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Four salt-tolerant and aromatics degrading strains used in this study were isolated from polluted technogenic soil on the territory of the Verkhnekamsk potash deposit (Russia). The strains were aerobic, Gram-stain-positive, non-motile, non-endospore-forming irregular rods, exhibiting a marked rod-coccus growth cycle. They contained lysine-based peptidoglycan, teichulosonic acid and poly(glycosyl phosphate) polymers in the cell walls. The major menaquinone was MK-9(H 2 ), the predominant fatty acids were saturated, anteiso- and iso-branched, and the major compounds of polar lipid profiles included phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and two glycolipids (monogalactosyldiacylglycerol and dimannosylglyceride). The strains showed the highest 16S rRNA gene sequence similarity to Arthrobacter crystallopoietes (99.6-99.9%), followed by A. mangrovi (98.3-98.5%) and A. globiformis, the type species of the genus Arthrobacter (97.6-97.8%). The values of overall genome related indices (ANI, dDDH, AAI and POCP) indicated that the target strains and A. crystallopoietes represented three species within a new genus. These species clearly differed from each other and from A. mangrovi and A. globiformis in the phenotypic traits, including the peptidoglycan type and the structures and compositions of cell wall glycopolymers. Based on the findings of this study and the previously published data, we provide the description of the new genus Crystallibacter gen. nov. with the type species Crystallibacter crystallifaciens comb. nov. (type strain, VKM Ac-1107  T ) and two newly revealed species, Crystallibacter permensis sp. nov. (type strain, B905 T  = VKM Ac-2550 T  = LMG 33113 T ) and Crystallibacter degradans sp. nov. (type strain, SF27 T  = VKM Ac-2063 T  = LMG 33112 T )., Competing Interests: Declarations. Conflict of interest: The authors declare no competing interests. Ethical approval: This article does not contain any studies with animals performed by any of the authors. Consent for publication: The manuscript is submitted with the consent of all authors., (© 2024. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)

In recent decades, most studies of microbial rhodopsins have focused on their identification and characterization in aquatic bacteria. In 2021, actinomycetes of the family Geodermatophilaceae, commonly inhabiting terrestrial ecosystems in hot and arid regions, have been reported to contain rhodopsins with DTEW, DTEF and NDQ amino acid motifs. An advanced bioinformatics analysis performed in this work additionally revealed NTQ rhodopsin and heliorhodopsins. The absorption maxima identified for rhodopsins from the above five groups ranged from 513 nm (NTQ rhodopsin) to 559 nm (heliorhodopsin). An assessment of pumping specificity showed that DTEW and DTEF rhodopsins possessed outward H + -transport activities. Ca 2+ ions were required for pumping if E. coli C43(DE3) was used as an expression strain, but were unnecessary in the case of E. coli BL21(DE3). For NDQ rhodopsin, outward H + -transport was detected in NaCl and KCl solutions at pH 5 and 6, but not at neutral pH. A weak Na + -efflux was observed for this rhodopsin at pH 6 and 7 in a NaCl solution only in the presence of proton ionophore. NTQ rhodopsin acted as an inward Cl - -, Br - -, and I - - pump, with a much weaker activity towards NO 3- . No pumping activity was detected for the heliorhodopsin tested. The finding of rhodopsins with novel properties further expands the rhodopsin landscape., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Puromycin (Puro) is a natural aminonucleoside antibiotic that inhibits protein synthesis by its incorporation into elongating peptide chains. The unique mechanism of Puro finds diverse applications in molecular biology, including the selection of genetically engineered cell lines, in situ protein synthesis monitoring, and studying ribosome functions. However, the key step of Puro biosynthesis remains enigmatic. In this work, pur6-guided genome mining is carried out to explore the natural diversity of Puro-like antibiotics. The diversity of biosynthetic gene cluster (BGC) architectures suggests the existence of distinct structural analogs of puromycin encoded by pur-like clusters. Moreover, the presence of tRNA Cys in some BGCs, i.e., cst -like clusters, leads us to the hypothesis that Pur6 utilizes aminoacylated tRNA as an activated peptidyl precursor, resulting in cysteine-based analogs. Detailed metabolomic analysis of Streptomyces sp. VKM Ac-502 containing cst -like BGC revealed the production of a cysteinyl-based analog of Puro-cystocin (Cst). Similar to puromycin, cystocin inhibits both prokaryotic and eukaryotic translation by the same mechanism. Aminonucleoside N-acetyltransferase CstC inactivated Cst, mediating antibiotic resistance in genetically modified bacteria and human cells. The substrate specificity of CstC originated from the steric hindrance of its active site. We believe that novel aminonucleosides and their inactivating enzymes can be developed through the directed evolution of the discovered biosynthetic machinery.

