Type Strain Research Articles

Salmonirosea aquatica gen. nov., sp. nov., a Novel Genus within the Family Spirosomaceae, Was Isolated from Brackish Water in the Republic of Korea.

A Gram-stain-negative, obligately aerobic, non-motile, rod-shaped bacterial strain designated SJW1-29T was isolated from brackish water samples collected from the Seomjin River, Republic of Korea. The purpose of this study was to characterize strain SJW1-29T and determine its taxonomic position as a potential new genus within the family Spirosomaceae. The strain grew within the range of 10-30 °C (optimum, 25 °C), pH 5.0-10.0 (optimum, 7.0), and 1-4% NaCl (optimum, 3%). Phylogenetic analysis based on the 16S rRNA gene revealed that strain SJW1-29T belongs to the family Spirosomaceae and is closely related to Persicitalea jodogahamensis Shu-9-SY12-35CT (91.3% similarity), Rhabdobacter roseus R491T (90.6%), and Arundinibacter roseus DMA-K-7aT (90.0%), while the similarities to strains within the order Cytophagales were lower than 90.0%. The genome is 7.1 Mbp with a G+C content of 50.7 mol%. The use of genome-relatedness indices confirmed that this strain belongs to a new genus. The major polar lipid profile consisted of phosphatidylethanolamine, and MK-7 was the predominant menaquinone. The predominant fatty acids were summed feature 3 (C16:1ω7c and/or C16:1ω6c), iso-C15:0, iso-C17:0 3-OH, and C16:0, representing more than 80% of the total fatty acids. The phenotypic, chemotaxonomic, genetic, and phylogenetic properties suggest that strain SJW1-29T represents a novel species within a new genus in the family Spirosomaceae, for which the name Salmonirosea aquatica gen. nov., sp. nov., is proposed. The type strain of Salmonirosea aquatica is SJW1-29T (=KCTC 72493T = NBRC 114061T = FBCC-B16924T).

Complete genome sequences of Thermus thermophilus strains isolated from Shirahama Hot Spring in Japan.

We isolated six Thermus thermophilus strains from Shirahama Hot Spring in Japan. Complete genome sequences, determined by combining Oxford Nanopore long-read and Illumina short-read sequence data, revealed that they showed >99.9% average nucleotide identities with each other and approximately 97% to the genome of the type strain HB8T.

Gilvimarinus gilvus sp. nov. and Gilvimarinus algae sp. nov., isolated from kelp seedlings.

Two novel rod-shaped, strictly aerobic, non-motile and Gram-stain-negative bacterial strains, designated SDUM040013T and SDUM040014T, were isolated from kelp seedlings in Weihai, PR China. Cells of strain SDUM040013T were 0.3-0.4 µm wide and 0.8-1.8 µm long, catalase-positive and oxidase-positive. Growth of SDUM040013T was observed at 0-37 °C (optimum, 28-30 °C) and pH 5.5-9 (optimum, pH 8.0) and in the presence of 1-8 % (w/v) NaCl (optimum, 2 %). The DNA G+C content of strain SDUM040013T was 50.5 %. Strain SDUM040013T showed the highest 16S rRNA gene sequence similarity (97.1 %) to Gilvimarinus chinensis. Cells of strain SDUM040014T were 0.4-0.5 µm wide and 1.0-1.4 µm long, catalase-positive and oxidase-positive. Growth of SDUM040014T was observed at 4-40 °C (optimum, 28-30 °C) and pH 5.5-9 (optimum, pH 8.5) and in the presence of 0-8 % (w/v) NaCl (optimum, 2 %). The DNA G+C content of strain SDUM040014T was 56.5 %. Strain SDUM040014T showed the highest 16S rRNA gene sequence similarity (96.2%) to Gilvimarinus polysaccharolyticus. The isoprenoid quinone of both strains was Q-8 and the predominant fatty acids were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), summed feature 8 (C18 : 1 ω7c) and C16 : 0. Diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine were the major polar lipids. Given these phenotypic and chemotaxonomic properties, as well as phylogenetic data, strains SDUM040013T and SDUM040014T were considered to represent two novel species of the genus Gilvimarinus, for which the names Gilvimarinus gilvus sp. nov. and Gilvimarinus algae sp. nov. are proposed. The type strains are SDUM040013T (=KCTC 8123T=MCCC 1H01413T) and SDUM040014T (=KCTC 8124T=MCCC 1H01414T), respectively.

