Chthoniobacter flavus gen. nov., sp. nov., the First Pure-Culture Representative of Subdivision Two, Spartobacteria classis nov., of the Phylum Verrucomicrobia

Abstract

The phylum Verrucomicrobia is increasingly recognized as an environmentally significant group of bacteria, particularly in soil habitats. At least six subdivisions of the Verrucomicrobia are resolved by comparative analysis of 16S rRNA genes, mostly obtained directly from environmental samples. To date, only two of these subdivisions (1 and 4) have characterized pure-culture representatives. We have isolated and characterized the first known pure-culture representative of subdivision 2. Strain Ellin428 is an aerobic heterotrophic bacterium that is able to grow with many of the saccharide components of plant biomass but does not grow with amino acids or organic acids other than pyruvate. Cells are yellow, rod-shaped, nonmotile, and gram-stain negative, and they contain peptidoglycan with direct cross-linkages of the A1γ meso-Dpm type. The isolate grows well at 25°C on a variety of standard biological media, including some used in the routine cultivation of bacteria from soil. The pH range for growth is 4.0 to 7.0. Low levels of menaquinones MK-10 and MK-11 were detected. The major cellular fatty acids are C14:0, a-C15:0, C16:1ω7c, and/or 2OH i-C15:0, and C16:0. The G+C content of the genomic DNA is 61 mol%. We propose a new genus and species, Chthoniobacter flavus gen. nov., sp. nov., with isolate Ellin428 as the type strain, and a new class for the subdivision to which it belongs, Spartobacteria classis nov. Environmental sequences indicate that the class Spartobacteria is largely represented by globally distributed, abundant, and active soil bacteria

Genome reduction in an abundant and ubiquitous soil bacterium ‘Candidatus Udaeobacter copiosus’

“…2). However, within the Spartobacteria class, the DA101 clade is clearly distinct from the clade containing Chthoniobacter flavus 11,12 , as DA101 shares only 92% 16S rRNA gene sequence identity with C. flavus. These findings indicate that DA101 is a representative of a new verrucomicrobial genus.…”

“…Because these two rRNA gene fragments have the same coverage as the genome (27×) and align to separate regions of one 16S rRNA gene, it is likely that Ca. U. copiosus encodes a single rRNA operon, similar to its closest relative C. flavus 11,12 and all other sequenced heterotrophic soil Verrucomicrobia (Supplementary Table 4). …”

“…Although Verrucomicrobia accounted for >50% of all bacterial 16S rRNA gene sequences in tallgrass prairie soils in the USA, >75% of these sequences were assigned to the class Spartobacteria 10 . Currently, the class Spartobacteria contains only a single described and sequenced isolate, Chthoniobacter flavus, a slow-growing aerobic heterotroph capable of using common components of plant biomass for growth 11,12 . Although Spartobacteria are prevalent in soils, they have also been observed in marine systems ('Spartobacteria baltica') 13 and as nematode symbionts (genus Xiphinematobacter) 14 .…”

Methane oxidation at 55°C and pH 2 by a thermoacidophilic bacterium belonging to the Verrucomicrobia phylum

“…2). The Verrucomicrobia lineage was proposed as a new division in 1997 (17) and has been further divided into five monophyletic subdivisions (18,19). The VTAM cluster is clearly separated from the other established subdivisions and …”

Soil resilience and recovery: rapid community responses to management changes

“…The most influential bacterial group according to SIMPER analysis, most abundant in grassland and least in bare fallow soil, was assigned to the Verrucomicrobia group DA101, belonging to the order Chthoniobacterales which is represented by a cultured isolate, Chthoniobacter flavus. The Chthoniobacterales are very common in soil (Sangwan et al 2004) but little is known of their biology. C. flavus is reported to grow on sugars, sugar polymers and pyruvate and to be unable to grow anaerobically by denitrification.…”