Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity

Abstract

In marine ecosystems, viruses exert control on the composition and metabolism of microbial communities, influencing overall biogeochemical cycling. Deep sea sediments associated with cold seeps are known to host taxonomically diverse microbial communities, but little is known about viruses infecting these microorganisms. Here, we probed metagenomes from seven geographically diverse cold seeps across global oceans to assess viral diversity, virus–host interaction, and virus-encoded auxiliary metabolic genes (AMGs). Gene-sharing network comparisons with viruses inhabiting other ecosystems reveal that cold seep sediments harbour considerable unexplored viral diversity. Most cold seep viruses display high degrees of endemism with seep fluid flux being one of the main drivers of viral community composition. In silico predictions linked 14.2% of the viruses to microbial host populations with many belonging to poorly understood candidate bacterial and archaeal phyla. Lysis was predicted to be a predominant viral lifestyle based on lineage-specific virus/host abundance ratios. Metabolic predictions of prokaryotic host genomes and viral AMGs suggest that viruses influence microbial hydrocarbon biodegradation at cold seeps, as well as other carbon, sulfur and nitrogen cycling via virus-induced mortality and/or metabolic augmentation. Overall, these findings reveal the global diversity and biogeography of cold seep viruses and indicate how viruses may manipulate seep microbial ecology and biogeochemistry.

Saline lakes on the Qinghai-Tibet Plateau harbor unique viral assemblages mediating microbial environmental adaption

“…Three hundred fifty-eight of 4,560 vOTUs could be linked to putative hosts, which represents 13.5% of the viral abundance in the six viromes of three lakes. This abundance is lower than in other environments, such as cold, deep-sea seep sediments, suggesting the uniqueness of the viral and microbial communities in the Qinghai-Tibet Plateau lakes (Li et al, 2021). Although most predicted vOTUs were linked to Bacteroidetes (90), Gammaproteobacteria (73), and other bacteria (51), the most abundant vOTUs (35.5% in relative abundance) were linked to Alphaproteobacteria, including the most abundant vOTU (vOTU_1374).…”

“…After comparing sequence similarity, tRNA sequences, CRISPR spacers, and oligonucleotide frequencies between prokaryotic metagenome-assembled genomes and vOTUs, putative hosts were predicted for 358 vOTUs of the six viromes (Figure 4), accounting for a relative abundance of 13.5% (Li et al, 2021). Most of the predicted vOTUs had narrow host ranges, with only 11 potentially exhibiting a broader host range across several classes.…”

A mixed blessing of viruses in wastewater treatment plants

“…Interestingly, only a minority of vOTUs derived from activated sludge (~1.4%) were shared with taxonomically known viruses from NCBI RefSeq (Figure 1b and Table S1), indicating that a large proportion of recovered viruses could not be assigned to known genus-level taxonomy. Among the classified viruses, 18 vOTUs belonged to Podoviridae, 11 vOTUs to Siphoviridae and 2 vOTUs to Myoviridae (Figure 1c), all of which were much lower than the classified viral quantities discovered in permafrost and deep sea sediments 5,7,18 , but comparable to that in glacier ice 36 . This suggests that activated sludge harbored diverse and especially the unknown viruses, which may impact the performance of such engineering systems.…”

“…Though this gene family was predicted to have no conserved motifs, the virus-derived CysH, also named as PAPS reductase and recovered from all three activated sludge samples, formed very similar tertiary structures to functionally known PAPS reductases (Figure 4e and Table S6). This homology suggested that viral cysH could enhance the biosynthesis of methionine and cysteine from sulfate assimilation in activated sludge, as well as in other ecosystems 7,[59][60][61][62] . Surprisingly, viral cysH genes formed discrete clusters from microbial ones and were manually divided into two clades based on the modeling structures (Figure S8 and Table S6).…”

“…Microorganisms in the forms of flocs or granules are long believed as the key responsible bio-catalysts of activated sludge, for removing nutrients and micropollutants 2 . Recent studies suggest viruses, usually many folds more than microbial population, have the potential to impact the activity and functionality of their microbial hosts in various habitats, including ocean 3 , freshwater 4 , permafrost 5 , and other natural ecosystems 6,7 . However, whether viruses have a contribution in artificial and engineering systems, for example in the activated sludge, and what are their exact roles remain poorly understood.…”