Peteryoungia algae sp. nov. isolated from seaweeds of Gouqi Island, China, and its unique genetic features among Peteryoungia strains.

A Gram-stain-negative, light khaki, strictly aerobic, rod-shaped, motile via multiple flagella, and catalase- and oxidase-positive bacterium, designated as SSM4.3T, was isolated from the seaweed of Gouqi Island in the East China Sea. The novel isolate grows at 0-5.0% NaCl concentrations (w/v) (optimum 1%), pH 5.0-9.0 (optimum pH 7.0), and 15-37°C (optimum 30°C). The 16S rRNA gene sequences-based phylogeny indicates that the novel marine isolate belongs to the family Rhizobiaceae and that it shared the greatest sequence similarity (98.9%) with Peteryoungia rhizophila CGMCC 1.15691T. This classification was also supported by phylogenetic analysis using core genes. The predominant fatty acids (≥ 10%) of the strain were identified as C18:1 ω7c/C18:1 ω6c. Q-10 was identified as the major isoprenoid quinone, with trace levels of Q-9 present. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The complete genome size of strain SSM4.3T is 4.39Mb with a DNA G+C content of 61.3%. The average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity values between the genomes of strain SSM4.3T and its closely related representatives were 74.80-86.93%, 20.00-32.30%, and 70.30-91.52%, respectively. Phylogenetic analysis, grounded on the core genes, reveals the evolutionary relationship between SSM4.3T and other Peteryoungia strains. Pan-genomics analysis of 8 previously classified Peteryoungia species and SSM4.3T revealed their unique genetic features and functions. Overall, strain SSM4.3T was considered to be a new species of the Peteryoungia genus; the name Peteryoungia algae sp. nov. has been proposed, with type strain SSM4.3T (= LMG 32561 = MCCC 1K07170).

Streptomyces odontomachi sp. nov., a novel actinobacterium with antimicrobial potential isolated from ants (Odontomachus simillimus Smith, 1858).

A new actinomycete strain, ODS25T, exhibited antimicrobial activity against Bacillus subtilis, Kocuria rhizophila, Staphylococcus aureus, Staphylococcus epidermidis, Candida albicans, Candida tropicalis, was isolated from the ants, Odontomachus simillimus, collected from National Science Museum Thailand, Pathum Thani, Thailand. A polyphasic technique was used to characterize the taxonomic position. The morphological and chemotaxonomic properties of the strain are typical of members of the genus Streptomyces. Strain ODS25T contained ll-diaminopimelic and glucose in the whole-cell hydrolysate. The major cellular fatty acids were iso-C16:0, iso-C15:0, and anteiso-C15:0. The polar lipids were phosphatidylethanolamine, phosphatidylinositol mannosides, phosphatidylinositol, diphosphatidylglycerol, phosphatidylglycerol, three unidentified phospholipids, three unidentified amino lipids and two unidentified lipids. The menaquinones were MK-9(H6), MK-9(H8), and MK-9(H4). The G + C content of the genomic DNA was 71.3%. The 16 S rRNA gene sequence analysis demonstrated that the strain had the highest similarity to Streptomyces lusitanus NBRC 13464T (98.07%) but shared the phylogenetic neighbour with Streptomyces sulfonofaciens JCM 5069T. Both digital DNA-DNA hybridization and average nucleotide identity values among strain ODS25T and its associated Streptomyces type strains fell within the values lower than the threshold for differentiate the strain to the same species. Based on the phenotypic characteristics and genotypic distinctiveness, strain ODS25T is considered a novel species within the genus Streptomyces, for which the name Streptomyces odontomachi sp. nov. is proposed. The type strain is ODS25T (=TBRC 16204T=NBRC 115862T).

Carotenoid-Producing Paracoccus aurantius sp. nov., Isolated from the West Coast of Dokdo Island, Republic of Korea.

