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Riemerella anatipestifer (Hendrickson and Hilbert 1932) Segers et al. 1993 is the type species of the genus Riemerella, which belongs to the family Flavobacteriaceae. The species is of in-terest because of the position of the genus in the phylogenetic tree and because of its role as a pathogen of commercially important avian species worldwide. This is the first completed genome sequence of a member of the genus Riemerella. The 2,155,121 bp long genome with its 2,001 protein-coding and 51 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Sequencing of bacterial and archaeal genomes has revolutionized our understanding of the many roles played by microorganisms. There are now nearly 1,000 completed bacterial and archaeal genomes available, most of which were chosen for sequencing on the basis of their physiology. As a result, the perspective provided by the currently available genomes is limited by a highly biased phylogenetic distribution. To explore the value added by choosing microbial genomes for sequencing on the basis of their evolutionary relationships, we have sequenced and analysed the genomes of 56 culturable species of Bacteria and Archaea selected to maximize phylogenetic coverage. Analysis of these genomes demonstrated pronounced benefits (compared to an equivalent set of genomes randomly selected from the existing database) in diverse areas including the reconstruction of phylogenetic history, the discovery of new protein families and biological properties, and the prediction of functions for known genes from other organisms. Our results strongly support the need for systematic phylogenomic efforts to compile a phylogeny-driven Genomic Encyclopedia of Bacteria and Archaea in order to derive maximum knowledge from existing microbial genome data as well as from genome sequences to come. © 2009 Macmillan Publishers Limited. All rights reserved.

Halogeometricum borinquense Montalvo-Rodríguez et al. 1998 is the type species of the ge-nus, and is of phylogenetic interest because of its distinct location between the halobacterial genera Haloquadratum and Halosarcina. H. borinquense requires extremely high salt (NaCl) concentrations for growth. It can not only grow aerobically but also anaerobically using ni-trate as electron acceptor. The strain described in this report is a free-living, motile, pleomor-phic, euryarchaeon, which was originally isolated from the solar salterns of Cabo Rojo, Puer-to Rico. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the halobacterial genus Halogeometricum, and this 3,944,467 bp long six replicon genome with its 3937 pro-tein-coding and 57 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

Several strains were isolated from subsurface soil of the Atacama Desert and were previously assigned to the Micromonospora genus. A polyphasic study was designed to determine the taxonomic affiliation of isolates 4G51 T , 4G53, and 4G57. All the strains showed chemotaxonomic properties in line with their classification in the genus Micromonospora, including meso-diaminopimelic acid in the cell wall peptidoglycan, MK-9(H 4 ) as major respiratory quinone, iso-C 15:0 and iso-C 16:0 as major fatty acids and diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol as major polar lipids. The 16S rRNA gene sequences of strains 4G51 T , 4G53, and 4G57 showed the highest similarity (97.9 %) with the type strain of Micromonospora costi CS1-12 T , forming an independent branch in the phylogenetic gene tree. Their independent position was confirmed with genome phylogenies, being most closely related to the type strain of Micromonospora kangleipakensis. Digital DNA-DNA hybridization and average nucleotide identity analyses between the isolates and their closest phylogenomic neighbours confirmed that they should be assigned to a new species within the genus Micromonospora for which the name Micromonospora sicca sp. nov. (4G51 T =PCM 3031 T =LMG 30756 T ) is proposed., 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 The Author(s). Published by Elsevier GmbH.. All rights reserved.)

