Genomic and Phenotypic Characterization of Chloracidobacterium Isolates Provides Evidence for Multiple Species.

Mohit Kumar Saini,Shin Haruta,Daniela I Drautz-Moses,Amaya M Garcia Costas,Istvan Albert,Donald A Bryant,Vera Thiel,Stephan C Schuster,Aswathy Sebastian,Marcus Tank,Satoshi Hanada,Nathan T Soulier,Yoshiki Shirotori

doi:10.3389/fmicb.2021.704168

Abstract

Chloracidobacterium is the first and until now the sole genus in the phylum Acidobacteriota (formerly Acidobacteria) whose members perform chlorophyll-dependent phototrophy (i.e., chlorophototrophy). An axenic isolate of Chloracidobacterium thermophilum (strain BT) was previously obtained by using the inferred genome sequence from an enrichment culture and diel metatranscriptomic profiling analyses in situ to direct adjustments to the growth medium and incubation conditions, and thereby a defined growth medium for Chloracidobacterium thermophilum was developed. These advances allowed eight additional strains of Chloracidobacterium spp. to be isolated from microbial mat samples collected from Mushroom Spring, Yellowstone National Park, United States, at temperatures of 41, 52, and 60°C; an axenic strain was also isolated from Rupite hot spring in Bulgaria. All isolates are obligately photoheterotrophic, microaerophilic, non-motile, thermophilic, rod-shaped bacteria. Chloracidobacterium spp. synthesize multiple types of (bacterio-)chlorophylls and have type-1 reaction centers like those of green sulfur bacteria. Light harvesting is accomplished by the bacteriochlorophyll a-binding, Fenna-Matthews-Olson protein and chlorosomes containing bacteriochlorophyll c. Their genomes are approximately 3.7 Mbp in size and comprise two circular chromosomes with sizes of approximately 2.7 Mbp and 1.0 Mbp. Comparative genomic studies and phenotypic properties indicate that the nine isolates represent three species within the genus Chloracidobacterium. In addition to C. thermophilum, the microbial mats at Mushroom Spring contain a second species, tentatively named Chloracidobacterium aggregatum, which grows as aggregates in liquid cultures. The Bulgarian isolate, tentatively named Chloracidobacterium validum, will be proposed as the type species of the genus, Chloracidobacterium. Additionally, Chloracidobacterium will be proposed as the type genus of a new family, Chloracidobacteriaceae, within the order Blastocatellales, the class Blastocatellia, and the phylum Acidobacteriota.

Highlights

Bacteria in the phylum Acidobacteria were first reported in 1997 (Kuske et al, 1997; Ludwig et al, 1997); the phylum was validly described in 2012 (Euzeby, 2012) and recently renamed Acidobacteriota (Oren et al, 2015; Whitman et al, 2018)
To understand better the properties of members of the genus Chloracidobacterium, additional isolates were sought from two hot spring systems
Seven of the eight remaining strains isolated in this study came from mat samples collected from the main effluent channel of Mushroom Spring, Yellowstone National Park (YNP)

Summary

Introduction

Bacteria in the phylum Acidobacteria were first reported in 1997 (Kuske et al, 1997; Ludwig et al, 1997); the phylum was validly described in 2012 (Euzeby, 2012) and recently renamed Acidobacteriota (Oren et al, 2015; Whitman et al, 2018). Discovered through bioinformatic analyses of metagenomic data from microbial mats associated with Octopus and Mushroom Springs in Yellowstone National Park (YNP), WY, United States, an initial enrichment culture containing “Candidatus (Ca.) Chloracidobacterium (C.) thermophilum” and growing on a defined medium was first described in 2007 (Bryant et al, 2007). Using clues obtained from the consensus genome sequence of the nonclonal enrichment culture (Garcia Costas et al, 2012a) and diel transcription profiles for the major organisms found in the mats of Mushroom Spring in situ (Liu et al, 2011, 2012), the growth medium was gradually amended and improved This culminated in the establishment of an axenic culture of C. thermophilum strain BT (2015) that grows well on a completely defined medium (Tank and Bryant, 2015a,b; Tank et al, 2018). It has been assumed that C. thermophilum strain BT (2015) potentially represents a novel family and perhaps a novel order (Dedysh and Yilmaz, 2018)

Methods

Results

Conclusion