Degradation Rates and Bacterial Community Compositions Vary among Commonly Used Bioplastic Materials in a Brackish Marine Environment

Plastic pollution threatens both terrestrial and aquatic ecosystems. As a result of the pressures of replacing oil-based materials and reducing the accumulation of litter in the environment, the use of bioplastics is increasing, despite little being known about their accurate biodegradation in natural conditions. Here, we investigated the weight attrition and degradation behavior of four different bioplastic materials compared to conventional oil-based polyethylene during a 1-year in situ incubation in the brackish Baltic Sea and in controlled 1 month biodegradation experiments in the laboratory. Bacterial communities were also investigated to verify whether putative plastic-degrading bacteria are enriched on bioplastics. Poly-l-lactic acid showed no signs of degradation, whereas poly(3-hydroxybutyrate/3-hydroxyvalerate) (PHB/HV), plasticized starch (PR), and cellulose acetate (CA) degraded completely or almost completely during 1-year in situ incubations. In accordance, bacterial taxa potentially capable of using complex carbon substrates and belonging, e.g., to class Gammaproteobacteria were significantly enriched on PHB/HV, PR, and CA. An increase in gammaproteobacterial abundance was also observed in the biodegradation experiments. The results show substantial differences in the persistence and biodegradation rates among bioplastics, thus highlighting the need for carefully selecting materials for applications with risk of becoming marine litter.

Sessilibacter corallicola gen. nov., sp. nov., a sessile bacterium isolated from coral Porites lutea

A Gram-stain-negative, non-spore-forming, motile, aerobic bacterium (strain C21T) was isolated from coral and identified using polyphasic identification approach. Global alignment of 16S rRNA gene sequences indicated that strain C21T shares 95.7 % sequence identity to its closest neighbour, Marinibactrum halimedae NBRC 110095T, followed by other type strains with identities of lower than 95 %. The average nucleotide identity and average amino acid identity values between strain C21T and M. halimedae NBRC 110095T were 69.6 and 64.8 %, respectively, indicating that strain C21T may represent a new species in a new genus. Phylogenetic analysis based on 16S rRNA gene and phylogenomic results indicated that strain C21T forms a distinct branch in the family Cellvibrionaceae. Cellular fatty acids and polar lipids could also readily distinguish strain C21T from closely related type strains. Therefore, strain C21T is suggested to represent a new species in a new genus, for which the name Sessilibacter corallicola gen. nov., sp. nov. is proposed. The type strain is C21T (=MCCC 1K03260T=KCTC 62317T).

Teredinibacter waterburyi sp. nov., a marine, cellulolytic endosymbiotic bacterium isolated from the gills of the wood-boring mollusc Bankia setacea (Bivalvia: Teredinidae) and emended description of the genus Teredinibacter

A cellulolytic, aerobic, gammaproteobacterium, designated strain Bs02^T, was isolated from the gills of a marine wood-boring mollusc, Bankia setacea (Bivalvia: Teredinidae). The cells are Gram-stain-negative, slightly curved motile rods (2-5×0.4-0.6 µm) that bear a single polar flagellum and are capable of heterotrophic growth in a simple mineral medium supplemented with cellulose as a sole source of carbon and energy. Cellulose, carboxymethylcellulose, xylan, cellobiose and a variety of sugars also support growth. Strain Bs02^T requires combined nitrogen for growth. Temperature, pH and salinity optima (range) for growth were 20 °C (range, 10-30 °C), 8.0 (pH 6.5-8.5) and 0.5 M NaCl (range, 0.0-0.8 M), respectively when grown on 0.5 % (w/v) galactose. Strain Bs02^T does not require magnesium and calcium ion concentrations reflecting the proportions found in seawater. The genome size is approximately 4.03 Mbp and the DNA G+C content of the genome is 47.8 mol%. Phylogenetic analyses based on 16S rRNA gene sequences, and on conserved protein-coding sequences, show that strain Bs02^T forms a well-supported clade with Teredinibacter turnerae. Average nucleotide identity and percentage of conserved proteins differentiate strain Bs02^T from Teredinibacter turnerae at threshold values exceeding those proposed to distinguish bacterial species but not genera. These results indicate that strain Bs02^T represents a novel species in the previously monotypic genus Teredinibacter for which the name Teredinibacter waterburyi sp. nov. is proposed. The strain has been deposited under accession numbers ATCC TSD-120^T and KCTC 62963^T.

