Paralimibaculum aggregatum gen. nov. sp. nov. and Biformimicrobium ophioploci gen. nov. sp. nov., two novel heterotrophs from brittle star Ophioplocus japonicus

Two novel Gram-stain-negative, strictly aerobic, halophilic and non-motile bacterial strains, designated NKW23T and NKW57T, were isolated from a brittle star Ophioplocus japonicus collected from a tidal pool in Wakayama, Japan. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that NKW23T represented a member of the family Paracoccaceae, with Limibaculum halophilum CAU 1123T as its closest relative (94.4% sequence identity). NKW57T was identified as representing a member of the family Microbulbiferaceae, with up to 94.9% sequence identity with its closest relatives. Both strains displayed average nucleotide identity (ANI) and digital DNA-DNA hybridisation (dDDH) values below the species delimitation threshold against their closest relatives. Additionally, amino acid identity (AAI) values of both strains fell below the genus-defining threshold. Phylogenetic trees based on genome sequences indicated that NKW23T formed a novel lineage, branching deeply prior to the divergence of the genera Limibaculum and Thermohalobaculum, with an evolutionary distance (ED) of 0.31-0.32, indicative of genus-level differentiation. NKW57T similarly formed a distinct lineage separate from the species of the genus Microbulbifer. The major respiratory quinones of NKW23T and NKW57T were ubiquinone-10 (Q-10) and Q-8, respectively. The genomic DNA G+C contents of NKW23T and NKW57T were 71.4 and 58.8%, respectively. On the basis of the physiological and phylogenetic characteristics, it was proposed that these strains should be classified as novel species representing two novel genera: Paralimibaculum aggregatum gen. nov., sp. nov., with strain NKW23T (=JCM 36220T=KCTC 8062T) as the type strain, and Biformimicrobium ophioploci gen. nov., sp. nov., with strain NKW57T (=JCM 36221T=KCTC 8063T) as the type strain.

Microbulbifer spongiae sp. nov., isolated from marine sponge Diacarnus erythraeanus

A novel bacterium, designated as MI-GT, was isolated from marine sponge Diacarnus erythraeanus. Cells of strain MI-GT are Gram-stain-negative, aerobic, and rod or coccoid-ovoid in shape. MI-GT is able to grow at 10-40 °C (optimum, 28 °C), with 1.0-8.0% (w/v) NaCl (optimum, 4.0%), and at pH 5.5-9.0 (optimum, pH 8.0). The 16S rRNA gene sequence of strain MI-GT shows 98.35, 97.32 and 97.25% similarity to those of Microbulbifer variabilis Ni-2088T, Microbulbifer maritimus TF-17T and Microbulbifer echini AM134T, respectively. Phylogenetic analysis also exhibits that strain MI-GT falls within a clade comprising members of the genus Microbulbifer (class Gammaproteobacteria). The genome size of strain MI-GT is 4478124 bp with a G+C content of 54.51 mol%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain MI-GT and other type strains are 71.61-76.44% (ANIb), 83.27-84.36% (ANIm) and 13.4-18.7% (dDDH), respectively. These values are significantly lower than the recommended threshold values for bacterial species delineation. Percentage of conserved proteins and average amino acid identity values among the genomes of strain MI-GT and other closely related species are 52.04-59.13% and 67.47-77.21%, respectively. The major cellular fatty acids of MI-GT are composed of summed feature 8 (C18 : 1 ω7c or C18 : 1 ω6c), iso-C11 : 0 3-OH, iso-C15 : 0, C16 : 0, and summed feature 9 (C17 : 1 iso ω9c or C16 : 0 10-methyl). The polar lipids of MI-GT mainly consist of phosphatidylethanolamine, phosphatidylglycerol, aminolipid, and two glycolipids. The major respiratory quinone is Q-8. Based on differential phenotypic and phylogenetic data, strain MI-GT is considered to represent a novel species of genus Microbulbifer, for which the name Microbulbifer spongiae sp. nov. is proposed. The type strain is MI-GT (=MCCC 1K07826T=KCTC 8081T).

