Microbulbifer litoralis sp. nov., Isolated from Seashore of Weizhou Island

A bacterium designated GXH0434T was isolated from sea shore samples collected from Weizhou Island, Beihai, Guangxi, China. The organism is motile, strictly aerobic, and possesses a rod-coccus cell cycle in association with the growth phase. It can grow at 15-45 °C (optimum 37 °C), at pH 6.0-11.0 (optimum 6.0), and at 0-20% (w/v) NaCl (optimum 5.0-8.0%). The strain is positive for peroxidase and oxidase activity, negative for Voges-Proskauer test, can hydrolyze Tween 20, Tween 60, Tween 80, casein, and is able to produce siderophore and has the function of nitrogen fixation. Molecular phylogenetic analysis based on 16S rRNA gene sequences indicated that GXH0434T was most closely related to Microbulbifer halophilus KCTC 12848T with the similarity of 97.2%, followed by Microbulbifer chitinilyticus JCM 16148T (97.1%) and Microbulbifer taiwanensis LMG 26125T (96.5%). The digital DNA-DNA hybridization and the average nucleotide identity values between GXH0434T and Microbulbifer halophilus KCTC 12848T were 28.90% and 83.38%, respectively, which were below thresholds of species delineation. The genomic DNA G+C content of the strain was 61.9%. The major fatty acids were iso-C15:0, C16:0, iso-C11:0 3-OH, iso-C11:0 and Summed features 8 (C18:0 ω7c and/or C18:0 ω6c). The major polar lipids detected in GXH0434T were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC). The major respiratory quinone was ubiquinone Q-8. Based on the above polyphasic classification indicated strain GXH0434T represents a novel species of the genus Microbulbifer, for which the name Microbulbifer litoralis sp. nov. is proposed. The type strain is GXH0434T (= MCCC 1K07158T = KCTC 92169T).

Microbulbifer okhotskensis sp. nov., isolated from a deep bottom sediment of the Okhotsk Sea

A Gram-negative, aerobic, non-motile bacterium КMM 9862^T was isolated from a deep bottom sediment sample obtained from the Okhotsk Sea, Russia. Based on the 16S rRNA gene and whole genome sequences analyses the novel strain КMM 9862^T fell into the genus Microbulbifer (class Gammaproteobacteria) sharing the highest 16S rRNA gene sequence similarities of 97.4% to Microbulbifer echini AM134^T and Microbulbifer epialgicus F-104^T, 97.3% to Microbulbifer pacificus SPO729^T, 97.1% to Microbulbifer variabilis ATCC 700307^T, and similarity values of < 97.1% to other recognized Microbulbifer species. The average nucleotide identity and digital DNA-DNA hybridization values between strain КMM 9862^T and M. variabilis ATCC 700307^T and M. thermotolerans DSM 19189^T were 80.34 and 77.72%, and 20.2 and 19.0%, respectively. Strain КMM 9862^T contained Q-8 as the predominant ubiquinone and C_16:0, C_16:1 ω7c, C_12:0, and C_10:0 3-OH as the major fatty acids. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, an unidentified aminophospholipid, an unidentified aminolipid, two unidentified phospholipids, phosphatidic acid, and an unidentified lipid. The DNA G+C content of 49.8% was calculated from the genome sequence. On the basis of the phylogenetic evidence and distinctive phenotypic characteristics, the marine bacterium KMM 9862^T is proposed to be classified as a novel species Microbulbifer okhotskensis sp. nov. The type strain of the species is strain KMM 9862^T (= KACC 22804^T).

From ecophysiology to cultivation methodology: filling the knowledge gap between uncultured and cultured microbes

Earth is dominated by a myriad of microbial communities, but the majority fails to grow under in situ laboratory conditions. The basic cause of unculturability is that bacteria dominantly occur as biofilms in natural environments. Earlier improvements in the culture techniques are mostly done by optimizing media components. However, with technological advancement particularly in the field of genome sequencing and cell imagining techniques, new tools have become available to understand the ecophysiology of microbial communities. Hence, it becomes easier to mimic environmental conditions in the culture plate. Other methods include co-culturing, emendation of growth factors, and cultivation after physical cell sorting. Most recently, techniques have been proposed for bacterial cultivation by employing genomic data to understand either microbial interactions (network-directed targeted bacterial isolation) or ecosystem engineering (reverse genomics). Hopefully, these techniques may be applied to almost all environmental samples, and help fill the gaps between the cultured and uncultured microbial communities.