In this study, a novel species within the genus Paracoccus was isolated from the coastal soil of Dokdo (Seodo) Island and investigated. We elucidated the novel species, designated MBLB3053T , through genomic analysis of novel functional microbial resources. Cells were gram-negative, non-motile, and coccoid, and the colony was light orange in color. Phylogenetic analysis based on the 16S rRNA gene showed that strain MBLB3053T was related to the genus Paracoccus, with 98.5% similarity to Paracoccus aestuariivivens. Comparative genome analysis also revealed the strain to be a novel species of the genus Paracoccus by average nucleotide identity and in silico DNA-DNA hybridization values. Through secondary metabolite analysis, terpene biosynthetic gene clusters associated with carotenoid biosynthesis were found in strain MBLB3053T . Using high-performance liquid chromatography, strain MBLB3053T was confirmed to produce carotenoids, including all-trans-astaxanthin, by comparison to the standard compound. Notably, the isolate was also confirmed to produce carotenoids that other closely related species did not produce. Based on this comprehensive polyphasic taxonomy, strain MBLB3053T represents a novel species within the genus Paracoccus, for which the name Paracoccus aurantius sp. nov is proposed. The type strain was MBL3053T (=KCTC 8269T =JCM 36634T ). These findings support the research and resource value of this novel species, which was isolated from the Dokdo environmental microbiome.

Draft genome sequence of multidrug resistant Proteus mirabilis strain MAD23

Genome sequencing became one of the important tools for diagnosis of microorganisms. Proteus mirabilis is an enteric Gramnegative bacterium causes gastrointestinal and urinary tract infections in human and animals. Here, the draft sequencing of Proteus mirabilis (MAD23) strain was performed. The strain was collected from Chinese duck cecum suffering from diarrhea. Bacteria was identified by biochemical tests and characteristic swarming pattern on the plate. Antimicrobial susceptibility test was performed by VITEC-2 MS system. Also, draft genome sequencing was conducted using the Illumina platform NovaSeq sequencer. The genome is about 3,729,695 bp long, GC content is of 38.9%., number of contigs is 123, largest contig is 137547pb, smallest contig is 513, total of protein-coding sequences (CDSs) is 3410, and number of RNA genes is 72. Genome Pairwise comparisons of Proteus mirabilis MAD23 with other vs. type strain was detected based on is DDH, GC content, δ- value, genome size and number of proteins. Neighbour-Joining phylogenetic trees show relationship between Proteus mirabilis MAD23 and the close strains of Proteus species based on 16S rRNA sequences. In addition, analysis of the sequence reveals presence of many antibiotic resistance genes as dfrA1, sul2, dfrA32, aadA2b, aph(3’)-Ia, aadA1, aph(6)-Id, aph(3’’)-Ib, ere(A), aadA1, aadA2b, tet(J), tet(C), floR, and Cat genes.These genes encoding the resistance to different antibiotics including Aminoglycosides, Macrolides, Aminocyclitol, Tetracycline and Amphenicol. This work is considered as an important study can help in more understanding of WGS in Proteus spp. and recognize the genes that related to antibiotic resistance in this pathogen.

Isolation and characterization of novel acetogenic Moorella strains for employment as potential thermophilic biocatalysts.

Thermophilic acetogenic bacteria have attracted attention as promising candidates for biotechnological applications such as syngas fermentation, microbial electrosynthesis, and methanol conversion. Here, we aimed to isolate and characterize novel thermophilic acetogens from diverse environments. Enrichment of heterotrophic and autotrophic acetogens was monitored by 16S rRNA gene-based bacterial community analysis. Seven novel Moorella strains were isolated and characterized by genomic and physiological analyses. Two Moorella humiferrea isolates showed considerable differences during autotrophic growth. The M. humiferrea LNE isolate (DSM 117358) fermented carbon monoxide (CO) to acetate, while the M. humiferrea OCP isolate (DSM 117359) transformed CO to hydrogen and carbon dioxide (H2 + CO2), employing the water-gas shift reaction. Another carboxydotrophic hydrogenogenic Moorella strain was isolated from the covering soil of an active charcoal burning pile and proposed as the type strain (ACPsT) of the novel species Moorella carbonis (DSM 116161T and CCOS 2103T). The remaining four novel strains were affiliated with Moorella thermoacetica and showed, together with the type strain DSM 2955T, the production of small amounts of ethanol from H2 + CO2 in addition to acetate. The physiological analyses of the novel Moorella strains revealed isolate-specific differences that considerably increase the knowledge base on thermophilic acetogens for future applications.

