Oceanimonas smirnovii sp. nov., a novel organism isolated from the Black Sea

Oceanimonas pelagia sp. nov., a novel biosurfactant-producing and plastic-degrading potential bacterium isolated from marine coastal sediment

A marine bacterial strain, named NTOU-MSR1T, was isolated from marine sediment of northern coast of Taiwan. This bacterium was Gram-stain-negative, aerobic, and motile, with a single flagellum. Its rod-shaped cells measured approximately 0.5-0.6 µm in width and 1.8-2.0 μm in length. NTOU-MSR1T grew at temperatures ranging from 10 to 45 °C, optimally at 30 °C. The pH range for growth was 7.0-10.0, with optimal growth at pH 7.0-8.0. It tolerated NaCl concentrations up to 12%. The cell membrane predominantly contained fatty acids such C16:1ω7c, C18:1ω7c, and C16:0. The overall genome relatedness indices indicated that strain NTOU-MSR1T had an average nucleotide identity (ANI) of 87.88% and a digital DNA-DNA hybridization (dDDH) value of 35.40% compared to its closest related species, O. marisflavi 102-Na3T. These values fell below the 95% and 70% threshold for species delineation, respectively. These findings suggested that the strain NTOU-MSR1T was a new member of the Oceanimonas genus. Its genomic DNA had a G + C content of 61.0 mol%. Genomic analysis revealed genes associated with the catechol branch of β- ketoadipate pathway for degrading polycyclic aromatic hydrocarbons, resistance to heavy metal, biosynthesis of polyhydroxybutyrate and the production of glycoside hydrolases (GH19, GH23, and GH103) for chitin and glycan digestion. Additionally, NTOU-MSR1T was capable of synthesizing biosurfactants and potentially degrading plastic. The proposed name for this new species is Oceanimonas pelagia, with the type strain designated as NTOU-MSR1T (= BCRC 81403T = JCM 36023T).

Assessment of Temporal Effects of a Mud Volcanic Eruption on the Bacterial Community and Their Predicted Metabolic Functions in the Mud Volcanic Sites of Niaosong, Southern Taiwan

The microbial communities inhabiting mud volcanoes have received more attention due to their noteworthy impact on the global methane cycle. However, the impact of temporal effects of volcanic eruptions on the microbial community’s diversity and functions remain poorly characterized. This study aimed to underpin the temporal variations in the bacterial community’s diversity and PICRUSt-predicted functional profile changes of mud volcanic sites located in southern Taiwan using 16S rRNA gene sequencing. The physicochemical analysis showed that the samples were slightly alkaline and had elevated levels of Na⁺, Cl⁻, and SO₄²⁻. Comparatively, the major and trace element contents were distinctly higher, and tended to be increased in the long-period samples. Alpha diversity metrics revealed that the bacterial diversity and abundance were lesser in the initial period, but increased over time. Instead, day 96 and 418 samples showed reduced bacterial abundance, which may have been due to the dry spell that occurred before each sampling. The initial-period samples were significantly abundant in haloalkaliphilic marine-inhabiting, hydrocarbon-degrading bacterial genera such as Marinobacter, Halomonas, Marinobacterium, and Oceanimonas. Sulfur-reducing bacteria such as Desulfurispirillum and Desulfofarcimen were found dominant in the mid-period samples, whereas the methanogenic archaeon Methanosarcina was abundant in the long-period samples. Unfortunately, heavy precipitation encountered during the mid and long periods may have polluted the volcanic site with animal pathogens such as Desulfofarcimen and Erysipelothrix. The functional prediction results showed that lipid biosynthesis and ubiquinol pathways were significantly abundant in the initial days, and the super pathway of glucose and xylose degradation was rich in the long-period samples. The findings of this study highlighted that the temporal effects of a mud volcanic eruption highly influenced the bacterial diversity, abundance, and functional profiles in our study site.