Microbulbifer harenosus sp. nov., an alginate-degrading bacterium isolated from coastal sand

A Gram-stain-negative, aerobic, rod-shaped bacterium with peritrichous flagella, designated strain HB161719^T, was isolated from coastal sand collected from Tanmen Port in Hainan, PR China. The isolate was found to grow with 2-11 % (w/v) NaCl, at 15-45 °C and pH 6.0-10.0, with an optima of 2-3 % NaCl, 37 °C and pH 7.0, respectively. Chemotaxonomic analysis showed that Q-8 was detected as the sole respiratory quinone and that iso-C_15 : 0 and summed features 3, 8 and 9 were the major cellular fatty acids. The G+C content of the genomic DNA was 58.2 mol%. Analysis of the 16S rRNA gene sequence of the strain showed an affiliation with the genus Microbulbifer, sharing 98.7, 98.4, 97.8 and 97.8 % sequence similarities to the closest relatives of Microbulbifer okinawensis ABABA23^T, Microbulbifer pacificus SPO729^T, Microbulbifer taiwanensis CC-LN1-12^T and Microbulbifer gwangyangensis GY2^T, respectively. Low DNA-DNA hybridization values showed that it formed a distinct genomic species. The combined phenotypic and molecular features supported that strain HB161719^T represents a novel species of the genus Microbulbifer, for which the name Microbulbifer harenosus sp. nov. is proposed. The type strain is HB161719^T (=CGMCC 1.13584^T=JCM 32688^T).

Microbulbifer echini sp. nov., isolated from the gastrointestinal tract of a purple sea urchin, Heliocidaris crassispina

A novel bacterium, designated as strain AM134T, was isolated from the gut of a purple sea urchin (Heliocidaris crassispina) gathered from the coastal waters of Dokdo, Korea. Strain AM134T was Gram-stain-negative, both catalase- and oxidase-positive, strictly aerobic and showed a rod-coccus cell cycle. Optimum growth occurred at 30 °C, in the presence of 2 % (w/v) NaCl and at pH 7. The 16S rRNA gene sequence analysis showed that strain AM134T belonged to the genus Microbulbifer in the family Alteromonadaceae and had high 16S rRNA gene sequence similarity (>97 %) with Microbulbifer epialgicus F-104T (98.9 % similarity) and Microbulbifer variabilis Ni-2088T (98.6 % similarity). The polar lipid profile of strain AM134T was composed of phosphatidylethanolamine, phosphatidylserine, three unidentified aminophospholipids, two unidentified phospholipids, an unidentified amino lipid and six unidentified lipids. The major respiratory quinone was identified as ubiquinone-8 (Q-8). The major cellular fatty acids were summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c) and C16 : 0. The DNA-DNA hybridization analysis showed that the strain shared less than 28 % genomic relatedness with Microbulbifer epialgicus DSM 18651T (27±3 %) and Microbulbifer variabilis ATCC 700307T (15±1 %). The G+C content of the genomic DNA was 56.1 mol%. The results of the phylogenetic, phenotypic and genotypic analyses suggest that strain AM134T represents a novel species in the genus Microbulbifer, for which the name Microbulbifer echini is proposed. The type strain is AM134T (=KACC 18258T=JCM 30400T).

Microbulbifer gwangyangensis sp. nov. and Microbulbifer pacificus sp. nov., isolated from marine environments