The taxonomic position of strain BMG 8361 T , isolated from sandstone collected in the Sahara Desert of Southern Tunisia, was refined through a polyphasic taxonomic investigation. Colonies of BMG 8361 T were pale-orange coloured, irregular with a dry surface and produced a diffusible pink or brown pigment depending on media. The Gram-positive cells were catalase-positive and oxidase-negative. The strain exhibited growth at 10-40 °C and pH values ranging from 5.5 to 9.0, with optima at 28-35 °C and pH 6.5-8.0. Additionally, BMG 8361 T demonstrated the ability to grow in the presence of up to 1 % NaCl (w/v) concentration. The peptidoglycan of the cell wall contained meso -diaminopimelic acid, glucose, galactose, xylose, ribose, and rhamnose. The predominant menaquinones consisted of MK-9(H 4 ) and MK-9. The main polar lipids were phosphatidylcholine, phosphatidylinositol, glycophosphatidylinositol, diphosphatidylglycerol, phosphatidylethanolamine, and two unidentified lipids. Major cellular fatty acids were iso-C 16 : 0 , iso-C 16 : 1  h, and C 17 : 1  ω 8 c . Phylogenetic analyses based on both the 16S rRNA gene and whole-genome sequences assigned strain BMG 8361 T within the genus Blastococcus . The highest pairwise sequence similarity observed in the 16S rRNA gene was 99.5 % with Blastococcus haudaquaticus AT 7-14 T . However, when considering digital DNA-DNA hybridization and average nucleotide identity, the highest values, 48.4 and 86.58 %, respectively, were obtained with Blastococcus colisei BMG 822 T . These values significantly undershoot the recommended thresholds for establishing new species, corroborating the robust support for the distinctive taxonomic status of strain BMG 8361 T within the genus Blastococcus . In conjunction with the phenotyping results, this compelling evidence leads to the proposal of a novel species we named Blastococcus brunescens sp. nov. with BMG 8361 T (=DSM 46845 T =CECT 8880 T ) as the type strain.

A comprehensive polyphasic investigation was conducted to elucidate the taxonomic position of an actinobacterium, designated BMG 814 T , which was isolated from the historic ruins of Carthage city in Tunisia. It grew as pink-orange pigmented colonies and displayed versatile growth capabilities, thriving within a temperature range of 20-40 °C, across a pH spectrum ranging from pH 5.5 to 10 and in the presence of up to 4 % NaCl. Chemotaxonomic investigations unveiled specific cell components, including diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylinositol, glycophosphatidylinositol, an unidentified aminoglycophospholipid, six unidentified aminolipids, two unidentified phospholipids and one unidentified lipid in its polar lipid profile. Furthermore, galactose, glucose and ribose were identified as the primary cell-wall sugars. Major menaquinones identified were MK-9(H 4 ), MK-9(H 2 ) and MK-9, while major fatty acids comprised iso-C 15 : 0 , iso-C 16 : 0 , C 17 : 1  ω 8 c and C 18 : 1  ω 9 c . Through phylogenetic analysis based on the 16S rRNA gene sequence, the strain was positioned within the genus Blastococcus , with Blastococcus capsiensis BMG 804 T showing the closest relationship (99.1 %). In light of this, draft genomes for both strains, BMG 814 T and BMG 804 T , were sequenced in this study, and comparative analysis revealed that strain BMG 814 T exhibited digital DNA-DNA hybridization and average nucleotide identity values below the recommended thresholds for demarcating new species with all available genomes of type strains of validly names species. Based on the polyphasic taxonomy assessment, strain BMG 814 T (=DSM 46848 T =CECT 8878 T ) was proposed as the type strain of a novel species named Blastococcus carthaginiensis sp. nov.

