- Volume 70, Issue 4, 2020

In 1983, Mycoplasma sp. strain 1220 was isolated in Hungary from the phallus lymph of a gander with phallus inflammation. Between 1983 and 2017, Mycoplasma sp. 1220 was also identified and isolated from the respiratory tract, liver, ovary, testis, peritoneum and cloaca of diseased geese in several countries. Seventeen studied strains produced acid from glucose and fructose but did not hydrolyse arginine or urea, and all grew under aerobic, microaerophilic and anaerobic conditions at 35 to 37 ˚C in either SP4 or pleuropneumonia-like organism medium supplemented with glucose and serum. Colonies on agar showed a typical fried-egg appearance and transmission electron microscopy revealed a typical mycoplasma cellular morphology. Molecular characterization included analysis of the following genetic loci: 16S rRNA, 23S rRNA, 16S–23S rRNA ITS, rpoB, rpoC, rpoD, uvrA, parC, topA, dnaE, fusA and pyk. The genome was sequenced for type strain 1220T. The 16S rRNA gene sequences of studied strains of Mycoplasma sp. 1220 shared 99.02–99.19 % nucleotide similarity with M. anatis strains but demonstrated ≤95.00–96.70 % nucleotide similarity to the 16S rRNA genes of other species of the genus Mycoplasma . Phylogenetic, average nucleotide and amino acid identity analyses revealed that the novel species was most closely related to Mycoplasma anatis . Based on the genetic data, we propose a novel species of the genus Mycoplasma , for which the name Mycoplasma anserisalpingitidis sp. nov. is proposed with the type strain 1220T (=ATCC BAA-2147T=NCTC 13513T=DSM 23982T). The G+C content is 26.70 mol%, genome size is 959110 bp.

Strain JC651T was isolated from a sediment sample collected from Chilika lagoon, which is one of the world’s most important brackish water lakes with estuarine characteristics. Colonies of this strain are light pink and cells are Gram-stain negative, spherical to pear shaped and form rosettes. Strain JC651T grows well up to pH 9.0 and tolerates up to 5 % NaCl (w/v). The respiratory quinone is MK6. The detected major fatty acids are C18 : 1 ω9c and C16 : 0. Its polar lipids are diphosphatidylglycerol, an unidentified phospholipid, phosphatidylglycerol and phosphatidylcholine. Strain JC651T shows highest 16S rRNA gene sequence similarity (97.8%) to the type species of the genus Roseimaritima , Roseimaritima ulvae UC8T. The genome size of strain JC651T is 6.2 Mb with a G+C content of 62.4 mol%. For the resolution of the phylogenetic congruence of the novel strain, the phylogeny was also reconstructed with the sequences of 92 core genes. Based on the phylogenetic analyses, low digital DNA–DNA hybridization values (19.5%), low (74.9%) genome average nucleotide identity results, chemotaxonomic characteristics and differential physiological properties, strain JC651T is recognized as a new species of the genus Roseimaritima for which we propose the name Roseimaritima sediminicola sp. nov. The type strain is JC651T (=KCTC 72178T=NBRC 113926T).

From a phlegmon in a dog an aerobic and facultatively anaerobic, indole-, oxidase- and catalase-negative, non-motile bacterium was isolated in 2019 in Germany that stained Gram-negative and showed a pleomorphic, rod-shaped, non-spore-forming appearance. Based on the results of 16S rRNA gene sequence analyses, strain IHIT1603-19T was assigned to the genus Streptobacillus with sequence similarities of 98.6, 98.0, 97.9, 97.1 and 94.4 % to the type strains of Streptobacillus felis , Streptobacillus notomytis , Streptobacillus ratti , Streptobacillus moniliformis and Streptobacillus hongkongensis , respectively. Strain IHIT1603-19T could also clearly be differentiated from other Streptobacillus species by rpoB, groEL and recA gene, nucleotide and amino acid sequence analyses as well as by core genome phylogeny. Regarding DNA–DNA relatedness, strain IHIT1603-19T demonstrated an average nucleotide identity of 83.00 and 82.28 % compared to S. felis 131000547T and S. moniliformis DSM 12112T, respectively. Chemotaxonomic and physiological data of strain IHIT1603-19T were in congruence with other closely related members of the family Leptotrichiaceae , represented by highly similar enzyme profiles and fatty acid patterns. MALDI-TOF MS analysis also proved suitable in unequivocally discriminating strain IHIT1603-19T from all currently described taxa of the genus Streptobacillus . On the basis of these data, we propose the novel species Streptobacillus canis sp. nov. with the type strain IHIT1603-19T (=DSM 110501T=CCUG 74118T=CIP 111795T). The G+C content of the DNA of the type strain is 26.6 mol%, genome size is 1.60 Mbp.

