Sulfitobacter faviae sp. nov., isolated from the coral Faviaveroni

Comparative Genomic Analysis of Cold-Water Coral-Derived Sulfitobacter faviae: Insights into Their Habitat Adaptation and Metabolism

Sulfitobacter is one of the major sulfite-oxidizing alphaproteobacterial groups and is often associated with marine algae and corals. Their association with the eukaryotic host cell may have important ecological contexts due to their complex lifestyle and metabolism. However, the role of Sulfitobacter in cold-water corals remains largely unexplored. In this study, we explored the metabolism and mobile genetic elements (MGEs) in two closely related Sulfitobacter faviae strains isolated from cold-water black corals at a depth of ~1000 m by comparative genomic analysis. The two strains shared high sequence similarity in chromosomes, including two megaplasmids and two prophages, while both contained several distinct MGEs, including prophages and megaplasmids. Additionally, several toxin-antitoxin systems and other types of antiphage elements were also identified in both strains, potentially helping Sulfitobacter faviae overcome the threat of diverse lytic phages. Furthermore, the two strains shared similar secondary metabolite biosynthetic gene clusters and genes involved in dimethylsulfoniopropionate (DMSP) degradation pathways. Our results provide insight into the adaptive strategy of Sulfitobacter strains to thrive in ecological niches such as cold-water corals at the genomic level.

Mesobacterium pallidum gen. nov., sp. nov., Heliomarina baculiformis gen. nov., sp. nov. and Oricola indica sp. nov., three novel Alphaproteobacteria members isolated from deep-sea water in the southwest Indian ridge

Three Gram-staining-negative, aerobic and rod-shaped strains, designated as T40-1T, T40-3T and JL-62T, were isolated from the deep-sea water in the southwest Indian ridge. For strain T40-1T, growth occurred at 15–37 °C (optimum, 28 °C), pH 6.0–9.0 (optimum, pH 7.5) and in the presence of 0.5–5.0 % NaCl (w/v; optimum, 2.0 %). Strain T40-3T could grow at 15–40 °C (optimum, 28 °C), with 0.5–11.0 % NaCl (optimum, 2.0 %, w/v) at pH 6.0–9.5 (optimum, 8.0). The temperature, pH and salinity ranges for growth of strain JL-62T were 15–40 °C (optimum, 30 °C), pH 5.5–9.0 (optimum, pH 7.5–8.0) and 0.5–9.0 % NaCl (w/v; optimum, 4.0 %). Ubiquinone-10 was the sole ubiquinone in all strains, the major fatty acids (>20 %) were summed feature 8 (C18 : 1  ω7c / C18 : 1  ω6c). The major polar lipids of strains T40-1T and T40-3T were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and diphosphatidylglycerol. Strain JL-62T contained phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and sulfoquinovosyldiacylglycerol as major polar lipids. Phylogenetic trees based on 16S rRNA gene and core-genomic sequences revealed affiliation of strains T40-1Tand T40-3T to the family Roseobacteraceae and formed two independent clades from other Roseobacteraceae genera, and those two strains had average nucleotide identities of 62.0–72.0 % to their phylogenetically related species which fell into to the genus boundary range, indicating that they represent two novel genera. While strain JL-62T represents a novel species in the genus Oricola belonging to the family Phyllobacteriaceae , which was supported by overall genomic relatedness index calculations. The DNA G+C contents of strains T40-1T, T40-3T and JL-62T were 66.5, 60.1 and 62.1 mol %, respectively. Based on the polyphasic taxonomic data, strains T40-1T (=MCCC M24557T=KCTC 82975T) and T40-3T (=MCCC 1K05135T=KCTC 82976T) are classified as representing two novel genera belonging to the family Roseobacteraceae with the names Mesobacterium pallidum gen. nov., sp. nov. and Heliomarina baculiformis gen. nov., sp. nov. are proposed, and strain JL-62T (=MCCC M24579T=KCTC 82974T) is proposed to represent a novel species within the genus Oricola with the name Oricola indica sp. nov. is proposed.

