Cargando…

Complete Genome of a Member of a New Bacterial Lineage in the Microgenomates Group Reveals an Unusual Nucleotide Composition Disparity Between Two Strands of DNA and Limited Metabolic Potential

The candidate phyla radiation is a large monophyletic lineage comprising unculturable bacterial taxa with small cell and genome sizes, mostly known from genomes obtained from environmental sources without cultivation. Here, we present the closed complete genome of a member of the superphylum Microge...

Descripción completa

Detalles Bibliográficos
Autores principales: Kadnikov, Vitaly V., Mardanov, Andrey V., Beletsky, Alexey V., Karnachuk, Olga V., Ravin, Nikolai V.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7143001/
https://www.ncbi.nlm.nih.gov/pubmed/32106565
http://dx.doi.org/10.3390/microorganisms8030320
_version_ 1783519512268636160
author Kadnikov, Vitaly V.
Mardanov, Andrey V.
Beletsky, Alexey V.
Karnachuk, Olga V.
Ravin, Nikolai V.
author_facet Kadnikov, Vitaly V.
Mardanov, Andrey V.
Beletsky, Alexey V.
Karnachuk, Olga V.
Ravin, Nikolai V.
author_sort Kadnikov, Vitaly V.
collection PubMed
description The candidate phyla radiation is a large monophyletic lineage comprising unculturable bacterial taxa with small cell and genome sizes, mostly known from genomes obtained from environmental sources without cultivation. Here, we present the closed complete genome of a member of the superphylum Microgenomates obtained from the metagenome of a deep subsurface thermal aquifer. Phylogenetic analysis indicates that the new bacterium, designated Ch65, represents a novel phylum-level lineage within the Microgenomates group, sibling to the candidate phylum Collierbacteria. The Ch65 genome has a highly unusual nucleotide composition with one strand of highly enriched in cytosine versus guanine throughout the whole length. Such nucleotide composition asymmetry, also detected in the members of Ca. Collierbacteria and Ca. Beckwithbacteria, suggests that most of the Ch65 chromosome is replicated in one direction. A genome analysis predicted that the Ch65 bacterium has fermentative metabolism and could produce acetate and lactate. It lacks respiratory capacity, as well as complete pathways for the biosynthesis of lipids, amino acids, and nucleotides. The Embden–Meyerhof glycolytic pathway and nonoxidative pentose phosphate pathway are mostly complete, although glucokinase, 6-phosphofructokinase, and transaldolase were not found. The Ch65 bacterium lacks secreted glycoside hydrolases and conventional transporters for importing sugars and amino acids. Overall, the metabolic predictions imply that Ch65 adopts the lifestyle of a symbiont/parasite, or a scavenger, obtaining resources from the lysed microbial biomass. We propose the provisional taxonomic assignment ‘Candidatus Chazhemtobacterium aquaticus’, genus ‘Chazhemtobacterium‘, family ‘Chazhemtobacteraceae‘ in the Microgenomates group.
format Online
Article
Text
id pubmed-7143001
institution National Center for Biotechnology Information
language English
publishDate 2020
publisher MDPI
record_format MEDLINE/PubMed
spelling pubmed-71430012020-04-14 Complete Genome of a Member of a New Bacterial Lineage in the Microgenomates Group Reveals an Unusual Nucleotide Composition Disparity Between Two Strands of DNA and Limited Metabolic Potential Kadnikov, Vitaly V. Mardanov, Andrey V. Beletsky, Alexey V. Karnachuk, Olga V. Ravin, Nikolai V. Microorganisms Article The candidate phyla radiation is a large monophyletic lineage comprising unculturable bacterial taxa with small cell and genome sizes, mostly known from genomes obtained from environmental sources without cultivation. Here, we present the closed complete genome of a member of the superphylum Microgenomates obtained from the metagenome of a deep subsurface thermal aquifer. Phylogenetic analysis indicates that the new bacterium, designated Ch65, represents a novel phylum-level lineage within the Microgenomates group, sibling to the candidate phylum