Publications by authors named "Hans-Peter Klenk"

487 Publications

Draft Genome Sequence of sp. Strain FB-8, Isolated from a Former Uranium Mining Area in Germany.

Microbiol Resour Announc 2021 Apr 8;10(14). Epub 2021 Apr 8.

Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany.

Here, we present the draft genome sequence of 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 species, indicating that FB-8 may be an environmentally important sp.
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http://dx.doi.org/10.1128/MRA.01035-19DOI Listing
April 2021

Ionizing-radiation-resistant Kocuria rhizophila PT10 isolated from the Tunisian Sahara xerophyte Panicum turgidum: Polyphasic characterization and proteogenomic arsenal.

Genomics 2021 Jan 3;113(1 Pt 1):317-330. Epub 2020 Dec 3.

Laboratory ″Energy and Matter for Development of Nuclear Sciences″ (LR16CNSTN02), National Center for Nuclear Sciences and Technology, Sidi Thabet Technopark, 2020, Tunisia; Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020, Ariana, Tunisia. Electronic address:

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.
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http://dx.doi.org/10.1016/j.ygeno.2020.11.029DOI Listing
January 2021

Draft genome sequence of Promicromonospora panici sp. nov., a novel ionizing-radiation-resistant actinobacterium isolated from roots of the desert plant Panicum turgidum.

Extremophiles 2021 Jan 26;25(1):25-38. Epub 2020 Oct 26.

Université de Lyon, Université Lyon 1, Lyon, France.

A novel strain of the genus Promicromonospora, designated PT9, was recovered from irradiated roots of the xerophyte Panicum turgidum collected from the Ksar Ghilane oasis in southern Tunisia. Strain PT9 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 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 and all sequenced type strains of the taxon. Phylogenomic analysis showed that isolate PT9 was most closely related to Promicromonospora soli CGMCC 4.7398. Phenotypic and phylogenomic analyses suggest that isolate PT9 represents a novel species of the genus Promicromonospora, for which the name Promicromonospora panici sp. nov. is proposed. The type strain is PT9 (LMG 31103 = DSM 108613).The isolate PT9 is an ionizing-radiation-resistant actinobacterium (D value = 2.6 kGy), with resistance to desiccation and hydrogen peroxide. The complete genome sequence of PT9 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.
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http://dx.doi.org/10.1007/s00792-020-01207-8DOI Listing
January 2021

Genomic Virulence Features of Two Novel Species sp. nov. and sp. nov., Isolated from Patients with Chronic Pulmonary Diseases.

Microorganisms 2020 Oct 1;8(10). Epub 2020 Oct 1.

Biodonostia, Infectious Diseases Area, Respiratory Infection and Antimicrobial Resistance Group; Osakidetza Basque Health Service, Donostialdea Integrated Health Organisation, Microbiology Department, 20014 San Sebastian, Spain.

Strains 335427 and 234509, 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 and 234509 and their closest phylogenetic neighbors NBRC 100129 and NBRC 100374 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 and 234509 have genome sizes of 8.49 Mpb and 8.07 Mpb, respectively, with G + C content of 68.5%. Isolate 335427 has C, C ωc, C and C 10 methyl as major fatty acids (>15%) and mycolic acids formed of 52-54 carbon atoms. However, only C ωc was detected for isolate 234509, which had mycolic acids with 44-56 carbon. Based on phenotypic and genetic data, strains 335427 (DSM 109819 = CECT 9924) and 234509 (DSM 111366 = CECT 30129) merit recognition as novel species, which are named sp. nov. and sp. nov., respectively. All the strains studied had homologous VF-associated genes to those described in , including experimentally verified virulence genes in humans related to tuberculosis. The GHIJ (nitrate reduction pathway) and AFGOJLMK (gas vesicles) genetic maps of strains 335427, 234509, NBRC 100129 and NBRC 100374 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 spp.
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http://dx.doi.org/10.3390/microorganisms8101517DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7600791PMC
October 2020

Mixotrophic Iron-Oxidizing Isolates from an Acid Mine Drainage-Affected Creek.

Appl Environ Microbiol 2020 11 24;86(24). Epub 2020 Nov 24.

