Micrococcineae

Abstract: An extensive Fourier-transform infrared (FT-IR) spectroscopy database for the identification of bacteria from the two suborders Micrococcineae and Corynebacterineae (Actinomycetales, Actinobacteria) as well as other morphologically similar genera was established. The database consists of averaged IR spectra from 730 reference strains, covering 220 different species out of 46 genera. A total of 192 species are represented by type strains. The identity of 352 reference strains was determined by comparative 16S rDNA sequence analysis and, if necessary, strains were reclassified accordingly. FT-IR frequency ranges, weights and reproducibility levels were optimized for this section of high-G+C gram-positive bacteria. In an internal validation, 98.1% of 208 strains were correctly identified at the species level. A simulated external validation which was carried out using 544 strains from 54 species out of 16 genera resulted in a correct identification of 87.3% at the species level and 95.4% at the genus level. The performance of this identification system is well within the range of those having been reported in the literature for the identification of coryneform bacteria by phenotypical methods. Coryneform and related taxa display a certain degree of overlapping distribution of different taxonomical markers, leading to a limited differentiation capacity of non-genotypical identification methods in general. However, easy handling, rapid identification within 25 h starting from a single colony, a satisfactory differentiation capacity and low cost, render FT-IR technology clearly superior over other routine methods for the identification of coryneform bacteria and related taxa.

Abstract: The Actinobacteria constitute one of the main phyla of Bacteria. Presently, no morphological and very few molecular characteristics are known which can distinguish species of this highly diverse group. In this work, we have analyzed the genomes of four actinobacteria (viz. Mycobacterium leprae TN, Leifsonia xyli subsp. xyli str. CTCB07, Bifidobacterium longum NCC2705 and Thermobifida fusca YX) to search for proteins that are unique to Actinobacteria. Our analyses have identified 233 actinobacteria-specific proteins, homologues of which are generally not present in any other bacteria. These proteins can be grouped as follows: (i) 29 proteins uniquely present in most sequenced actinobacterial genomes; (ii) 6 proteins present in almost all actinobacteria except Bifidobacterium longum and another 37 proteins absent in B. longum and few other species; (iii) 11 proteins which are mainly present in Corynebacterium, Mycobacterium and Nocardia (CMN) subgroup as well as Streptomyces, T. fusca and Frankia sp., but they are not found in Bifidobacterium and Micrococcineae; (iv) 8 proteins that are specific for T. fusca and Streptomyces species, plus 2 proteins also present in the Frankia species; (v) 13 proteins that are specific for the Corynebacterineae or the CMN group; (vi) 14 proteins only found in Mycobacterium and Nocardia; (vii) 24 proteins unique to different Mycobacterium species; (viii) 8 proteins specific to the Micrococcineae; (ix) 85 proteins which are distributed sporadically in actinobacterial species. Additionally, many examples of lateral gene transfer from Actinobacteria to Magnetospirillum magnetotacticum have also been identified. The identified proteins provide novel molecular means for defining and circumscribing the Actinobacteria phylum and a number of subgroups within it. The distribution of these proteins also provides useful information regarding interrelationships among the actinobacterial subgroups. Most of these proteins are of unknown function and studies aimed at understanding their cellular functions should reveal common biochemical and physiological characteristics unique to either all actinobacteria or particular subgroups of them. The identified proteins also provide potential targets for development of drugs that are specific for actinobacteria.

Abstract: Despite advancing knowledge about the functional role of actinomycetes in degrading lignocellulosic materials, definitive knowledge concerning the diversity and dynamics of the actinomycetal community in composting is still lacking. In this study, real-time polymerase chain reaction (PCR) coupled with denaturing gradient gel electrophoresis (DGGE) and clone library construction were applied to investigate actinomycetal diversity and dynamics in a pilot-scale composting. Quantitative real-time PCR data revealed that actinomycetes accounted for 18–86 % of bacteria and that the fraction peaked during the maturing phase, indicating that Actinobacteria were critical to the compost ecosystem. Qualitatively, actinomycetal communities displayed distinct temporal variations during composting. Fourteen distinct genera of actinomycetes and an unknown group were observed in manure composts. Redundancy analysis indicated that temperature exerted an influence over the actinomycetal communities. Specifically, pathogenic Corynebacterium species dominated in the initial phase, whereas the genera Saccharomonospora and Thermobifida were abundant in the thermophilic phase. In maturing composts, mesophilic Micrococcineae members were most prevalent. The dominant thermophiles along with Micrococcineae may jointly facilitate the degradation of lignocellulosic materials during composting. Together, our research revealed a more detailed ecological and potential functional role for actinomycetes in the compost ecology.

Abstract: The taxonomic positions of two actinobacterial strains isolated from Mariana Trench sediment were established using a combination of genotypic and phenotypic data. The strains, isolates MT2.1T and MT2.2T, formed a distinct phyletic line in the Micrococcineae 16S rRNA gene tree together with Dermacoccus abyssi NCIMB 14084T. The isolates had chemical and phenotypic properties typical of members of the genus Dermacoccus and could be distinguished sharply from one another and from the type strains of Dermacoccus abyssi and Dermacoccus nishinomiyaensis using DNA–DNA relatedness data. A range of phenotypic properties served to distinguish the two novel strains from one another and from the type strains of established Dermacoccus species. The G+C contents of the DNAs of strains MT2.1T and MT2.2T were 66.8 and 69.1 mol%, respectively. It is evident that the two isolates merit recognition as novel species within the genus Dermacoccus. The names proposed for these taxa are Dermacoccus barathri sp. nov. (type strain MT2.1T=DSM 17574T=NCIMB 14081T) and Dermacoccus profundi sp. nov. (type strain MT2.2T=DSM 17575T=NCIMB 14084T).