Phylogenetic Relationships and Functional Genes: Distribution of a Gene (mnxG) encoding a putative manganese-oxidizing enzyme in Bacillus species

Abstract

Several Bacillus and Paenibacillus species were isolated from Fe and Mn oxide minerals precipitating at a deep subsurface oxic-anoxic interface at Henderson Molybdenum Mine, Empire, CO. The isolates were investigated for their Mn(II)-oxidizing potential and interrogated for possession of the mnxG gene, a gene that codes for a putative Mn(II)-oxidizing enzyme in Bacillus species. Seven of eight Bacillus species were capable of Mn(II) oxidation; however, the mnxG gene was detected in only one isolate. Using sequences of known Bacillus species both with and without amplifiable mnxG genes and Henderson Mine isolates, the 16S rRNA and mnxG gene phylogenies were compared to determine if 16S rRNA sequences could be used to predict the presence or absence of an amplifiable mnxG gene within the genomes of the isolates. We discovered a strong correspondence between 16S rRNA sequence similarity and the presence/absence of an amplifiable mnxG gene in the isolates. The data revealed a complex phylogenetic distribution of the mnxG gene in which vertical inheritance and gene loss influence the distribution of the gene among the Bacillus species included in this study. Comparisons of 16S rRNA and functional gene phylogenies can be used as a tool to aid in unraveling the history and dispersal of the mnxG gene within the Bacillus clade.

FIG. 1.

Maximum parsimony bootstrap 50% majority rule consensus tree based on mnxG amino acid sequences. Bootstrap values are indicated at selected nodes and are based on 100 bootstrap replicates. The SG-1 cluster is labeled and is consistent across both the 16S rRNA and mnxG gene trees. The HM06-02 cluster is also labeled.

FIG. 2.

Fifty-percent majority rule consensus phylogenetic tree based on 16S rRNA sequences of Bacillus species. Henderson Mine isolates are in boldface type, and the single asterisk indicates the mnxG-positive Bacillus organism isolated in this study. Consensus values are indicated at select nodes and are based on 9,000 Bayesian trees. The SG-1 and the HM06-02 clusters are labeled.

FIG. 3.

Histogram depicting the probabilities of numbers of gains and losses of the mnxG gene needed to explain the observed data.

FIG. 4.

Histogram comparing the number of changes needed within the trees constructed by Bayesian analysis to explain the distribution of the mnxG gene in the observed data versus the randomized data. Note that the distribution of observed values falls to the left of the distribution of random values; this indicates that the null hypothesis can be rejected.