The Sahara Desert, one of the most extreme ecosystems in the planet, constitutes an unexplored source of microorganisms such as mycelial bacteria. In this study, we investigated the diversity of halophilic actinobacteria in soils collected from five regions of the Algerian Sahara. A total of 23 halophilic actinobacterial strains were isolated by using a humic-vitamin agar medium supplemented with 10% NaCl. The isolated halophilic strains were subjected to taxonomic analysis using a polyphasic approach, which included morphological, chemotaxonomic, physiological (numerical taxonomy), and phylogenetic analyses. The isolates showed abundant growth in CMA (complex medium agar) and TSA (tryptic soy agar) media containing 10% NaCl, and chemotaxonomic characteristics were consistent with their assignment to the genus Nocardiopsis . Analysis of the 16S rRNA sequence of 23 isolates showed five distinct clusters and a similarity level ranging between 98.4% and 99.8% within the Nocardiopsis species. Comparison of their physiological characteristics with the nearest species showed significant differences with the closely related species. Halophilic Nocardiopsis isolated from Algerian Sahara soil represents a distinct phyletic line suggesting a potential new species. Furthermore, the isolated strains of halophilic Nocardiopsis were screened for their antagonistic properties against a broad spectrum of microorganisms by the conventional agar method (agar cylinders method) and found to have the capacity to produce bioactive secondary metabolites. Except one isolate (AH37), all isolated Nocardiopsis showed moderate to high biological activities against Pseudomonas syringae and Salmonella enterica , and some isolates showed activities against Agrobacterium tumefaciens , Serratia marcescens , and Klebsiella pneumoniae . However, no isolates were active against Bacillus subtilis , Aspergillus flavus , or Aspergillus niger . The obtained finding implies that the unexplored extreme environments such as the Sahara contain many new bacterial species as a novel drug source for medical and industrial applications., Competing Interests: The authors declare no competing interests., (Copyright © 2023 Farida Boudjelal et al.)

A nitrogen-fixing actinobacterium strain (Cc1.17 T ) isolated from a root nodule of Colletia cruciata was subjected to polyphasic taxonomic studies. The strain was characterized by the presence of meso -diaminopimelic acid in its peptidoglycan, galactose, glucose, mannose, rhamnose, ribose and xylose as cell-wall sugars, phosphatidylinositol, diphosphatidylglycerol, glycophospholipids, phosphatidylglycerol, glycophospholipid and uncharacterized lipids as its polar lipids, and C 16 : 0 , iso - C 16 : 0 , C 17 : 1 ω9 and C 18 : 1 ω 9 as major fatty acids (>10 %). Strain Cc1.17 T showed 16S rRNA gene sequence similarities of 97.4-99.8 % to validly named Frankia species. Phylogenetic trees based on 16S rRNA gene and genome sequences placed strain Cc1.17 T in a new lineage within the genus Frankia . Digital DNA-DNA hybridization and average nucleotide identity values between strain Cc1.17 T and its closest phylogenomic neighbours were well below the thresholds recommended for prokaryotic species delineation. Therefore, strain Cc1.17 T (=DSM 43829 T =CECT 9313 T ) merits recognition as the type strain of a new species for which the name Frankia colletiae sp. nov. is proposed.

The status of four Frankia strains isolated from a root nodule of Alnus glutinosa was established in a polyphasic study. Taxogenomics and phenotypic features show that the isolates belong to the genus Frankia. All four strains form extensively branched substrate mycelia, multilocular sporangia, vesicles, lack aerial hyphae, but contain meso-diaminopimelic acid as the diamino acid of the peptidoglycan, galactose, glucose, mannose, ribose, xylose and traces of rhamnose as cell wall sugars, iso-C 16:0 as the predominant fatty acid, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol as the major polar lipids, have comparable genome sizes to other cluster 1, Alnus-infective strains with structural and accessory genes associated with nitrogen fixation. The genome sizes of the isolates range from 7.0 to 7.7 Mbp and the digital DNA G + C contents from 71.3 to 71.5 %. The four sequenced genomes are rich in biosynthetic gene clusters predicted to express for novel specialized metabolites, notably antibiotics. 16S rRNA gene and whole genome sequence analyses show that the isolates fall into two lineages that are closely related to the type strains of Frankia alni and Frankia torreyi. All of these taxa are separated by combinations of phenotypic properties and by digital DNA:DNA hybridization scores which indicate that they belong to different genomic species. Based on these results, it is proposed that isolates Agncl-4 T and Agncl-10, and Agncl-8 T and Agncl-18, be recognised as Frankia gtarii sp. nov. and Frankia tisai sp. nov. respectively, with isolates Agncl-4 T (=DSM 107976 T  = CECT 9711 T ) and Agncl-8 T (=DSM 107980 T  = CECT 9715 T ) as the respective type strains., (Crown Copyright © 2022. Published by Elsevier GmbH. All rights reserved.)