Department of Biological Sciences, University of Delaware, Newark, Delaware, USA

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: FB-6 and 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 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 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 genomes. The FB strains fall within a relatively novel group of strains that includes another strain (b6) with solid evidence of Fe oxidation. Most isolates, including the FB strains, have the putative iron oxidation gene , but only the two FB strains possess the putative Fe oxidase genes The two FB strain genomes contain the highest numbers of strain-specific gene clusters, greatly increasing the known genetic potential. Our results revealed that the FB strains are two distinct novel species of with the genetic potential for bioremediation of AMD via iron oxidation. 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 species that are mildly acidophilic to neutrophilic and that have two genetic pathways for iron oxidation. These species are well positioned to naturally attenuate AMD as it discharges across the landscape.
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http://dx.doi.org/10.1128/AEM.01424-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7688216PMC
November 2020

High-quality draft genome sequences of DSM 14164, DSM 17497, DSM 15088, DSM 21245 and DSM 16006: taxonomic considerations.

Access Microbiol 2019 29;1(10):e000067. Epub 2019 Oct 29.

Department of Biology-Microbiology, Universitat de les Illes Balears, Palma de, Mallorca, Spain.

is the bacterial genus of Gram-negative bacteria with the highest number of recognized species. It is divided phylogenetically into three lineages and at least 11 groups of species. The group of species is one of the most versatile and best studied. It comprises 15 species with validly published names. As a part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) project, we present the genome sequences of the type strains of five species included in this group: (DSM 14164), (DSM 17497), (DSM 15088) (DSM 21245) and (DSM 16006). These strains represent species of environmental and also of clinical interest due to their pathogenic properties against humans and animals. Some strains of these species promote plant growth or act as plant pathogens. Their genome sizes are among the largest in the group, ranging from 5.3 to 6.3 Mbp. In addition, the genome sequences of the type strains in the taxonomy were analysed via genome-wide taxonomic comparisons of ANIb, gANI and GGDC values among 130 strains classified within the group. The results demonstrate that at least 36 genomic species can be delineated within the phylogenetic group of species.
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http://dx.doi.org/10.1099/acmi.0.000067DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7491935PMC
October 2019

sp. nov., a home for a gifted strain isolated from Indonesian sand dune soil.

Int J Syst Evol Microbiol 2020 Sep;70(9):4874-4882

School of Natural and Environmental Sciences, Ridley Building 2, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.

A polyphasic study was undertaken to establish the position of a strain, isolate PRKS01-65, 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 . Comparative 16S rRNA gene sequence analyses showed that the isolate was most closely related to C34 (99.9 % similarity) and loosely associated with the type strains of (98.7 % similarity) and (98.9 % similarity). Multilocus sequence analyses based on five conserved housekeeping gene alleles confirmed the close relationship between the isolate and C34, although both strains belonged to a well-supported clade that encompassed the type strains of , , , , and . 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 C34. 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 (=NCIMB 15211=CCMM B1302=ICEBB-03) be classified as sp. nov. The genome of the isolate contains several biosynthetic gene clusters with the potential to produce new natural products.
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http://dx.doi.org/10.1099/ijsem.0.004346DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7656270PMC
September 2020

Roadmap for naming uncultivated Archaea and Bacteria.

Nat Microbiol 2020 08 8;5(8):987-994. Epub 2020 Jun 8.

Biology Department, Portland State University, Portland, OR, USA.

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.
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http://dx.doi.org/10.1038/s41564-020-0733-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7381421PMC
August 2020

sp. nov. a novel plant growth-promoting bacterium with potential use in phytoremediation.

Int J Syst Evol Microbiol 2020 May;70(5):3287-3294

School of Natural and Environmental Sciences (SNES), Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.

Strain RA15 was isolated from the rhizosphere of the halophyte plant growing in the Odiel marshes (Huelva, Spain). RA15 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 (Cω7 and/or Cω6), C8 and C. The polar lipids profile comprised phosphatidylglycerol and phosphatidylethanolamine as the most abundant representatives. Phylogenetic analyses confirmed the well-supported affiliation of strain RA15 within the genus , close to the type strains of , and . Results of comparative phylogenetic and phenotypic studies between strain RA15 and its closest related species suggest that RA15 could be a new representative of the genus , for which the name sp. nov. is proposed. The type strain is RA15 (=CECT 9079=LMG 29860). The whole genome has 5.3 Mb and the G+C content is 40.4 mol%.
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http://dx.doi.org/10.1099/ijsem.0.004167DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7395622PMC
May 2020

Genome-based classification of Micromonospora craterilacus sp. nov., a novel actinobacterium isolated from Nemrut Lake.