Discovery of α-Glucosidase Inhibitors from Marine Microorganisms: Optimization of Culture Conditions and Medium Composition

Various studies showed that the suppression of α-glucosidase activity can impede the glucose absorption in our body, and therefore, it can be used to treat type 2 diabetes. Hence, the compounds with anti-α-glucosidase have gained considerable attention because of their potential application in diabetes treatment. In previous literature studies, these anti-α-glucosidase compounds were extracted from plants and fungus. Less studies are being conducted to identify the anti-α-glucosidase compounds in the microbial community. In this study, 23 marine bacterial strains were screened for their potential to suppress the α-glucosidase activity. The highest inhibitory activity was exhibited by isolated L06 which was identified as Oceanimonas smirnovii EBL6. The cultivation conditions, such as temperature and pH, were optimized to increase the production of α-glucosidase inhibitors by Oceanimonas smirnovii EBL6 strain. The result findings showed that the highest yield of α-glucosidase inhibitors can be obtained at the culture time of 120 h, fermentation temperature of 30 °C, and pH 4.6. Under these conditions, the inhibitory activity of α-glucosidase can reach 81%. The IC₅₀ of n-butanol extract was 13.89 μg/ml, while standard acarbose was 31.16 μg/ml. Overall, these findings suggest that Oceanimonas smirnovii produces α-glucosidase inhibitors and could been applied in the biochemical and medicinal fields in the future.

Dongshaea marina gen. nov., sp. nov., a facultatively anaerobic marine bacterium that ferments glucose with gas production

Two isolates of heterotrophic, facultatively anaerobic, marine bacteria, designated DM1 and DM2^T, were recovered from a lagoon sediment sample of Dongsha Island, Taiwan. Cells were Gram-reaction-negative rods. Nearly all of the cells were non-motile and non-flagellated during the late exponential to early stationary phase of growth, while a few of the cells exhibited motility with monotrichous flagellation. The two isolates required NaCl for growth and grew optimally at about 30 °C, 2-3 % NaCl and pH 7-8. They grew aerobically and could achieve anaerobic growth by fermenting d-glucose or other carbohydrates with production of acids and the gases, including CO₂ and H₂. Ubiquinone Q-8 was the only respiratory quinone. Cellular fatty acids were predominated by C_16 : 0, C_18 : 1ω7c and C_16 : 1ω7c. The major polar lipid was phosphatidylethanolamine. Strains DM1 and DM2^T had DNA G+C contents of 52.0 and 51.8 mol%, respectively, as determined by HPLC analysis. Phylogenetic analyses based on 16S rRNA gene sequences clearly indicated that the two isolates formed a distinct genus-level lineage in the family Aeromonadaceae of the class Gammaproteobacteria and was an outgroup with respect to a stable supragenic clade comprising species of the genera Oceanimonas, Oceanisphaera and Zobellella. The phylogenetic data and those from chemotaxonomic, physiological and morphological characterizations support the establishment of a novel species and genus inside the family Aeromonadaceae, for which the name Dongshaea marina gen. nov., sp. nov. is proposed. The type strain is DM2^T (=BCRC 81069^T=JCM 32096^T).

Oceanimonas marisflavi sp. nov., a polycyclic aromatic hydrocarbon-degrading marine bacterium