Cyanobacterial strain ARC8 was isolated from seepage coming into the river Dračice, Františkov, Czech Republic, and was characterized using a polyphasic approach. Strain ARC8 showed a typical Nostoc -like morphology and in-depth morphological characterization indicated that it is a member of the genus Nostoc . Furthermore, in the 16S rRNA gene phylogeny inferred using Bayesian inference, maximum likelihood and neighbour joining methods, strain ARC8 clustered within the Nostoc sensu stricto clade. The phylogenetic distance and the positioning of strain ARC8 also indicated that it is a member of the genus Nostoc . Furthermore, the rbcL gene phylogeny along with the 16S–23S ITS secondary structure analysis also supported the findings from the 16S rRNA gene tree. In accordance with the International Code of Nomenclature for Algae, Fungi and Plants we describe a novel species of Nostoc with the name Nostoc neudorfense sp. nov.

A Gram-reaction-negative, motile by gliding, rod-shaped bacterium, designated strain GH4-78T, was isolated from the tidal mudflat of a beach in the Republic of Korea. Cells were aerobic, catalase-positive, oxidase-negative and produced cream-coloured colonies. Q-8 was the only isoprenoid quinone. The major fatty acids were summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c), summed feature 3 (C16 : 1  ω6c and/or C16 : 1  ω7c) and C16 : 0. The major polar lipids are phosphatidylethanolamine and phosphatidylglycerol. Results of phylogenetic analyses based on 16S rRNA gene sequences revealed that strain GH4-78T formed a distinct lineage with Halioglobus sediminis (98.2 % sequence similarity). The DNA G+C content was 59.9 mol%. The average nucleotide identity value with the closest relative was 82.90 %. On the basis of the results from phenotypic, chemotaxonomic, phylogenetic and phylogenomic analyses, strain GH4-78T (=KCTC 62383T=DSM 106349T) represents a novel species of a new genus in the family Halieaceae , for which the name Seongchinamella unica gen. nov., sp. nov. is proposed. Moreover, the transfers of Halioglobus sediminis Han et al. 2019 to Seongchinamella sediminis comb. nov. and Halioglobus lutimaris Shi et al. 2018 to Pseudohalioglobus gen. nov. as Pseudohalioglobus lutimaris comb. nov. are also proposed, with the emended description of the genus Halioglobus .

An aerobic and Gram-stain-negative bacterial strain, designated UKS-15T, was isolated from lake water in the Republic of Korea. Results of 16S rRNA gene sequence and phylogenetic analyses indicated that the novel isolate belongs to the genus Lysobacter and was most closely related to Lysobacter xinjiangensis RCML-52T (98.0 %), Lysobacter mobilis 9 NM-14T (97.4 %) and Lysobacter humi FJY8T (97.2 %). The DNA G+C content was 69.1 mol%. Strain UKS-15T possessed ubiquinone-8 (Q-8) as the sole respiratory quinone and the fatty acid profile comprised iso-C15 : 0, iso-C17 : 0 and summed feature 9 (iso-C17 : 1 ω9c and/or C16 : 0 10-methyl) as its major components. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and one unidentified aminophospholipid. Moreover, the physiological and biochemical results and low level of DNA–DNA relatedness (<22.0 %) allowed the phenotypic and genotypic differentiation of strain UKS-15T from other Lysobacter species. Therefore, on the basis of the data from this polyphasic taxonomic study, strain UKS-15T should represent a novel species of the genus Lysobacter , for which the name Lysobacter lacus sp. nov. is proposed. The type strain is UKS-15T (=JCM 30983T=KACC 18719T).