Antonie Van Leeuwenhoek 2020 Jun 14;113(6):791-801. Epub 2020 Feb 14.

Department of Biology, Faculty of Science and Arts, Ondokuz Mayis University, Samsun, Turkey.

A novel actinobacterial strain, designated NA12, 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 showed that the strain closely related to M. radicis AZ1-13, M. zingiberis PLAI 1-1, M. craniella LHW63014 and M. endophytica 202201 with pairwise sequence identity values ranging from 99.4 to 99.3%. Digital DNA-DNA hybridization values between strain NA12 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 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) and MK-9(H). Major fatty acids were iso-C and Cω8c. Based upon the consensus of phenotypic and phylogenetic analyses as well as whole genome comparisons, strain NA12 (DSM 100982 = KCTC 39647) is proposed to represent the type strain of a novel species, Micromonospora craterilacus sp. nov.
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http://dx.doi.org/10.1007/s10482-020-01390-wDOI Listing
June 2020

Genome-guided analysis allows the identification of novel physiological traits in Trichococcus species.

BMC Genomics 2020 Jan 8;21(1):24. Epub 2020 Jan 8.

Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708, WE, Wageningen, The Netherlands.

Background: The genus Trichococcus currently contains nine species: T. flocculiformis, T. pasteurii, T. palustris, T. collinsii, T. patagoniensis, T. ilyis, T. paludicola, T. alkaliphilus, and T. shcherbakoviae. In general, Trichococcus species can degrade a wide range of carbohydrates. However, only T. pasteurii and a non-characterized strain of Trichococcus, strain ES5, have the capacity of converting glycerol to mainly 1,3-propanediol. Comparative genomic analysis of Trichococcus species provides the opportunity to further explore the physiological potential and uncover novel properties of this genus.

Results: In this study, a genotype-phenotype comparative analysis of Trichococcus strains was performed. The genome of Trichococcus strain ES5 was sequenced and included in the comparison with the other nine type strains. Genes encoding functions related to e.g. the utilization of different carbon sources (glycerol, arabinan and alginate), antibiotic resistance, tolerance to low temperature and osmoregulation could be identified in all the sequences analysed. T. pasteurii and Trichococcus strain ES5 contain a operon with genes encoding necessary enzymes for 1,3-PDO production from glycerol. All the analysed genomes comprise genes encoding for cold shock domains, but only five of the Trichococcus species can grow at 0 °C. Protein domains associated to osmoregulation mechanisms are encoded in the genomes of all Trichococcus species, except in T. palustris, which had a lower resistance to salinity than the other nine studied Trichococcus strains.

Conclusions: Genome analysis and comparison of ten Trichococcus strains allowed the identification of physiological traits related to substrate utilization and environmental stress resistance (e.g. to cold and salinity). Some substrates were used by single species, e.g. alginate by T. collinsii and arabinan by T. alkaliphilus. Strain ES5 may represent a subspecies of Trichococcus flocculiformis and contrary to the type strain (DSM 2094), is able to grow on glycerol with the production of 1,3-propanediol.
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http://dx.doi.org/10.1186/s12864-019-6410-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6950789PMC
January 2020

Genome analysis of the marine bacterium Kiloniella laminariae and first insights into comparative genomics with related Kiloniella species.

Arch Microbiol 2020 May 16;202(4):815-824. Epub 2019 Dec 16.

GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Marine Symbioses, Düsternbrooker Weg 20, 24105, Kiel, Germany.

