Diversity of Bathyarchaeia viruses in metagenomes and virus-encoded CRISPR system components

Abstract

Bathyarchaeia represent a class of archaea common and abundant in sedimentary ecosystems. Here we report 56 metagenome-assembled genomes of Bathyarchaeia viruses identified in metagenomes from different environments. Gene sharing network and phylogenomic analyses led to the proposal of four virus families, including viruses of the realms Duplodnaviria and Adnaviria, and archaea-specific spindle-shaped viruses. Genomic analyses uncovered diverse CRISPR elements in these viruses. Viruses of the proposed family "Fuxiviridae" harbor an atypical Type IV-B CRISPR-Cas system and a Cas4 protein that might interfere with host immunity. Viruses of the family "Chiyouviridae" encode a Cas2-like endonuclease and two mini-CRISPR arrays, one with a repeat identical to that in the host CRISPR array, potentially allowing the virus to recruit the host CRISPR adaptation machinery to acquire spacers that could contribute to competition with other mobile genetic elements or to inhibit host defenses. These findings present an outline of the Bathyarchaeia virome and offer a glimpse into their counter-defense mechanisms.

Keywords: Bathyarchaeia; Cas4 protein; Type IV-B CRISPR-Cas system; virus.

Figure 1

Distribution of identified viruses across the evolutionary tree of the Bathyarchaeia; (A) maximum likelihood tree of Bathyarchaeia was reconstructed based on the modified set of 51 marker genes; the outgroup was taken from Ren et al. [116] and includes representatives of the phyla Euryarchaeota, Crenarchaeota, Aigarchaeota, and Thaumarchaeota; Bathyarchaeia orders are highlighted in different background colors; viruses identified in this study are indicated with colored symbols denoting the respective virion architectures, and their corresponding hosts are highlighted with the same color; red icosahedron represents viruses in the realm Duplodnaviria, green rod represents viruses in the realm Adnaviria, and blue spindle represents the spindle-shaped virus; (B) subtypes of CRISPR-Cas systems distributed in different Bathyarchaeia orders: Bifang, Bifangarchaeales; Jinwu, Jinwuousiales; Houtu, Houtuarculales; Wuzhiqi, Wuzhiqiibiales; Zhuque, Zhuquarculales; Baize, Baizomonadales; only high-quality MAGs were selected.

Figure 2

Ecological distribution of Bathyarchaeia and their viruses; the number of Bathyarchaeia orders in different types of habitats are shown by the bar chart, with the number of detected viral sequences discovered in the genomes shown in the circles above the corresponding bars; viruses identified in this study by matching CRISPR spacers (the distribution of these viruses aligns with their hosts’ habitats) are marked with symbols that denote their respective virion architectures, placed above their corresponding hosts; MAGs from public databases and from our previous study are denoted by grey and black circles, respectively, with the quantity displayed inside the circles.

Figure 3

Classification of Bathyarchaeia viruses based on the whole-genome protein-sharing network with other prokaryotic viruses; the whole-genome protein-sharing network analysis was constructed using vConTACT2 v.0.11.3 for the taxonomic assignment of 56 Bathyarchaeia viral genomes; Bathyarchaeia virus clusters are outlined with a rectangle in the complete network; Bathyarchaeia viruses are assigned to four distinct groups (numbered within circles), including one large cluster; viral clusters (VCs) are indicated by the colored spheres within the inset; the proposed virus families with complete genomes are separated by dashed lines and appended with the corresponding names; the light pink and light blue clusters outside of the inset represent archaeal and bacterial viruses, respectively; the networks were visualized with Cytoscape v.3.9.1.

Figure 4

Maps of complete genomes of Bathyarchaeia viruses; (A) Genome map of Fuxivirus; (B) genome map of Kunpengvirus; (C) genome map of Huangdivirus; (D) genome map of Chiyouvirus; genes annotated by HHblits with a probability greater than 95% are shown as different colors; genes related to Type IV B CRISPR-Cas system, Cas4, and Cas2 are indicated in rose pink, mini-CRISPR array in vibrant orange, genes specific to viruses in dark blue, predicted Acr in black, other annotated genes in light blue; the positions of targeted protospacers are indicated with red circle; the organization of CRISPR mini-arrays is shown above the genome maps; in Chiyouvirus CRISPR Array 1, the self-targeting spacers are highlighted in light blue and purple; their corresponding target sites on the genome are marked with circles in the same color; transmembrane proteins of Chiyouvirus predicted using CCTOP [117] server are indicated with red asterisks; fdetailed gene annotations are in Supplementary Table S4.