In the course of screening the surface soils of ancient copper mines and smelters (East Harz, Germany) an aerobic, non-motile and halotolerant actinobacterium forming small rods or cocci was isolated. The strain designated F300T developed creamy to yellow colonies on tryptone soy agar and grew optimally at 28 °C, pH 7–8 and with 0.5–2 % (m/v) NaCl. Its peptidoglycan was of type A4α l-Lys–l-Glu (A11.54). The menaquinone profile was dominated by MK-8(II, III-H4) and contained minor amounts of MK-8(H2), MK-8(H6) and MK-9(H4). The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, mono and diacylated phosphatidylinositol dimannosides, and components that were not fully characterized, including two phospholipids, two glycolipids and an uncharacterized lipid. Major whole-cell sugars were rhamnose and ribose. The fatty acid profile contained mainly iso and anteiso branched fatty acids (anteiso-C15 : 0, iso-C14 : 0) and aldehydes/dimethylacetals (i.e. not fatty acids). Sequence analysis of its genomic DNA and subsequent analysis of the data placed the isolate in the group currently defined by members of the genera Ruania and Haloactinobacterium (family Ruaniaceae , order Micrococcales ) as a sister taxon to the previously described species Haloactinobacterium glacieicola , sharing an average nucleotide identity and average amino acid identity values of 85.3 and 85.7 %, respectively. Genotypic and chemotaxonomic analyses support the view that strain F300T (=DSM 108350T=CIP 111667T) is the type strain of a new genus and new species for which the name Occultella aeris gen. nov., sp. nov. is proposed. Based on revised chemotaxonomic and additional genome based data, it is necessary to discuss and evaluate the results in the light of the classification and nomenclature of members of the family Ruaniaceae , i.e. the genera Haloactinobacterium and Ruania . Consequently, the reclassification of Haloactinobacterium glacieicola as Occultella glacieicola comb. nov. and Haloactinobacterium album as Ruania alba comb. nov., with an emended description of the genus Ruania are proposed.

No abstract

The 16S rRNA profiling of 27 soil samples of three ancient mining areas of the East Harz region (Germany) indicated a group of rare bacteria which is related to extreme conditions such as salinity, higher temperature and alkalinity. Beside Hadesarchaea, it involves a significant number of sequences of Rubritepida, Polymorphobacter, Crinalium, Aliterella, Imperialibacter, Mizugakiibacter, Ekhidna, Mumia and Isoptericola, too. The appearance of such types may be related to the ground material which was brought onto the surface by the ancient mining activities dating back into the period between the fifteenth and the beginning nineteenth centuries. It is assumed that the RNA profiling reflects local soil bacteria communities which store a certain memory of previous environmental conditions. This ecological memory could be related on the one hand to the minerals and the mining activities centuries before, but on the other hand it could hint to the possibility of storage of bacteria in the geological sediments of late Perm (Zechstein), which has been deposited about 250 million years ago. The findings can be interpreted by the possibility of persistence of special types of soil bacteria at the ancient mining places. In addition, a possible relevance of the re-activation of very old microorganisms from deep subsurface layers for the recent microbial communities should be taken into account.

Soils are complex ecosystem, and their function in the environment is mainly determined by the microbial communities. Metal-tolerant micro-organisms have an important function in the formation of soil and the development of microbial communities in all areas where heavy metals are released by natural erosion processes or by human activities. The investigation of dose-dependent growth and behaviour is an essential part of the search for heavy metal-tolerant microorganism communities and their characterization. In this study, next-generation sequencing was used for the analysis of soil sample and reduced communities and droplet-based microfluidics was used to assess the growth behaviour of unknown bacterial communities and single strains in response to different heavy metal ions. Highly resolved dose-response functions of the bacterial communities reflect the specific character in their concentration-dependent response to different culture media and heavy metals of copper, nickel and cobalt. Besides the characterization of community responses, they allowed to characterize newly isolated strains. Concentration-dependent growth patterns of the micro-organisms in the droplets could be observed. The investigation demonstrates the potential of droplet-based microfluidics for miniaturized eco-toxicological studies and their suitability for the discovery of novel strains with special tolerance features.

We present a new methodological approach for the assessment of the susceptibility of Rhodococcus erythropolis strains from specific sampling sites in response to increasing heavy metal concentration (Cu2+, Ni2+, and Co2+) using the droplet-based microfluid technique. All isolates belong to the species R. erythropolis identified by Sanger sequencing of the 16S rRNA. The tiny step-wise variation of metal concentrations from zero to the lower mM range in 500 nL droplets not only provided accurate data for critical metal ion concentrations but also resulted in a detailed visualization of the concentration-dependent response of bacterial growth and autofluorescence activity. As a result, some of the isolates showed similar characteristics in heavy metal tolerance against Cu2+, Ni2+, and Co2+. However, significantly different heavy metal tolerances were found for other strains. Surprisingly, samples from the surface soil of ancient copper mining areas supplied mostly strains with a moderate sensitivity to Cu2+, Ni2+, and Co2+, but in contrast, a soil sample from an excavation site of a medieval city that had been covered for about eight centuries showed an extremely high tolerance against cobalt ion (up to 36 mM). The differences among the strains not only may be regarded as results of adaptation to the different environmental conditions faced by the strains in nature but also seem to be related to ancient human activities and temporal partial decoupling of soil elements from the surface. This investigation confirmed that microfluidic screening offers empirical characterization of properties from same species which has been isolated from sites known to have different human activities in the past.