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Title: Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum

Abstract

Five closely related populations of bacteria from the Candidate Phylum (CP) Peregrinibacteria, part of the bacterial Candidate Phyla Radiation (CPR), were sampled from filtered groundwater obtained from an aquifer adjacent to the Colorado River near the town of Rifle, CO, USA. Here, we present the first complete genome sequences for organisms from this phylum. These bacteria have small genomes and, unlike most organisms from other lineages in the CPR, have the capacity for nucleotide synthesis. They invest significantly in biosynthesis of cell wall and cell envelope components, including peptidoglycan, isoprenoids via the mevalonate pathway, and a variety of amino sugars including perosamine and rhamnose. The genomes encode an intriguing set of large extracellular proteins, some of which are very cysteine-rich and may function in attachment, possibly to other cells. Strain variation in these proteins is an important source of genotypic variety. Overall, the cell envelope features, combined with the lack of biosynthesis capacities for many required cofactors, fatty acids, and most amino acids point to a symbiotic lifestyle. Furthermore, phylogenetic analyses indicate that these bacteria likely represent a new class within the Peregrinibacteria phylum, although they ultimately may be recognized as members of a separate phylum. In conclusion, we proposemore » the provisional taxonomic assignment as ‘Candidatus Peribacter riflensis’, Genus Peribacter, Family Peribacteraceae, Order Peribacterales, Class Peribacteria in the phylum Peregrinibacteria.« less

Authors:
 [1]; ORCiD logo [1];  [1];  [1];  [1];  [1];  [2];  [3]
  1. Univ. of California, Berkeley, CA (United States)
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  3. Univ. of California, Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1257633
Alternate Identifier(s):
OSTI ID: 1378772
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
PeerJ
Additional Journal Information:
Journal Volume: 4; Journal ID: ISSN 2167-8359
Publisher:
PeerJ Inc.
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Peregrinibacteria; candidate phyla radiation; metagenomics; complete genomes; strain variation

Citation Formats

Anantharaman, Karthik, Brown, Christopher T., Burstein, David, Castelle, Cindy J., Probst, Alexander J., Thomas, Brian C., Williams, Kenneth H., and Banfield, Jillian F. Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum. United States: N. p., 2016. Web. doi:10.7717/peerj.1607.
Anantharaman, Karthik, Brown, Christopher T., Burstein, David, Castelle, Cindy J., Probst, Alexander J., Thomas, Brian C., Williams, Kenneth H., & Banfield, Jillian F. Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum. United States. doi:10.7717/peerj.1607.
Anantharaman, Karthik, Brown, Christopher T., Burstein, David, Castelle, Cindy J., Probst, Alexander J., Thomas, Brian C., Williams, Kenneth H., and Banfield, Jillian F. Thu . "Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum". United States. doi:10.7717/peerj.1607. https://www.osti.gov/servlets/purl/1257633.
@article{osti_1257633,
title = {Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum},
author = {Anantharaman, Karthik and Brown, Christopher T. and Burstein, David and Castelle, Cindy J. and Probst, Alexander J. and Thomas, Brian C. and Williams, Kenneth H. and Banfield, Jillian F.},
abstractNote = {Five closely related populations of bacteria from the Candidate Phylum (CP) Peregrinibacteria, part of the bacterial Candidate Phyla Radiation (CPR), were sampled from filtered groundwater obtained from an aquifer adjacent to the Colorado River near the town of Rifle, CO, USA. Here, we present the first complete genome sequences for organisms from this phylum. These bacteria have small genomes and, unlike most organisms from other lineages in the CPR, have the capacity for nucleotide synthesis. They invest significantly in biosynthesis of cell wall and cell envelope components, including peptidoglycan, isoprenoids via the mevalonate pathway, and a variety of amino sugars including perosamine and rhamnose. The genomes encode an intriguing set of large extracellular proteins, some of which are very cysteine-rich and may function in attachment, possibly to other cells. Strain variation in these proteins is an important source of genotypic variety. Overall, the cell envelope features, combined with the lack of biosynthesis capacities for many required cofactors, fatty acids, and most amino acids point to a symbiotic lifestyle. Furthermore, phylogenetic analyses indicate that these bacteria likely represent a new class within the Peregrinibacteria phylum, although they ultimately may be recognized as members of a separate phylum. In conclusion, we propose the provisional taxonomic assignment as ‘Candidatus Peribacter riflensis’, Genus Peribacter, Family Peribacteraceae, Order Peribacterales, Class Peribacteria in the phylum Peregrinibacteria.},
doi = {10.7717/peerj.1607},
journal = {PeerJ},
number = ,
volume = 4,
place = {United States},
year = {2016},
month = {1}
}

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    Works referencing / citing this record:

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