Kiloniella laminariae is a true marine bacterium and the first member of the family and order, the Kiloniellaceae and Kiloniellales. K. laminariae LD81 (= DSM 19542) was isolated from the marine macroalga Saccharina latissima and is a mesophilic, typical marine chemoheterotrophic aerobic bacterium with antifungal activity. Phylogenetic analysis of 16S rRNA gene sequence revealed the similarity of K. laminariae LD81 not only with three validly described species of the genus Kiloniella, but also with undescribed isolates and clone sequences from marine samples in the range of 93.6-96.7%. We report on the analysis of the draft genome of this alphaproteobacterium and describe some selected features. The 4.4 Mb genome has a G + C content of 51.4%, contains 4213 coding sequences including 51 RNA genes as well as 4162 protein-coding genes, and is a part of the Genomic Encyclopaedia of Bacteria and Archaea (GEBA) project. The genome provides insights into a number of metabolic properties, such as carbon and sulfur metabolism, and indicates the potential for denitrification and the biosynthesis of secondary metabolites. Comparative genome analysis was performed with K. laminariae LD81 and the animal-associated species Kiloniella majae M56.1 from a spider crab, Kiloniella spongiae MEBiC09566 from a sponge as well as Kiloniella litopenai P1-1 from a white shrimp, which all inhabit quite different marine habitats. The analysis revealed that the K. laminariae LD81 contains 1397 unique genes, more than twice the amount of the other species. Unique among others is a mixed PKS/NRPS biosynthetic gene cluster with similarity to the biosynthetic gene cluster responsible for the production of syringomycin.
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http://dx.doi.org/10.1007/s00203-019-01791-0DOI Listing
May 2020

Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies.

Sci Data 2019 11 26;6(1):285. Epub 2019 Nov 26.

DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA.

Metagenomic sequence data from defined mock communities is crucial for the assessment of sequencing platform performance and downstream analyses, including assembly, binning and taxonomic assignment. We report a comparison of shotgun metagenome sequencing and assembly metrics of a defined microbial mock community using the Oxford Nanopore Technologies (ONT) MinION, PacBio and Illumina sequencing platforms. Our synthetic microbial community BMock12 consists of 12 bacterial strains with genome sizes spanning 3.2-7.2 Mbp, 40-73% GC content, and 1.5-7.3% repeats. Size selection of both PacBio and ONT sequencing libraries prior to sequencing was essential to yield comparable relative abundances of organisms among all sequencing technologies. While the Illumina-based metagenome assembly yielded good coverage with few misassemblies, contiguity was greatly improved by both, Illumina + ONT and Illumina + PacBio hybrid assemblies but increased misassemblies, most notably in genomes with high sequence similarity to each other. Our resulting datasets allow evaluation and benchmarking of bioinformatics software on Illumina, PacBio and ONT platforms in parallel.
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http://dx.doi.org/10.1038/s41597-019-0287-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6879543PMC
November 2019

Pseudomonas khazarica sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from Khazar Sea sediments.

Antonie Van Leeuwenhoek 2020 Apr 25;113(4):521-532. Epub 2019 Nov 25.

Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran.

A novel Gram-negative, aerobic, motile and rod-shaped bacterium with the potential to biodegrade polycyclic aromatic hydrocarbons, was isolated from Khazar (Caspian) Sea. Strain TBZ2 grows in the absence of NaCl and tolerates up to 8.5% NaCl. Growth occurred at pH 3.0-10.0 (optimum, pH 6.0-7.0) and 10-45 °C (optimum, 30 °C). The major fatty acids are Cω7C, Cω7C/ C iso 2-OH, C, C C 3-OH, C 3-OH. The major polar lipids include diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and the predominant respiratory quinone is ubiquinone Q-9. The 16S rRNA gene sequence analysis showed that strain TBZ2 is a member of the genus Pseudomonas with the highest similarity to P. oleovorans subsp. oleovorans DSM 1045 (98.83%), P. mendocina NBRC 14162 (98.63%), P. oleovorans subsp. lubricantis RS1 (98.61%) and P. alcaliphila JCM 10630 (98.49%) based on EzBioCloud server. Phylogenetic analyses using housekeeping genes (16S rRNA, rpoD, gyrB and rpoB) and genome sequences demonstrated that the strain TBZ2 formed a distinct branch closely related to the type strains of P. mendocina and P. guguanensis. Digital DNA-DNA hybridisation and average nucleotide identity values between strain TBZ2 and its closest relatives, P. mendocina NBRC 14162 (25.3%, 81.5%) and P. guguanensis JCM 18146 (26.8%, 79.0%), rate well below the designed threshold for assigning prokaryotic strains to the same species. On the basis of phenotypic, chemotaxonomic, genomic and phylogenetic results, it is recommended that strain TBZ2 is a novel species of the genus Pseudomonas, for which the name Pseudomonas khazarica sp. nov., is proposed. The type strain is TBZ2 (= LMG 29674 = KCTC 52410).
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http://dx.doi.org/10.1007/s10482-019-01361-wDOI Listing
April 2020

Polyphasic classification of strains isolated from the Karakum Desert and description of sp. nov., sp. nov., sp. nov. and sp. nov.

