Ultra-small bacteria and their phages discovered through metagenomics in a sub-arctic degrading permafrost ecosystem

Abstract

Patescibacteriota is a diverse bacterial phylum characterized by ultra-small cell size, streamlined genome, incomplete metabolism and episymbiotic lifestyle. While Patescibacteriota have been detected across a wide range of ecosystem types, their phages are not widely described. We utilized metagenomics to explore these less characterized parts of the microbiome in a sporadic permafrost ecosystem, with samples from palsa and peat soils, small ponds and streams. We retrieved 33 high-quality metagenome assembled genomes (MAGs) of Patescibacteriota, mainly from the classes Minisyncoccia and Saccharimonadia. Minisyncoccia was a dominant class in the thawing soils and thaw ponds, whereas the Saccharimonadia was more abundant in the frozen palsa soil layers. The distribution of the Patescibacteria classes was also reflected in their metabolic potential. For example, gluconeogenesis pathway was complete only in MAGs from the class Minisyncoccia, whereas cytochrome o ubiquinol oxidase was mainly found from the MAGs of the class Saccharimondia. The viral community analysis yielded 16 354 viral operational taxonomic units (vOTUs), which represented mainly tailed dsDNA viruses from the class Caudoviricetes. Based on genome size, 16 vOTUs were qualified as jumbophages and one as a megaphage. Similar to the bacterial community, the viral community composition differed across sample types. The most common hosts for bacterial viruses were phyla Pseudomonadota, Acidobacteriota and Actinomycetota. A further 196 vOTUs were in silico linked to Patescibacteriota hosts. The Patescibacteriota phages were diverse, with only two vOTUs representing the same genus. The relative abundance of Patescibacteriota-associated phages was especially high in frozen palsa soils, largely following the same pattern of abundance as Patescibacteriota.