Novel Caudovirales associated with Marine Group I Thaumarchaeota assembled from metagenomes

Abstract

Summary Marine Group I (MGI) Thaumarchaeota are some of the most abundant microorganisms in the deep ocean and responsible for much of the ammonia oxidation occurring in this environment. In this work, we present 35 sequences assembled from metagenomic samples of the first uncultivated Caudovirales viruses associated with Thaumarchaeota, which we designated marthavirus. Most of the sequences were obtained from cellular metagenomes confirming that they represent an important tool to study environmental viral communities due to cells retrieved while undergoing viral lysis. Metagenomic recruitment showed that this viral population is formed by very divergent entities with high intrapopulation homogeneity. However, metatranscriptomic analyses revealed the same differential expression profile with the capsid as major transcript, indicative of viruses during the lytic cycle. The cobalamine biosynthesis gene cobS, an auxiliary metabolic gene, was also highly expressed during the infection. These analyses expand our understanding of the global diversity of archaeal viruses.

Genome-resolved viral and cellular metagenomes revealed potential key virus-host interactions in a deep freshwater lake

“…and thus are important players in the nitrogen and carbon cycles of lakes. In marine systems, members of MGI are also dominant in the deep aphotic layer, and recent studies have reported the presence of several putative MGI viruses(Chow et al, 2015;Labonté et al, 2015), including those encoding AMGs such as amoC(Ahlgren et al, 2019) and cobS(López-Pérez et al, 2018). The present study predicted one Ca.…”

“…Members of MGI dominate the hypolimnion of deep freshwater lakes(26) (Table S4) and thus are important players in the nitrogen and carbon cycles of lakes. In marine systems, members of MGI are also dominant in the deep aphotic layer, and recent studies have reported the presence of several putative MGI viruses(105,106), including those encoding AMGs such as amoC(107) and cobS(86). The present study predicted Most of these virus-host interactions were newly discovered, and their characterization was facilitated by LBMAGs (SI Results and Discussion).…”

“…Functional annotation of viral genes (SI Dataset S1) revealed that LBVGs encoded AMGs that have previously been identified in marine viromes (8,49,77,85,86). LBVGs, respectively, and LBVG_98 contained both (SI Dataset S1).…”

Integrated mobile genetic elements in Thaumarchaeota

“…In addition to proviruses related to tailed viruses of the order Caudovirales , which have been previously observed in thaumarchaeal genomes and also detected by several metagenomics studies (Chow et al ., ; Labonté et al ., ; Ahlgren et al ., ; López‐Pérez et al ., ), we identified proviruses encoding the DJR MCP, one of the most widely distributed and diverse groups of dsDNA viruses in all three domains of life (Krupovic and Bamford, ; Krupovic and Koonin, ; Yutin et al ., ). Although the number of identified archaeal viruses with the DJR MCP is small, phylogenetic analysis suggests a coevolution of this virus group with the major archaeal lineages, including Thaumarchaeota.…”

Metagenome Mining Reveals Hidden Genomic Diversity of Pelagimyophages in Aquatic Environments

“…In this study, we analyzed 26 new sequences of myophages that putatively infect the SAR11 clade retrieved by mining aquatic metagenomes. This alternative approach to culture-dependent methods has succeeded in discovering new viruses from uncultured microbes earlier (32,33). Together, these findings increased sixfold the SAR11 myophage repertoire and allowed us to discover different PMP clades, including the first myophage specific of the freshwater genus Ca.…”