Two novel Gram-stain-negative, chemoheterotrophic and strictly aerobic bacteria, strains GY2T and SPO729T, were isolated from a tidal flat at Gwangyang Bay in Korea and a marine sponge sample from the Pacific Ocean, respectively. The two strains were halotolerant, catalase- and oxidase-positive, and non-motile rods. Optimum temperature and pH for growth of both strains were observed to be 35 °C and pH 7.0–7.5, but optimum salinity for strain SPO729T [2–3 % (w/v)] was slightly higher than that for strain GY2T (1–2 %). The major cellular fatty acids of both strains were C16 : 0, iso-C15 : 0, iso-C17 : 0, iso-C17 : 1ω9c, C18 : 1ω7c, iso-C11 : 0 and iso-C11 : 0 3-OH. The genomic DNA G+C contents of strains GY2T and SPO729T were 55.1 and 57.9 mol%, respectively, and ubiquinone 8 (Q-8) was detected as the sole respiratory quinone from the two strains. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains GY2T and SPO729T formed tight phyletic lineages with members of the genus Microbulbifer . Strain GY2T was closely related to Microbulbifer okinawensis ABABA23T (98.2 %), strain SPO729T (98.0 %) and Microbulbifer donghaiensis CN85T (97.0 %); strain SPO729T was closely related to M. okinawensis ABABA23T (98.3 %) and M. donghaiensis CN85T (98.2 %). The DNA–DNA relatedness values of strain GY2T with M. okinawensis ABABA23T, strain SPO729T and M. donghaiensis CN85T were 40.0±2.1 %, 13.1±3.9 % and 16.2±5.8 %, respectively, whereas those of strain SPO729T with M. okinawensis ABABA23T and M. donghaiensis CN85T were 48.0±4.0 % and 34.6±9.3 %, respectively. On the basis of phenotypic and molecular features, it is concluded that the two strains GY2T and SPO729T represent two novel species of the genus Microbulbifer , for which the names Microbulbifer gwangyangensis sp. nov. and Microbulbifer pacificus are proposed; the type strains are GY2T ( = KACC 16189T = JCM 17800T) and SPO729T ( = KCCM 42667T = JCM 14507T), respectively.

Microbulbifer marinus sp. nov. and Microbulbifer yueqingensis sp. nov., isolated from marine sediment

Two Gram-negative, aerobic strains, Y215T and Y226T, were isolated from sediment from Yueqing Bay, Zhejiang Province, China. The two novel strains were both positive for oxidase activity, nitrate reduction, and aesculin and casein decomposition, but negative for gelatin and tyrosine decomposition. Catalase activity, and starch and Tween 80 decomposition differed between the two strains. Cells of both novel strains were rod-shaped in young cultures and ovoid in older cultures. Optimum NaCl concentration and pH range for growth of both strains were 2.0–3.0 % (w/v) and 7.0–8.0, respectively, whereas the optimum growth temperature for strain Y215T (25–30 °C) was lower than that for strain Y226T (30–37 °C). The genomic DNA G+C contents of strains Y215T and Y226T were 54.0 and 56.7 mol%, respectively. The major fatty acids in both isolates were iso-C15 : 0 and iso-C17 : 1ω9c, which was also the case in the reference strains apart from Microbulbifer salipaludis, which possessed C18 : 1ω7c as the predominant fatty acid. The predominant isoprenoid quinone was Q-8 and the major polar lipids of both strains were phosphatidylethanolamine, phosphatidylglycerol and an unknown glycolipid. Both strains had highest 16S rRNA gene sequence similarity to members of the genus Microbulbifer. Strain Y215T was closely related to the type strains of Microbulbifer maritimus (97.6 %) and Microbulbifer donghaiensis (97.5 %), whereas strain Y226T was closely related to the type strain of M. salipaludis (97.6 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strains Y215T and Y226T fell into two separate clusters. The DNA–DNA relatedness values of strain Y215T with M. maritimus TF-17T and M. donghaiensis CN85T were 34.1 and 32.8 %, respectively, whereas that between strain Y226T and M. salipaludis SM-1T was 38.0 %; these values are significantly lower than the threshold value for the delineation of bacterial species. On the basis of their distinct taxonomic characteristics, the two isolates represent two novel species of the genus Microbulbifer, for which the names Microbulbifer marinus sp. nov. and Microbulbifer yueqingensis sp. nov. are proposed; the type strains are Y215T ( = CGMCC 1.10657T = JCM 17211T) and Y226T ( = CGMCC 1.10658T = JCM 17212T), respectively.