Polymer degrading marine Microbulbifer bacteria: an un(der)utilized source of chemical and biocatalytic novelty

Microbulbifer is a genus of halophilic bacteria that are commonly detected in the commensal marine microbiomes. These bacteria have been recognized for their ability to degrade polysaccharides and other polymeric materials. Increasingly, Microbulbifer genomes indicate these bacteria to be an untapped reservoir for novel natural product discovery and biosynthetic novelty. In this review, we summarize the distribution of Microbulbifer bacteria, activities of the various polymer degrading enzymes that these bacteria produce, and an up-to-date summary of the natural products that have been isolated from Microbulbifer strains. We argue that these bacteria have been hiding in plain sight, and contemporary efforts into their genome and metabolome mining are going to lead to a proliferation of Microbulbifer-derived natural products in the future. We also describe, where possible, the ecological interactions of these bacteria in marine microbiomes.

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).

Microbulbifer hainanensis sp. nov., a moderately halopilic bacterium isolated from mangrove sediment

A new bacterium was successfully isolated from a mangrove sediment sample in Haikou City, Hainan Province, China. The organism is a Gram-negative, rod-shaped, non-motile and strictly aerobic bacterium, named NBU-8HK146^T. Strain NBU-8HK146^T was able to grow at temperatures of 10-40 °C, at salinities of 0-11% (w/v) and at pH 5.5-9.5. Veoges-Proskauer, methyl red reaction and hydrolysis of Tween 20 were negative. Catalase and oxidase activities, H₂S production, hydrolysis of starch, casein, Tweens 40, 60 and 80 were positive. The major cellular fatty acids were C_16:0, iso-C_15:0 and summed feature 9. The major respiratory quinone was ubiquinone-8 (Q-8). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and two unidentified glycolipids. According to 16S rRNA gene sequence similarities, strain NBU-8HK146^T shared 98.0%, 97.9%, 97.7%, 97.6% and 97.3% similarities to the species with validated name Microbulbifer taiwanensis CC-LN1-12^T, Microbulbifer rhizosphaerae Cs16b^T, Microbulbifer marinus Y215^T, Microbulbifer donghaiensis CN85^T and Microbulbifer aggregans CCB-MM1^T, respectively. Phylogenetic analyses indicated that strain NBU-8HK146^T formed a distinct lineage with strains Microbulbifer taiwanensis CC-LN1-12^T and Microbulbifer marinus Y215^T. Both digital DNA-DNA hybridization values (19.5-22.7%) and average nucleotide identity values (73.2-78.9%) between strain NBU-8HK146^T and related species of genus Microbulbifer were below the species delineation cutoffs. The DNA G+C content was 58.9 mol%. Many proteins involving in the adaption of osmotic stress in the salt environment of mangrove were predicted in genome of strain NBU-8HK146^T. From phenotypic, genotypic, phylogenetic and chemotaxonomic characteristics, strain NBU-8HK146^T can be regarded as a new Microbulbifer species for which the name Microbulbifer hainanensis. The type strain is NBU-8HK146^T (= KCTC 82226^T = MCCC 1K04737^T).

Bulbimidazoles A-C, Antimicrobial and Cytotoxic Alkanoyl Imidazoles from a Marine Gammaproteobacterium Microbulbifer Species

Three new alkanoyl imidazoles, designated bulbimidazoles A-C (1-3), were found from the culture extract of the gammaproteobacterium Microbulbifer sp. DC3-6 isolated from a stony coral of the genus Tubastraea. The absolute configuration of the anteiso-methyl substitution in 1 was established to be a mixture of (R)- and (S)-configurations in a ratio of 9:91 by applying the Ohrui-Akasaka method. Compounds 1-3 displayed unique broad-spectrum antimicrobial activity against Gram-positive and -negative bacteria and fungi with MICs ranging from 0.78 to 12.5 μg/mL. They also exhibited cytotoxicity toward P388 murine leukemia cells with IC₅₀ in the micromolar range.