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).

Agarilytica rhodophyticola gen. nov., sp. nov., isolated from Gracilaria blodgettii

A novel Gram-stain-negative, rod-shaped, non-spore-forming, aerobic, agarolytic bacterium, designated 017^T, was isolated from Gracilaria blodgettii collected at the coast of Lingshui county, Hainan province, China. Optimal growth occurred at 28-33 °C (range 15-40 °C), with 3 % (w/v) NaCl (range 2-4 %) and at pH 8.0 (range pH 6.5-8.5). Cells of strain 017^T were motile and formed yellow colonies on marine agar 2216. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 017^T shared the highest similarity with Teredinibacter turnerae T7902^T (94.4 %). The predominant polar lipids of the novel isolate consisted of phosphatidylglycerol, phosphatidylethanolamine, aminophospholipid and some other unknown lipids. Major cellular fatty acids (>10 %) were C16 : 0, C18 : 1ω7c and summed feature 3 (C16 : 1ω7c/iso-C15 : 0 2-OH), and the sole respiratory lipoquinone was Q-8. The DNA G+C content of strain 017^T was 40.2 mol%. Comparative analysis of 16S rRNA gene sequences and phenotypic characterization indicated that strain 017^T represents a novel species in a new genus of the family Cellvibrionaceae, order Cellvibrionales, for which the name Agarilytica rhodophyticola gen. nov., sp. nov. is proposed. The type strain of Agarilytica rhodophyticola is 017^T (=KCTC 42584^T=MCCC 1H00123^T).

Marinibactrum halimedae gen. nov., sp. nov., a gammaproteobacterium isolated from a marine macroalga

Phylogenetic and taxonomic characterization was performed for a bacterium, designated strain Q-192T, isolated from the surface of the green macroalga Halimeda sp., collected from the subtropical Ishigaki Island, Japan. The isolate was a polysaccharide-producing, Gram-stain-negative, aerobic, rod-shaped, motile bacterium with a polar flagellum. The isolate was slightly halophilic, required Na+, Mg2+ and Ca2+ ions for growth, but did not require growth factors. The only isoprenoid quinone was ubiquinone-8.The major cellular fatty acids were C18 : 1ω7c, C16 : 0 and C14 : 0. The main hydroxy fatty acid was C10 : 0 3-OH. The DNA G+C content was 45.9 mol%. Phylogenetic analysis of 16S rRNA gene sequences placed the isolate in the class Gammaproteobacteria. The phylogenetically closest relatives with validly published names were Pseudomaricurvus alkylphenolicus KU41GT, Teredinibacter turnerae T7902T, Pseudoteredinibacter isoporae SW-11T and Simiduia agarivorans SA1T with sequence similarities of 94.5, 94.1, 93.7 and 93.6 %, respectively. The isolate was distinguished from members of these genera by a combination of DNA G+C content, chemotaxonomic characteristics (respiratory quinone system, fatty acid profile and polar lipid composition) and other phenotypic features. Based on phylogenetic, genotypic, chemotaxonomic and phenotypic characteristics, strain Q-192T is considered to represent a novel species of a new genus, for which the name Marinibactrum halimedae gen. nov., sp. nov. is proposed. The type strain of Marinibactrum halimedae is Q-192T ( = NBRC 110095T = NCIMB 14932T).

Pseudomaricurvus alcaniphilus sp. nov., a marine bacterium isolated from tidal flat sediment and emended descriptions of the genus Pseudomaricurvus, Pseudomaricurvus alkylphenolicus Iwaki et al. 2014 and Maricurvus nonylphenolicus Iwaki et al. 2012