Mesobaculum littorinae gen. nov., sp. nov., a novel bacterium isolated from a sea snail Littorina scabra

Members within the family Rhodbacteraceae are morphologically and genetically highly diverse, and originate mostly from coastal marine environments. In this study, a novel species of this family, designated M0103^T, was isolated from the surface of a sea snail Littorina scabra. Strain M0103^T is Gram-stain-negative, halophilic, non-motile and non-Bacteriochlorophyll a-producing bacterium. Several phenotypic characteristics of the isolate were similar to other species within this family, such as the sole respiratory quinone Q-10 and major fatty acid components C_18 : 1  ω7c, C_18 : 0 and C_16 : 0. Strain M0103^T contains a diphosphatidylglycerol, a phosphatidylglycerol, a phosphatidylcholine, a phosphatidy ethanolamine, a phosphatidylinositol, five unidentified phospholipids and four unidentified polar lipids. Based on the 16S rRNA gene sequence analysis, this isolate showed the closest phylogenetic relationship with 'Palleronia pontilimi' GH1-23^T (95.1 %). Values of average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) of genome sequences were of 70.1-76.4 % and 18.3-20.9 % between the isolate and 24 closely related type strains. Analysis the 4.0 Mb genome of strain M0103^T revealed several putative genes associated with cellular stress resistance, which may play protective roles for the isolate in the adaptation to a marine environment. Phylogenetic, phenotypic and chemotaxonomic analyses suggested that strain M0103^T represents a novel genus and novel species of the family Rhodobacteraceae, for which the name Mesobaculum littorinae gen. nov., sp. nov. is proposed. The type strain is M0103^T (=MCCC 1K03619^T=KCTC 62358^T).

Sulfitobacter aestuariivivens sp. nov., isolated from a tidal flat

A Gram-stain-negative, aerobic, non-flagellated, coccoid, ovoid or rod-shaped bacterial strain, TSTF-M16^T, was isolated from a tidal flat on the Yellow Sea, Republic of Korea. The neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that strain TSTF-M16^T fell within a clade comprising the type strains of Sulfitobacter species. Strain TSTF-M16^T exhibited 16S rRNA gene sequence similarities of 98.5 and 98.1 % to the type strains of Sulfitobacter mediterraneus and Sulfitobacter sabulilitoris, respectively, and 96.2-97.8 % to the type strains of the other Sulfitobacter species. The average nucleotide identity and digital DNA-DNA hybridization values between the genomic sequences of strain TSTF-M16^T and the type strains of 16 Sulfitobacter species were 70.6-74.2 and 17.9-19.0 %, respectively. The DNA G+C content of strain TSTF-M16^T from genomic sequence data was 59.26 mol%. Strain TSTF-M16^T contained Q-10 as the predominant ubiquinone and C_18 : 1  ω7c as the major fatty acid. The major polar lipids of strain TSTF-M16^T were phosphatidylcholine, phosphatidylglycerol, one unidentified aminolipid and one unidentified lipid. Distinguished phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain TSTF-M16^T is separated from recognized Sulfitobacter species. On the basis of the data presented here, strain TSTF-M16^T is considered to represent a novel species of the genus Sulfitobacter, for which the name Sulfitobacter aestuariivivens sp. nov. is proposed. The type strain is TSTF-M16^T (=KACC 21645^T=NBRC 114501^T).

Sulfitobacter alexandrii sp. nov., a new microalgae growth-promoting bacterium with exopolysaccharides bioflocculanting potential isolated from marine phycosphere

Marine phycosphere harbors unique cross-kingdom associations with enormous ecological significance in aquatic ecosystems as well as relevance for algal biotechnology industry. During our investigating the microbial composition and bioactivity of marine phycosphere microbiota (PM), a novel lightly yellowish and versatile bacterium designated strain AM1-D1^T was isolated from cultivable PM of marine dinoflagellate Alexandrium minutum amtk4 that produces high levels of paralytic shellfish poisoning toxins (PSTs). Strain AM1-D1^T demonstrates notable bioflocculanting bioactivity with bacterial exopolysaccharides (EPS), and microalgae growth-promoting (MGP) potential toward its algal host. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain AM1-D1^T was affiliated to the members of genus Sulfitobacter within the family Rhodobacteraceae, showing the highest sequence similarity of 97.9% with Sulfitobacter noctilucae NB-68^T, and below 97.8% with other type strains. The complete genome of strain AM1-D1^T consisted of a circular 3.84-Mb chromosome and five circular plasmids (185, 95, 15, 205 and 348 Kb, respectively) with the G+C content of 64.6%. Low values obtained by phylogenomic calculations on the average nucleotide identity (ANI, 77.2%), average amino acid identity (AAI, 74.7%) and digital DNA-DNA hybridization (dDDH, 18.6%) unequivocally separated strain AM1-D1^T from its closest relative. The main polar lipids were identified as phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, diphosphatidylglycerol, one unidentified phospholipid and one unidentified lipid. The predominant fatty acids (> 10%) were C_18:1 ω7c, C_19:0 cyclo ω8c and C_16:0. The respiratory quinone was Q-10. The genome of strain AM1-D1^T was predicted to encode series of gene clusters responsible for sulfur oxidation (sox) and utilization of dissolved organic sulfur exometabolites from marine dinoflagellates, taurine (tau) and dimethylsulfoniopropionate (DMSP) (dmd), as well as supplementary vitamin B₁₂ (cob), photosynthesis carotenoids (crt) which are pivotal components during algae-bacteria interactions. Based on the evidences by the polyphasic characterizations, strain AM1-D1^T represents a novel species of the genus Sulfitobacter, for which the name Sulfitobacter alexandrii sp. nov. is proposed. The type strain is AM1-D1^T (= CCTCC 2017277T = KCTC 62491^T).

