phoH-carrying virus communities responded to multiple factors and their correlation network with prokaryotes in sediments along Bohai Sea, Yellow Sea, and East China Sea in China

Bacteriophages carry auxiliary metabolic genes related to energy, sulfur and phosphorus metabolism during a harmful algal bloom in a freshwater lake

Cyanophages play an important role in nutrient cycling in lakes since they can modulate the metabolism of cyanobacteria. A proper understanding of the impact of cyanophage infection on the metabolism and ecology of cyanobacteria is critical during a complete cycle of harmful algal bloom (HAB). The ecology of cyanophages in marine environments has been well-delineated, but cyanophages in freshwater lakes remain less studied. Here, we studied the diversity of cyanophages and their impact on host ecology and metabolism through the succession of HAB in Utah Lake, which is a shallow eutrophic freshwater lake, in 2019. We collected water samples at three different periods from two locations in freshwater Utah Lake. The three sampling periods represented the pre-bloom, peak-bloom, and post-bloom events. We observed that the Utah Lake virome was dominated by families Myoviridae, Siphoviridae, and Podoviridae under the order Caudovirales. We detected photosystem-related genes, sulfur assimilation genes, and pho regulon (phosphorus metabolism) genes in genomes of predicted cyanophages. We were able to capture the changes in relative abundance and expression of functional genes in genomes of cyanophage at different stages of the bloom. We observed higher relative abundance and expression of cyanophage-encoded pho-regulon genes in the "pre-bloom" period. The higher expression of pho-regulon genes in P-limited ecosystem of Utah Lake indicated the possible contribution of cyanophage to enhance the fitness of the host cyanobacteria. Our study provides some insightful findings on the role of cyanophages in controlling the ecology and relative abundance of host cyanobacteria in freshwater lakes.

Macroalgal virosphere assists with host-microbiome equilibrium regulation and affects prokaryotes in surrounding marine environments

The microbiomes in macroalgal holobionts play vital roles in regulating macroalgal growth and ocean carbon cycling. However, the virospheres in macroalgal holobionts remain largely underexplored, representing a critical knowledge gap. Here we unveil that the holobiont of kelp (Saccharina japonica) harbors highly specific and unique epiphytic/endophytic viral species, with novelty (99.7% unknown) surpassing even extreme marine habitats (e.g. deep-sea and hadal zones), indicating that macroalgal virospheres, despite being closest to us, are among the least understood. These viruses potentially maintain microbiome equilibrium critical for kelp health via lytic-lysogenic infections and the expression of folate biosynthesis genes. In-situ kelp mesocosm cultivation and metagenomic mining revealed that kelp holobiont profoundly reshaped surrounding seawater and sediment virus-prokaryote pairings through changing surrounding environmental conditions and virus-host migrations. Some kelp epiphytic viruses could even infect sediment autochthonous bacteria after deposition. Moreover, the presence of ample viral auxiliary metabolic genes for kelp polysaccharide (e.g. laminarin) degradation underscores the underappreciated viral metabolic influence on macroalgal carbon cycling. This study provides key insights into understanding the previously overlooked ecological significance of viruses within macroalgal holobionts and the macroalgae-prokaryotes-virus tripartite relationship.

Genomic diversity and ecological distribution of marine Pseudoalteromonas phages

Pseudoalteromonas, with a ubiquitous distribution, is one of the most abundant marine bacterial genera. It is especially abundant in the deep sea and polar seas, where it has been found to have a broad metabolic capacity and unique co-existence strategies with other organisms. However, only a few Pseudoalteromonas phages have so far been isolated and investigated and their genomic diversity and distribution patterns are still unclear. Here, the genomes, taxonomic features and distribution patterns of Pseudoalteromonas phages are systematically analyzed, based on the microbial and viral genomes and metagenome datasets. A total of 143 complete or nearly complete Pseudoalteromonas-associated phage genomes (PSAPGs) were identified, including 34 Pseudoalteromonas phage isolates, 24 proviruses, and 85 Pseudoalteromonas-associated uncultured viral genomes (UViGs); these were assigned to 47 viral clusters at the genus level. Many integrated proviruses (n = 24) and filamentous phages were detected (n = 32), suggesting the prevalence of viral lysogenic life cycle in Pseudoalteromonas. PSAPGs encoded 66 types of 249 potential auxiliary metabolic genes (AMGs) relating to peptidases and nucleotide metabolism. They may also participate in marine biogeochemical cycles through the manipulation of the metabolism of their hosts, especially in the phosphorus and sulfur cycles. Siphoviral and filamentous PSAPGs were the predominant viral lineages found in polar areas, while some myoviral and siphoviral PSAPGs encoding transposase were more abundant in the deep sea. This study has expanded our understanding of the taxonomy, phylogenetic and ecological scope of marine Pseudoalteromonas phages and deepens our knowledge of viral impacts on Pseudoalteromonas. It will provide a baseline for the study of interactions between phages and Pseudoalteromonas in the ocean.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-022-00160-z.

The smallest in the deepest: the enigmatic role of viruses in the deep biosphere

It is commonly recognized that viruses control the composition, metabolism, and evolutionary trajectories of prokaryotic communities, with resulting vital feedback on ecosystem functioning and nutrient cycling in a wide range of ecosystems. Although the deep biosphere has been estimated to be the largest reservoir for viruses and their prokaryotic hosts, the biology and ecology of viruses therein remain poorly understood. The deep virosphere is an enigmatic field of study in which many critical questions are still to be answered. Is the deep virosphere simply a repository for deeply preserved, non-functioning virus particles? Or are deep viruses infectious agents that can readily infect suitable hosts and subsequently shape microbial populations and nutrient cycling? Can the cellular content released by viral lysis, and even the organic structures of virions themselves, serve as the source of bioavailable nutrients for microbial activity in the deep biosphere as in other ecosystems? In this review, we synthesize our current knowledge of viruses in the deep biosphere and seek to identify topics with the potential for substantial discoveries in the future.