A Gram-stain-negative, strictly aerobic, motile and rod-shaped bacterial strain, designated 102-Na3^T, was isolated from sediment of Sinduri beach in Taean, Republic of Korea. Strain 102-Na3^T grew optimally at 28-37 °C, at pH 7.0-11.0 and in the presence of 1-3 % (w/v) NaCl, but NaCl was not an absolute requirement for growth. The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain 102-Na3^T joined the clade comprising the type strains of Oceanimonasspecies. Strain 102-Na3^T exhibited 16S rRNA gene sequence similarity values of 98.8, 98.3 and 98.0 % to the type strains of Oceanimonas doudoroffii MBIC1298^T, Oceanimonas baumannii GB6^T and Oceanimonas smirnovii 31-13^T, respectively. Strain 102-Na3^T contained summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c), C16 : 0 and C12 : 0 as major fatty acids. The major quinone was ubiquinone-8. The polar lipids were composed of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and two unidentified amino lipids. The DNA G+C content was 56.8 mol%. Strain 102-Na3^T exhibited DNA-DNA relatedness values of 25.7, 21.7 and 14.8 % to the type strains of O. doudoroffii, O. baumannii and O. smirnovii, respectively. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain 102-Na3^T is separated from recognized species of the genus Oceanimonas. On the basis of the data presented, strain 102-Na3^T (=KCTC 62271^T=JCM 32358^T=DSM 106032^T) is considered the type strain of a novel species of the genus Oceanimonas, for which the name Oceanimonas marisflavi sp. nov. is proposed.

Modeling of growth kinetics for an isolated marine bacterium, Oceanimonas sp. BPMS22 during the production of a trypsin inhibitor

Protease inhibitors significantly control physiologically relevant protease activities. Protease inhibitors from marine microbial sources are unique due to their rough living environmental conditions. In the present study, a protein protease inhibitor (PI) was produced from marine Oceanimonas sp. BPMS22. Seven different media were screened for the growth of the bacterium and production of PI. Different carbon and nitrogen sources were screened and optimized for the specific protease inhibitor activity. Three different growth models were checked for the best fit of the bacterial growth. A modified Gompertz model was selected as the best model for the growth of Oceanimonas sp. BPMS22 with the maximum specific growth rate of 0.165 hr^-1 and doubling time of 4.2 hr. The production of PI takes place during the non-growing phase of the bacterial growth. A kinetic model for the production of PI during non-growing phase was used for studying various process parameters. From the model, the maximum trypsin inhibitor formation rate of 0.3802 IU per mg of biomass per hour was observed at 49.91 hr.

Genome Sequence of Oceanimonas doudoroffii ATCC 27123T

Oceanimonas doudoroffii ATCC 27123^T is an obligately aerobic Gram-negative rod of the class Gammaproteobacteria. It was first isolated from surface seawater off the coast of Oahu, HI, USA, in 1972. The predicted genome size is 3,832,938 bp (G+C content, 60.03%), which contains 3,524 predicted coding sequences.

Characterization of Phosphoenolpyruvate Carboxylase from Oceanimonas smirnovii in Escherichia coli

In this study, phosphoenolpyruvate carboxylase (PEPC) derived from Oceanimonas smirnovii (OS) was expressed as a soluble protein in Escherichia coli BL21(DE3). We isolated OS-PEPC (a recombinant PEPC protein) by his-tag purification. The purified protein showed a single band upon analysis with SDS-PAGE, and it had an apparent molecular mass of 98 kDa. Pufied OS-PEPC showed a specific activity value of 21.8 ± 0.495 U/mg protein. Especially, OS-PEPC showed the enzymatic activity between 40 and 50 °C. It maintained enzymatic activity in basic pH conditions (pH value, 9-10). We also measured OS-PEPC PEP and HCO3 (-) saturation kinetics and confirmed the effect of divalent cation on OS-PEPC activity.

Complete genome sequence of Oceanimonas sp. GK1, a halotolerant bacterium from Gavkhouni Wetland in Iran

Oceanimonas sp. GK1 (IBRC-M 10197) is a marine halotolerant gammaproteobacterium which was characterized as producing large amounts of poly-β-hydroxybutyrate. Here we present the whole-genome sequence of Oceanimonas sp. GK1, which consists of a single circular chromosome of 3,514,537 bp and two plasmids 8,462 and 4,245 bp in length.