The phylum Actinobacteria includes important human pathogens like Mycobacterium tuberculosis and Corynebacterium diphtheriae and renowned producers of secondary metabolites of commercial interest, yet only a small part of its diversity is represented by sequenced genomes. Here, we present 824 actinobacterial isolate genomes in the context of a phylum-wide analysis of 6,700 genomes including public isolates and metagenome-assembled genomes (MAGs). We estimate that only 30%-50% of projected actinobacterial phylogenetic diversity possesses genomic representation via isolates and MAGs. A comparison of gene functions reveals novel determinants of host-microbe interaction as well as environment-specific adaptations such as potential antimicrobial peptides. We identify plasmids and prophages across isolates and uncover extensive prophage diversity structured mainly by host taxonomy. Analysis of >80,000 biosynthetic gene clusters reveals that horizontal gene transfer and gene loss shape secondary metabolite repertoire across taxa. Our observations illustrate the essential role of and need for high-quality isolate genome sequences., Competing Interests: The authors declare no competing financial interests., (© 2022 The Authors.)

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 CO 2 fixation pathways and a battery of enzymes able to degrade complex carbohydrates were also identified in Blastococcus genomes., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Montero-Calasanz, Yaramis, Rohde, Schumann, Klenk and Meier-Kolthoff.)

A genome led phylophasic study was designed to determine the taxonomic status of a strain, DSM 45956, recovered from a Saharan desert soil. A wealth of taxonomic data, including average nucleotide identity and DNA:DNA hybridization (DDH) values, showed that the isolate and the type strains of Actinopolyspora lacussalsi and Actinopolyspora righensis belong to the same species. Consequently, it is proposed that A. righensis is a heterotypic synonym of A. lacussalsi. Similarly, DDH values and associated phenotypic data show that A. lacussalsi contains two subspecies, A. lacussalsi subsp. lacussalsi and A. lacussalsi subsp. righensis which includes isolate DSM 45956., (© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

A novel Gram-negative, facultative anaerobic, rod-shaped, and non-motile bacterium with bio-degradation potential of polycyclic aromatic hydrocarbons (PAHs) and uranium bio-reduction, designated as RCRI7 T , was isolated from Qurugöl Lake water near Tabriz city. Strain RCRI7 T can grow in the absence of NaCl and tolerates up to 3% NaCl (optimum, 0-0.5%), at the temperature range of 4-45 °C (optimum, 30 °C) and a pH range of 6-9 (optimum, pH 7 ± 0.5). Results of phylogenetic analysis based on 16S rRNA gene sequence indicated that strain RCRI7 T is affiliated with the genus Shewanella, most closely related to Shewanella xiamenensis S4 T (99.1%) and Shewanella putrefaciens JCM 20190 T (98.9%). The genomic DNA G+C content of strain RCRI7 T is 41 mol%. The major fatty acids are C 16:1 ω9c, C 18:1 ω9c and iso-C 17:1 ω5c. The OrthoANI and ANIb values between RCRI7 T and Shewanella xiamenensis S4 T were 87.4% and 87.7%, and between RCRI7 T and Shewanella putrefaciens JCM 20190 T were 79.5% and 79.7%, respectively. Strain RCRI7 T displayed dDDH values of 30.2% and 39.8% to Shewanella xiamenensis S4 T and Shewanella putrefaciens JCM 20190 T , respectively. The major polar lipids include phosphatidylglycerol (PG) and phosphatidylethanolamine (PE). The respiratory quinone is Q8. Based on the polyphasic evidence presented in this paper, strain RCRI7 T is considered to represent a novel species, with bioremediation potential, in the genus Shewanella, for which the name Shewanella azerbaijanica sp. nov. is proposed. The type strain is RCRI7 T (= JCM 17276 T ) (= KCTC 62476 T )., (© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