A novel Gram-reaction-negative, rod-shaped, aerobic and motile strain, designated MEBiC06469T, was isolated from tidal flat sediment of the Taean province, South Korea. Strain MEBiC06469T produced ivory-coloured colonies on marine agar 2216 medium and could degrade carboxymethyl-cellulose. On the basis of 16S rRNA gene sequence similarity, the closest relative was Pseudomaricurvus alkylphenolicus KU41GT with 96.5 % similarity. The isolate was catalase-positive but oxidase-negative. Growth was observed at 16-38 °C (optimum, 32 °C), at pH 6.0-9.0 (optimum, pH 7.5) and in the presence of 0.0-8.0 % (w/v) NaCl (optimum, 1.5 %). The only isoprenoid quinone was Q-8.The dominant fatty acids were summed feature 3 (comprised of C15 : 0 2-OH and/or C16 : 1ω7c; 20.4 %) and C17 : 1ω8c (30.9 %), summed feature 8 (comprised of C18 : 1ω7c and/or C18 : 1ω6c; 9.5 %), C16 : 0 (9.0 %), C15 : 1ω8c (5.3 %), and C11 : 0 3-OH (5.2 %). Based on these phenotypic properties and phylogenetic data, strain MEBiC06469T should be classified as a novel species within the genus Pseudomaricurvus for which the name Pseudomaricurvus alcaniphilus sp. nov. is proposed. The type strain is MEBiC06469T ( = KCCM 42976T = JCM 18313T). Emended descriptions of the genus Pseudomaricurvus, Pseudomaricurvus alkylphenolicusIwaki et al. 2014, and Maricurvus nonylphenolicusIwaki et al. 2012 are also provided.

Cloning and Characterization of a Novel Agarase from a Newly Isolated Bacterium Simiduia sp. Strain TM-2 Able to Degrade Various Seaweeds

A new bacterial strain capable of reducing thalli of various seaweeds (red, green, and brown algae) was isolated from marine sediments of Uozu in Toyama Prefecture, Japan. We designated the strain Simiduia sp. TM-2 based on analyses of the 16S rRNA gene and gyrB gene sequences and its biochemical and morphological characteristics. Zymography methods revealed numerous active bands of alginate lyases, cellulases, and agarases in the cells and culture supernatants of TM-2, showing that the strain possessed multiple polysaccharide lyases. A novel agarase gene (agaTM2) was cloned from TM-2 and expressed in Escherichia coli. The resulting DNA sequence contained an open reading frame of 1764 bp that encoded a protein of 587 amino acids with an estimated molecular mass of 64 kDa and pI of 4.62. The deduced amino acid sequence, AgaTM2, had a typical signal peptide followed by a glycoside hydrolase family 16 catalytic domain and two carbohydrate-binding modules 6. A BLAST search indicated that AgaTM2 shared 75.5 % amino acid sequence identity with agarase from Simiduia agarivorans SA1. The cloned and purified AgaTM2 protein showed optimal activity at 35 °C and pH 8.0, and its thermostability increased in the presence of calcium ions. AgaTM2 degraded agarose to tetraose and hexaose.

High molecular weight dissolved organic matter enrichment selects for methylotrophs in dilution to extinction cultures

The role of bacterioplankton in the cycling of marine dissolved organic matter (DOM) is central to the carbon and energy balance in the ocean, yet there are few model organisms available to investigate the genes, metabolic pathways, and biochemical mechanisms involved in the degradation of this globally important carbon pool. To obtain microbial isolates capable of degrading semi-labile DOM for growth, we conducted dilution to extinction cultivation experiments using seawater enriched with high molecular weight (HMW) DOM. In total, 93 isolates were obtained. Amendments using HMW DOM to increase the dissolved organic carbon concentration 4x (280 μM) or 10x (700 μM) the ocean surface water concentrations yielded positive growth in 4–6% of replicate dilutions, whereas <1% scored positive for growth in non-DOM-amended controls. The majority (71%) of isolates displayed a distinct increase in cell yields when grown in increasing concentrations of HMW DOM. Whole-genome sequencing was used to screen the culture collection for purity and to determine the phylogenetic identity of the isolates. Eleven percent of the isolates belonged to the gammaproteobacteria including Alteromonadales (the SAR92 clade) and Vibrio. Surprisingly, 85% of isolates belonged to the methylotrophic OM43 clade of betaproteobacteria, bacteria thought to metabolically specialize in degrading C1 compounds. Growth of these isolates on methanol confirmed their methylotrophic phenotype. Our results indicate that dilution to extinction cultivation enriched with natural sources of organic substrates has a potential to reveal the previously unsuspected relationships between naturally occurring organic nutrients and the microorganisms that consume them.