A Gram-stain-negative, non-spore-forming, motile, aerobic, rod-shaped bacteria strain, designated LCB8T, was isolated from the insect Teleogryllus occipitalis captured from a deserted cropland in Shuangliu district, Chengdu, PR China. Phylogenetic analysis on the basis of 16S rRNA gene sequence indicated that the strain represented a member of the genus Ochrobactrum , family Brucellaceae , class Alphaproteobacteria. Ochrobactrum pecoris CCUG 60088T (97.9 %) and Ochrobactrum haematophilum CCUG 38531T (98.8 %) were identified as the most closely related phylogenetic neighbours of strain LCB8T. The novel strain was able to grow at salt concentrations of 0–4.5 % (w/v), pH 5–9 and temperatures of 20–42 °C. The major quinone system was ubiquinone Q-10, the major fatty acids were C18 : 1ω7c, C16 : 0 and C18 : 0. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylmonomethylethanolamine, diphosphatidylglycerol and four undefined aminolipids. The major polyamines were putrescine and spermidine. Genome sequencing revealed a genome size of 4.76 Mbp and a DNA G+C content of 57.1 mol%. These phenotypic, genotypic and chemotaxonomic traits excellently supported the affiliation of LCB8T to the genus Ochrobactrum . Pairwise determined whole-genome average nucleotide identity (ANI) values indicated that strain LCB8T represents a novel species, for which we propose the name Ochrobactrum teleogrylli sp. nov. with the type strain LCB8T (=KCTC 72031T=CGMCC 1.13984T).

A Gram-negative, moderately halophilic and facultatively aerobic bacterium, designated strain GTF13T, was isolated from a sea tidal flat. Cells were curved rods and motile by a single polar flagellum showing catalase and oxidase activities. Growth was observed at 20–37 °C, pH 5.0–8.5 and 1.0–6.0 % (w/v) NaCl. Strain GTF13T contained C16:0, summed feature 3 (comprising C16 : 1  ω6c/C16 : 1  ω7c), summed feature 8 (comprising C18 : 1  ω6c/C18 : 1  ω7c) and C12 : 0 3-OH as major fatty acids and ubiquinone-9 and ubiquinone-8 as major quinones. Phosphatidylethanolamine and two unidentified phospholipids were detected as major polar lipids. The G+C content of the genomic DNA was 59.8 mol%. Strain GTF13T was most closely related to Simiduia agarivorans SA1T, Endozoicomonas montiporae CL-33T and Pseudomonas segetis FR1439T, belonging to different families or orders of the class Gammaproteobacteria , with less than 92.0 % 16S rRNA gene sequence similarities. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain GTF13T formed a phylogenetic lineage with the family Litoricolaceae , but the genome-based phylogenomic tree showed that strain GTF13T formed a distinct phylogenetic lineage within the order Oceanospirillales . The very low 16S rRNA gene sequence similarities and distinct phylogenetic relationships, together with distinct phenotypic and chemotaxonomic properties, served to differentiate strain GTF13T from phylogenetically closely related families. Here, strain GTF13T is proposed as a novel genus and species, for which the name Aestuariirhabdus litorea gen. nov., sp. nov. is proposed, within a new family Aestuariirhabdaceae fam. nov. of the order Oceanospirillales . The type strain is GTF13T (=KACC 19788T=JCM 32043T).