Isolation and biosynthesis of an unsaturated fatty acid with unusual methylation pattern from a coral-associated bacterium Microbulbifer sp

(2Z,4E)-3-Methyl-2,4-decadienoic acid (1) was identified as a major metabolite from a culture extract of a marine bacterium Microbulbifer which was collected from a stony coral Porites sp. NMR-based spectroscopic analysis revealed that 1 is an unsaturated fatty acid in which a methyl group is located in an uncommon position as a natural product. Feeding experiments of ¹³C-labeled precursors clarified that ʟ-methionine-derived methylation takes place at the carbon which is derived from the carbonyl carbon of acetate. Compound 1 showed weak growth inhibition against Saccharomyces cerevisiae.

Complete genome sequence of Microbulbifer sp. CCB-MM1, a halophile isolated from Matang Mangrove Forest, Malaysia

Microbulbifer sp. CCB-MM1 is a halophile isolated from estuarine sediment of Matang Mangrove Forest, Malaysia. Based on 16S rRNA gene sequence analysis, strain CCB-MM1 is a potentially new species of genus Microbulbifer. Here we describe its features and present its complete genome sequence with annotation. The genome sequence is 3.86 Mb in size with GC content of 58.85%, harbouring 3313 protein coding genes and 92 RNA genes. A total of 71 genes associated with carbohydrate active enzymes were found using dbCAN. Ectoine biosynthetic genes, ectABC operon and ask_ect were detected using antiSMASH 3.0. Cell shape determination genes, mreBCD operon, rodA and rodZ were annotated, congruent with the rod-coccus cell cycle of the strain CCB-MM1. In addition, putative mreBCD operon regulatory gene, bolA was detected, which might be associated with the regulation of rod-coccus cell cycle observed from the strain.

A taxonomic framework for emerging groups of ecologically important marine gammaproteobacteria based on the reconstruction of evolutionary relationships using genome-scale data

In recent years a large number of isolates were obtained from saline environments that are phylogenetically related to distinct clades of oligotrophic marine gammaproteobacteria, which were originally identified in seawater samples using cultivation independent methods and are characterized by high seasonal abundances in coastal environments. To date a sound taxonomic framework for the classification of these ecologically important isolates and related species in accordance with their evolutionary relationships is missing. In this study we demonstrate that a reliable allocation of members of the oligotrophic marine gammaproteobacteria (OMG) group and related species to higher taxonomic ranks is possible by phylogenetic analyses of whole proteomes but also of the RNA polymerase beta subunit, whereas phylogenetic reconstructions based on 16S rRNA genes alone resulted in unstable tree topologies with only insignificant bootstrap support. The identified clades could be correlated with distinct phenotypic traits illustrating an adaptation to common environmental factors in their evolutionary history. Genome wide gene-content analyses revealed the existence of two distinct ecological guilds within the analyzed lineage of marine gammaproteobacteria which can be distinguished by their trophic strategies. Based on our results a novel order within the class Gammaproteobacteria is proposed, which is designated Cellvibrionales ord. nov. and comprises the five novel families Cellvibrionaceae fam. nov., Halieaceae fam. nov., Microbulbiferaceae fam. nov., Porticoccaceae fam. nov., and Spongiibacteraceae fam. nov.