A new actinobacterium strain, designated BMG 823 T , was isolated from a limestone sample collected in Tunisia. Its taxonomic position was scrutinized using a polyphasic approach. Colonies of strain BMG 823 T were pink orange-coloured, regular and had a moist surface. Cells are Gram-stain-positive, catalase-negative and oxidase-negative. The strain grew at pH 5.5-9, 10-40 °C and in presence of up to 4 % NaCl (w/v). Chemotaxonomically, strain BMG 823 T was characterized by cell-wall type III containing meso -diaminopimelic acid as diamino acid, glucose, ribose and rhamnose as whole-cell sugars, MK-9(H 4 ) as predominant menaquinone, and phosphatidylcholine, diphosphadidylglycerol, phosphatidethanolamine, phosphatidylcholine, phosphatidylinositol, unidentified glycolipid, unidentified aminophospholipids and unidentified glycophospholipid as major polar lipids. The fatty acid profile consisted of iso-C 16 : 0 and iso-C 17 : 1  ω 9. Phylogenetic trees based on 16S rRNA gene and genome sequences placed strain BMG 823 T within the genus Blastococcus and separated it from all type strains of validly published species. Comparison of 16S rRNA gene sequence similarity, digital DNA-DNA hybridization and average nucleotide identity indicated that strain BMG 823 T was most closely related to Blastococcus litoris DSM 106127 T and Blastococcus colisei BMG 822 T with pairwise values well below the species differentiation thresholds. The distinct phenotypic and genotypic features of strain BMG 823 T (=DSM 46838 T =CECT 8881 T ) within the genus Blastococcus warrant its recognition as the type strain for the new species for which we propose the name Blastococcus tunisiensis sp. nov.

Advanced physicochemical and chemical absorption methods for chlorinated ethenes are feasible but incur high costs and leave traces of pollutants on the site. Biodegradation of such pollutants by anaerobic or aerobic bacteria is emerging as a potential alternative. Several mycobacteria including Mycolicibacterium aurum L1, Mycolicibacterium chubuense NBB4, Mycolicibacterium rhodesiae JS60, Mycolicibacterium rhodesiae NBB3 and Mycolicibacterium smegmatis JS623 have previously been described as assimilators of vinyl chloride (VC). In this study, we compared nucleotide sequence of VC cluster and performed a taxogenomic evaluation of these mycobacterial species. The results showed that the complete VC cluster was acquired by horizontal gene transfer and not intrinsic to the genus Mycobacterium sensu lato . These results also revealed the presence of an additional xcb F1 gene that seems to be involved in Coenzyme M biosynthesis, which is ultimately used in the VC degradation pathway. Furthermore, we suggest for the first time that S/N-Oxide reductase encoding gene was involved in the dissociation of the SsuABC transporters from the organosulfur, which play a crucial role in the Coenzyme M biosynthesis. Based on genomic data, M. aurum L1, M. chubuense NBB4 , M. rhodesiae JS60, M. rhodesiae NBB3 and M. smegmatis JS623 were misclassified and form a novel species within the genus Mycobacterium sensu lato . Mycolicibacterium aurum L1 T (CECT 8761 T  = DSM 6695 T ) was the subject of polyphasic taxonomic studies and showed ANI and dDDH values of 84.7 and 28.5% with its close phylogenetic neighbour, M. sphagni ATCC 33027 T . Phenotypic, chemotaxonomic and genomic data considering strain L1 T (CECT 8761 T  = DSM 6695 T ) as a type strain of novel species with the proposed name, Mycolicibacterium vinylchloridicum sp. nov., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Cortés-Albayay, Sangal, Klenk and Nouioui.)

A novel hyperthermophilic archaeon, termed strain T7324 T , was isolated from a mixed sulfate-reducing consortium recovered from hot water produced from a deep North Sea oil reservoir. The isolate is a strict anaerobic chemo-organotroph able to utilize yeast extract or starch as a carbon source. The genes for a number of sugar degradation enzymes and glutamate dehydrogenase previously attributed to the sulfate reducing strain of the consortium ( Archaeoglobus fulgidus strain 7324) were identified in the nearly completed genome sequence. Sequence analysis of the 16S rRNA gene placed the strain in the Thermococcus genus, but with an average nucleotide identity that is less than 90% to its closest relatives. Phylogenomic treeing reconstructions placed the strain on a distinct lineage clearly separated from other Thermococcus spp. The results indicate that the strain T7324 T represents a novel species, for which the name Thermococcus bergensis sp. nov. is proposed. The type strain is T7324 T (=DSM 27149 T = KCTC 15808 T ).