In the course of screening halophilic bacteria in Urmia Lake in Iran, which is being threatened by dryness, a novel Gram-negative, moderately halophilic, heterotrophic and short rod-shaped bacteria was isolated and characterized. The bacterium was isolated from a water specimen and designated as TBZ3T. Colonies were found to be creamy yellow, with catalase- and oxidase-positive activities. The growth of strain TBZ3T was observed to be at 10–45 °C (optimum, 30 °C), at pH 6.0–9.0 (optimum, pH 7.0) and in the presence of 0.5–20 % (w/v) NaCl (optimum, 7.5 %). Strain TBZ3T contained C16 : 0, cyclo-C19 : 0  ω8c, summed feature 3 (comprising C16 : 1  ω7c and/or C16 : 1  ω6c) and summed feature 8 (comprising C18 : 1  ω7c and/or C18 : 1  ω6c) as major fatty acids and ubiquinone-9 as the only respiratory isoprenoid quinone. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, glycolipid, unidentified phospholipid and unidentified polar lipids were detected as the major polar lipids. Strain TBZ3T was found to be most closely related to Halomonas saccharevitans AJ275T , Halomonas denitrificans M29T and Halomonas sediminicola CPS11T with the 16S rRNA gene sequence similarities of 98.93, 98.15 and 97.60 % respectively and in phylogenetic analysis strain TBZ3T grouped with Halomonas saccharevitans AJ275T contained within a large cluster within the genus Halomonas . Based on phenotypic, chemotaxonomic and molecular properties, strain TBZ3T represents a novel species of the Halomonas genus, for which the name Halomonas urmiana sp. nov. is proposed. The type strain is TBZ3T (=DSM 22871T=LMG 25416T).

A novel thermotolerant bacterial strain was isolated from a hot spring in a Tibetan geothermal field. Phylogenetic analysis of the 16S rRNA gene sequence of the novel strain showed that it belongs to a distinct lineage far from any known taxa. The new isolate shared the highest pairwise sequence identity with Phreatobacter cathodiphilus S-12T (92.8 % similarity) according to the 16S rRNA gene sequences. Cells were Gram-stain-negative, aerobic, rod-shaped and formed white round colonies. The strain grew at the ranges of 28–45 °C (optimum, 37 °C), pH 5.0–7.0 (optimum, pH 6.0) and 0–2 % NaCl. The strain was positive for catalase and oxidase. The major respiratory quinone was ubiquinone Q-10. Polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine. The major fatty acids were summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c). The DNA G+C content was 68.3 mol%. Based on these distinguishing properties, this strain is proposed to represent a new species of a new genus Rhabdaerophilum calidifontis gen. nov., sp. nov., within a new family Rhabdaerophilaceae fam. nov. The type strain of the type species of Rhabdaerophilum calidifontis is SYSU G02060T (=KCTC 72351T=CGMCC 1.17070T).

A novel Gram-negative, obligately aerobic, rod-shaped and non-motile bacterium, designated strain K13M18T, was isolated from the intestinal tract of a Korean indigenous fish, oily bitterling (Acheilognathus koreensis). Strain K13M18T formed creamy-pink colonies on a marine agar plate. Results of phylogenetic analysis based on the 16S rRNA gene sequence similarity indicated that strain K13M18T was most closely related to Tabrizicola sediminis DRYC-M-16T, sharing 97.62 % similarity with that strain. Strain K13M18T belonged to the genus Tabrizicola , which formed a cluster with Tabrizicola aquatica RCRI19T, Tabrizicola fusiformis SY72T, Tabrizicola sediminis DRYC-M-16T and Tabrizicola alkalilacus DJCT in a phylogenetic tree based on the 16S rRNA gene sequences. Strain K13M18T grown optimally in 0 % (w/v) NaCl, at pH 7 and 30 °C, in a marine broth medium. The predominant cellular fatty acids were C18 : 1 ω7c and C18 : 1 ω6c. The major respiratory isoprenoid quinone was ubiquinone Q-10. Polar lipids of strain K13M18T contained phosphatidylcholine, phosphatidylglycerol, phosphatidylinositol, diphosphatidylglycerol, six unidentified aminophospholipids, one unidentified aminolipid and an unidentified lipid. Based on genome sequencing, the DNA G+C content of strain K13M18T was 64.08 mol %, with an average nucleotide identity value, calculated by a comparative genomic analysis of strains K13M18T and T. sediminis DRYC-M-16T, of 74.82 %. Based on the phylogenetic, genotypic, and phenotypic information, strain K13M18T is proposed to be a novel species of the genus Tabrizicola . The type strain is K13M18T (=KCTC 62659T=JCM 33230T).