TFIIB-Termination Factor Interaction Affects Termination of Transcription on Genome-Wide Scale.

Apart from its well-established role in the initiation of transcription, the general transcription factor TFIIB has been implicated in the termination step as well. The ubiquity of TFIIB involvement in termination as well as mechanistic details of its termination function, however, remain largely unexplored. Using GRO-seq analyses, we compared the terminator readthrough phenotype in the sua7-1 mutant (TFIIBsua7-1) and the isogenic wild type (TFIIBWT) strains. Approximately 74% of genes analyzed exhibited a 2-3-fold increase in readthrough of the poly(A)-termination signal in the TFIIBsua7-1 mutant compared to TFIIBWT cells. To understand the mechanistic basis of TFIIB's role in termination, we performed the mass spectrometry of TFIIB-affinity purified from chromatin and soluble cellular fractions-from TFIIBsua7-1 and TFIIBWT cells. TFIIB purified from the chromatin fraction of TFIIBWT cells exhibited significant enrichment of CF1A and Rat1 termination complexes. There was, however, a drastic decrease in TFIIB interaction with CF1A and Rat1 complexes in the TFIIBsua7-1 mutant. ChIP assays revealed about a 90% decline in the recruitment of termination factors in the TFIIBsua7-1 mutant compared to wild type cells. The overall conclusion of these results is that TFIIB affects the termination of transcription on a genome-wide scale, and the TFIIB-termination factor interaction plays a crucial role in the process.

Analysis on shear band development under large strain torsion of amorphous glassy polymers

Unlike the shear band development of metals generally regarded as the precursor to failure, the shear banding process in amorphous glassy polymers is known to influence both the strengthening and fracturing behaviors. Complementary to the previous experimental work in the literature on the shear band development under torsion under limited cases, the finite element (FE) analysis has been conducted to investigate the general shear banding behaviors in terms of the initiation and propagation in more detail. The FE model has been established by incorporating the Boyce-Parks-Argon (BPA) constitutive model with the full-network modification via a user material subroutine in ABAQUS. A series of nondimensional quantities were used to discuss the mesh sensitivity and the effects of predefined imperfections, specimen geometry, and torsion mode. Besides, by altering the extents of the intrinsic material softening and the strain hardening, the shear banding behaviors of typical materials under typical temperature and strain rate conditions are equivalently investigated. The validity of the simulation has been qualitatively validated by directly comparing with the experimental results from the literature.

Functional genomics and taxonomic insights into heavymetaltolerant novel bacterium Brevibacterium metallidurans sp. nov. NCCP-602T isolated from tannery effluent in Pakistan.

The strain designated NCCP-602T was isolated from tannery effluent, and displayed aerobic, gram-positive, rod-shaped cells that were characterized by oxidase negative, catalase positive, and non-motile features. The most favourable growth conditions were observed at a temperature of 30°C, pH 7.0, and NaCl concentration of 1% (w/v). It tolerated heavy metals at high concentrations of chromium (3600 ppm), copper (3300 ppm), cadmium (3000 ppm), arsenic (1200 ppm) and lead (1500 ppm). The results of phylogenetic analysis, derived from sequences of the 16S rRNA gene, indicated the position of strain NCCP-602T within genus Brevibacterium and showed that it was closely related to Brevibacterium ammoniilyticum JCM 17537T. Strain NCCP-602T formed a robust branch that was clearly separate from closely related taxa. A comparison of 16S rRNA gene sequence similarity and dDDH values between the closely related type strains and strain NCCP-602T provided additional evidence supporting the classification of strain NCCP-602T as a distinct novel genospecies. The polar lipid profile included diphosphatidylglycerol, glycolipid, phospholipids and amino lipids. MK-7 and MK-8 were found as the respiratory quinones, while anteiso-C15:0, iso-C15:0, iso-C16:0, iso-C17:0, and anteiso-C17:0 were identified as the predominant cellular fatty acids (> 10%). Considering the convergence of phylogenetic, phenotypic, chemotaxonomic, and genotypic traits, it is suggested that strain NCCP-602T be classified as a distinct species Brevibacterium metallidurans sp. nov. within genus Brevibacterium with type strain NCCP-602T (JCM 18882T = CGMCC1.62055T).