Int J Syst Evol Microbiol 2020 Jan;70(1):636-647

Department of Molecular Biology and Genetics, Faculty of Sciences and Arts, Ondokuz Mayis University, 55139, Samsun, Turkey.

Five actinobacteria isolates, KC201, KC401, KC310, KC712 and 6K102, were recovered from the Karakum Desert during an investigation of novel actinobacteria with biotechnological potential. A polyphasic approach confirmed the affiliation of the strains to the genus . The strains showed chemotaxonomic and morphological properties consistent with their classification in the genus . Furthermore, these strains clearly distinguished and formed well supperted clades in phylogenetic and phylogenomic trees. Low ANI and dDDH values and distinguishing phenotypic properties between isolates KC201, KC310, KC712 and 6K102 showed that these strains belonged to novel species, the names proposed for these taxa are sp. nov., sp. nov., sp. nov. and sp. nov., with the type strains KC310 (=CGMCC 4.7331 =DSM 102919 =KCTC 39774), KC712 (=CGMCC 4.7334 =DSM 102925 =KCTC 39776), KC201 (=CGMCC 4.7339 =DSM 102917 =KCTC 39781) and 6K102 (=CGMCC 4.7541 =JCM 32916), respectively.
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http://dx.doi.org/10.1099/ijsem.0.003808DOI Listing
January 2020

Draft Genome Sequence of Mn(II)-Oxidizing Bacterium sp. Strain AB_14.

Microbiol Resour Announc 2019 Oct 24;8(43). Epub 2019 Oct 24.

Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany.

Biological Mn(II) oxidation produces reactive manganese oxides that help to mitigate metal contamination in the environment. Here, we present the genome of sp. strain AB_14, a species of Mn(II)-oxidizing bacteria (MOB) that is notable for its ability to catalyze Mn oxidation at low pH (5.5).
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http://dx.doi.org/10.1128/MRA.01024-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6813393PMC
October 2019

Micromonospora orduensis sp. nov., isolated from deep marine sediment.

Antonie Van Leeuwenhoek 2020 Mar 19;113(3):397-405. Epub 2019 Oct 19.

Department of Molecular Biology and Genetics, Faculty of Art and Science, Ondokuz Mayis University, 55139, Samsun, Turkey.

A novel actinobacterial strain, designated S2509, was isolated from marine sediment collected by a dredge at a depth of 45 m along Melet River offshore of the southern Black Sea coast, Ordu, Turkey. The cell wall peptidoglycan of strain was found to contain meso-diaminopimelic acid and 3-OH-diaminopimelic acid. The whole cell sugars detected were arabinose, glucose, rhamnose, ribose and xylose. The diagnostic phospholipids of strain S2509 were found to be diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, a glycolipid and two unidentified phospholipids. The predominant menaquinones were identified as MK-9(H), MK-9(H), MK-10(H), MK-9(H), MK-10(H) and MK-10(H). The major cellular fatty acids were found to be iso-C, iso-C and 10-methyl C. The taxonomic position of the strain was established using a polyphasic approach, showing that S2509 strain belongs to the genus Micromonospora. Phylogenetic analysis based on the 16S rRNA gene sequence of strain S2509 showed that it is closely related to the type strain of Micromonospora chokoriensis DSM 45160 (99.37% sequence similarity), and phylogenetically clustered with Micromonospora inaquosa LB39 (99.37%), Micromonospora lupini Lupac 14N (99.16%), Micromonospora violae NEAU-zh8 (99.23%) and Micromonospora taraxaci NEAU-P5 (99.03%). The phylogenetic analysis based on the gyrB gene sequence of strain S2509 confirmed its close relationship with M. chokoriensis JCM 13247 (96.5% sequence similarity). Whole genome sequences confirmed by digital DNA-DNA hybridization analysis that the strain S2509 represents a novel species in the genus Micromonospora, for which the name Micromonospora orduensis sp. nov. is proposed. The type strain is S2509 (=DSM 45926 = KCTC 29201).
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http://dx.doi.org/10.1007/s10482-019-01349-6DOI Listing
March 2020

sp. nov., isolated from growing in the Odiel marshes(Spain) and emended descriptions of and .