β-Lactam antibiotic-degrading enzymes from non-pathogenic marine organisms: a potential threat to human health

Metallo-β-lactamases (MBLs) are a family of Zn(II)-dependent enzymes that inactivate most of the commonly used β-lactam antibiotics. They have emerged as a major threat to global healthcare. Recently, we identified two novel MBL-like proteins, Maynooth IMipenemase-1 (MIM-1) and Maynooth IMipenemase-2 (MIM-2), in the marine organisms Novosphingobium pentaromativorans and Simiduia agarivorans, respectively. Here, we demonstrate that MIM-1 and MIM-2 have catalytic activities comparable to those of known MBLs, but from the pH dependence of their catalytic parameters it is evident that both enzymes differ with respect to their mechanisms, with MIM-1 preferring alkaline and MIM-2 acidic conditions. Both enzymes require Zn(II) but activity can also be reconstituted with other metal ions including Co(II), Mn(II), Cu(II) and Ca(II). Importantly, the substrate preference of MIM-1 and MIM-2 appears to be influenced by their metal ion composition. Since neither N. pentaromativorans nor S. agarivorans are human pathogens, the precise biological role(s) of MIM-1 and MIM-2 remains to be established. However, due to the similarity of at least some of their in vitro functional properties to those of known MBLs, MIM-1 and MIM-2 may provide essential structural insight that may guide the design of as of yet elusive clinically useful MBL inhibitors.

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.

Simiduia curdlanivorans sp. nov., a curdlan-degrading bacterium isolated from the junction between the ocean and a freshwater spring, and emended description of the genus Simiduia

A Gram-stain-negative, aerobic, non-spore-forming, non-flagellated and rod-shaped bacterial strain, designated DMCK3-4(T), was isolated from the zone where the ocean and a freshwater spring meet at Jeju island, South Korea. Strain DMCK3-4(T) grew optimally at 30 °C, at pH 7.0-8.0 and in the presence of 2.0% (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain DMCK3-4(T) clustered with the strains of three members of the genus Simiduia, with which it exhibited 97.0-99.0% sequence similarity. Sequence similarities to the type strains of the other species with validly published names were less than 92.2%. Strain DMCK3-4(T) contained Q-8 as the predominant ubiquinone and summed feature 3 (C(16:1)ω7c and/or C(16:1)ω6c), C(17:1)ω8c, C(16:0), C(17:0) and C(18:1)ω7c as the major fatty acids. The major polar lipids of strain DMCK3-4(T) were phosphatidylethanolamine, phosphatidylglycerol, two unidentified glycolipids, one unidentified lipid and one unidentified aminolipid. The DNA G+C content of strain DMCK3-4(T) was 51.8 mol% and its mean DNA-DNA relatedness values with Simiduia agarivorans KCTC 23176(T), Simiduia areninigrae KCTC 23293(T) and Simiduia litorea NRIC 0917(T) were 23-34%, respectively. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain DMCK3-4(T) is distinct from other species of the genus Simiduia. On the basis of the data presented, strain DMCK3-4(T) is considered to represent a novel species of the genus Simiduia, for which the name Simiduia curdlanivorans sp. nov. is proposed. The type strain is DMCK3-4(T) ( = KCTC 42075(T) =CECT 8570(T)). An emended description of the genus Simiduia is also proposed.

Simiduia litorea sp. nov., isolated from seashore sediments of the Sea of Japan

An aerobic, Gram-stain-negative, agarolytic rod-shaped bacterium, designated KMM 9504T, was isolated from a sediment sample collected from the seashore of the Sea of Japan. Comparative 16S rRNA gene sequence analysis showed that strain KMM 9504T belonged to the genus Simiduia as it was most closely related to Simiduia areninigrae KCTC 23293T (97.3 % sequence similarity). Strain KMM 9504T was characterized by the major ubiquinone Q-8, and by the predominance of C16 : 1ω7c, C17 : 1ω8c, followed by C16 : 0, C15 : 0, C17 : 0 and C12 : 1 in its fatty acid profile. Polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unknown aminophospholipid, an unknown aminolipid, unknown phospholipids, and unknown lipids. Based on the distinctive phenotypic characteristics, phylogenetic analysis and DNA–DNA hybridization results, it is concluded that strain KMM 9504T represents a novel species of the genus Simiduia , for which the name Simiduia litorea sp. nov. is proposed. The type strain of the species is strain KMM 9504T ( = NRIC 0917T = JCM 19759T).

