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

被引:37
作者
Anantharaman, Karthik [1 ]
Brown, Christopher T. [2 ]
Burstein, David [1 ]
Castelle, Cindy J. [1 ]
Probst, Alexander J. [1 ]
Thomas, Brian C. [1 ]
Williams, Kenneth H. [3 ]
Banfield, Jillian F. [1 ,3 ]
机构
[1] Univ Calif Berkeley, Dept Earth & Planetary Sci, Berkeley, CA 94720 USA
[2] Univ Calif Berkeley, Dept Plant & Microbial Biol, Berkeley, CA 94720 USA
[3] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Earth Sci, Berkeley, CA 94720 USA
来源
PEERJ | 2016年 / 4卷
关键词
Peregrinibacteria; Candidate phyla radiation; Metagenomics; Complete genomes; Strain variation; PREDICTION; ALIGNMENT; CELL;
D O I
10.7717/peerj.1607
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
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.
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页数:14
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