Description of Geodermatophilus bullaregiensis sp. nov

Taxonomic Diversity and Functional Traits of Soil Bacterial Communities under Radioactive Contamination: A Review

Studies investigating the taxonomic diversity and structure of soil bacteria in areas with enhanced radioactive backgrounds have been ongoing for three decades. An analysis of data published from 1996 to 2024 reveals changes in the taxonomic structure of radioactively contaminated soils compared to the reference, showing that these changes are not exclusively dependent on contamination rates or pollutant compositions. High levels of radioactive exposure from external irradiation and a high radionuclide content lead to a decrease in the alpha diversity of soil bacterial communities, both in laboratory settings and environmental conditions. The effects of low or moderate exposure are not consistently pronounced or unidirectional. Functional differences among taxonomic groups that dominate in contaminated soil indicate a variety of adaptation strategies. Bacteria identified as multiple-stress tolerant; exhibiting tolerance to metals and antibiotics; producing antioxidant enzymes, low-molecular antioxidants, and radioprotectors; participating in redox reactions; and possessing thermophilic characteristics play a significant role. Changes in the taxonomic and functional structure, resulting from increased soil radionuclide content, are influenced by the combined effects of ionizing radiation, the chemical toxicity of radionuclides and co-contaminants, as well as the physical and chemical properties of the soil and the initial bacterial community composition. Currently, the quantification of the differential contributions of these factors based on the existing published studies presents a challenge.

Genotype-phenotype correlations within the Geodermatophilaceae

The integration of genomic information into microbial systematics along with physiological and chemotaxonomic parameters provides for a reliable classification of prokaryotes. In silico analysis of chemotaxonomic traits is now being introduced to replace characteristics traditionally determined in the laboratory with the dual goal of both increasing the speed of the description of taxa and the accuracy and consistency of taxonomic reports. Genomics has already successfully been applied in the taxonomic rearrangement of Geodermatophilaceae (Actinomycetota) but in the light of new genomic data the taxonomy of the family needs to be revisited. In conjunction with the taxonomic characterisation of four strains phylogenetically located within the family, we conducted a phylogenetic analysis of the whole proteomes of the sequenced type strains and established genotype-phenotype correlations for traits related to chemotaxonomy, cell morphology and metabolism. Results indicated that the four isolates under study represent four novel species within the genus Blastococcus. Additionally, the genera Blastococcus, Geodermatophilus and Modestobacter were shown to be paraphyletic. Consequently, the new genera Trujillonella, Pleomorpha and Goekera were proposed within the Geodermatophilaceae and Blastococcus endophyticus was reclassified as Trujillonella endophytica comb. nov., Geodermatophilus daqingensis as Pleomorpha daqingensis comb. nov. and Modestobacter deserti as Goekera deserti comb. nov. Accordingly, we also proposed emended descriptions of Blastococcus aggregatus, Blastococcus jejuensis, Blastococcus saxobsidens and Blastococcus xanthilyniticus. In silico chemotaxonomic results were overall consistent with wet-lab results. Even though in silico discriminatory levels varied depending on the respective chemotaxonomic trait, this approach is promising for effectively replacing and/or complementing chemotaxonomic analyses at taxonomic ranks above the species level. Finally, interesting but previously overlooked insights regarding morphology and ecology were revealed by the presence of a repertoire of genes related to flagellum synthesis, chemotaxis, spore production and pilus assembly in all representatives of the family. A rich carbon metabolism including four different CO₂ fixation pathways and a battery of enzymes able to degrade complex carbohydrates were also identified in Blastococcus genomes.

Direct comparison of bacterial communities in soils contaminated with different levels of radioactive cesium from the first Fukushima nuclear power plant accident

The Great East Japan Earthquake caused a serious accident at the first Fukushima nuclear power plant (NPP), which in turn released a large amount of radionuclides. Little attention has been paid to in-situ soil microorganisms exposed to radioactive contamination by the actual NPP accident. We herein investigated bacterial communities in the radioactive cesium (Cs)-contaminated and non-contaminated soils by high-throughput sequencing. The uppermost and ectorhizosphere soil samples were collected from the base of mugwort grown in the same soil type with the same soil-use history in order to compare the bacterial communities at geographically separated areas. The concentrations of radioactive Cs in the soils ranged from 10 to 563,000 Bq ¹³⁷Cs/kg dry soil, with the highest concentration being detected at 1 km from the NPP. Alpha-diversity indices, i.e., Chao1, Shannon and Simpson reciprocal, of the sequence data showed the lower bacterial diversity in the most highly Cs-contaminated soil. Principal coordinate analysis with principle components 1 and 3 based on unweighted UniFrac distances indicated the significant difference in bacterial communities of the most contaminated area from those of the other areas. Operational taxonomic unit-based assay revealed higher abundance of the radio-resistant Geodermatophilus bullaregiensis relative in the most contaminated soil. Thus, it was strongly suggested that the radioactive accident facilitated the growth and/or survival of radio-resistant bacteria in the Cs-contaminated soils. The results of this study show that information on the soil type, vegetation and soil-use history enhances the direct comparison of geographically distant soil bacterial communities exposed to different levels of radioactive contamination.

