Hiding in Plain Sight: The Globally Distributed Bacterial Candidate Phylum PAUC34f.

Michael L Chen,Gerhard J Herndl,Josep M Gasol,Julia M Brown,Duane P Moser,Nikolai V Ravin,Tanja Woyke,Eric D Becraft,Maria Pachiadaki,Ramunas Stepanauskas,Jessica K Jarett,Takuro Nunoura

doi:10.3389/fmicb.2020.00376

Abstract

Bacterial candidate phylum PAUC34f was originally discovered in marine sponges and is widely considered to be composed of sponge symbionts. Here, we report 21 single amplified genomes (SAGs) of PAUC34f from a variety of environments, including the dark ocean, lake sediments, and a terrestrial aquifer. The diverse origins of the SAGs and the results of metagenome fragment recruitment suggest that some PAUC34f lineages represent relatively abundant, free-living cells in environments other than sponge microbiomes, including the deep ocean. Both phylogenetic and biogeographic patterns, as well as genome content analyses suggest that PAUC34f associations with hosts evolved independently multiple times, while free-living lineages of PAUC34f are distinct and relatively abundant in a wide range of environments.

Highlights

Recent advances in cultivation-independent techniques such as metagenomics and singlecell genomics have enabled the study of the coding potential of many “candidate phyla” – uncultivated microbial lineages that are distinct from well-classified bacterial and archaeal phyla (Rinke et al, 2013; Brown et al, 2015; Castelle et al, 2015; Anantharaman et al, 2016; Hug et al, 2016; Parks et al, 2017)
16S rRNA sequence (Kamke et al, 2014; Astudillo-García et al, 2017) identified PAUC34f as a sister-clade to the candidate phylum Latescibacteria, a widely distributed, putatively saprophytic group (Youssef et al, 2015; Farag et al, 2017), and distantly related to the candidate phylum Poribacteria, a group that represents a substantial fraction of sponge microbiomes (Taylor et al, 2007a; Schmitt et al, 2012; Kamke et al, 2014; Steinert et al, 2017)
Using metagenomic assembly and binning of sponge-associated DNA, two composite genomes of PAUC34f were analyzed recently, significantly expanding our understanding of this group’s phylogeny and metabolic potential. These analyses revealed the potential for degradation of sponge- and algaederived carbohydrates, phosphate transport and storage, and signatures of host-association, including eukaryotic-like proteins (Astudillo-García et al, 2017)

Summary

Introduction

Recent advances in cultivation-independent techniques such as metagenomics and singlecell genomics have enabled the study of the coding potential of many “candidate phyla” – uncultivated microbial lineages that are distinct from well-classified bacterial and archaeal phyla (Rinke et al, 2013; Brown et al, 2015; Castelle et al, 2015; Anantharaman et al, 2016; Hug et al, 2016; Parks et al, 2017). Using metagenomic assembly and binning of sponge-associated DNA, two composite genomes (metagenomeassembled genomes, or “MAGs”) of PAUC34f were analyzed recently, significantly expanding our understanding of this group’s phylogeny and metabolic potential. These analyses revealed the potential for degradation of sponge- and algaederived carbohydrates, phosphate transport and storage, and signatures of host-association, including eukaryotic-like proteins (Astudillo-García et al, 2017)

Methods

Results

Conclusion