A Gram-stain-negative, non-motile and ovoid bacterial strain, designated 4-2T, was isolated from oil-contaminated water which was collected from Xinjiang Province, north-west PR China. The 16S rRNA gene sequence analysis showed that strain 4-2T belonged to the genus Paracoccus . The species with highest similarity to strain 4-2T was Paracoccus saliphilus YIM 90738T (97.83 %), followed by ‘ Paracoccus siganidrum ’ M26 (97.83 %) and Paracoccus endophyticus SYSUP0003T (97.25 %). The average nucleotide identity values between 4-2T and three type strains were 84.69, 77.88 and 74.07 %, respectively. The genomic DNA G+C content of strain 4-2T was 61.4 mol%. Chemotaxonomical characteristic results showed that the respiratory quinone was ubiquinone Q-10 and the major fatty acids were summed feature 8 (C18 : 1 ω7c or C18 : 1 ω6c) and C19 : 0 cyclo ω8c. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, unidentified phospholipids, an unidentified aminolipid and an unidentified polar lipid. The predominant polyamines were putrescine, cadaverine and spermidine. On the basis of phenotypic, chemotaxonomic and phylogenetic inferences, strain 4-2T represents a novel species of the genus Paracoccus , for which the name Paracoccus alkanivorans sp. nov. is proposed. The type strain is 4-2T (=CGMCC 1.13669T=LMG 30882T).

Two strains, WS 5063T and WS 5067, isolated from raw cow’s milk and skimmed milk concentrate, could be affiliated as members of the same, hitherto unknown, Pseudomonas species by 16S rRNA and rpoD gene sequences. Multilocus sequence and average nucleotide identity (ANIm) analyses based on draft genome sequences confirmed the discovery of a novel Pseudomonas species. It was most closely related to Pseudomonas synxantha DSM 18928T with an ANIm of 91.4 %. The DNA G+C content of WS 5063T was 60.0 mol %. Phenotypic characterizations showed that the isolates are rod-shaped, motile, catalase- and oxidase-positive, and aerobic. Growth occurred at 4–34 °C and at pH values of pH 5.5–8.0. Both strains showed strong β-haemolysis on blood agar. The major cellular polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The dominant quinone was Q-9 (90 %), but noticeable amounts of Q-8 (9 %) and traces of Q-7 were also detected. Fatty acid profiles were typical for Pseudomonas species and exhibited C16 : 0 as a major component. Based on these results, we conclude that both strains belong to a novel species, for which the name Pseudomonas haemolytica sp. nov. is proposed. The type strain is WS 5063T (=DSM 108987T=LMG 31232T) and an additional strain is WS 5067 (=DSM 108988=LMG 31233).

A Gram-negative rod from the Yersinia genus was isolated from a clinical case of yersiniosis in the United Kingdom. Long read sequencing data from an Oxford Nanopore Technologies (ONT) MinION in conjunction with Illumina HiSeq reads were used to generate a finished quality genome of this strain. Overall Genome Related Index (OGRI) of the strain was used to determine that it was a novel species within Yersinia , despite biochemical similarities to Yersinia enterocolitica . The 16S ribosomal RNA gene accessions are MN434982-MN434987 and the accession number for the complete and closed chromosome is CP043727. The type strain is SRR7544370T (=NCTC 14382T/=LMG 31573T).