Int J Syst Evol Microbiol 2020 Jan;70(1):220-227

School of Natural and Environmental Sciences (SNES), Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.

Strain EAR18 was isolated as an endophyte from the roots of a halophyte plant, , growing in the Odiel marshes (Huelva, Spain). Cells of strain EAR18 were Gram- stain-negative, motile, non-spore-forming aerobic rods. It grew optimally on tryptic soy agar supplemented with 2.5 % NaCl (w/v), at pH 7 and 30 °C for 48 h. It tolerated NaCl from 0 to 25 % (w/v). It presented Q9 as the major quinone and C cyclo 8, summed feature 8 (Cω7 and/or Cω6) and C as the predominant fatty acids. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and four unidentified phospholipids. The results of phylogenetic analysis based on 16S rRNA gene sequences revealed that strain EAR18 formed a well-supported clade with species B6 and TRM 0175 (similarities of 98.3 and 96.1 % respectively). Furthermore, digital DNA-DNA hybridization analysis resulted in values of 20.4 % with TRM 0175 and 35.50 % with B6, and ANIb/ANIm results in values of 73.8 %/84.2 % with TRM 0175 and 86.8 %/89.4 % with B6. Based on phylogeny and differential phenotypic properties in comparison with its closest related species, strain EAR18 is suggested to represent a new species in the genus , for which the name sp. nov. is proposed. The type strain is EAR18 (=CECT 9077=LMG 29859). The whole genome was sequenced, and it had a total length of 4.6 Mbp and a G+C content of 64.9 mol%.
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http://dx.doi.org/10.1099/ijsem.0.003742DOI Listing
January 2020

sp. nov., a rapidly growing scotochromogenic strain isolated from .

Int J Syst Evol Microbiol 2019 Nov;69(11):3465-3471

School of Natural and Environmental Sciences, Ridley Building 2, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.

A polyphasic study was undertaken to establish the taxonomic provenance of a rapidly growing strain, CECT 8783, recovered from the plant L. in Yunnan Province, China. Phylogenetic analyses based upon 16S rRNA and whole-genome sequences showed that the strain formed a distinct branch within the evolutionary radiation of the genus . The strain was most closely related to DSM 44221 with 98.4 % 16S rRNA gene sequence similarity, but was distinguished readily from this taxon by a combination of chemotaxonomic and phenotypic features and by low average nucleotide identity and digital DNA-DNA hybridization values of 79.5 and 21.1 %, respectively. Consequently, the strain is considered, to represent a novel species of for which the name sp. nov is proposed; the type strain is I10A-01893 (=CECT 8783=KCTC 19843=DSM 45590).
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http://dx.doi.org/10.1099/ijsem.0.003644DOI Listing
November 2019

sp. nov., a novel actinobacterium isolated from a high altitude Atacama Desert soil.

Int J Syst Evol Microbiol 2019 Nov;69(11):3426-3436

School of Natural and Environmental Sciences, Ridley Building 2, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.

A strain, designated 5R2A7, isolated from a high altitude Atacama Desert soil was examined by using a polyphasic approach. Strain 5R2A7 was found to have morphological, chemotaxonomic and cultural characteristics typical of members of the genus The cell wall contains - and -diaminopimelic acid, the major whole-cell sugars are glucose, ribose and xylose, the predominant menaquinones MK-10(H), MK-10(H), MK-10(H) and MK-9(H), the major polar lipids diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and an unknown glycolipid, and the predominant cellular fatty acids -C, -C and 10-methyl C. The digital genomic DNA G+C content is 72.3 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain 5R2A7 was closely related to DSM 44875 (99.8 %) and CR30 (99.7 %), and was separated readily from the latter, its closest phylogenetic neighbour, based on and multilocus sequence data, by low average nucleotide identity (92.59 %) and DNA-DNA relatedness (51.7 %) values calculated from draft genome assemblies and by a range of chemotaxonomic and phenotypic properties. Consequently, strain 5R2A7 is considered to represent a novel species of for which the name sp. nov. is proposed. The type strain is 5R2A7 (=LMG 30755=CECT 9656).
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http://dx.doi.org/10.1099/ijsem.0.003634DOI Listing
November 2019

Genomic Insights Into Plant-Growth-Promoting Potentialities of the Genus .

