Comparative genomic analysis of Parageobacillus thermoglucosidasius strains with distinct hydrogenogenic capacities

Abstract

Background: The facultatively anaerobic thermophile Parageobacillus thermoglucosidasius produces hydrogen gas (H₂) by coupling CO oxidation to proton reduction in the water-gas shift (WGS) reaction via a carbon monoxide dehydrogenase-hydrogenase enzyme complex. Although little is known about the hydrogenogenic capacities of different strains of this species, these organisms offer a potentially viable process for the synthesis of this alternative energy source.

Results: The WGS-catalyzed H₂ production capacities of four distinct P. thermoglucosidasius strains were determined by cultivation and gas analysis. Three strains (DSM 2542^T, DSM 2543 and DSM 6285) were hydrogenogenic, while the fourth strain (DSM 21625) was not. Furthermore, in one strain (DSM 6285) H₂ production commenced earlier in the cultivation than the other hydrogenogenic strains. Comparative genomic analysis of the four strains identified extensive differences in the protein complement encoded on the genomes, some of which are postulated to contribute to the different hydrogenogenic capacities of the strains. Furthermore, polymorphisms and deletions in the CODH-NiFe hydrogenase loci may also contribute towards this variable phenotype.

Conclusions: Disparities in the hydrogenogenic capacities of different P. thermoglucosidasius strains were identified, which may be correlated to variability in their global proteomes and genetic differences in their CODH-NiFe hydrogenase loci. The data from this study may contribute towards an improved understanding of WGS-catalysed hydrogenogenesis by P. thermoglucosidasius.

Keywords: Biohydrogen production; Comparative genomics; DSM 6285; Parageobacillus thermoglucosidasius; Water-gas shift reaction.

Fig. 1

Growth curves of four P. thermoglucosidasius strains. The strains were cultivated in mLB medium in stoppered serum bottles with an initial gas atmosphere consisting of 50% CO and 50% air. DSM 2542^T (green) and DSM 2543 (black) reached their maximum absorbance after ~ 6 h while there was still O₂ present. DSM 6285 (blue) reached its maximum absorbance OD₆₀₀ = 0.537 ± 0.02 after ~ 36 h during the anaerobic phase. The non hydrogenogenic strain DSM 21625 (orange) reached its maximum (OD₆₀₀ = 0.645 ± 0.032) after 9.39 h and decreased to a final value of OD₆₀₀ = 0.292 ± 0.021 at the end of the cultivation

Fig. 2

CO consumption and H₂ production of the hydrogenogenic strains during the cultivation with an initial gas atmosphere of 50% CO and 50% air. DSM 2542^T (green) and DSM 2543 (black) started to produce H₂ after ~ 36 h (dotted lines). They achieved a final yield of 1.08 CO/H₂ (DSM 2542^T) and 0.95 CO/H₂ (DSM 2543). P. thermoglucosidasius DSM 6285 (blue) started the hydrogen production already after ~ 16 h. For DSM 21625 no hydrogen was detected (orange)

Fig. 3

Genome properties of the compared P. thermoglucosidasius strains. The isolation source, genome size, number of contigs, G + C % and number of proteins encoded on the genome are indicated. Similarly, the number of predicted plasmids and integrated phages are shown. The dendrograms at either end show the phylogenetic relationships of the strains on the basis of digital DNA-DNA hybridization values (left) and OrthoANI values (right), respectively

Fig. 4

Venn diagram of protein families shared among or unique to the four compared P. thermoglucosidasius strains

Fig. 5

Schematic diagram of the CODH-NiFe group 4a hydrogenase locus of the compared P. thermoglucosidasius strains. Genes involved in the synthesis of the CODH are represented by green arrows, while blue arrows indicate those genes required for the synthesis and functioning of the NiFe group 4a hydrogenase. Flanking genes are coloured in yellow. Black arrows below each locus indicate the operonic structure of the CODH-NiFe group 4a hydrogenase loci. The inset shows alignments of the indels occurring upstream and downstream of the cooC gene in P. thermoglucosidasius DSM 21625. The orange arrow below the Indel 1 alignment indicates the consensus sequence for the Hpr transcription factor binding site. cooC, cooS and cooF code for a CO dehydrogenase maturation factor, phcA-phcL code for an H₂ evolving hydrogenase