MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.

MxaF gene, a gene encoding alpha subunit of methanol dehydrogenase in and false growth of acetic acid bacteria on methanol

MxaF gene, a gene encoding alpha subunit of methanol dehydrogenase, was investigated for acetic acid bacteria, and growth on methanol was examined for the bacteria by using various media. Of 21 strains of acetic acid bacteria studied, Acidomonas methanolica strains showed the presence of mxaF gene exclusively, and grew on a defined medium containing methanol. Further, none of the strains tested of which the growth on methanol had been previously reported, except for Acidomonas methanolica, showed the presence of mxaF gene or the growth on methanol. Precautions were taken against false growth on compounds used for identification of bacteria.

Genera and species in acetic acid bacteria

Taxonomic studies of acetic acid bacteria were historically surveyed. The genus Acetobacter was first introduced in 1898 with a single species, Acetobacter aceti. The genus Gluconobacter was proposed in 1935 for strains with intense oxidation of glucose to gluconic acid rather than oxidation of ethanol to acetic acid and no oxidation of acetate. The genus "Acetomonas" was described in 1954 for strains with polar flagellation and no oxidation of acetate. The proposals of the two generic names were due to confusion, and "Acetomonas" was a junior subjective synonym of Gluconobacter. The genus Acetobacter was in 1984 divided into two subgenera, Acetobacter and Gluconoacetobacter. The latter was elevated to the genus Gluconacetobacter in 1998. In the acetic acid bacteria, ten genera are presently recognized and accommodated to the family Acetobacteraceae, the Alphaproteobacteria: Acetobacteer, Gluconobacter, Acidomonas, Gluconacetobacter, Asaia, Kozakia, Swaminathania, Saccharibacter, Neoasaia and Granulibacter. In contrast, the genus Frateuria, strains of which were once named 'pseudacetic acid bacteria', was classified into the Gammaproteobacteria. The genus Gluconacetobacter was phylogenetically divided into two groups: the Gluconacetobacter liquefaciens group and the Gluconacetobacter xylinus group. The two groups were discussed taxonomically.

Emendation of the genus Acidomonas Urakami, Tamaoka, Suzuki and Komagata 1989

The genus Acidomonas and the species Acidomonas methanolica were recharacterized by using the type strain (NRIC 0498T), three reference strains and 10 methanol-utilizing bacteria that were isolated from activated sludge from three different sewage-treatment plants in Tokyo. Based on 16S rDNA sequences, all strains formed a single cluster within the Acetobacteraceae that was clearly different from the genera Acetobacter, Gluconobacter, Gluconacetobacter, Asaia and Kozakia. The 14 strains were identified as a single species, Acidomonas methanolica, by DNA–DNA similarities, showed DNA G+C contents that ranged from 62 to 63 mol% and had Q-10 as the major quinone, accounting for >87 % of total ubiquinones. Cells of Acidomonas methanolica had a single polar flagellum (or occasionally polar tuft flagella); this differs from a previous study that described peritrichous flagella. Oxidation of acetate was positive for all strains, but oxidation of lactate was weakly positive and varied with strains. Dihydroxyacetone was not produced from glycerol. Pantothenic acid was an essential requirement for growth. The strains tested grew at mostly the same extent at pH 3·0–8·0. Therefore, Acidomonas methanolica should be regarded as acidotolerant, not acidophilic. The descriptions of the genus Acidomonas and the species Acidomonas methanolica Urakami, Tamaoka, Suzuki and Komagata 1989 are emended with newly obtained data.

The genus Gluconobacter and its applications in biotechnology

Organisms of the genus Gluconobacter have been widely utilized within the biotechnology industry for many decades, due to their unique metabolic characteristics. The metabolic features that render Gluconobacter so useful in biotransformation processes, vitamin synthesis, and, as the biological element in sensor systems, are critically evaluated, and the relevance of recent biochemical genetic studies to current and future industrial Gluconobacter processes is discussed. The impact of recombinant gene technology on the status of Gluconobacter processes and the potential use of such techniques in clarifying aspects of the physiology of Gluconobacter is reviewed.