Aliidiomarina shirensis sp. nov., a halophilic bacterium isolated from Shira Lake in Khakasia, southern Siberia, and a proposal to transfer Idiomarina maris to the genus Aliidiomarina

Strain AIST, an aerobic halophilic, Gram-reaction-negative, heterotrophic bacterium isolated from the water of Shira Lake in Khakasia, southern Siberia, was characterized using a polyphasic approach. Our analysis of the 16S rRNA gene sequences showed that ‘Aliidiomarina haloalkalitolerans’, ‘Aliidiomarina sanyensis’, Idiomarina maris and AIST formed a distinct lineage. The sequence similarities between AIST and the type strains of species of the genera Idiomarina and Aliidiomarina were 91.6–95.1 % and 94.0–96.9 %, respectively. The major isoprenoid quinone of AIST was ubiquinone 8 (Q-8). Predominant cellular fatty acids were iso-C17 : 0, iso-C15 : 0 and summed feature 9. The genomic DNA G+C content was 45.8 mol%. It is concluded that AIST represents a novel species of the genus Aliidiomarina , and the name Aliidiomarina shirensis sp. nov. is herein proposed for it. The type strain is AIST ( = JCM 17761T = BCRC 80327T). Based on its fatty acid profile and our phylogenetic analysis, we propose that Idiomarina maris be transferred to the genus Aliidiomarina .

Reclassification of [Glaciecola] lipolytica and [ Aestuariibacter] litoralis in Aliiglaciecola gen. nov., as Aliiglaciecola lipolytica comb. nov. and Aliiglaciecola litoralis comb. nov., respectively

Following phylogenetic analysis based on 16S rRNA gene sequences, together with DNA G+C contents and differential chemotaxonomic and physiological characteristics, a new genus with the name Aliiglaciecola gen. nov. is proposed to more appropriately accommodate two recognized species of the genera Glaciecola and Aestuariibacter . Accordingly, [Glaciecola] lipolytica and [ Aestuariibacter] litoralis should be reassigned to the novel genus as Aliiglaciecola lipolytica comb. nov. (type strain, E3T = JCM 15139T = CGMCC 1.7001T) and Aliiglaciecola litoralis comb. nov. (type strain, KMM 3894T = JCM 15896T = NRIC 0754T), respectively. Aliiglaciecola lipolytica is proposed as the type species of this new genus. Physiologically, the combined characteristics of positive reactions for nitrate reduction and growth at 4 °C and 36 °C distinguish the new genus from the genera Aestuariibacter and Glaciecola by one to three traits. Moreover, the new genus is also distinguished from the genus Glaciecola by the fatty acid profile and distinguished from the genus Aestuariibacter by the differences of major isoprenoid quinone (MK-7 vs Q-8) and DNA G+C content (40.8–43.0 mol% vs 48.0–54.0 mol%).

Complete Genome Sequence of Simiduia agarivorans SA1(T), a Marine Bacterium Able To Degrade a Variety of Polysaccharides

Simiduia agarivorans strain SA1(T) is able to degrade a variety of polysaccharides found in marine algae, plants, and animals. The genome of S. agarivorans SA1(T) consists of a single chromosome (4,309,711 bp), and its information may provide insights into the polysaccharide-degrading capability, cell division, flagellar motility, and chemotaxis of this bacterium.

Kangiella taiwanensis sp. nov. and Kangiella marina sp. nov., marine bacteria isolated from shallow coastal water

Two Gram-negative, heterotrophic, aerobic, marine bacteria, designated strains KT1T and KM1T, were isolated from seawater samples collected from the shallow coastal regions of northern Taiwan. Cells grown in broth cultures were non-flagellated rods. NaCl was required for growth. Optimal growth occurred with 2–5 % NaCl, at 25–30 °C and at pH 8. They grew aerobically and were not capable of anaerobic growth by fermenting d-glucose or other carbohydrates. Q-8 was the only isoprenoid quinone. The major polar lipid detected in strain KT1T was phosphatidylmonomethylethanolamine, whereas those detected in KM1T were phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine and an unidentified phospholipid. Cellular fatty acids were nearly all iso-branched, with iso-C15 : 0 as the most abundant component (54.6–57.2 % of the total). Strains KT1T and KM1T had DNA G+C contents of 43.9 and 46.3 mol%, respectively. The two strains shared 98.1 % 16S rRNA gene sequence similarity; levels of similarity with the type strains of species of the genus Kangiella were 95.6–98.4 %. Data from the present taxonomic study conducted using a polyphasic approach revealed that the isolates could be classified as representatives of two novel species of the genus Kangiella , for which the names Kangiella taiwanensis sp. nov. (type strain KT1T = BCRC 80330T = JCM 17727T) and Kangiella marina sp. nov. (type strain KM1T = BCRC 80329T = JCM 17728T) are proposed.