Front Microbiol 2019 4;10:1457. Epub 2019 Jul 4.

School of Natural and Environmental Sciences, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom.

This study was designed to determine the plant growth promoting (PGP) potential of members of the genus . To this end, the genomes of 21 representative strains were examined for genes associated directly or indirectly with plant growth. All of the genomes contained genes that encoded for products associated with the biosynthesis of auxins [indole-3-glycerol phosphate synthases, anthranilate phosphoribosyltransferases (D), anthranilate synthases, and aminases (A and B)], cytokinins (11 well-conserved genes within the predicted biosynthetic gene cluster), siderophores, and nitrogenases ( operon except for atypical ) as well as genes that modulate the effects of biotic and abiotic environmental stress (e.g., alkyl hydroperoxide reductases, aquaporin Z, heat shock proteins). In contrast, other genes were associated with strains assigned to one or more of four host-specific clusters. The genes encoding for phosphate solubilization (e.g., low-affinity inorganic phosphate transporters) and lytic enzymes (e.g., cellulases) were found in cluster 1 genomes, while other genes were found only in cluster 3 genomes (e.g., alkaline phosphatases, extracellular endoglucanases, pectate lyases) or cluster 4 and subcluster 1c genomes (e.g., NAD(P) transhydrogenase genes). Genes encoding for chitinases were found only in the genomes of the type strains of , , , and . In short, these genome analyses provide an insight into the PGP abilities of strains of known taxonomic provenance. This is the first study designed to establish the underlying genetic basis of cytokinin production in strains. Also, the discovery of additional genes in the biosynthetic gene cluster involved in cytokinin production opens up the prospect that may have novel molecular mechanisms for cytokinin biosynthesis.
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http://dx.doi.org/10.3389/fmicb.2019.01457DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6624747PMC
July 2019

Genomic Insight into Three Marine sp. Strains from the Gulf of California.

Microbiol Resour Announc 2019 Jul 11;8(28). Epub 2019 Jul 11.

School of Natural and Environmental Science, Newcastle University, Newcastle upon Tyne, United Kingdom.

Three actinomycete strains, designated BL1, BL4, and CV4, were isolated from sediment samples from the Gulf of California in 2009 together with nearly 300 other actinobacteria. Genome mining and analysis of their ∼6.4-Mb sequences confirmed the bioprospecting potential of these three bacteria belonging to the genus .
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http://dx.doi.org/10.1128/MRA.01673-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6624776PMC
July 2019

Editorial: Actinobacteria in Special and Extreme Habitats: Diversity, Function Roles and Environmental Adaptations, Second Edition.

Front Microbiol 2019 30;10:944. Epub 2019 Apr 30.

National Agricultural Research Center, Bio-resources Conservation Institute, Islamabad, Pakistan.

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http://dx.doi.org/10.3389/fmicb.2019.00944DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6503213PMC
April 2019

Isolation, characterization and analysis of bacteriophages from the haloalkaline lake Elmenteita, Kenya.

PLoS One 2019 25;14(4):e0215734. Epub 2019 Apr 25.

Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.

As a step towards better understanding of diversity and biology of phages and their hosts in haloalkaline Lake Elmenteita, phages were isolated from sediment samples and overlying water using indigenous bacteria as hosts. 17 seemingly different phages of diverse morphotypes with different dimensions and partly exhibiting remarkably unusual ultrastructures were revealed by transmission electron microscopy. 12 clonal phage isolates were further characterized. Infection capability of the phages was optimum at 30-35°C and in alkali condition with optimum at pH 10-12. Structural protein profiles and restriction fragment length polymorphism analyses patterns were distinct for each of the phage type. Complete nucleotide sequences of phages vB-VmeM-32, vB_EauS-123 and vB_BhaS-171 genomes varied in size from 30,926-199,912 bp and G + C content of between 36.25-47.73%. A range of 56-260 potential open reading frames were identified and annotated. The results showed that the 12 phages were distinct from each other and confirmed the presence and diversity of phages in extreme environment of haloalkaline Lake Elmenteita. The phages were deposited at the German Collection of Microorganisms and Cell Cultures and three of their genomes uploaded to NCBI GenBank.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215734PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6483233PMC
February 2020

Modestobacter italicus sp. nov., isolated from Carrara marble quarry and emended descriptions of the genus Modestobacter and the species Modestobacter marinus, Modestobacter multiseptatus, Modestobacter roseus and Modestobacter versicolor.