Aquibium pacificus sp. nov., a Novel Mixotrophic Bacterium from Bathypelagic Seawater in the Western Pacific Ocean.

A novel Gram-stain-negative, facultatively anaerobic, and mixotrophic bacterium, designated as strain LZ166T, was isolated from the bathypelagic seawater in the western Pacific Ocean. The cells were short rod-shaped, oxidase- and catalase-positive, and motile by means of lateral flagella. The growth of strain LZ166T was observed at 10-45 °C (optimum 34-37 °C), at pH 5-10 (optimum 6-8), and in the presence of 0-5% NaCl (optimum 1-3%). A phylogenetic analysis based on the 16S rRNA gene showed that strain LZ166T shared the highest similarity (98.58%) with Aquibium oceanicum B7T and formed a distinct branch within the Aquibium genus. The genomic characterization, including average nucleotide identity (ANI, 90.73-76.79%), average amino identity (AAI, 88.50-79.03%), and digital DNA-DNA hybridization (dDDH, 36.1-22.2%) values between LZ166T and other species within the Aquibium genus, further substantiated its novelty. The genome of strain LZ166T was 6,119,659 bp in size with a 64.7 mol% DNA G+C content. The predominant fatty acid was summed feature 8 (C18:1ω7c and/or C18:1ω6c). The major polar lipids identified were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), glycolipid (GL), and phosphatidylglycerol (PG), with ubiquinone-10 (Q-10) as the predominant respiratory quinone. The genomic annotation indicated the presence of genes for a diverse metabolic profile, including pathways for carbon fixation via the Calvin-Benson-Bassham cycle and inorganic sulfur oxidation. Based on the polyphasic taxonomic results, strain LZ166T represented a novel species of the genus Aquibium, for which the name Aquibium pacificus sp. nov. is proposed, with the type strain LZ166T (=MCCC M28807T = KACC 23148T = KCTC 82889T).

Isolation and Genetic Characterization of Genotype VII Velogenic Pathotype Newcastle Disease Virus from Commercial Chicken Farms in Central Ethiopia, Distinct from the Local Vaccine Strains.

Newcastle disease (ND) is caused by virulent strains of avian paramyxovirus type 1, also known as Newcastle disease virus (NDV). Despite vaccination, the frequency of reported outbreaks in Ethiopia has increased. From January to June 2022, an active outbreak investigation was conducted in six commercial chicken farms across areas of central Ethiopia to identify the circulating NDV strains. Thirty pooled tissue specimens were collected from chickens suspected of being infected with NDV. A questionnaire survey of farm owners and veterinarians was also carried out to collect information on the farms and the outbreak status. NDV was isolated using specific-pathogen-free (SPF)-embryonated chicken eggs and detected using haemagglutination and the reverse transcriptase-polymerase chain reaction (RT-PCR). The genotype and virulence of field NDV isolates were determined using phylogenetic analysis of fusion (F) protein gene sequences and the mean death time (MDT) test in SPF-embryonated chicken eggs. The questionnaire results revealed that ND caused morbidity (23.1%), mortality (16.3%), case fatality (70.8%), and significant economic losses. Eleven of thirty tissue specimens tested positive for NDV using haemagglutination and RT-PCR. The MDT testing and sequence analysis revealed the presence of virulent NDV classified as genotype VII of class II velogenic pathotype and distinct from locally used vaccine strains (genotype II). The amino acid sequences of the current virulent NDV fusion protein cleavage site motif revealed 112RRQKR↓F117, unlike the locally used avirulent vaccine strains (112GRQGR↓L117). The epidemiological data, MDT results, cleavage site sequence, and phylogenetic analysis all indicated that the present NDV isolates were virulent. The four NDV sequences were deposited in GenBank with accession numbers F gene (PP726912-15) and M gene (PP726916-19). The genetic difference between avirulent vaccine strains and circulating virulent NDV could explain the low level of protection provided by locally used vaccines. Further studies are needed to better understand the circulating NDV genotypes in different production systems.

