GAL08, an Uncultivated Group of Acidobacteria, Is a Dominant Bacterial Clade in a Neutral Hot Spring

Frontiers in Microbiology

Microbiology

Susanne Krause¹  Peter F. Dunfield¹  Chantel C. Furgason¹  Triet M. Tran¹  Andriy Sheremet¹  Ilona A. Ruhl¹  Stephen E. Grasby²  Jessica K. Jarett³  Tanja Woyke³  Robert M. Bowers³ 

[1] Department of Biological Sciences, University of Calgary, Calgary, AB, Canada;Department of Geoscience, University of Calgary, Calgary, AB, Canada;Geological Survey of Canada, Calgary, AB, Canada;U.S. Department of Energy Joint Genome Institute, Berkeley, CA, United States;

关键词: Acidobacteria;    Acidobacteriota;    uncultivated bacterium;    GAL08;    hot spring;    thermophile;    single-cell genomics;   

DOI  :  10.3389/fmicb.2021.787651

 received in 2021-10-01, accepted in 2021-11-29,  发布年份 2022

来源: Frontiers

【 摘 要 】

GAL08 are bacteria belonging to an uncultivated phylogenetic cluster within the phylum Acidobacteria. We detected a natural population of the GAL08 clade in sediment from a pH-neutral hot spring located in British Columbia, Canada. To shed light on the abundance and genomic potential of this clade, we collected and analyzed hot spring sediment samples over a temperature range of 24.2–79.8°C. Illumina sequencing of 16S rRNA gene amplicons and qPCR using a primer set developed specifically to detect the GAL08 16S rRNA gene revealed that absolute and relative abundances of GAL08 peaked at 65°C along three temperature gradients. Analysis of sediment collected over multiple years and locations revealed that the GAL08 group was consistently a dominant clade, comprising up to 29.2% of the microbial community based on relative read abundance and up to 4.7 × 105 16S rRNA gene copy numbers per gram of sediment based on qPCR. Using a medium quality threshold, 25 single amplified genomes (SAGs) representing these bacteria were generated from samples taken at 65 and 77°C, and seven metagenome-assembled genomes (MAGs) were reconstructed from samples collected at 45–77°C. Based on average nucleotide identity (ANI), these SAGs and MAGs represented three separate species, with an estimated average genome size of 3.17 Mb and GC content of 62.8%. Phylogenetic trees constructed from 16S rRNA gene sequences and a set of 56 concatenated phylogenetic marker genes both placed the three GAL08 bacteria as a distinct subgroup of the phylum Acidobacteria, representing a candidate order (Ca. Frugalibacteriales) within the class Blastocatellia. Metabolic reconstructions from genome data predicted a heterotrophic metabolism, with potential capability for aerobic respiration, as well as incomplete denitrification and fermentation. In laboratory cultivation efforts, GAL08 counts based on qPCR declined rapidly under atmospheric levels of oxygen but increased slightly at 1% (v/v) O2, suggesting a microaerophilic lifestyle.

【 授权许可】

Unknown   
Copyright © 2022 Ruhl, Sheremet, Furgason, Krause, Bowers, Jarett, Tran, Grasby, Woyke and Dunfield.