Simiduia areninigrae sp. nov., an agarolytic bacterium isolated from sea sand

During a study intended to screen for agar-degrading bacteria, strain M2-5T was isolated from black sand off the shore of Jeju Island, Republic of Korea. Strain M2-5T exhibited agarase activity; the β-agarase gene of the isolate had 62 % amino acid sequence identity to the β-agarase gene of Microbulbifer thermotolerans JAMB A94T. The isolate was closely related to members of the genus Simiduia but was clearly discernible from reported Simiduia species, based on a polyphasic analysis. Cells of strain M2-5T were Gram-negative, catalase- and oxidase-positive, motile rods. The DNA G+C content was 53.3 mol%. The predominant isoprenoid quinone was Q-8. The major cellular fatty acids were C17 : 1ω8c (25.9 %), summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c; 17.2 %) and C17 : 0 (15.0 %). Phylogenetic analysis using 16S rRNA gene sequences showed that strain M2-5T had 96.6 % gene sequence similarity to Simiduia agarivorans SA1T, the most closely related type strain of the genus Simiduia . These results suggest that strain M2-5T represents a novel species in the genus Simiduia , for which the name Simiduia areninigrae sp. nov. is proposed; the type strain is M2-5T ( = KCTC 23293T = NCAIM B 02424T).

Aliidiomarina taiwanensis gen. nov., sp. nov., isolated from shallow coastal water

A Gram-negative, heterotrophic, aerobic, marine bacterium, designated AIT1T, was isolated from a seawater sample collected in the shallow coastal region of Bitou Harbour, New Taipei City, Taiwan. Cells grown in broth cultures were straight or slightly curved rods that were motile by means of a single polar flagellum. Strain AIT1T required NaCl for growth, grew optimally at 30–40 °C and with 1.5–5.0 % NaCl, and was incapable of anaerobic growth by fermentation of glucose or other carbohydrates. The isoprenoid quinones consisted of Q-8 (95.2 %) and Q-9 (4.8 %). The major polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The cellular fatty acids were predominantly iso-branched and included iso-C17 : 0 (26.5 %), summed feature 9 (comprising iso-C17 : 1ω9c and/or 10-methyl C16 : 0; 25.9 %) and iso-C15 : 0 (20.5 %). The DNA G+C content was 51.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain AIT1T formed a distinct lineage within the class Gammaproteobacteria and was most closely related to members of the genus Idiomarina in the family Idiomarinaceae (91.5–93.9 % 16S rRNA gene sequence similarity). The phylogenetic data, together with chemotaxonomic, physiological and morphological data, revealed that the isolate should be classified as a representative of a novel species in a new genus in the family Idiomarinaceae, for which the name Aliidiomarina taiwanensis gen. nov., sp. nov. is proposed. The type strain is AIT1T ( = JCM 16052T = BCRC 80035T = NCCB 100321T).

Rheinheimera nanhaiensis sp. nov., isolated from marine sediments, and emended description of the genus Rheinheimera Brettar et al. 2002 emend. Merchant et al. 2007