Here, we present the draft genome sequence of Bordetella sp. strain FB-8, a mixotrophic iron-oxidizing bacterium isolated from creek sediment in the former uranium-mining district of Ronneburg, Germany. To date, iron oxidation has not been reported in Bordetella species, indicating that FB-8 may be an environmentally important Bordetella sp.

A new strain belonging to the genus Kocuria, designed PT10, was isolated from irradiated roots of the xerophyte Panicum turgidum. Isolate PT10 is a Gram-positive, coccoid, aerobic and ionizing-radiation (IR)-resistant actinobacterium. PT10 has shown an ability to survive under extreme conditions, such as gamma irradiation, desiccation and high concentration of hydrogen peroxide. Phenotypic, chemotaxonomic and comparative genome analyses support the assignment of strain PT10 (LMG 31102 = DSM 108617) as Kocuria rhizophila. The complete genome sequence of PT10 consists of one chromosome (2,656,287 bps), with a 70.7% G + C content and comprises 2481 protein-coding sequences. A total of 1487 proteins were identified by LC-MS/MS profiling. In silico analyses revealed that the proteome of the oxidation-tolerant PT10 possesses several features explaining its IR-resistant phenotype and many adaptive pathways implicated in response to environmental pressures - desiccation, cold, reactive oxygen species and other stressors., (Copyright © 2020 Elsevier Inc. All rights reserved.)

A novel strain of the genus Promicromonospora, designated PT9 T , was recovered from irradiated roots of the xerophyte Panicum turgidum collected from the Ksar Ghilane oasis in southern Tunisia. Strain PT9 T is aerobic, non-spore-forming, Gram- positive actinomycete that produces branched hyphae and forms white to yellowish-white colonies. Chemotaxonomic features, including fatty acids, whole cell sugars and polar lipid profiles, support the assignment of PT9 T to the genus Promicromonospora. The genomic relatedness indexes based on DNA-DNA hybridization and average nucleotide identity values revealed a significant genomic divergence between strain PT9 T and all sequenced type strains of the taxon. Phylogenomic analysis showed that isolate PT9 T was most closely related to Promicromonospora soli CGMCC 4.7398 T . Phenotypic and phylogenomic analyses suggest that isolate PT9 T represents a novel species of the genus Promicromonospora, for which the name Promicromonospora panici sp. nov. is proposed. The type strain is PT9 T (LMG 31103 T  = DSM 108613 T ).The isolate PT9 T is an ionizing-radiation-resistant actinobacterium (D 10 value = 2.6 kGy), with resistance to desiccation and hydrogen peroxide. The complete genome sequence of PT9 T consists of 6,582,650 bps with 71.2% G+C content and 6291 protein-coding sequences. This genome will help to decipher the microbial genetic bases for ionizing-radiation resistance mechanisms including the response to oxidative stress.

