Abstract
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.
Highlights
The phylum Acidobacteria is one of the most abundant and phylogenetically diverse bacterial phyla in nature (Hugenholtz et al, 1998)
GAL08 was detected in five out of six Dewar Creek sediments collected at temperatures between 22.5 and 32.2◦C (Supplementary Figure 2); the very low relative abundance (0.01% or below) of GAL08 reads at these low temperatures makes it difficult to discern whether GAL08 is capable of growth at these temperatures or whether some cells are dispersing downstream from hotter upstream areas and not growing in the cooler areas
average nucleotide identity (ANI) comparisons of genomes obtained through single-cell sequencing revealed the coexistence of at least three species of DChs_GAL08, with Species 1 being dominant across all sampling years
Summary
The phylum Acidobacteria is one of the most abundant and phylogenetically diverse bacterial phyla in nature (Hugenholtz et al, 1998). The phylum has informally been divided into 26 subgroups based on 16S rRNA gene phylogeny, with subgroups 1, 3, 4, and 6 being the most abundant globally (Barns et al, 1999). The division of the phylum into subgroups was originally proposed by Hugenholtz et al (1998), who considered a subgroup to be any group of two or more 16S rRNA sequences that were reproducibly monophyletic and unaffiliated with all other sequences within the phylum. The 26 subgroups do not correspond to any particular taxonomic rank but instead correspond to different class, order, or family rank taxa in release 132 of the Silva rRNA gene database (Pruesse et al, 2012). The Silva database lists 21 classes within Acidobacteria, while the GTDB genome-based database lists 14 classes and proposes the alternative phylum name Acidobacteriota (Oren et al, 2015; Parks et al, 2018). There are only 5 classes with validly published names: Acidobacteria, Blastocatellia, Holophagae, Vicinamibacteria, and Thermoanaerobaculia (Dedysh and Yilmaz, 2018; Parte, 2018)
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