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Some (bacilli) like it hot: genomics of Geobacillus species.

Studholme DJ - Microb Biotechnol (2014)

View Article: PubMed Central - PubMed

Affiliation: Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK.

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The genus Geobacillus includes thermophilic Gram-positive spore-forming bacteria that form a phylogenetically coherent clade within the family Bacillaceae... Genome sequences are also available for some other thermophilic members of the Bacillaceae, such as Paenibacillus lautus (Mead et al., ) and Bacillus coagulans (Xu et al., ) and for Geobacillus-infecting bacteriophage (Marks and Hamilton, ), but these will not be discussed here... However, the availability of complete genome sequence data enables phylogenetic analysis based on single-nucleotide variants over the entire core genome, offering much greater resolution (Fig.  3A)... According to the core-genome-wide phylogenetic analysis, the two strains assigned as G.  kaustophilus do not form a phylogenetically coherent monophyletic clade... Nucleotide sequence identities between clades are much lower; between G.  kaustophilus and G.  thermoglucosidans, there is approximately 84% identity... The considerable amount of reticulation in the phylogenetic network (Fig.  3A) suggests significant horizontal genetic transfer within and among these species... CAMR12739... The NG80-2 genome sequence also enabled discovery of the first nitrous oxide reductase gene from a Gram-positive, and a novel thermophilic long-chain alkane monooxygenase (Feng et al., )... Specifically, they used the genome sequence to clone two promoters and incorporated them into plasmid vectors: one for inducible gene expression and one constitutive... The authors also mention that they tried other promoters that did not work so well; presumably, the availability of the genome sequence allowed them to relatively quickly screen a number of candidates until they found the best ones... Only then can we rationally design genetic interventions to predictably manipulate metabolism... And finally, palaeo-genomics of ancient Geobacillus spores, which may be viable after billions of years of dormancy, might shed light on population-genetics and evolutionary processes over timescales that we previously assumed to be intractable (Nicholson, ; Zeigler, ).

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Phylogenetic relationships among sequenced strains of Geobacillus inferred from a multiple sequence alignment of recN sequences. The circles indicate strains whose genomes have been sequenced, as listed in Table 1. The triangles indicate type strains of the various Geobacillus species; recN sequences from these are taken from a previous phylogenetic analysis by Zeigler (2005). The maximum-likelihood tree was generated using mega6 (Tamura et al., 2013).
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fig02: Phylogenetic relationships among sequenced strains of Geobacillus inferred from a multiple sequence alignment of recN sequences. The circles indicate strains whose genomes have been sequenced, as listed in Table 1. The triangles indicate type strains of the various Geobacillus species; recN sequences from these are taken from a previous phylogenetic analysis by Zeigler (2005). The maximum-likelihood tree was generated using mega6 (Tamura et al., 2013).

Mentions: At the time of writing (28 July 2014), 29 Geobacillus genome sequences are available (Table 1). These include representatives of all the major phylogenetic groups within the genus and include representatives of the species G. thermoleovorans, G. kaustophilus, G. thermocatenulatus, G. thermodenitrificans, G. stearothermophilus, G. caloxylosilyticus and G. thermoglucosidans (formerly G. thermoglucosidasius) as well as several strains that have not been assigned to named species (Fig. 2). Genome sequences are also available for some other thermophilic members of the Bacillaceae, such as Paenibacillus lautus (Mead et al., 2012) and Bacillus coagulans (Xu et al., 2013) and for Geobacillus-infecting bacteriophage (Marks and Hamilton, 2014), but these will not be discussed here. The team who sequenced the genome of Geobacillus sp. MAS1 described this strain as ‘G. thermopakistaniensis’, but this is not a validly named species and no justification was provided for its proposal as a new species (Siddiqui et al., 2014). On the basis of its recN sequence, a useful phylogenetic marker for Geobacillus spp. (Zeigler, 2005), strain MAS1 is closely related to the type strains of G. kaustophilus and G. thermoleovorans (Fig. 2). Strain NUB3621 was described as ‘G. stearothermophilus’ but as has been previously noted (Studholme et al., 1999; Zeigler, 2005; Blanchard et al., 2014), this strain is phylogenetically distinct from B. stearothermophilus sensu strictu and is more closely related to G. caldoxylsilyticus and, to a lesser extent, G. thermoglucosidans (Fig. 2). For more than half of the sequenced genomes, papers have been published describing and/or announcing the sequence data and usually indicating the particular features of the strain that motivated its sequencing. An insightful discussion of the biological lessons from Geobacillus genomes was previously published earlier this year, including surveys of genes involved in breakdown of plant-derived lignocellulose (Zeigler, 2005); but at that time, only 10 genome sequences were available.


Some (bacilli) like it hot: genomics of Geobacillus species.