Two novel yellow-pigmented, rod-shaped and non-motile coryneform actinobacteria, strains VKM Ac-2596 T and VKM Ac-2761, were isolated from a plant Tanacetum vulgare (Asteraceae) infested by foliar nematode Aphelenchoides sp. The strains exhibited the highest 16S rRNA gene sequence similarities to Rathayibacter agropyri CA4 T (99.71%), Rathayibacter rathayi DSM 7485 T (99.65%) and Rathayibacter iranicus VKM Ac-1602 T (99.65%). The pairwise average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between VKM Ac-2596 T and VKM Ac-2671 towards the type strains of Rathayibacter species did not exceed 85.24% and 29.40%, respectively, that are well below the thresholds for species delineation. The target strains had key chemotaxonomic properties typical of the genus Rathayibacter, namely, the DAB-based peptidoglycan, rhamnose and mannose as the predominant sugars and a rhamnomannan in the cell, the major menaquinone MK-10 and fatty acids of iso-anteiso type, with a large proportion of anteiso-15:0. The strains showed clear differences from the recognized Rathayibacter species in several phenotypic characteristics, including the difference in the composition of cell wall glycopolymers. Based on the results obtained in this study and the data published previously, we provide a description of a new species, Rathayibacter tanaceti sp. nov., with DL-642 T (= VKM Ac-2596 T  = LMG 33114 T ) as the type strain., (© 2024. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Draft genome sequences of 11 strains of putative new species of Geodermatophilaceae were generated using Illumina technology. The genome sizes ranged from 4.19 to 4.99 Mb, with G+C contents of 73.5% to 74.6%, and contained genes for microbial rhodopsins. This study will contribute to our knowledge of the ecology and diversity of members of the family Geodermatophilaceae ., Competing Interests: The authors declare no conflict of interest.

Draft genome sequences of 9 strains of known and putative new species of Microbacteriaceae isolated from insect- and nematode-damaged plants were generated using Illumina technology. The data obtained will contribute to the development of the genome-based prokaryote taxonomy and the knowledge on the biology of the microbial group investigated.

Draft genome sequences of 28 strains of Microbacteriaceae from plants infested by plant-parasitic nematodes were obtained using Illumina technology. The sequence data will provide useful baseline information for the development of comparative genomics and systematics of Microbacteriaceae and facilitate understanding of molecular mechanisms involved in interactions between plants and nematode-associated bacterial complexes., (Copyright © 2021 Tarlachkov et al.)

Draft genome sequences of 13 bacterial strains from the family Microbacteriaceae were generated using Illumina technology. The genome sizes varied from 3.0 to 4.8 Mb, and the DNA G+C content was 68.1 to 72.5%. The sequences obtained will contribute to the development of genome-based taxonomy and understanding of molecular interactions between bacteria and plants., (Copyright © 2020 Tarlachkov et al.)

Complete and draft genome sequences of 12 Rathayibacter strains were generated using Oxford Nanopore and Illumina technologies. The genome sizes of these strains are 3.21 to 4.61 Mb, with high G+C content (67.2% to 72.7%) genomic DNA. Genomic data will provide useful baseline information for natural taxonomy and comparative genomics of members of the genus Rathayibacter ., (Copyright © 2020 Tarlachkov et al.)

Motivation: A small amount of research is focused on investigation of rhodopsins in cultivated bacteria isolated from non-aquatic environments. Furthermore, the abundance of these proteins in strains from hot and arid habitats was not reported previously. Since there is an insignificant amount of such isolates, the enigmatic role of the rhodopsins in dry ecological niches is still poorly understood. The members of the family Geodermatophilaceae could be used as interesting objects to search for new rhodopsin genes that will provide novel insights into versatility and importance of these proteins in non-aquatic conditions., Results: This is the first report of the abundance of different rhodopsins in cultivated bacteria isolated from hot and arid ecological niches. A total of 31 rhodopsin genes were identified in 51 analyzed genomes of strains belonging to the family Geodermatophilaceae. Overall, 88% of the strains harbouring rhodopsins are isolated from non-aquatic environments. It was found that 82% of strains belonging to the genus Geodermatophilus have at least one gene as compared to 38% of strains of other genera which contain rhodopsins. Analysis of key amino acids revealed two types of the studied proteins: DTE type (putative proton pump) and NDQ type (putative sodium pump). Proton pumps were divided into two subtypes (DTEW and DTEF) according to phylogenetic analysis and the presence of highly conserved tryptophan or phenylalanine at position 182. Among all studied rhodopsins DTEF subtype is the most unique one, identified only in this family., Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author(s) 2019. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

