Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum
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 f...
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PeerJ Inc.
2016-01-01
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| author | Karthik Anantharaman Christopher T. Brown David Burstein Cindy J. Castelle Alexander J. Probst Brian C. Thomas Kenneth H. Williams Jillian F. Banfield |
| author_facet | Karthik Anantharaman Christopher T. Brown David Burstein Cindy J. Castelle Alexander J. Probst Brian C. Thomas Kenneth H. Williams Jillian F. Banfield |
| author_sort | Karthik Anantharaman |
| collection | DOAJ |
| description | 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. 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. We propose the provisional taxonomic assignment as ‘Candidatus Peribacter riflensis’, Genus Peribacter, Family Peribacteraceae, Order Peribacterales, Class Peribacteria in the phylum Peregrinibacteria. |
| first_indexed | 2024-03-09T06:30:53Z |
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| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:30:53Z |
| publishDate | 2016-01-01 |
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| spelling | doaj.art-4740f9c19b8f42cba1751be238512fec2023-12-03T11:05:03ZengPeerJ Inc.PeerJ2167-83592016-01-014e160710.7717/peerj.1607Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylumKarthik Anantharaman0Christopher T. Brown1David Burstein2Cindy J. Castelle3Alexander J. Probst4Brian C. Thomas5Kenneth H. Williams6Jillian F. Banfield7Department of Earth and Planetary Sciences, University of California, Berkeley, California, United StatesDepartment of Plant and Microbial Biology, University of California, Berkeley, California, United StatesDepartment of Earth and Planetary Sciences, University of California, Berkeley, California, United StatesDepartment of Earth and Planetary Sciences, University of California, Berkeley, California, United StatesDepartment of Earth and Planetary Sciences, University of California, Berkeley, California, United StatesDepartment of Earth and Planetary Sciences, University of California, Berkeley, California, United StatesEarth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United StatesDepartment of Earth and Planetary Sciences, University of California, Berkeley, California, United StatesFive 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. 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. We propose the provisional taxonomic assignment as ‘Candidatus Peribacter riflensis’, Genus Peribacter, Family Peribacteraceae, Order Peribacterales, Class Peribacteria in the phylum Peregrinibacteria.https://peerj.com/articles/1607.pdfPeregrinibacteriaCandidate phyla radiationMetagenomicsComplete genomesStrain variation |
| spellingShingle | Karthik Anantharaman Christopher T. Brown David Burstein Cindy J. Castelle Alexander J. Probst Brian C. Thomas Kenneth H. Williams Jillian F. Banfield Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum PeerJ Peregrinibacteria Candidate phyla radiation Metagenomics Complete genomes Strain variation |
| title | Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum |
| title_full | Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum |
| title_fullStr | Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum |
| title_full_unstemmed | Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum |
| title_short | Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum |
| title_sort | analysis of five complete genome sequences for members of the class peribacteria in the recently recognized peregrinibacteria bacterial phylum |
| topic | Peregrinibacteria Candidate phyla radiation Metagenomics Complete genomes Strain variation |
| url | https://peerj.com/articles/1607.pdf |
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