Collierbacteria. The Ch65 genome has a highly unusual nucleotide composition with one strand of highly enriched in cytosine versus guanine throughout the whole length. Such nucleotide composition asymmetry, also detected in the members of Ca. Collierbacteria and Ca. Beckwithbacteria, suggests that most of the Ch65 chromosome is replicated in one direction. A genome analysis predicted that the Ch65 bacterium has fermentative metabolism and could produce acetate and lactate. It lacks respiratory capacity, as well as complete pathways for the biosynthesis of lipids, amino acids, and nucleotides. The Embden–Meyerhof glycolytic pathway and nonoxidative pentose phosphate pathway are mostly complete, although glucokinase, 6-phosphofructokinase, and transaldolase were not found. The Ch65 bacterium lacks secreted glycoside hydrolases and conventional transporters for importing sugars and amino acids. Overall, the metabolic predictions imply that Ch65 adopts the lifestyle of a symbiont/parasite, or a scavenger, obtaining resources from the lysed microbial biomass. We propose the provisional taxonomic assignment ‘Candidatus Chazhemtobacterium aquaticus’, genus ‘Chazhemtobacterium‘, family ‘Chazhemtobacteraceae‘ in the Microgenomates group. MDPI 2020-02-25 /pmc/articles/PMC7143001/ /pubmed/32106565 http://dx.doi.org/10.3390/microorganisms8030320 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Kadnikov, Vitaly V.
Mardanov, Andrey V.
Beletsky, Alexey V.
Karnachuk, Olga V.
Ravin, Nikolai V.
Complete Genome of a Member of a New Bacterial Lineage in the Microgenomates Group Reveals an Unusual Nucleotide Composition Disparity Between Two Strands of DNA and Limited Metabolic Potential
title Complete Genome of a Member of a New Bacterial Lineage in the Microgenomates Group Reveals an Unusual Nucleotide Composition Disparity Between Two Strands of DNA and Limited Metabolic Potential
title_full Complete Genome of a Member of a New Bacterial Lineage in the Microgenomates Group Reveals an Unusual Nucleotide Composition Disparity Between Two Strands of DNA and Limited Metabolic Potential
title_fullStr Complete Genome of a Member of a New Bacterial Lineage in the Microgenomates Group Reveals an Unusual Nucleotide Composition Disparity Between Two Strands of DNA and Limited Metabolic Potential
title_full_unstemmed Complete Genome of a Member of a New Bacterial Lineage in the Microgenomates Group Reveals an Unusual Nucleotide Composition Disparity Between Two Strands of DNA and Limited Metabolic Potential
title_short Complete Genome of a Member of a New Bacterial Lineage in the Microgenomates Group Reveals an Unusual Nucleotide Composition Disparity Between Two Strands of DNA and Limited Metabolic Potential
title_sort complete genome of a member of a new bacterial lineage in the microgenomates group reveals an unusual nucleotide composition disparity between two strands of dna and limited metabolic potential
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7143001/
https://www.ncbi.nlm.nih.gov/pubmed/32106565
http://dx.doi.org/10.3390/microorganisms8030320
work_keys_str_mv AT kadnikovvitalyv completegenomeofamemberofanewbacteriallineageinthemicrogenomatesgrouprevealsanunusualnucleotidecompositiondisparitybetweentwostrandsofdnaandlimitedmetabolicpotential
AT mardanovandreyv completegenomeofamemberofanewbacteriallineageinthemicrogenomatesgrouprevealsanunusualnucleotidecompositiondisparitybetweentwostrandsofdnaandlimitedmetabolicpotential
AT beletskyalexeyv completegenomeofamemberofanewbacteriallineageinthemicrogenomatesgrouprevealsanunusualnucleotidecompositiondisparitybetweentwostrandsofdnaandlimitedmetabolicpotential
AT karnachukolgav completegenomeofamemberofanewbacteriallineageinthemicrogenomatesgrouprevealsanunusualnucleotidecompositiondisparitybetweentwostrandsofdnaandlimitedmetabolicpotential
AT ravinnikolaiv completegenomeofamemberofanewbacteriallineageinthemicrogenomatesgrouprevealsanunusualnucleotidecompositiondisparitybetweentwostrandsofdnaandlimitedmetabolicpotential