Zobellella denitrificans gen. nov., sp. nov. and Zobellella taiwanensis sp. nov., denitrifying bacteria capable of fermentative metabolism

Two denitrifying strains of heterotrophic, facultatively anaerobic bacteria, designated ZD1T and ZT1T, were isolated from sediment samples collected from mangrove ecosystems in Taiwan. The isolates were Gram-negative. Cells grown in broth cultures were straight rods that were motile by means of a single polar flagellum. The isolates grew optimally in 1–3 % NaCl, but NaCl was not an absolute requirement for growth; only strain ZT1T grew in 13–14 % NaCl. Both isolates grew between 10 and 45 °C, with optimum growth at 30–35 °C. They were capable of anaerobic growth by denitrifying metabolism using nitrate or nitrous oxide as terminal electron acceptors or, alternatively, by fermenting glucose, sucrose or mannitol as substrates. C18 : 1 ω7c was the most abundant fatty acid (32.6–35.7 %). The other major fatty acids included C16 : 1 ω7c (27.5–29.4 %) and C16 : 0 (20.1–22.0 %). The two isolates had 16S rRNA gene sequence similarity of 96.8 % and shared 94.1–96.8 % sequence similarity with the most closely related species, Oceanimonas doudoroffii, Oceanimonas baumannii, Oceanimonas smirnovii and Oceanisphaera litoralis. They could be distinguished from these species in that they were capable of fermentative metabolism, had relatively high DNA G+C contents (62.0–64.0 mol%) and contained C18 : 1 ω7c instead of C16 : 1 ω7c as the most abundant fatty acid. Characterization data accumulated in this study revealed that the two denitrifying isolates could be classified as representatives of two novel species in a new genus, Zobellella gen. nov., with Zobellella denitrificans sp. nov. (type strain ZD1T=BCRC 17493T=JCM 13380T) as the type species and Zobellella taiwanensis sp. nov. (type strain ZT1T=BCRC 17494T=JCM 13381T) as a second species.

Validation of publication of new names and new combinations previously effectively published outside the IJSEM

The purpose of this announcement is to effect the valid publication of the following new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries (i.e. documents certifying deposition and availability of type strains). It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors' names will be included in the author index of the present issue and in the volume author index. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in bacteriological nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.

Notification of changes in taxonomic opinion previously published outside the IJSEM

The Bacteriological Code deals with the nomenclature of prokaryotes. This may include existing names (the Approved Lists of Bacterial Names) as well as new names and new combinations. In this sense the Code is also dealing indirectly with taxonomic opinions. However, as with most codes of nomenclature there are no mechanisms for formally recording taxonomic opinions that do not involve the creation of new names or new combinations. In particular, it would be desirable for taxonomic opinions resulting from the creation of synonyms or emended descriptions to be made widely available to the public. In 2004, the Editorial Board of the International Journal of Systematic and Evolutionary Microbiology (IJSEM) agreed unanimously that it was desirable to cover such changes in taxonomic opinions (i.e. the creation of synonyms or the emendation of circumscriptions) previously published outside the IJSEM, and to introduce a List of Changes in Taxonomic Opinion [Notification of changes in taxonomic opinion previously published outside the IJSEM; Euzéby et al. (2004). Int J Syst Evol Microbiol 54, 1429-1430]. Scientists wishing to have changes in taxonomic opinion included in future lists should send one copy of the pertinent reprint or a photocopy or a PDF file thereof to the IJSEM Editorial Office or to the Lists Editor. It must be stressed that the date of proposed taxonomic changes is the date of the original publication not the date of publication of the list. Taxonomic opinions included in the List of Changes in Taxonomic Opinion cannot be considered as validly published nor, in any other way, approved by the International Committee on Systematics of Prokaryotes and its Judicial Commission. The names that are to be used are those that are the 'correct names' (in the sense of Principle 6) in the opinion of the bacteriologist, with a given circumscription, position and rank. A particular name, circumscription, position and rank does not have to be adopted in all circumstances. Consequently, the List of Changes in Taxonomic Opinion must be considered as a service to bacteriology and it has no 'official character', other than providing a centralized point for registering/indexing such changes in a way that makes them easily accessible to the scientific community.