The candidate phylum Poribacteria by single-cell genomics: new insights into phylogeny, cell-compartmentation, eukaryote-like repeat proteins, and other genomic features.
The candidate phylum Poribacteria is one of the most dominant and widespread members of the microbial communities residing within marine sponges. Cell compartmentalization had been postulated along with their discovery about a decade ago and their phylogenetic association to the Planctomycetes, Verrucomicrobia, Chlamydiae superphylum was proposed soon thereafter. In the present study we revised these features based on genomic data obtained from six poribacterial single cells. We propose that Poribacteria form a distinct monophyletic phylum contiguous to the PVC superphylum together with other candidate phyla. Our genomic analyses supported the possibility of cell compartmentalization in form of bacterial microcompartments. Further analyses of eukaryote-like protein domains stressed the importance of such proteins with features including tetratricopeptide repeats, leucin rich repeats as well as low density lipoproteins receptor repeats, the latter of which are reported here for the first time from a sponge symbiont. Finally, examining the most abundant protein domain family on poribacterial genomes revealed diverse phyH family proteins, some of which may be related to dissolved organic posphorus uptake.
Department of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of Wuerzburg, Wuerzburg, Germany.
Janine
J
Kamke
Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America.
Christian
C
Rinke
Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America.
Patrick
P
Schwientek
Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America.
Kostas
K
Mavromatis
Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America.
Natalia
N
Ivanova
Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America ; Center for Biotechnology, Bielefeld University, Bielefeld, Germany.
Alexander
A
Sczyrba
Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America.
Tanja
T
Woyke
Department of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of Wuerzburg, Wuerzburg, Germany.
Ute
U
Hentschel
D000818:Animals; D001419:Bacteria / Q000145:classification / Q000166:cytology / Q000235:genetics*; D001426:Bacterial Proteins / Q000235:genetics; D014644:Genetic Variation; D016680:Genome, Bacterial / Q000235:genetics; D023281:Genomics / Q000379:methods*; D010802:Phylogeny; D011161:Porifera / Q000382:microbiology*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D059010:Single-Cell Analysis / Q000379:methods*
D001426:Bacterial Proteins; D012336:RNA, Ribosomal, 16S