The draft genome sequence of the type strain Saccharopolyspora hirsuta subsp. hirsuta VKM Ac-666 was sequenced. This moderately thermophilic actinobacterial strain of sugarcane bagasse origin is able to transform different steroid substrates., (Copyright © 2020 Lobastova et al.)

The 23-membered macrolide tacrolimus (FK506) is an important immunosuppressant that is widely used in the prevention of graft rejection and in the treatment of inflammatory skin diseases and immune diseases. We report here the draft genome sequence of the FK506 producer Streptomyces tsukubensis VKM Ac-2618D., (Copyright © 2019 Poshekhontseva et al.)

Draft genome sequences of 11 bacteria belonging to the family Microbacteriaceae were obtained using Illumina technology. The genomes of these strains have sizes from 3.14 to 4.30 Mb with their genomic DNA characterized as having high G+C contents (above 65%). These genomic data will be useful for natural taxonomy and comparative genomic studies of bacterial strains of the family Microbacteriaceae.

A rod-shaped, non-endospore-forming and non-motile bacterium, strain DL-329 T , was isolated from the above-ground part of a plant, Androsace koso-poljanskii Ovcz. (Primulaceae), at the the State Natural Reserve 'Belogorie', Russia. On the basis of 16S rRNA gene sequence comparisons, the strain clustered with members of the genus Rathayibacter, showing the highest sequence similarity to Rathayibacter tritici (98.89 %), Rathayibacter rathayi (98.82 %) and Rathayibacter festucae (98.82 %). The DNA hybridization experiments demonstrated that strain DL-329 T represents a separate genomic species. The results of comparative studies of physiological and chemotaxonomic characteristics, including cell-wall sugar patterns, polar lipid profiles, and the matrix-assisted laser desorption/ionization time-of-flight mass spectra of bacterial cells, allowed clear differentiation of VKM Ac-2121 T from the recognized Rathayibacter species at the phenotypic level. Based on the data obtained, a new species, Rathayibacter oskolensis sp. nov., is proposed, with DL-329 T (=VKM Ac-2121 T =LMG 22542 T ) as the type strain.

The cell walls of two strains of the genus Promicromonospora (phylum Actinobacteria) were found to include non-phosphorylated anionic glycopolymers with pyruvic acid acetals of R-configuration. The cell wall of the type strain P. citrea 665 T contains two glycopolymers of the sort, including the Kdn-teichulosonic acid with the repeating unit →6)-α-d-Gl≿p/→6)-α-d-Gl≿p3SO 3 - -(1 → 4)-α-[7,9Pyr]-Kdn-(2→, and the galactan with the repeating unit →3)-α-[4,6Pyr]-d-Galp-2OAc-(1 → . The cell wall of Promicromonospora sp.VKM Ac-1028 contains the teichuronic acid with the repeating unit →6)-α-d-Gl≿p-(1 → 4)-β-[2,3Pyr]-d-GlcpA-(1 → . The detected glycopolymer structures are reported for the first time. Presented results expand the notion on the diversity of the organic world and on the role of the structures and composition of cell wall polymers in bacterial taxonomy. The glycopolymer structures were established by using a combination of chemical methods, NMR- and IR-spectroscopy, and ESI MS., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

A draft genome sequence of Rathayibacter sp. strain VKM Ac-2630 was derived using Ion Torrent sequencing technology. The genome size of this strain is 3.88 Mb, with an average G+C content of 72.0%. Genomic evidence of an aerobic mode of respiration and a heterotrophic lifestyle of this bacterium was obtained., (Copyright © 2017 Starodumova et al.)

The draft genome of "Rathayibacter tanaceti" VKM Ac-2596 is 3.17 Mb in size with an average G+C content of 70.7% and comprises at least two nonidentical copies of ribosomal small subunit (SSU-rRNA) genes. The semiconductor sequencing platform Ion Torrent was used., (Copyright © 2016 Vasilenko et al.)