Microbulbifer taiwanensis sp. nov., isolated from coastal soil

A Gram-negative, non-spore-forming rod (CC-LN1-12(T)) was isolated from coastal soil samples of Lutao Island (Green Island), Taiwan, and its taxonomic position was studied. 16S rRNA gene sequence analysis showed that isolate CC-LN1-12(T) was grouped into the Microbulbifer cluster, with the highest similarities to Microbulbifer okinawensis ABABA23(T) (97.9 %), Microbulbifer maritimus TF-17(T) (97.7 %) and Microbulbifer donghaiensis CN85(T) (97.7 %), similarities to all other species of the genus Microbulbifer were lower than 96.8 %. The polyamine pattern contained the major compounds spermidine and cadaverine. The fatty acid profile, comprising the major fatty acids iso-C(15 : 0), iso-C(17 : 1)ω9c, C(18 : 1)ω7c and iso-C(11 : 0) 3-OH as the major hydroxylated fatty acid, supported the affiliation of strain CC-LN1-12(T) to the genus Microbulbifer. DNA-DNA hybridizations between strain CC-LN1-12(T) and Microbulbifer okinawensis ABABA23(T), M. donghaiensis CN85(T) and M. maritimus JCM 12187(T) resulted in relatedness values of 21.5 % (14.3 %, reciprocal analysis), 35.9 % (48.5 %, reciprocal analysis) and 48.1 % (52.1 %, reciprocal analysis), respectively. From these data, as well as from physiological and biochemical tests, strain CC-LN1-12(T) could be clearly differentiated from the most closely related species of the genus Microbulbifer. It is concluded that strain CC-LN1-12(T) represents a novel species, for which the name Microbulbifer taiwanensis sp. nov. is proposed. The type strain is CC-LN1-12(T) ( = LMG 26125(T) = CCM 7856(T)).

Microbulbifer chitinilyticus sp. nov. and Microbulbifer okinawensis sp. nov., chitin-degrading bacteria isolated from mangrove forests

Three chitin-degrading strains representing two novel species were isolated from mangrove forests in Okinawa, Japan. The isolates, ABABA23(T), ABABA211 and ABABA212(T), were Gram-negative, non-spore-forming, strictly aerobic chemo-organotrophs. The novel strains produced Q-8 as the major isoprenoid quinone component. The predominant fatty acids were iso-C₁₅:₀ and C₁₆:₀. On the basis of 16S rRNA gene sequence analysis, the isolates were closely affiliated with members of the genus Microbulbifer. The DNA G+C contents of strains ABABA23(T) and ABABA212(T) were 57.8 and 60.2 mol%, respectively. DNA-DNA relatedness values between these two strains and Microbulbifer reference strains were significantly lower than 70 %, the generally accepted threshold level below which strains are considered to belong to separate species. Based on differences in taxonomic characteristics, the three isolates represent two novel species of the genus Microbulbifer, for which the names Microbulbifer chitinilyticus sp. nov. (type strain, ABABA212(T) = JCM 16148(T) = NCIMB 14577(T)) and Microbulbifer okinawensis sp. nov. (type strain, ABABA23(T) = JCM 16147(T) = NCIMB 14576(T); reference strain, ABABA211) are proposed.

Arenicella xantha gen. nov., sp. nov., a gammaproteobacterium isolated from a marine sandy sediment

A Gram-negative, aerobic, yellow-pigmented, rod-shaped, non-motile bacterium, strain KMM 3895T, was isolated from a marine sandy sample collected offshore from the Sea of Japan. Phylogenetic analysis based on the 16S rRNA gene sequence placed strain KMM 3895T in the class Gammaproteobacteria, forming a separate branch, sharing 89.5 % sequence similarity with Nitrincola lacisaponensis 4CAT and 88–87 % similarity with the other members of the cluster, including members of Kangiella, Spongiibacter, Alcanivorax and Microbulbifer. The major isoprenoid quinone was Q-8. Polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, aminophospholipid and an unknown phospholipid. Fatty acid analysis revealed C16 : 1 ω7, iso-C16 : 0, iso-C18 : 0 and C18 : 1 ω7 as dominant components. The DNA G+C content was determined to be 48.1 mol%. Based on its unique phenotypic characteristics and phylogenetic distance, the marine coastal sediment isolate KMM 3895T should be classified as a representative of a novel genus and species, for which the name Arenicella xantha gen. nov., sp. nov. is proposed. The type strain of Arenicella xantha is KMM 3895T (=NRIC 0759T =JCM 16153T).