Atacama desert is a source of new Micromonospora strains: description of Micromonospora sicca sp. nov

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 4G51T, 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(H4) as major respiratory quinone, iso-C15:0 and iso-C16:0 as major fatty acids and diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol as major polar lipids. The 16S rRNA gene sequences of strains 4G51T, 4G53, and 4G57 showed the highest similarity (97.9 %) with the type strain of Micromonospora costi CS1-12T, 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. (4G51T=PCM 3031T=LMG 30756T) is proposed.

A New Convenient Method to Assess Antibiotic Resistance and Antimicrobial Efficacy against Pathogenic Clostridioides difficile Biofilms.

Clostridioides difficile is a widely distributed anaerobic pathogen. C. difficile infection is a serious problem in healthcare. Its biofilms have been found to exhibit biocorrosivity, albeit very little, but sufficient for it to correlate with biofilm growth/health. This work demonstrated the use of a disposable electrochemical biofilm test kit using two solid-state electrodes (a 304 stainless steel working electrode, and a graphite counter electrode, which also served as the reference electrode) in a 10 mL serum vial. It was found that the C. difficile 630∆erm Adp-4 mutant had a minimum inhibitory concentration (MIC) for vancomycin twice that of the 630∆erm wild type strain in biofilm prevention (2 ppm vs. 1 ppm by mass) on 304 stainless steel. Glutaraldehyde, a commonly used hospital disinfectant, was found ineffective at 2% (w/w) for the prevention of C. difficile 630∆erm wild type biofilm formation, while tetrakis(hydroxymethyl)phosphonium sulfate (THPS) disinfectant was very effective at 100 ppm for both biofilm prevention and biofilm killing. These antimicrobial efficacy data were consistent with sessile cell count and biofilm imaging results. Furthermore, the test kit provided additional transient biocide treatment information. It showed that vancomycin killed C. difficile 630∆erm wild type biofilms in 2 d, while THPS only required minutes.

Microbacterium humicola sp. nov., Microbacterium terrisoli sp. nov., Paenibacillus pedocola sp. nov., Paenibacillus silviterrae sp. nov., Flavobacterium terrisoli sp. nov., and Aquabacterium humicola sp. nov., isolated from soil.

Four Gram-stain-positive and two Gram-stain-negative bacterial strains, designated as W4T, FW7T, TW48T, UW52T, PT-3T, and RJY3T, were isolated from soil samples collected from the Republic of Korea. The 16S rRNA gene sequence analysis showed that strains W4T and FW7T belonged to the genus Microbacterium, strains TW48T and UW52T were affiliated to the genus Paenibacillus, strain PT-3T was related to the genus Flavobacterium, and strain RJY3T was associated with the genus Aquabacterium. The closest phylogenetic taxa to W4T, FW7T, TW48T, UW52T, PT-3T, and RJY3T were Microbacterium bovistercoris NEAU-LLET (97.7 %), Microbacterium protaetiae DFW100M-13T (97.9 %), Paenibacillus auburnensis JJ-7T (99.6 %), Paenibacillus allorhizosphaerae JJ-447T (95.7 %), Flavobacterium buctense T7T (97.1 %), and Aquabacterium terrae S2T (99.5 %), respectively. Average nucleotide identity and digital DNA-DNA hybridization values between the novel strains and related reference type strains were <95.0 % and <70.0 %, respectively. The major cellular fatty acid in strains W4T, FW7T TW48T, and UW52T was antiso-C15 : 0. Similarly, strain PT-3T revealed iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH, and iso-C15 : 0 3-OH as its principal fatty acids. On the other hand, RJY3T exhibited summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0, summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), and C12 : 0 as its predominant fatty acids. Overall, the polyphasic taxonomic data indicated that strains W4T, FW7T, TW48T, UW52T, PT-3T, and RJY3T represent novel species within the genera Microbacterium, Paenibacillus, Flavobacterium, and Aquabacterium. Accordingly, we propose the names Microbacterium humicola sp. nov., with the type strain W4T (=KCTC 49888T=NBRC 116001T), Microbacterium terrisoli sp. nov., with the type strain FW7T (=KCTC 49859T=NBRC 116000T), Paenibacillus pedocola sp. nov., with the type strain TW48T (=KCTC 43470T=NBRC 116017T), Paenibacillus silviterrae sp. nov., with the type strain UW52T (=KCTC 43477T=NBRC 116018T), Flavobacterium terrisoli sp. nov., with the type strain PT-3T (=KCTC 92106T=NBRC 116012T), and Aquabacterium humicola sp. nov., with the type strain RJY3T (=KCTC 92105T=NBRC 115831T).

