PMID- 27058507
OWN - NLM
STAT- MEDLINE
DCOM- 20170918
LR  - 20220321
IS  - 1751-7370 (Electronic)
IS  - 1751-7362 (Print)
IS  - 1751-7362 (Linking)
VI  - 10
IP  - 11
DP  - 2016 Nov
TI  - Phylogenomic analysis of Candidatus 'Izimaplasma' species: free-living 
      representatives from a Tenericutes clade found in methane seeps.
PG  - 2679-2692
LID - 10.1038/ismej.2016.55 [doi]
AB  - Tenericutes are a unique class of bacteria that lack a cell wall and are 
      typically parasites or commensals of eukaryotic hosts. Environmental 16S rDNA 
      surveys have identified a number of tenericute clades in diverse environments, 
      introducing the possibility that these Tenericutes may represent 
      non-host-associated, free-living microorganisms. Metagenomic sequencing of 
      deep-sea methane seep sediments resulted in the assembly of two genomes from a 
      Tenericutes-affiliated clade currently known as 'NB1-n' (SILVA taxonomy) or 'RF3' 
      (Greengenes taxonomy). Metabolic reconstruction revealed that, like cultured 
      members of the Mollicutes, these 'NB1-n' representatives lack a tricarboxylic 
      acid cycle and instead use anaerobic fermentation of simple sugars for substrate 
      level phosphorylation. Notably, the genomes also contained a number of unique 
      metabolic features including hydrogenases and a simplified electron transport 
      chain containing an RNF complex, cytochrome bd oxidase and complex I. On the 
      basis of the metabolic potential predicted from the annotated genomes, we devised 
      an anaerobic enrichment media that stimulated the growth of these Tenericutes at 
      10  degrees C, resulting in a mixed culture where these organisms represented ~60% of the 
      total cells by targeted fluorescence in situ hybridization (FISH). Visual 
      identification by FISH confirmed these organisms were not directly associated 
      with Eukaryotes and electron cryomicroscopy of cells in the enrichment culture 
      confirmed an ultrastructure consistent with the defining phenotypic property of 
      Tenericutes, with a single membrane and no cell wall. On the basis of their 
      unique gene content, phylogenetic placement and ultrastructure, we propose these 
      organisms represent a novel class within the Tenericutes, and suggest the names 
      Candidatus 'Izimaplasma sp. HR1' and Candidatus 'Izimaplasma sp. HR2' for the two 
      genome representatives.
FAU - Skennerton, Connor T
AU  - Skennerton CT
AUID- ORCID: 0000-0003-1320-4873
AD  - Division of Geological and Planetary Sciences, California Institute of 
      Technology, Pasadena, CA, USA.
FAU - Haroon, Mohamed F
AU  - Haroon MF
AD  - Australian Center for Ecogenomics, School of Chemistry and Molecular Biosciences, 
      University of Queensland, St Lucia, Queensland, Australia.
FAU - Briegel, Ariane
AU  - Briegel A
AD  - Division of Biology and Biological Engineering, California Institute of 
      Technology, Pasadena, CA, USA.
FAU - Shi, Jian
AU  - Shi J
AD  - Division of Biology and Biological Engineering, California Institute of 
      Technology, Pasadena, CA, USA.
FAU - Jensen, Grant J
AU  - Jensen GJ
AD  - Division of Biology and Biological Engineering, California Institute of 
      Technology, Pasadena, CA, USA.
AD  - Howard Hughes Medical Institute, California Institute of Technology, Pasadena, 
      CA, USA.
FAU - Tyson, Gene W
AU  - Tyson GW
AD  - Australian Center for Ecogenomics, School of Chemistry and Molecular Biosciences, 
      University of Queensland, St Lucia, Queensland, Australia.
AD  - The Advanced Water Management Center, University of Queensland, St Lucia, 
      Queensland, Australia.
FAU - Orphan, Victoria J
AU  - Orphan VJ
AD  - Division of Geological and Planetary Sciences, California Institute of 
      Technology, Pasadena, CA, USA.
LA  - eng
GR  - HHMI/Howard Hughes Medical Institute/United States
PT  - Journal Article
DEP - 20160408
PL  - England
TA  - ISME J
JT  - The ISME journal
JID - 101301086
RN  - 0 (DNA, Bacterial)
RN  - 0 (RNA, Ribosomal, 16S)
RN  - OP0UW79H66 (Methane)
SB  - IM
MH  - DNA, Bacterial/genetics
MH  - Genome, Bacterial
MH  - Genomics
MH  - In Situ Hybridization, Fluorescence
MH  - Methane/analysis/*metabolism
MH  - *Phylogeny
MH  - RNA, Ribosomal, 16S/genetics
MH  - Seawater/analysis/*microbiology
MH  - Tenericutes/classification/*genetics/isolation & purification/metabolism
PMC - PMC5113845
EDAT- 2016/10/26 06:00
MHDA- 2017/09/19 06:00
PMCR- 2017/11/01
CRDT- 2016/04/09 06:00
PHST- 2016/01/13 00:00 [received]
PHST- 2016/02/29 00:00 [revised]
PHST- 2016/03/04 00:00 [accepted]
PHST- 2016/10/26 06:00 [pubmed]
PHST- 2017/09/19 06:00 [medline]
PHST- 2016/04/09 06:00 [entrez]
PHST- 2017/11/01 00:00 [pmc-release]
AID - ismej201655 [pii]
AID - 10.1038/ismej.2016.55 [doi]
PST - ppublish
SO  - ISME J. 2016 Nov;10(11):2679-2692. doi: 10.1038/ismej.2016.55. Epub 2016 Apr 8.