title: Comparative Genomics of Candidate Phylum TM6 Suggests That Parasitism Is Widespread and Ancestral in This Lineage.
abstract: Candidate phylum TM6 is a major bacterial lineage recognized through culture-independent rRNA surveys to be low abundance members in a wide range of habitats; however, they are poorly characterized due to a lack of pure culture representatives. Two recent genomic studies of TM6 bacteria revealed small genomes and limited gene repertoire, consistent with known or inferred dependence on eukaryotic hosts for their metabolic needs. Here, we obtained additional near-complete genomes of TM6 populations from agricultural soil and upflow anaerobic sludge blanket reactor metagenomes which, together with the two publicly available TM6 genomes, represent seven distinct family level lineages in the TM6 phylum. Genome-based phylogenetic analysis confirms that TM6 is an independent phylum level lineage in the bacterial domain, possibly affiliated with the Patescibacteria superphylum. All seven genomes are small (1.0-1.5 Mb) and lack complete biosynthetic pathways for various essential cellular building blocks including amino acids, lipids, and nucleotides. These and other features identified in the TM6 genomes such as a degenerated cell envelope, ATP/ADP translocases for parasitizing host ATP pools, and protein motifs to facilitate eukaryotic host interactions indicate that parasitism is widespread in this phylum. Phylogenetic analysis of ATP/ADP translocase genes suggests that the ancestral TM6 lineage was also parasitic. We propose the name Dependentiae (phyl. nov.) to reflect dependence of TM6 bacteria on host organisms.
authors.affiliation: Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia.
authors.forename: Yun Kit
authors.initials: YK
authors.lastname: Yeoh
authors.affiliation: Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan.
authors.forename: Yuji
authors.initials: Y
authors.lastname: Sekiguchi
authors.affiliation: Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia.
authors.forename: Donovan H
authors.initials: DH
authors.lastname: Parks
authors.affiliation: Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia p.hugenholtz@uq.edu.au.
authors.forename: Philip
authors.initials: P
authors.lastname: Hugenholtz
mesh_terms: D000255:Adenosine Triphosphate / Q000235:genetics / Q000378:metabolism; D001421:Bacteria, Anaerobic / Q000235:genetics*; D016680:Genome, Bacterial; D006790:Host-Parasite Interactions / Q000235:genetics; D054892:Metagenome / Q000235:genetics; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D012988:Soil Microbiology
chemical_list: D012336:RNA, Ribosomal, 16S; D000255:Adenosine Triphosphate
keywords: candidate phylum TM6; comparative genomics; parasitism; soil.; upflow anaerobic sludge blanket