Natural attenuation of heavy metals occurs via coupled microbial iron cycling and metal precipitation in creeks impacted by acid mine drainage (AMD). Here, we describe the isolation, characterization, and genomic sequencing of two iron-oxidizing bacteria (FeOB) species: Thiomonas ferrovorans FB-6 and Thiomonas metallidurans FB-Cd, isolated from slightly acidic (pH 6.3), Fe-rich, AMD-impacted creek sediments. These strains precipitated amorphous iron oxides, lepidocrocite, goethite, and magnetite or maghemite and grew at a pH optimum of 5.5. While Thiomonas spp. are known as mixotrophic sulfur oxidizers and As oxidizers, the FB strains oxidized Fe, which suggests they can efficiently remove Fe and other metals via coprecipitation. Previous evidence for Thiomonas sp. Fe oxidation is largely ambiguous, possibly because of difficulty demonstrating Fe oxidation in heterotrophic/mixotrophic organisms. Therefore, we also conducted a genomic analysis to identify genetic mechanisms of Fe oxidation, other metal transformations, and additional adaptations, comparing the two FB strain genomes with 12 other Thiomonas genomes. The FB strains fall within a relatively novel group of Thiomonas strains that includes another strain (b6) with solid evidence of Fe oxidation. Most Thiomonas isolates, including the FB strains, have the putative iron oxidation gene cyc2 , but only the two FB strains possess the putative Fe oxidase genes mtoAB The two FB strain genomes contain the highest numbers of strain-specific gene clusters, greatly increasing the known Thiomonas genetic potential. Our results revealed that the FB strains are two distinct novel species of Thiomonas with the genetic potential for bioremediation of AMD via iron oxidation. IMPORTANCE As AMD moves through the environment, it impacts aquatic ecosystems, but at the same time, these ecosystems can naturally attenuate contaminated waters via acid neutralization and catalyzing metal precipitation. This is the case in the former Ronneburg uranium-mining district, where AMD impacts creek sediments. We isolated and characterized two iron-oxidizing Thiomonas species that are mildly acidophilic to neutrophilic and that have two genetic pathways for iron oxidation. These Thiomonas species are well positioned to naturally attenuate AMD as it discharges across the landscape., (Copyright © 2020 American Society for Microbiology.)

Strains 335427 T and 234509 T , isolated from two 76-year-old patients with chronic pulmonary diseases, were the subject of polyphasic taxonomic studies and comparative genomic analyses for virulence factors. The 16 rRNA gene sequence similarity between strains 335427 T and 234509 T and their closest phylogenetic neighbors Nocardia asiatica NBRC 100129 T and Nocardia abscessus NBRC 100374 T were 99.5% and 100%, respectively. Digital DNA-DNA hybridization values between the aforementioned studied strains were well below the 70% threshold for assigning prokaryotic strains to a novel species. Strains 335427 T and 234509 T have genome sizes of 8.49 Mpb and 8.07 Mpb, respectively, with G + C content of 68.5%. Isolate 335427 T has C 16:0 , C 18:1 ω 9 c, C 18:0 and C 18:0 10 methyl as major fatty acids (>15%) and mycolic acids formed of 52-54 carbon atoms. However, only C 18:1 ω 9 c was detected for isolate 234509 T , which had mycolic acids with 44-56 carbon. Based on phenotypic and genetic data, strains 335427 T (DSM 109819 T = CECT 9924 T ) and 234509 T (DSM 111366 T = CECT 30129 T ) merit recognition as novel species, which are named Nocardia barduliensis sp. nov. and Nocardia gipuzkoensis sp. nov., respectively. All the strains studied had homologous VF-associated genes to those described in M. tuberculosis , including experimentally verified virulence genes in humans related to tuberculosis. The nar GHIJ (nitrate reduction pathway) and gvp AFGOJLMK (gas vesicles) genetic maps of strains 335427 T , 234509 T , NBRC 100129 T and NBRC 100374 T showed the same syntenic block and raise the question of whether their functions are interlinked during the infection of the human host. However, further research is required to decipher the role of the gas vesicle in the pathogenicity mechanism of Nocardia spp.

A polyphasic study was undertaken to establish the position of a Streptomyces strain, isolate PRKS01-65 T , recovered from sand dune soil collected at Parangkusumo, Yogyakarta Province, Java, Indonesia. A combination of chemotaxonomic, cultural and morphological properties confirmed its position in the genus of Streptomyces . Comparative 16S rRNA gene sequence analyses showed that the isolate was most closely related to Streptomyces leeuwenhoekii C34 T (99.9 % similarity) and loosely associated with the type strains of Streptomyces chiangmaiensis (98.7 % similarity) and Streptomyces glomeratus (98.9 % similarity). Multilocus sequence analyses based on five conserved housekeeping gene alleles confirmed the close relationship between the isolate and S. leeuwenhoekii C34 T , although both strains belonged to a well-supported clade that encompassed the type strains of S. glomeratus , Streptomyces griseomycini , Streptomyces griseostramineus , Streptomyces labedae , Streptomyces lomondensis and Streptomyces spinoverrucosus . A comparison of the draft genome sequence generated for the isolate with corresponding whole genome sequences of its closest phylogenomic neighbours showed that it formed a well-separated lineage with S. leeuwenhoekii C34 T . These strains can also be distinguished using a combination of phenotypic properties and by average nucleotide identity and digital DNA-DNA hybridization similarities of 94.3 and 56 %, values consistent with their classification in different species. Based on this wealth of data it is proposed that isolate PRKS01-65 T (=NCIMB 15211 T =CCMM B1302 T =ICEBB-03 T ) be classified as Streptomyces harenosi sp. nov. The genome of the isolate contains several biosynthetic gene clusters with the potential to produce new natural products.