Characterization of multidrug resistance in Vibrio species isolated from marine invertebrates from Andaman Sea

This study describes the abundance of multidrug-resistant Vibrios associated with marine invertebrate hosts from the Andaman Sea, India. Thirty-eight Vibrio strains were isolated from surface mucus layers of coral Porites, Goniastrea, Pocillopora, Fungia, and eggs of spiny lobster (Panulirus penicillatus). Phenotypically, the majority of strains exhibited growth at a wide range of temperatures, salt tolerance, and diverse nutritional requirements. All the strains had more than 97% 16S rRNA sequence similarity with type species of the genus Vibrio where Vibrio fortis, and Vibrio alginolyticus were predominant. Multilocus Sequence Analysis (MLSA) using eight housekeeping genes namely ftsZ, gapA, gyrB, mreB, pyrH, recA, rpoA, and topA distributed the strains into 6 reported clades i.e., Harveyi, Ponticus, Nereis, Orientalis, Splendidus, and Mediterranei where nearly half of the total strains represented the clade Harveyi, followed by the clade Splendidus. Likewise, the PFGE profile indicated genomic heterogeneity among the strains resulting in their distribution in five major clusters. Resistance to different antimicrobials was tested following the disc diffusion method where all strains were found susceptible to chloramphenicol (30 µg) and resistant to streptomycin (10 µg), vancomycin (30 µg), sulfamethoxazole-trimethoprim (25 µg). Moreover, the resistant phenotype to other antimicrobials confirmed the abundance of multidrug resistance strains in this marine environment.

Description of Sulfitobacter sediminilitoris sp. nov., isolated from a tidal flat

A Gram-stain-negative bacterial strain, JBTF-M27T, was isolated from a tidal flat from Yellow Sea, Republic of Korea. Neighbor-joining phylogenetic tree of 16S rRNA gene sequences showed that strain JBTF-M27T fell within the clade comprising the type strains of Sulfitobacter species. Strain JBTF-M27T exhibited the highest 16S rRNA gene sequence similarity (98.8%) to the type strain of S. porphyrae. Genomic ANI and dDDH values of strain JBTF-M27T between the type strains of Sulfitobacter species were less than 76.1 and 19.2%, respectively. Mean DNA-DNA relatedness value between strain JBTF-M27T and the type strain of S. porphyrae was 21%. DNA G + C content of strain JBTF-M27T from genome sequence was 57.8% (genomic analysis). Strain JBTF-M27T contained Q-10 as the predominant ubiquinone and C18:1ω7c as the major fatty acid. The major polar lipids of strain JBTF-M27T were phosphatidylcholine, phosphatidylglycerol and one unidentified aminolipid. Distinguished phenotypic properties, along with the phylogenetic and genetic distinctiveness, revealed that strain JBTF-M27T is separated from recognized Sulfitobacter species. On the basis of the data presented, strain JBTF-M27T ( = KACC 21648T = NBRC 114356T) is considered to represent a novel species of the genus Sulfitobacter, for which the name Sulfitobacter sediminilitoris sp. nov. is proposed.