Marinicella litoralis gen. nov., sp. nov., a gammaproteobacterium isolated from coastal seawater

A Gram-negative, aerobic, greyish–yellowish-pigmented, stenohaline, rod-shaped, non-motile bacterium, strain KMM 3900T, was isolated from a coastal seawater sample collected from the Sea of Japan. Based on phylogenetic analysis, strain KMM 3900T was positioned within the Gammaproteobacteria on a separate branch adjacent to members of the genera Reinekea and Kangiella, sharing less than 88 % 16S rRNA gene sequence similarity with all recognized species of the Gammaproteobacteria. The major isoprenoid quinone was Q-8. Polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and two unknown phospholipids. Fatty acid analysis revealed iso-C15 : 0, C16 : 1 ω7c and C16 : 0 as the dominant components. The DNA G+C content was 43.8 mol%. Based on its unique phenotypic characteristics and phylogenetic remoteness, marine isolate KMM 3900T is considered to represent a novel genus and species, for which the name Marinicella litoralis gen. nov., sp. nov. is proposed. The type strain of Marinicella litoralis is KMM 3900T (=NRIC 0758T =JCM 16154T).

Characterization of Microbulbifer strain CMC-5, a new biochemical variant of Microbulbifer elongatus type strain DSM6810T isolated from decomposing seaweeds

A Gram-negative, rod-shaped, non-spore forming, non-motile and moderate halophilic bacteria designated as strain CMC-5 was isolated from decomposing seaweeds by enrichment culture. The growth of strain CMC-5 was assessed in synthetic seawater-based medium containing polysaccharide. The bacterium degraded and utilized agar, alginate, carrageenan, xylan, carboxymethyl cellulose and chitin. The strain was characterized using a polyphasic approach for taxonomic identification. Cellular fatty acid analysis showed the presence of iso-C(15:0) as major fatty acid and significant amounts of iso-C(17:1x9c) and C(18:1x7c). Phylogenetic analysis based on 16S rDNA sequence indicated that strain CMC-5 is phylogenetically related to Microbulbifer genus and 99% similar to type strain Microbulbifer elongatus DSM6810T. However in contrast to Microbulbifer elongatus DSM6810T, strain CMC-5 is non-motile, utilizes glucose, galactose, inositol and xylan, does not utilize fructose and succinate nor does it produce H2S. Further growth of bacterial strain CMC-5 was observed when inoculated in seawater-based medium containing sterile pieces of Gracilaria corticata thalli. The bacterial growth was associated with release of reducing sugar in the broth suggesting its role in carbon recycling of polysaccharides from seaweeds in marine ecosystem.

Umboniibacter marinipuniceus gen. nov., sp. nov., a marine gammaproteobacterium isolated from the mollusc Umbonium costatum from the Sea of Japan

Two bacterial strains, KMM 3891(T) and KMM 3892, were isolated from internal tissues of the marine mollusc Umbonium costatum collected from the Sea of Japan. The novel isolates were Gram-negative, aerobic, faint pink-reddish-pigmented, rod-shaped, non-motile, stenohaline and psychrotolerant bacteria that were unable to degrade most tested complex polysaccharides. Polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Fatty acid analysis revealed C(17 : 1)omega6c, C(17 : 0), C(16 : 0) and C(16 : 1)omega7c as the dominant components. The major isoprenoid quinone was Q-7. The DNA G+C content of strain KMM 3891(T) was 51.7 mol%. According to phylogenetic analysis of 16S rRNA gene sequences, strains KMM 3891(T) and KMM 3892 were positioned within the Gammaproteobacteria as a separate branch, sharing <93 % sequence similarity to their phylogenetic relatives including Saccharophagus degradans, Microbulbifer species, Endozoicomonas elysicola, Simiduia agarivorans and Teredinibacter turnerae. Based on phenotypic characterization and phylogenetic distance, the novel marine isolates KMM 3891(T) and KMM 3892 represent a new genus and species, for which the name Umboniibacter marinipuniceus gen. nov., sp. nov. is proposed. The type strain of Umboniibacter marinipuniceus is KMM 3891(T) (=NRIC 0753(T) =JCM 15738(T)).