Gilvimarinus polysaccharolyticus sp. nov., an agar-digesting bacterium isolated from seaweed, and emended description of the genus Gilvimarinus

A taxonomic study was carried out on strain YN3(T), which was isolated from a seaweed sample taken from the coast of Weihai, China. The bacterium was Gram-stain-negative, rod-shaped, and could grow at pH 5.0-10.0 and 4-32 °C in the presence of 0-9.0 % (w/v) NaCl. Strain YN3(T) was positive for the hydrolysis of polysaccharides, such as agar, starch and xylan. The predominant respiratory quinone was ubiquinone-8. The major fatty acids were C16 : 1ω7c and/or iso-C15 : 0 2-OH, C16 : 0 and C18 : 1ω7c. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, and two unidentified glycolipids. The genomic DNA G+C content was 49.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YN3(T) should be assigned to the genus Gilvimarinus. 'Gilvimarinus agarilyticus' KCTC 23325 and Gilvimarinus chinensis QM42(T) had the closest phylogenetic relationship to strain YN3(T), and showed 97.9 % and 95.8 % sequence similarities, respectively. On the basis of phenotypic, chemotaxonomic and genotypic data and DNA-DNA hybridization studies, we propose that strain YN3(T) represents a novel species of the genus Gilvimarinus, for which the name Gilvimarinus polysaccharolyticus sp. nov. is proposed. The type strain is YN3(T) ( = KCTC 32438(T) = JCM 19198(T)). An emended description of the genus Gilvimarinus is also presented.

Pleionea mediterranea gen. nov., sp. nov., a gammaproteobacterium isolated from coastal seawater

A Gram-negative, aerobic, cream-pigmented, non-motile, non-spore-forming straight rod, strain MOLA115T, was isolated from a coastal water sample from the Mediterranean Sea. On the basis of phylogenetic analysis of the 16S rRNA gene sequences, strain MOLA115T was shown to belong to the Gammaproteobacteria , adjacent to members of the genera Marinicella , Arenicella and Kangiella , sharing less than 89 % 16S rRNA gene sequence similarity with strains of all recognized species within the Gammaproteobacteria . The only isoprenoid quinone was ubiquinone-8. Polar lipids in strain MOLA115T included phosphatidylethanolamine, an aminolipid, phosphatidylglycerol and an aminophospholipid. Fatty acid analysis revealed iso-C15 : 0 and iso-C17 : 1ω9c to be the dominant components. The DNA G+C content was 44.5 mol%. Based upon the phenotypic and phylogenetic data, we propose that strain MOLA115T should be considered to represent a novel species in a new genus, for which the name Pleionea mediterranea gen. nov., sp. nov. is proposed. The type strain of Pleionea mediterranea is MOLA115T ( = CIP 110343T = DSM 25350T).

Microbulbifer mangrovi sp. nov., a polysaccharide-degrading bacterium isolated from an Indian mangrove

A rod-shaped, Gram-negative, non-motile, aerobic and non-endospore forming bacterium, designated strain DD-13T, was isolated from the mangrove ecosystem of Goa, India. Strain DD-13T degraded polysaccharides such as agar, alginate, chitin, cellulose, laminarin, pectin, pullulan, starch, carrageenan, xylan and β-glucan. The optimum pH and temperature for growth was 7 and 36 °C, respectively. The strain grew optimally in the presence of 3 % NaCl (w/v). The DNA G+C content was 61.4 mol%. The predominant fatty acid of strain DD-13T was iso-C15 : 0. Ubiquinone-8 was detected as the major respiratory lipoquinone. Phylogenetic studies based on 16S rRNA gene sequence analysis demonstrated that strain DD-13T formed a coherent cluster with species of the genus Microbulbifer . Strain DD-13T exhibited 16S rRNA gene sequence similarity levels of 98.9–97.1 % with Microbulbifer hydrolyticus IRE-31T, Microbulbifer salipaludis JCM 11542T, Microbulbifer agarilyticus JAMB A3T, Microbulbifer celer KCTC 12973T and Microbulbifer elongatus DSM 6810T. However, the level of DNA–DNA relatedness between strain DD-13T and the five type strains of these species of the genus Microbulbifer were in the range of 26–33 %. Additionally, strain DD-13T demonstrates several phenotypic differences from these type strains of species of the genus Microbulbifer . Thus strain DD-13T represents a novel species of the genus Microbulbifer , for which the name Microbulbifer mangrovi sp. nov. is proposed with the type strain DD-13T ( = KCTC 23483T = JCM 17729T).

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.