A Gram-negative, facultatively aerobic, oxidase- and catalase-positive, rod-shaped bacterium, designated strain E407-8T, was isolated from a sediment sample from the South China Sea. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain E407-8T was affiliated with the genus Rheinheimera, sharing the highest sequence similarity with Rheinheimera pacifica KMM 1406T (97.5 %) and Rheinheimera aquimaris SW-353T (97.4 %) and showing less than 97 % sequence similarity to the type strains of other recognized Rheinheimera species. Levels of DNA–DNA relatedness of strain E407-8T to R. pacifica DSM 17616T and R. aquimaris JCM 14331T were 25.2 % (25.3 % in the duplicate measurement) and 9.4 % (6.5 %), respectively. The bacterium could grow at 10–48 °C (optimum 37 °C) and in the presence of 0–8 % (w/v) NaCl (optimum 0.5–2.5 %). The major cellular fatty acids of strain E407-8T were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C17 : 1ω8c, C16 : 0 and C18 : 1ω7c. The predominant respiratory quinone was ubiquinone Q-8. The DNA G+C content was 51.0 mol%. Based on the results of our polyphasic taxonomic study, strain E407-8T represents a novel species in the genus Rheinheimera, for which the name Rheinheimera nanhaiensis sp. nov. is proposed. The type strain is E407-8T ( = CCTCC AB 209089T  = KACC 14030T). An emended description of the genus Rheinheimera Brettar et al. 2002 emend. Merchant et al. 2007 is also proposed.

Agarivorans gilvus sp. nov. isolated from seaweed

A novel agarase-producing, non-endospore-forming marine bacterium, WH0801T, was isolated from a fresh seaweed sample collected from the coast of Weihai, China. Preliminary characterization based on 16S rRNA gene sequence analysis showed that WH0801T shared 96.1 % similarity with Agarivorans albus MKT 106T, the type species of the genus Agarivorans. A polyphasic taxonomic study was conducted and confirmed the phylogenetic affiliation of strain WH0801T to the genus Agarivorans. Isolate WH0801T produces light-yellow-pigmented colonies; cells are Gram-stain-negative, straight or curved rods, which are motile with a single polar flagellum. Strain WH0801T grew in 0.5–5 % NaCl, with optimum growth at 3 % NaCl, and its optimal pH and cultivation temperature were 8.4–8.6 and 28–32 °C, respectively. Data from biochemical tests, whole-cell fatty acid profiling, 16S rRNA gene sequence studies and DNA–DNA hybridization clearly indicated that isolate WH0801T represented a novel species within the genus Agarivorans, for which the name Agarivorans gilvus sp. nov. is proposed. The type strain of Agarivorans gilvus sp. nov. is WH0801T (=NRRL B-59247T =CGMCC 1.10131T).

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).

Porticoccus litoralis gen. nov., sp. nov., a gammaproteobacterium isolated from the Yellow Sea

A marine bacterium, designated IMCC2115T, was isolated from coastal seawater (Yellow Sea, Korea) using a high throughput cultivation method based on dilution-to-extinction, and taxonomically investigated. Cells of the strain formed tiny, beige to off-white colonies and were Gram-stain-negative, obligately aerobic, chemoheterotrophic, non-motile cocci. Based on 16S rRNA gene sequence comparisons, the strain was most closely related to the genera Marinimicrobium (92.0–92.4 %) and Microbulbifer (91.6–92.8 %), but phylogenetic trees showed that the strain formed a distinct phyletic line in the class Gammaproteobacteria adjacent to the OM60 and SAR92 clades. The DNA G+C content of the strain was 47.8 mol% and the predominant cellular fatty acids were anteiso-C15 : 0 (67.6 %), anteiso-C17 : 0 (14.4 %) and C16 : 0 (6.9 %). The 16S rRNA gene sequence analyses and phenotypic and chemotaxonomic tests allowed the differentiation of IMCC2115T from other related genera in the class Gammaproteobacteria. Therefore, strain IMCC2115T (=KCCM 42369T =NBRC 102686T) is proposed as the representative of a new genus and species, for which the name Porticoccus litoralis gen. nov., sp. nov. is proposed.

Valuable processes and products from marine intertidal microbial communities

Microbial communities are ubiquitous in marine intertidal environments. These communities, which grow preferentially as biofilms on natural and artificial surfaces, carry out key processes contributing to the functioning of coastal environments and providing valuable services to human society, including carbon cycling, primary productivity, trophic linkage, and transfer and removal of pollutants. In addition, their surface-associated life style greatly influences the integrity and performance of marine infrastructure and archaeological heritage materials. The fluctuating conditions of the intertidal zone make it an extreme environment to which intertidal biofilm organisms must adapt at varying levels. This requirement has probably favored the development and spread of specific microorganisms with particular physiological and metabolic processes. These organisms may have potential biotechnological utility, in that they may provide novel secondary metabolites, biopolymers, lipids, and enzymes and even processes for the production of energy in a sustainable manner.