A cellulolytic, aerobic, gammaproteobacterium, designated strain Bs02T, was isolated from the gills of a marine wood-boring mollusc, Bankia setacea (Bivalvia: Teredinidae). The cells are Gram-stain-negative, slightly curved motile rods (2–5×0.4–0.6 µm) that bear a single polar flagellum and are capable of heterotrophic growth in a simple mineral medium supplemented with cellulose as a sole source of carbon and energy. Cellulose, carboxymethylcellulose, xylan, cellobiose and a variety of sugars also support growth. Strain Bs02T requires combined nitrogen for growth. Temperature, pH and salinity optima (range) for growth were 20 °C (range, 10–30 °C), 8.0 (pH 6.5–8.5) and 0.5 M NaCl (range, 0.0–0.8 M), respectively when grown on 0.5 % (w/v) galactose. Strain Bs02T does not require magnesium and calcium ion concentrations reflecting the proportions found in seawater. The genome size is approximately 4.03 Mbp and the DNA G+C content of the genome is 47.8 mol%. Phylogenetic analyses based on 16S rRNA gene sequences, and on conserved protein-coding sequences, show that strain Bs02T forms a well-supported clade with Teredinibacter turnerae . Average nucleotide identity and percentage of conserved proteins differentiate strain Bs02T from Teredinibacter turnerae at threshold values exceeding those proposed to distinguish bacterial species but not genera. These results indicate that strain Bs02T represents a novel species in the previously monotypic genus Teredinibacter for which the name Teredinibacter waterburyi sp. nov. is proposed. The strain has been deposited under accession numbers ATCC TSD-120T and KCTC 62963T.

Six Helicobacter -like isolates were recovered from 15 gastric mucosa samples of red foxes (Vulpes vulpes) shot by hunters in the surroundings of Ljubljana, Slovenia. Gram-negative, tightly coiled, intensely motile, 7–15 µm long and ≤1 µm wide bacteria grew on the biphasic blood agar plates. By using a genus-specific polymerase chain reaction (PCR), all isolates were confirmed as Helicobacter sp. and subsequently subjected to whole-genome sequencing (WGS). Five isolates showed a genome-wide average nucleotide identity (ANI) value of <95 % to the previously described Helicobacter species and one isolate was classified as Helicobacter felis . In the five unidentified isolates, the 16S rRNA gene sequence similarity to the type strains of all Helicobacter species ranged from 98.6 to 98.9 %. Their taxonomic status was established using a polyphasic taxonomic approach comprising the core genome-based phylogeny, morphological and phenotypic characteristics, including an analysis of matrix-assisted laser desorption/ionisation time-of-flight (MALDI-TOF) mass spectra. Phylogeny revealed the existence of three novel and well-supported clusters, with Helicobacter bizzozeronii and Helicobacter baculiformis being the most closely related species. The isolates also differed from the previously described species in their MALDI-TOF profiles and some biochemical characteristics. In conclusion, the data presented herein indicate that the obtained isolates, excluding H. felis isolate, represent three novel Helicobacter species, for which the names Helicobacter labacensis sp. nov., Helicobacter mehlei sp. nov., and Helicobacter vulpis sp. nov. are proposed, with isolates L9T (=DSM 108823T=CRBIP 111719T), L15T (=DSM 108730T=CCUG 72910T) and L2T (=DSM 108727T=CCUG 72909T) as type strains, respectively.

As the current episode of Acute Oak Decline (AOD) continues to affect native British oak in the United Kingdom, ongoing isolations from symptomatic and healthy oak have yielded a large Pseudomonas species population. These strains could be divided into taxa representing three potential novel species. Recently, two of these taxa were described as novel Pseudomonas species in the Pseudomonas fluorescens lineage. Here, we demonstrate using a polyphasic approach that the third taxon represents another novel Pseudomonas species. The 16S rRNA gene sequencing assigned the strains to the Pseudomonas aeruginosa lineage, while multilocus sequence analysis (based on partial gyrB, rpoB and rpoD sequences) placed the 13 strains in a single cluster on the border of the Pseudomonas stutzeri group. Whole genome intra-species comparisons (based on average nucleotide identity and in silico DNA–DNA hybridization) confirmed that the strains belong to a single taxon, while the inter-species comparisons with closest phylogenetic relatives yielded similarity values below the accepted species threshold. Therefore, we propose these strains as a novel species, namely Pseudomonas kirkiae sp. nov., with the type strain FRB 229T (P4CT=LMG 31089T=NCPPB 4674T). The phylogenetic analyses performed in this study highlighted the difficulties in assigning novel species to the genus Pseudomonas due to its polyphyletic nature and close relationship to the genus Azotobacter . We further propose that a thorough taxonomic re-evaluation of the genus Pseudomonas is essential and should be performed in the near future.