Int J Syst Evol Microbiol 2019 Jun 16;69(6):1537-1545. Epub 2019 Apr 16.

5​Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Italy.

A Gram-reaction-positive, aerobic bacterial strain showing coccoid cells and designated as BC 501 was isolated from a black patina of the surface of a Carrara marble blockin the Gioia quarry in Tuscany, Italy. A polyphasic study was carried out to clarify the taxonomic status of BC 501 within the evolutionary radiation of the genus Modestobacter. Phenotypic and genotypic characteristics as well as phylogenetic distinctiveness confirmed that it represents a novel species of the genus Modestobacter, for which the name Modestobacteritalicus sp. nov. is proposed. The type strain is BC 501 (=DSM 44449=CECT 9708). Emended descriptions of the genus Modestobacter and the species Modestobacter marinus, Modestobacter multiseptatus, Modestobacter roseus and Modestobacter versicolor are also proposed.
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http://dx.doi.org/10.1099/ijsem.0.003282DOI Listing
June 2019

Uncovering the potential of novel micromonosporae isolated from an extreme hyper-arid Atacama Desert soil.

Sci Rep 2019 03 18;9(1):4678. Epub 2019 Mar 18.

School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon Tyne, UK.

The taxonomic status, biotechnological and ecological potential of several Micromonospora strains isolated from an extreme hyper arid Atacama Desert soil were determined. Initially, a polyphasic study was undertaken to clarify the taxonomic status of five micromonosporae, strains LB4, LB19, LB32, LB39 and LB41, isolated from an extreme hyper-arid soil collected from one of the driest regions of the Atacama Desert. All of the isolates were found to have chemotaxonomic, cultural and morphological properties consistent with their classification in the genus Micromonospora. Isolates LB32 and LB39 were distinguished from their nearest phylogenetic neighbours and proposed as new species, namely as Micromonospora arida sp. nov. and Micromonospora inaquosa sp. nov., respectively. Eluted methanol extracts of all of the isolates showed activity against a panel of bacterial and fungal indicator strains, notably against multi-drug resistant Klebsiella pneumoniae ATCC 700603 while isolates LB4 and LB41 showed pronounced anti-tumour activity against HepG2 cells. Draft genomes generated for the isolates revealed a rich source of novel biosynthetic gene clusters, some of which were unique to individual strains thereby opening up the prospect of selecting especially gifted micromonosporae for natural product discovery. Key stress-related genes detected in the genomes of all of the isolates provided an insight into how micromonosporae adapt to the harsh environmental conditions that prevail in extreme hyper-arid Atacama Desert soils.
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http://dx.doi.org/10.1038/s41598-019-38789-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6423291PMC
March 2019

Comparative genomic analysis of eight novel haloalkaliphilic bacteriophages from Lake Elmenteita, Kenya.

PLoS One 2019 14;14(2):e0212102. Epub 2019 Feb 14.

Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, Braunschweig, Germany.

We report complete genome sequences of eight bacteriophages isolated from Haloalkaline Lake Elmenteita found on the floor of Kenyan Rift Valley. The bacteriophages were sequenced, annotated and a comparative genomic analysis using various Bioinformatics tools carried out to determine relatedness of the bacteriophages to each other, and to those in public databases. Basic genome properties like genome size, percentage coding density, number of open reading frames, percentage GC content and gene organizations revealed the bacteriophages had no relationship to each other. Comparison to other nucleotide sequences in GenBank database showed no significant similarities hence novel. At the amino acid level, phages of our study revealed mosaicism to genes with conserved domains to already described phages. Phylogenetic analyses of large terminase gene responsible for DNA packaging and DNA polymerase gene for replication further showed diversity among the bacteriophages. Our results give insight into diversity of bacteriophages in Lake Elmenteita and provide information on their evolution. By providing primary sequence information, this study not only provides novel sequences for biotechnological exploitation, but also sets stage for future studies aimed at better understanding of virus diversity and genomes from haloalkaline lakes in the Rift Valley.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0212102PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6375668PMC
November 2019