Antarcticimicrobium sediminis gen. nov., sp. nov., isolated from Antarctic intertidal sediment, transfer of Ruegeria lutea to Antarcticimicrobium gen. nov. as Antarcticimicrobium luteum comb. nov

A Gram-stain-negative, aerobic, non-flagellated and rod- or ovoid-shaped bacterium, designated as strain S4J41^T, was isolated from Antarctic intertidal sediment. The isolate grew at 0-37 °C and with 0.5-10 % (w/v) NaCl. It reduced nitrate to nitrite and hydrolysed Tween 80 and gelatin. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain S4J41^T constituted a distinct phylogenetic line within the family Rhodobacteraceae and was closely related with some species in the genera Ruegeria, Phaeobacter, Pseudopuniceibacterium, Sulfitobacter, Puniceibacterium and Poseidonocella with 98.6-95.7 % 16S rRNA gene sequence similarities. The major cellular fatty acids were C_16 : 0, summed feature 8 (C_18 : 1  ω7c and/or C_18 : 1  ω6c) and C_18 : 0 and the major polar lipids were phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, phosphatidylethanolamine and one unidentified aminolipid. The sole respiratory quinone was Q-10. The genomic DNA G+C content of strain S4J41^T was 60.3 mol%. Based on the phylogenetic, chemotaxonomic and phenotypic data obtained in this study, strain S4J41^T is considered to represent a novel species in a new genus within the family Rhodobacteraceae, for which the name Antarcticimicrobium sediminis gen. nov., sp. nov. is proposed. The type strain is S4J41^T (=MCCC 1K03508^T=KCTC 62793^T). Moreover, the transfer of Ruegeria lutea Kim et al. 2019 to Antarcticimicrobium gen. nov. as Antarcticimicrobium luteum comb. nov. (type strain 318-1^T=JCM 30927^T=KCTC 72105^T) is also proposed.

Sulfitobacter profundi sp. nov., isolated from deep seawater

A Gram-stain-negative, rod-shaped, obligately aerobic, chemoheterotrophic bacterium which is motile by means of a single polar flagellum, designated SAORIC-263^T, was isolated from deep seawater of the Pacific Ocean. Phylogenetic analyses based on 16S rRNA gene sequences and genomebased phylogeny revealed that strain SAORIC-263^T belonged to the genus Sulfitobacter and shared 96.1-99.9% 16S rRNA gene sequence similarities with Sulfitobacter species. Wholegenome sequencing of strain SAORIC-263^T revealed a genome size of 3.9Mbp and DNA G+C content of 61.3 mol%. The SAORIC-263^T genome shared an average nucleotide identity and digital DNA-DNA hybridization of 79.1-88.5% and 18.9-35.0%, respectively, with other Sulfitobacter genomes. The SAORIC-263^T genome contained the genes related to benzoate degradation, which are frequently found in deep-sea metagenome. The strain contained summed feature 8 (C_18:1ω7c), C_18:1ω7c 11-methyl, and C_16:0 as the predominant cellular fatty acids as well as ubiquinone-10 (Q-10) as the major respiratory quinone. The major polar lipids of the strain were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, and aminolipid. On the basis of taxonomic data obtained in this study, it is suggested that strain SAORIC-263^T represents a novel species of the genus Sulfitobacter, for which the name Sulfitobacter profundi sp. nov. is proposed. The type strain is SAORIC-263^T (= KACC 21183^T = NBRC 113428^T).

Proposal for transfer of Oceanibulbus indolifex Wagner-Döbler et al. 2004 to the genus Sulfitobacter as Sulfitobacter indolifex comb. nov

A polyphasic taxonomic study was undertaken to clarify the exact position of type strain HEL-45T of OceanibulbusindolifexWagner-Döbler et al. 2004. A combination of physiological properties of HEL-45T were similar to those of its closest relatives, Sulfitobacterdelicatus KMM 3584T and Sulfitobacterdubius KMM 3554T. The results of 16S rRNA gene sequences analysis indicated that HEL-45T and the two relatives shared 99.6 % similarity and formed a coherent cluster in the phylogenetic tree. The close relationship between HEL-45T and the two relatives was underpinned by the results for chemotaxonomic characters, including the fatty acids, quinone and polar lipids. The digital DNA-DNA hybridization values and between HEL-45T and the two relatives were 25.9 and 31.6 %, respectively, which were well below the 70 % threshold value recommended for delineation of bacterial species. The comparative phenotypic and genotypic analyses supported the incorporation of Oceanibulbusindolifex into the genus Sulfitobacter as Sulfitobacterindolifex comb. nov.; the type strain is HEL-45T (=MCCC 1A11773T=DSM 14862T=NCIMB 13983T).