A bacterial strain, designated GEM5T, was isolated from sand soil samples from the Qinghai–Tibet Plateau. The polyphasic study confirmed the affiliation of the isolate with the genus Massilia . GEM5T had Gram-stain-negative, non-spore-forming and rod-shaped cells and grew at 4–30 °C, pH 6–8 and with 0–2 % (w/v) NaCl. Its cell wall contained ribose. Q8 was the predominant respiratory quinone, and summed feature 3 (C16 : 1ω6c/ω7c) and C16 : 0 were the major components of the fatty acids. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified phospholipid, an unidentified aminolipid and four unidentified lipids. The DNA G+C content was 65.1 mol%. The phylogenetic analysis based on the 16S rRNA gene showed a stable clade being formed by GEM5T, Massilia timonae CCUG 45783T (97.94 %) and Massilia oculi CCUG 43427AT (97.58 %). The average nucleotide identity (ANIb) values between GEM5T and M. timonae CCUG 45783T, M.oculi CCUG 43427AT were 91.3 and 91.7 %, respectively. On the basis of the morphological, physiological and chemotaxonomic pattern, it was proposed that strain GEM5T (=JCM 32744T=CICC 24458T) should be classified as representing a member of the genus Massilia with the name Massilia arenae sp. nov.

Pectobacterium strains isolated from potato stems in Finland, Poland and the Netherlands were subjected to polyphasic analyses to characterize their genomic and phenotypic features. Phylogenetic analysis based on 382 core proteins showed that the isolates clustered closest to Pectobacterium polaris but could be divided into two clades. Average nucleotide identity (ANI) analysis revealed that the isolates in one of the clades included the P. polaris type strain, whereas the second clade was at the border of the species P. polaris with a 96 % ANI value. In silico genome-to-genome comparisons between the isolates revealed values below 70%, patristic distances based on 1294 core proteins were at the level observed between closely related Pectobacterium species, and the two groups of bacteria differed in genome size, G+C content and results of amplified fragment length polymorphism and Biolog analyses. Comparisons between the genomes revealed that the isolates of the atypical group contained SPI-1-type Type III secretion island and genes coding for proteins known for toxic effects on nematodes or insects, and lacked many genes coding for previously characterized virulence determinants affecting rotting of plant tissue by soft rot bacteria. Furthermore, the atypical isolates could be differentiated from P. polaris by their low virulence, production of antibacterial metabolites and a citrate-negative phenotype. Based on the results of a polyphasic approach including genome-to-genome comparisons, biochemical and virulence assays, presented in this report, we propose delineation of the atypical isolates as a novel species Pectobacterium parvum, for which the isolate s0421T (CFBP 8630T=LMG 30828T) is suggested as a type strain.

A gamma radiation-resistant and pink-pigmented bacterial strain, designated as 17Sr1-39T, was isolated from a gamma ray-irradiated soil sample collected in the Republic of Korea. Cells were Gram-stain-negative, strictly aerobic, flagellated, asporogenous, rod-shaped and methylotrophic. Results of 16S rRNA gene sequence analysis showed that strain 17Sr1-39T was phylogenetically related to Methylobacterium currus PR1016AT (97.3 %), Methylobacterium aquaticum DSM 16371T (97.2 %), Methylobacterium platani PMB02T (97.0 %), Methylobacterium frigidaeris IER25-16T (96.6 %), Methylobacterium terrae 17Sr1-28T (96.6 %) and Methylobacterium organophilum JCM 2833T (93.4 %). The G+C content calculated based on the genome sequence was 70.4 mol%. The average nucleotide identity and in silico DNA–DNA hybridization values between strain 17Sr1-39T and M. currus , M. aquaticum , M. platani , M. frigidaeris , M. terrae and M. organophilum were 77.3–89.9 and 22–38.2 %, respectively. The predominant fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The predominant quinone was ubiquinone 10 and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Based on the data from phenotypic tests and genotypic differences between strain 17Sr1-39T and its close phylogenetic relatives, strain 17Sr1-39T represented a new species belonging to the genus Methylobacterium , for which the name Methylobacterium terricola sp. nov. (=KACC 52905T=NBRC 112874T) is proposed.