Insights into the dynamics between viruses and their hosts in a hot spring microbial mat

Abstract

Our current knowledge of host–virus interactions in biofilms is limited to computational predictions based on laboratory experiments with a small number of cultured bacteria. However, natural biofilms are diverse and chiefly composed of uncultured bacteria and archaea with no viral infection patterns and lifestyle predictions described to date. Herein, we predict the first DNA sequence-based host–virus interactions in a natural biofilm. Using single-cell genomics and metagenomics applied to a hot spring mat of the Cone Pool in Mono County, California, we provide insights into virus–host range, lifestyle and distribution across different mat layers. Thirty-four out of 130 single cells contained at least one viral contig (26%), which, together with the metagenome-assembled genomes, resulted in detection of 59 viruses linked to 34 host species. Analysis of single-cell amplification kinetics revealed a lack of active viral replication on the single-cell level. These findings were further supported by mapping metagenomic reads from different mat layers to the obtained host–virus pairs, which indicated a low copy number of viral genomes compared to their hosts. Lastly, the metagenomic data revealed high layer specificity of viruses, suggesting limited diffusion to other mat layers. Taken together, these observations indicate that in low mobility environments with high microbial abundance, lysogeny is the predominant viral lifestyle, in line with the previously proposed “Piggyback-the-Winner” theory.

Tracking Double-Stranded DNA Bacteriophages and Their Hosts in a Deep Freshwater Lake by Integrating Metagenomics and The Hi-C Technique

“…Similarly, in cone pool virome research, only three bacteriophage-host link events were detected by CRISPR [10]. Twenty-six (1.28%, 26/2034 total viral genomes) bacteriophages had host information identi ed by the CRISPR-based method in two freshwater habitats [27].…”

“…Following a previous virome study in hot spring, we used VirSorter and sequence BLASTN comparison to the IMG/VR database to detect viral genomes in the unbinned fraction of the assembled contigs [10,60,82]. First, the contigs (> 10 kb) classi ed as VirSorter categories 1-2 (viral genomes) and 4-5 (integrated viral contigs) were rst picked as candidate viral contigs.…”

“…However, the rapid development of viral metagenomics and bioinformatics has provided an opportunity to overcome these obstacles [5,6]. In recent years, large amounts of viral genomes, most of which are novel bacteriophages, have been identi ed from a variety of environments, such as marine environments [7,8], freshwater environments [9], hot spring mats [10], rhizosphere soils [11], and mangroves [12]. The ndings of these studies indicated that bacteriophages interacting with their hosts (bacteria and archaea), acted as key partners in multiple ecosystems.…”

“…However, this novel technology was limited in the types of host cell envelopes and bacteriophage isolations that could be analyzed. Single-cell genome sequencing technology could represent direct experimental evidence of bacteriophage-host links and was used in previous aquatic virome studies [10,35,36]. However, with this method, bacteriophages in active replication might not be detected effectively, and single ampli ed host genomes could not be reconstructed on a large scale.…”

Table_1.XLSX

“…For example, the metagenomes of microbialites of Cuatro Ciénegas, Mexico, were found to contain a large number of genes involved in sensory and regulatory systems as well as cell communication suggesting a coordination between cyanobacteria and heterotrophs (Breitbart et al, 2009). Additionally, evidence of viral-microbe interactions has been shown in microbial mat and stromatolite communities (Jarett et al, 2020;White et al, 2020). Viruses may contribute to structure morphogenesis through modulating microbial diversity and impacting microbial metabolism and ecosystem function through infection and the recycling of key nutrients.…”