Studholme DJ - Microb Biotechnol (2014)

Phylogenetic relationships among sequenced strains of Geobacillus inferred from a multiple sequence alignment of recN sequences. The circles indicate strains whose genomes have been sequenced, as listed in Table 1. The triangles indicate type strains of the various Geobacillus species; recN sequences from these are taken from a previous phylogenetic analysis by Zeigler (2005). The maximum-likelihood tree was generated using mega6 (Tamura et al., 2013).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4321371&req=5

fig02: Phylogenetic relationships among sequenced strains of Geobacillus inferred from a multiple sequence alignment of recN sequences. The circles indicate strains whose genomes have been sequenced, as listed in Table 1. The triangles indicate type strains of the various Geobacillus species; recN sequences from these are taken from a previous phylogenetic analysis by Zeigler (2005). The maximum-likelihood tree was generated using mega6 (Tamura et al., 2013).
Mentions: At the time of writing (28 July 2014), 29 Geobacillus genome sequences are available (Table 1). These include representatives of all the major phylogenetic groups within the genus and include representatives of the species G. thermoleovorans, G. kaustophilus, G. thermocatenulatus, G. thermodenitrificans, G. stearothermophilus, G. caloxylosilyticus and G. thermoglucosidans (formerly G. thermoglucosidasius) as well as several strains that have not been assigned to named species (Fig. 2). Genome sequences are also available for some other thermophilic members of the Bacillaceae, such as Paenibacillus lautus (Mead et al., 2012) and Bacillus coagulans (Xu et al., 2013) and for Geobacillus-infecting bacteriophage (Marks and Hamilton, 2014), but these will not be discussed here. The team who sequenced the genome of Geobacillus sp. MAS1 described this strain as ‘G. thermopakistaniensis’, but this is not a validly named species and no justification was provided for its proposal as a new species (Siddiqui et al., 2014). On the basis of its recN sequence, a useful phylogenetic marker for Geobacillus spp. (Zeigler, 2005), strain MAS1 is closely related to the type strains of G. kaustophilus and G. thermoleovorans (Fig. 2). Strain NUB3621 was described as ‘G. stearothermophilus’ but as has been previously noted (Studholme et al., 1999; Zeigler, 2005; Blanchard et al., 2014), this strain is phylogenetically distinct from B. stearothermophilus sensu strictu and is more closely related to G. caldoxylsilyticus and, to a lesser extent, G. thermoglucosidans (Fig. 2). For more than half of the sequenced genomes, papers have been published describing and/or announcing the sequence data and usually indicating the particular features of the strain that motivated its sequencing. An insightful discussion of the biological lessons from Geobacillus genomes was previously published earlier this year, including surveys of genes involved in breakdown of plant-derived lignocellulose (Zeigler, 2005); but at that time, only 10 genome sequences were available.

View Article: PubMed Central - PubMed

Affiliation: Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK.

AUTOMATICALLY GENERATED EXCERPT
Please rate it.

The genus Geobacillus includes thermophilic Gram-positive spore-forming bacteria that form a phylogenetically coherent clade within the family Bacillaceae... Genome sequences are also available for some other thermophilic members of the Bacillaceae, such as Paenibacillus lautus (Mead et al., ) and Bacillus coagulans (Xu et al., ) and for Geobacillus-infecting bacteriophage (Marks and Hamilton, ), but these will not be discussed here... However, the availability of complete genome sequence data enables phylogenetic analysis based on single-nucleotide variants over the entire core genome, offering much greater resolution (Fig.  3A)... According to the core-genome-wide phylogenetic analysis, the two strains assigned as G.  kaustophilus do not form a phylogenetically coherent monophyletic clade... Nucleotide sequence identities between clades are much lower; between G.  kaustophilus and G.  thermoglucosidans, there is approximately 84% identity... The considerable amount of reticulation in the phylogenetic network (Fig.  3A) suggests significant horizontal genetic transfer within and among these species... CAMR12739... The NG80-2 genome sequence also enabled discovery of the first nitrous oxide reductase gene from a Gram-positive, and a novel thermophilic long-chain alkane monooxygenase (Feng et al., )... Specifically, they used the genome sequence to clone two promoters and incorporated them into plasmid vectors: one for inducible gene expression and one constitutive... The authors also mention that they tried other promoters that did not work so well; presumably, the availability of the genome sequence allowed them to relatively quickly screen a number of candidates until they found the best ones... Only then can we rationally design genetic interventions to predictably manipulate metabolism... And finally, palaeo-genomics of ancient Geobacillus spores, which may be viable after billions of years of dormancy, might shed light on population-genetics and evolutionary processes over timescales that we previously assumed to be intractable (Nicholson, ; Zeigler, ).

Show MeSH