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)).

Aliagarivorans marinus gen. nov., sp. nov. and Aliagarivorans taiwanensis sp. nov., facultatively anaerobic marine bacteria capable of agar degradation

Two agarolytic strains of Gram-negative, heterotrophic, facultatively anaerobic, marine bacteria, designated AAM1T and AAT1T, were isolated from seawater samples collected in the shallow coastal region of An-Ping Harbour, Tainan, Taiwan. Cells grown in broth cultures were straight rods that were motile by means of a single polar flagellum. The two isolates required NaCl for growth and grew optimally at about 25-30 degrees C, in 2-4% NaCl and at pH 8. They grew aerobically and could achieve anaerobic growth by fermenting D-glucose or other sugars. The major isoprenoid quinone was Q-8 (79.8-92.0%) and the major cellular fatty acids were summed feature 3 (C16:1omega7c and/or iso-C15:0 2-OH; 26.4-35.6%), C18:1omega7c (27.1-31.4%) and C16:0 (14.8-16.3%) in the two strains. Strains AAM1T and AAT1T had DNA G+C contents of 52.9 and 52.4 mol%, respectively. The two strains had a 16S rRNA gene sequence similarity of 98.6% and shared 84.9-92.4% sequence similarity with the type strains of Agarivorans albus (91.2-92.4%), eight Alteromonas species (84.9-87.1%), two Aestuariibacter species (86.0-87.0%), Bowmanella denitrificans (86.1-86.7%), eight Glaciecola species (85.0-87.9%) and Salinimonas chungwhensis (85.9-86.1%). Despite their high sequence similarity, strains AAM1T and AAT1T had a DNA-DNA relatedness value of only 4.5%. The data obtained from these polyphasic taxonomic studies revealed that the two agarolytic isolates could be classified as representatives of two novel species in a new genus, Aliagarivorans gen. nov., with Aliagarivorans marinus sp. nov. [type strain is AAM1T (=BCRC 17888T=JCM 15522T)] as the type species and Aliagarivorans taiwanensis sp. nov. [type strain is AAT1T (=BCRC 17889T=JCM 15537T)] as a second species.

Pseudidiomarina marina sp. nov. and Pseudidiomarina tainanensis sp. nov. and reclassification of Idiomarina homiensis and Idiomarina salinarum as Pseudidiomarina homiensis comb. nov. and Pseudidiomarina salinarum comb. nov., respectively

Two Gram-negative strains of heterotrophic, aerobic, marine bacteria, designated PIM1T and PIN1T, were isolated from seawater samples collected from the shallow coastal region of An-Ping Harbour, Tainan, Taiwan. Cells grown in broth cultures were straight rods and non-motile. The two isolates required NaCl for growth and grew optimally at 30-35 degrees C and 2-5 % NaCl. They grew aerobically and were not capable of anaerobic growth by fermentation of glucose or other carbohydrates. The cellular fatty acids were predominantly iso-branched, with iso-C(15 : 0) (17.0-21.4 %), iso-C(17 : 0) (18.2-21.0 %) and iso-C(17 : 1)omega9c (15.7-16.6 %) as the most abundant components. The predominant isoprenoid quinone was Q-8 (95.2-97.1 %). Strains PIM1T and PIN1T had DNA G+C contents of 46.6 and 46.9 mol%, respectively. Phylogeny based on 16S rRNA gene sequences and DNA-DNA hybridization, together with data from physiological, morphological and chemotaxonomic characterizations, indicated that the two isolates should be classified as representatives of two novel species of the genus Pseudidiomarina of the family Idiomarinaceae, for which the names Pseudidiomarina marina sp. nov. (type strain PIM1T=BCRC 17749T=JCM 15083T) and Pseudidiomarina tainanensis sp. nov. (type strain PIN1T=BCRC 17750T=JCM 15084T) are proposed. In addition, based on the characterization data obtained in this study, it is proposed that Idiomarina homiensis and Idiomarina salinarum should be reclassified as Pseudidiomarina homiensis comb. nov. and Pseudidiomarina salinarum comb. nov., respectively.