Methylomonas rivi sp. nov., Methylomonas rosea sp. nov., Methylomonas aurea sp. nov. and Methylomonas subterranea sp. nov., type I methane-oxidizing bacteria isolated from a freshwater creek and the deep terrestrial subsurface.

Four methane-oxidizing bacteria, designated as strains WSC-6T, WSC-7T, SURF-1T, and SURF-2T, were isolated from Saddle Mountain Creek in southwestern Oklahoma, USA, and the Sanford Underground Research Facility (SURF) in Lead, South Dakota, USA. The strains were Gram-negative, motile, short rods that possessed intracytoplasmic membranes characteristic of type I methanotrophs. All four strains were oxidase-negative and weakly catalase-positive. Colonies ranged from pale pink to orange in colour. Methane and methanol were the only compounds that could serve as carbon and energy sources for growth. Strains WSC-6T and WSC-7T grew optimally at lower temperatures (25 and 20 °C, respectively) compared to strains SURF-1T and SURF-2T (40 °C). Strains WSC-6T and SURF-2T were neutrophilic (optimal pH of 7.5 and 7.3, respectively), while strains WSC-7T and SURF-1T were slightly alkaliphilic, with an optimal pH of 8.8. The strains grew best in media amended with ≤0.5% NaCl. The major cellular fatty acids were C14 : 0, C16 : 1 ω8c, C16 : 1 ω7c, and C16 : 1 ω5c. The DNA G+C content ranged from 51.5 to 56.0 mol%. Phylogenetic analyses indicated that the strains belonged to the genus Methylomonas, with each exhibiting 98.6-99.6% 16S rRNA gene sequence similarity to closely related strains. Genome-wide estimates of relatedness (84.5-88.4% average nucleotide identity, 85.8-92.4% average amino acid identity and 27.4-35.0% digital DNA-DNA hybridization) fell below established thresholds for species delineation. Based on these combined results, we propose to classify these strains as representing novel species of the genus Methylomonas, for which the names Methylomonas rivi (type strain WSC-6T=ATCC TSD-251T=DSM 112293T), Methylomonas rosea (type strain WSC-7T=ATCC TSD-252T=DSM 112281T), Methylomonas aurea (type strain SURF-1T=ATCC TSD-253T=DSM 112282T), and Methylomonas subterranea (type strain SURF-2T=ATCC TSD-254T=DSM 112283T) are proposed.

A hotspot of diversity: novel Shewanella species isolated from Baltic Sea sediments delineate a sympatric species complex.

Two bacterial strains, SP1S1-4T and SP2S1-2T, were isolated from sediment samples collected in the Stockholm archipelago in November 2021. Following whole-genome sequencing, these strains were identified as tentatively belonging to two novel Shewanella genospecies, based on digital DNA-DNA hybridization, as implemented in the Type Strain Genome Server. Shewanella septentrionalis, Shewanella baltica and Shewanella hafniensis were, in this order and within a narrow genomic relatedness range, their closest genotypic relatives. Additional sampling and sequencing efforts led to the retrieval of distinct isolates that were monophyletic with SP1S1-4T and SP2S1-2T, respectively, based on phylogenomic analysis of whole-genome sequences. Comparative analyses of genome sequence data, which included blast-based average nucleotide identity, core genome-based and core proteome-based phylogenomics, in addition to MALDI-TOF MS-based protein profiling, confirmed the distinctness of the putative novel genospecies with respect to their closest genotypic relatives. A comprehensive phenotypic characterisation of SP1S1-4T and SP2S1-2T revealed only minor differences with respect to the type strains of S. septentrionalis, S. baltica and S. hafniensis. Based on the collective phylogenomic, proteomic, and phenotypic evidence presented here, we describe two novel genospecies within the genus Shewanella, for which the names Shewanella scandinavica sp. nov. and Shewanella vaxholmensis sp. nov. are proposed. The type strains are, respectively, SP2S1-2T (=CCUG 76457T=CECT 30688T), with a draft genome sequence of 5 041 805 bp and a G+C content of 46.3 mol%, and SP1S1-4T (=CCUG 76453T=CECT 30684T), with a draft genome sequence of 4 920147 bp and a G+C content of 46.0 mol%. Our findings suggest the existence of a species complex formed by the species S. baltica, S. septentrionalis, S. scandinavica sp. nov., and S. vaxholmensis sp. nov., with S. hafniensis falling in the periphery, where distinct genomic species clusters could be identified. However, this does not exclude the possibility of a continuum of genomic diversity within this sedimental ecosystem, as discussed herein with additional sequenced isolates.

