P-related phage and Fonsibacter suggested that these phage infect Fonsibacter Similar phage were detected in Lake Mendota, Wisconsin, where Fonsibacter is also present. A search of related phage revealed the worldwide distribution of some genotypes in freshwater ecosystems, suggesting their substantial role in shaping indigenous microbial assemblages and influence on biogeochemical cycling. However, the uv-Fonsiphage-EPL and one group of HTVC010P-related phage have a more limited distribution in freshwater ecosystems. Overall, the findings provide insights into the genomic features of phage that infect Fonsibacter and expand understanding of the ecology and evolution of these important bacteria.IMPORTANCE Fonsibacter represents a significant microbial group of freshwater ecosystems. Although the genomic and metabolic features of these bacteria have been well studied, no phage infecting them has been reported. In this study, we reconstructed complete genomes of Fonsibacter and infecting phage and revealed their close relatedness to the phage infecting marine SAR11 members. Also, we illustrated that phage that infect Fonsibacter are widely distributed in freshwater habitats. In summary, the results contribute new insights into the ecology and evolution of Fonsibacter and phage.
Highlights
Fonsibacter (LD12 subclade) is among the most abundant bacterioplankton in freshwater ecosystems
A metagenomics-assembled genome from the freshwater Lake Baikal was phylogenetically assigned to Pelagibacter [4], and phylogenetic analyses of 16S rRNA genes suggested the existence of several marine SAR11 subtypes in freshwater lakes [8]
Freshwater samples were collected from an end pit lake (EPL) in Alberta, Canada
Summary
Fonsibacter (LD12 subclade) is among the most abundant bacterioplankton in freshwater ecosystems These bacteria belong to the order Pelagibacterales (SAR11) and are related to Pelagibacter (marine SAR11), which dominates many marine habitats. We reconstructed complete genomes of Fonsibacter and infecting phage and revealed their close relatedness to the phage infecting marine SAR11 members. Heterotrophic SAR11 bacteria (Alphaproteobacteria; Pelagibacterales) are often very abundant in marine and freshwater ecosystems [1,2,3,4]. Comparative genomic analyses showed many proteins shared between Fonsibacter and Pelagibacter (marine SAR11), but metabolic divergence was detected [2]. We performed genome-resolved metagenomic analyses on microbial communities from freshwater ecosystems to reconstruct genomes of Fonsibacter bacteria and their phage. The distribution of some related phage in freshwater ecosystems suggests the broad ecological significance of Fonsibacter phage. The findings shed light on the ecology of Fonsibacter and reveal aspects of phage and host evolutionary history
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