Metagenome Across a Geochemical Gradient of Indian Stone Ruins Found at Historic Sites in Tamil Nadu, India

Although stone surfaces seem unlikely to be habitable, they support microbial life. Life on these surfaces are subjected to many varying harsh conditions and require the inhabitants to exhibit resistance to environmental factors including UV irradiation, toxic metal exposure, and fluctuating temperatures and humidity. Here we report the effect of hosting stone geochemistry on the microbiome of stone ruins found in Tamil Nadu, India. The microbial communities found on the two lithologies, granite and granodiorite, hosted distinct populations of bacteria. Geochemical composition analysis of sampled stones revealed quartz mineral content as a major driver of microbial community structure, particularly promoting community richness and proportions of Cyanobacteria and Deinococcus-Thermus. Other geochemical parameters including ilmenite, albite, anorthite, and orthoclase components or elemental concentrations (Ti, Fe, Mn, Na, and K) also influenced community structure to a lesser degree than quartz. Core members of the stone microbiome community found on both lithologies were also identified and included Cyanobacteria (Chroococcidiopsaceae and Dapisostemonum CCIBt 3536), Rubrobacter, and Deinococcus. A cluster of taxa including Sphingomonas, Geodermatophilus, and Truepera were mostly found in the granodiorite samples. Community diversity correlated with quartz mineral content in these samples may indicate that the microbial communities that attach to quartz surfaces may be transient and regularly changing. This work has expanded our understanding of built-stone microbial community structure based on lithology and geochemistry.

Geodermatophilus chilensis sp. nov., from soil of the Yungay core-region of the Atacama Desert, Chile

A polyphasic study was undertaken to establish the taxonomic status of three representative Geodermatophilus strains isolated from an extreme hyper-arid Atacama Desert soil. The strains, isolates B12^T, B20 and B25, were found to have chemotaxonomic and morphological properties characteristic of the genus Geodermatophilus. The isolates shared a broad range of chemotaxonomic, cultural and physiological features, formed a well-supported branch in the Geodermatophilus 16S rRNA gene tree in which they were most closely associated with the type strain of Geodermatophilus obscurus. They were distinguished from the latter by BOX-PCR fingerprint patterns and by chemotaxonomic and other phenotypic properties. Average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between the whole genome sequences of isolate B12^T and G. obscurus DSM 43160^T were 89.28%, 87.27% and 37.4%, respectively, metrics consistent with its classification as a separate species. On the basis of these data, it is proposed that the isolates be assigned to the genus Geodermatophilus as Geodermatophilus chilensis sp. nov. with isolate B12^T (CECT 9483^T=NCIMB 15089^T) as the type strain. Analysis of the whole genome sequence of G. chilensis B12^T with 5341 open reading frames and a genome size of 5.5Mb highlighted genes and gene clusters that encode for properties relevant to its adaptation to extreme environmental conditions prevalent in extreme hyper-arid Atacama Desert soils.

Genome-Scale Data Call for a Taxonomic Rearrangement of Geodermatophilaceae

Geodermatophilaceae (order Geodermatophilales, class Actinobacteria) form a comparatively isolated family within the phylum Actinobacteria and harbor many strains adapted to extreme ecological niches and tolerant against reactive oxygen species. Clarifying the evolutionary history of Geodermatophilaceae was so far mainly hampered by the insufficient resolution of the main phylogenetic marker in use, the 16S rRNA gene. In conjunction with the taxonomic characterisation of a motile and aerobic strain, designated YIM M13156T and phylogenetically located within the family, we here carried out a phylogenetic analysis of the genome sequences now available for the type strains of Geodermatophilaceae and re-analyzed the previously assembled phenotypic data. The results indicated that the largest genus, Geodermatophilus, is not monophyletic, hence the arrangement of the genera of Geodermatophilaceae must be reconsidered. Taxonomic markers such as polar lipids and fatty-acids profile, cellular features and temperature ranges are indeed heterogeneous within Geodermatophilus. In contrast to previous studies, we also address which of these features can be interpreted as apomorphies of which taxon, according to the principles of phylogenetic systematics. We thus propose a novel genus, Klenkia, with the type species Klenkia marina sp. nov. and harboring four species formerly assigned to Geodermatophilus, G. brasiliensis, G. soli, G. taihuensis, and G. terrae. Emended descriptions of all species of Geodermatophilaceae are provided for which type-strain genome sequences are publicly available. Our study again demonstrates that the principles of phylogenetic systematics can and should guide the interpretation of both genomic and phenotypic data.