Genome-based reclassification of Williamsia marianensis as a later heterotypic synonym of Williamsia muralis.

The present study used whole-genome data to clarify the taxonomic assignment of two closely related Williamsia species. Genomic information for 10 type strains was available at the time of conducting this analysis. One group of type strains was found to be conspecific, namely Williamsia muralis Kämpfer et al. 1999 and Williamsia marianensis Pathom-aree et al. 2006. The 16S rRNA gene sequences showed 99 % similarity between these type strains. Whole-genome-based comparisons showed that Williamsia muralis DSM 44343T and Williamsia marianensis DSM 44944T shared 98.07 % average nucleotide identity, 98.29 % average amino acid identity and 84.80 % digital DNA-DNA hybridization values. These values exceeded the threshold values for bacterial species delineation. Further, phylogenomic analysis based on the core genomes of the strains under study confirmed that Williamsia muralis DSM 44343T and Williamsia marianensis DSM 44944T formed a monophyletic clade. Based on this evidence, we propose the reclassification of Williamsia marianensis Pathom-aree et al. 2006 as a later heterotypic synonym of Williamsia muralis Kämpfer et al. 1999.

Gilvirhabdus luticola gen. nov., sp. nov., a mesophilic and halophilic bacterium isolated from tidal flat sediment.

Two novel bacteria, MJ-SS3T and MJ-SS4, were isolated from tidal flat sediment sampled in Gochang, Republic of Korea. The isolates were Gram-stain-negative, aerobic, non-motile, rod-shaped, yellow-coloured, oxidase-positive, and catalase-positive. Strains MJ-SS3T and MJ-SS4 grew at 20-37 °C (optimum, 30 °C), at pH 6-8 (optimum, pH 7.0) and in the presence of 0-7 % (w/v) NaCl (optimum, 2.0 % NaCl). Strains MJ-SS3T and MJ-SS4 showed 99.9 % 16S rRNA gene sequence similarity. Phylogenetic analysis based on genome and 16S rRNA gene sequences indicated that strains MJ-SS3T and MJ-SS4 were affiliated with the family Flavobacteriaceae and most closely related to Formosa maritima 1494T (95.3 %), Hanstruepera flava NBU2984T (95.2 %), Yeosuana marina JLT21T (95.2 %), Meridianimaribacter flavus NH57NT (95.1 %), and Geojedonia litorea YCS-16T (95.1 %). The major respiratory quinone was menaquinone-6. The major identified polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, and amino lipids. The major cellular fatty acids of strain MJ-SS3T were iso-C15 : 1 G (24.6 %), iso-C15 : 0 (21.6 %), and iso-C17 : 0 3-OH (15.8 %). The genome length of strain MJ-SS3T is 3.1 Mbp (DNA G+C content, 32.5 mol%) and it has 2822 coding and 59 tRNA genes. The average amino acid identity and average nucleotide identity values, as well as biochemical, phylogenetic, and physiological characteristics, strongly supported the genotypic and phenotypic differentiation of strains MJ-SS3T and MJ-SS4 from other members of the family Flavobacteriaceae. Hence, strains MJ-SS3T and MJ-SS4 are considered to represent a novel species of a new genus in the family Flavobacteriaceae, for which the Gilvirhabdus luticola gen. nov., sp. nov. is proposed. The type strain is MJ-SS3T (=KCTC 102114T=KEMB 20189T=JCM 36595T), with reference strain MJ-SS4 (=KCTC 102115=KEMB 20190).