The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as 'type material', thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity.

A novel actinobacterial strain, designated NA12 T , was isolated from coastal sediment sample of Nemrut Lake, a crater lake in eastern Anatolia, Turkey. The taxonomic position of the strain was established using a polyphasic approach. Cultural and chemotaxonomic characteristics of the strain were consistent with its classification within the family Micromonosporaceae. The 16S rRNA gene sequence analysis of strain NA12 T showed that the strain closely related to M. radicis AZ1-13 T , M. zingiberis PLAI 1-1 T , M. craniella LHW63014 T and M. endophytica 202201 T with pairwise sequence identity values ranging from 99.4 to 99.3%. Digital DNA-DNA hybridization values between strain NA12 T and the closely related type strains were ranged from 41.0 to 18.3% while the average nucleotide identity values were between 87.3 and 86.5%, which are well below the designed cut-off points of 70 and 95%, respectively. The G + C content of genomic DNA was 71.5%. Whole-cell hydrolysates of strain NA12 T contained 3-hydroxydiaminopimelic acid and meso-diaminopimelic acid. Cell-wall sugars were composed of arabinose, fucose, glucose, mannose, rhamnose and xylose. The polar lipid profile contained phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol, phosphatidylglycerol, glycophospholipid, amino-phospholipid and two unidentified phospholipids. The predominant menaquinones were MK-9(H 6 ) and MK-9(H 4 ). Major fatty acids were iso-C 16:0 and C 17:1 ω8c. Based upon the consensus of phenotypic and phylogenetic analyses as well as whole genome comparisons, strain NA12 T (DSM 100982 T  = KCTC 39647 T ) is proposed to represent the type strain of a novel species, Micromonospora craterilacus sp. nov.

Strain RA15 T was isolated from the rhizosphere of the halophyte plant Arthrocnemum macrostachyum growing in the Odiel marshes (Huelva, Spain). RA15 T cells were Gram stain-negative, non-spore-forming, aerobic rods and formed cream-coloured, opaque, mucoid, viscous, convex, irregular colonies with an undulate margin. Optimal growth conditions were observed on tryptic soy agar (TSA) plates supplemented with 2.5 % NaCl (w/v) at pH 7.0 and 28 °C, although it was able to grow at 4-32 °C and at pH values of 5.0-9.0. The NaCl tolerance range was from 0 to 15 %. The major respiratory quinone was Q8 but Q9 was also present. The most abundant fatty acids were summed feature 3 (C 16 : 1   ω7 c and/or C 16 : 1   ω6 c ), C 17 : 1  ω 8 c and C 16 : 0 . The polar lipids profile comprised phosphatidylglycerol and phosphatidylethanolamine as the most abundant representatives. Phylogenetic analyses confirmed the well-supported affiliation of strain RA15 T within the genus Pseudoalteromonas , close to the type strains of Pseudoalteromonas neustonica , Pseudoalteromonas prydzensis and Pseudoalteromonas mariniglutinosa . Results of comparative phylogenetic and phenotypic studies between strain RA15 T and its closest related species suggest that RA15 T could be a new representative of the genus Pseudoalteromonas , for which the name Pseudoalteromonas rhizosphaerae sp. nov. is proposed. The type strain is RA15 T (=CECT 9079 T =LMG 29860 T ). The whole genome has 5.3 Mb and the G+C content is 40.4 mol%.