Geodermatophilus daqingensis sp. nov., isolated from petroleum-contaminated soil

A novel Gram-positive actinobacterium, designated WT-2-1^T, was isolated from a sample of petroleum-contaminated soil collected in Daqing, Heilongjiang province, China and characterised using a polyphasic taxonomic approach. The optimal growth for strain WT-2-1^T was found to be at 25-35 °C and at pH 6.0-9.0 and with 0-4% (w/v) NaCl, forming blackish green-coloured colonies. Chemotaxonomic and molecular characteristics of the isolate match those described for members of the genus Geodermatophilus. The peptidoglycan was found to contain meso-diaminopimelic acid; galactose, glucose and xylose were detected as diagnostic sugars. The main phospholipids were identified as diphosphatidylglycerol, phosphatidylcholine, phosphatidylinositol, phosphatidylethanolamine and phosphatidylglycerol; MK-9(H₄) was the dominant menaquinone present. The major cellular fatty acids were identified as iso-C_16:0 and iso-C_15:0. 16S rRNA gene sequence analysis showed that strain WT-2-1^T is a member of the genus Geodermatophilus, with high sequence similarities to Geodermatophilus aquaeductus BMG801^T (98.4%), Geodermatophilus saharensis CF5/5^T (98.4%), Geodermatophilus bullaregiensis BMG841^T (98.3%) and Geodermatophilus normandii CF5/3^T (98.3%). Based on the phenotypic characteristics, phylogenetic data and DNA-DNA hybridization results, the isolate is concluded to represent a novel species of the genus Geodermatophilus, for which the name Geodermatophilus daqingensis sp. nov. is proposed. The type strain is WT-2-1^T (=CGMCC 4.7381^T = DSM 104001^T).

Blastococcus capsensis sp. nov., isolated from an archaeological Roman pool and emended description of the genus Blastococcus, B. aggregatus, B. saxobsidens, B. jejuensis and B. endophyticus

A novel Gram-reaction-positive actinobacterium, designated BMG 804T, was isolated from an archaeological Roman pool located in Gafsa, Tunisia. The strain grew as dry bright orange colonies at 30 °C and pH 6.0-8.0. It contained meso-diaminopimelic acid in the cell wall. The whole-cell sugars consisted of glucose, rhamnose and ribose. Polar lipids present were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol, an unidentified glycolipid and two unidentified phospholipids. MK-9(H4) was the predominant menaquinone. The fatty acid profile contained major amounts (>5 %) of C17 : 1ω8c, C16 : 1ω7c, iso-C15 : 0, iso-C16 : 0 and iso-C16 : 1H. The 16S rRNA gene sequence of BMG 804T showed 99.4 % as highest sequence similarity with Blastococcussaxobsidens. DNA-DNA hybridization between strain BMG 804T and B.saxobsidens DSM 44509T was 48.6±6.6 %. The G+C content of the DNA was 73.7 mol%. On the basis of the phenotypic and genotypic characteristics, including DNA-DNA hybridization results, BMG 804T (=DSM 46835T=CECT 8876T) is proposed as the type strain of a novel species Blastococcuscapsensis sp. nov. Emended descriptions of the genus Blastococcus and the species Blastococcus aggregatus, B. saxobsidens, Blastococcus jejuensis and Blastococcus endophyticus are also proposed.

Geodermatophilus pulveris sp. nov., a gamma-radiation-resistant actinobacterium isolated from the Sahara desert

A black-pigmented, aerobic actinobacterium, tolerant to ionizing radiation, designated BMG 825T, was isolated from desert limestone dust in Tunisia. The strain grew within the temperature range 10-40 °C, at pH 5.5-11.0 and in the presence of 2 % NaCl. The DNA G+C content was 75.7 mol%, and its cell-wall peptidoglycan contained meso-diaminopimelic acid. Sugars of whole-cell hydrolysates were galactose, glucose, and trace amounts of ribose and mannose. The predominant menaquinone was MK-9(H4), and the major fatty acids were iso-C16 : 0 and C16 : 1ω7c. The polar lipid profile comprised phosphatidylcholine, phosphatidylinositol, diphosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine and an unspecified glycolipid. 16S rRNA gene sequence analysis revealed that the strain fell into the genus Geodermatophilus, showing the highest similarity with Geodermatophilus poikilotrophus DSM 44209T (99.1 %). DNA-DNA hybridization results, phylogenetic distinctiveness and phenotypic properties supported the classification of this strain as a representative of a novel species of the genus Geodermatophilus, for which the name Geodermatophilus pulveris sp. nov. is proposed. The type strain is BMG 825T (=CECT 9003T=DSM 46839‏T).

List of new names and new combinations previously effectively, but not validly, published

The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries. It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in the nomenclature of prokaryotes. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.