Polaribacter ponticola sp. nov., isolated from seawater, reclassification of Polaribacter undariae as a later heterotypic synonym of Polaribacter sejongensis, and emended description of Polaribacter sejongensis Kim et al. 2013

A Gram-stain-negative, yellow-pigmented, and strictly aerobic bacterium, designated as strain MSW5T, was isolated from seawater of the Yellow Sea in South Korea. The cells were non-motile rods exhibiting oxidase- and catalase-positive activities. Growth was observed at 15-25 °C (optimum, 25 °C) and pH 5.0-9.0 (optimum, pH 7.0-8.0) and in the presence of 1.0-5.0% (w/v) NaCl (optimum, 2.0%). Menaquinone-6 was the sole respiratory quinone, and iso-C15 : 0, summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c), iso-C15 : 0 3-OH, and C15 : 1  ω6c were the major cellular fatty acids. Major polar lipids included phosphatidylethanolamine, two unidentified aminolipids, and three unidentified lipids. Phylogenetic analyses based on 16S rRNA gene sequences and 92 concatenated core protein sequences revealed that strain MSW5T formed a distinct lineage within the genus Polaribacter. The genome of strain MSW5T was 3582 kb in size with a 29.1 mol% G+C content. Strain MSW5T exhibited the highest similarity to Polaribacter atrinae WP25T, with a 97.9% 16S rRNA gene sequence similarity. However, the average nucleotide identity and digital DNA-DNA hybridization values were 79.4 and 23.3%, respectively, indicating that strain MSW5T represents a novel species. Based on its phenotypic, chemotaxonomic, and phylogenetic characteristics, strain MSW5T is proposed to represent a novel species, with the name Polaribacter ponticola sp. nov. The type strain is MSW5T (=KACC 22340T=NBRC 116025T). In addition, whole genome sequence comparisons and phenotypic features suggested that Polaribacter sejongensis and Polaribacter undariae belong to the same species, with P. undariae proposed as a later heterotypic synonym of P. sejongensis. An emended description of Polaribacter sejongensis is also proposed.

Effects of Hyphomonas Strains on the Growth of Red Algae Pyropia Species by Attaching Specifically to Their Rhizoids

Bacteria and marine macroalgae form close associations, while various bacteria affect the morphogenesis and growth of macroalgae. Hyphomonas strains exhibit normal morphogenetic activity in protoplasts of the red alga Pyropia yezoensis (nori). However, the effects of the bacteria on the growth of Pyropia from protoplast cells to regenerated thalli remain unknown. Here, we assessed the growth of P. yezoensis and Pyropia tenera using combined cultures of three Hyphomonas strains (LNM10-16, SCM-2, and LNM-9) and three algal media (artificial seawater with vitamins, artificial seawater, and natural seawater) over 7 weeks. Third week after culture, the three Hyphomonas strains showed almost similar levels of normal growth activity for both Pyropia species. However, at 7 weeks, significant differences were observed among the three Hyphomonas strains in terms of length, length-to-width ratio, and normal morphology of Pyropia thalli. LNM10-16 significantly promoted the thalli length and length-to-width ratios of both Pyropia species in artificial seawater without vitamins and natural seawater, compared with the other two Hyphomonas strains. P. yezoensis cultured in artificial seawater with vitamins showed a much higher demand for LNM10-16 in development of the thalli length than P. tenera. These results may be explained by differences in the growth activities of Hyphomonas strains and the nutrient requirements of Pyropia species. Furthermore, the bacteria were more specifically attached to the rhizoid surfaces of both species. This study is the first to reveal that Hyphomonas strains affect the growth of Pyropia species by attaching to their rhizoids.

Adaptive genetic traits in pelagic freshwater microbes

Pelagic microbes have adopted distinct strategies to inhabit the pelagial of lakes and oceans and can be broadly categorized in two groups: free-living, specialized oligotrophs and patch-associated generalists or copiotrophs. In this review, we aim to identify genomic traits that enable pelagic freshwater microbes to thrive in their habitat. To do so, we discuss the main genetic differences of pelagic marine and freshwater microbes that are both dominated by specialized oligotrophs and the difference to freshwater sediment microbes, where copiotrophs are more prevalent. We phylogenomically analysed a collection of >7700 metagenome-assembled genomes, classified habitat preferences on different taxonomic levels, and compared the metabolic traits of pelagic freshwater, marine, and freshwater sediment microbes. Metabolic differences are mainly associated with transport functions, environmental information processing, components of the electron transport chain, osmoregulation and the isoelectric point of proteins. Several lineages with known habitat transitions (Nitrososphaeria, SAR11, Methylophilaceae, Synechococcales, Flavobacteriaceae, Planctomycetota) and the underlying mechanisms in this process are discussed in this review. Additionally, the distribution, ecology and genomic make-up of the most abundant freshwater prokaryotes are described in details in separate chapters for Actinobacteriota, Bacteroidota, Burkholderiales, Verrucomicrobiota, Chloroflexota, and 'Ca. Patescibacteria'.

Colwellia maritima sp. nov. and Polaribacter marinus sp. nov., isolated from seawater

Two Gram-stain-negative, catalase- and oxidase-positive, and aerobic bacteria, strains MSW7^T and MSW13^T, were isolated from seawater. Cells of strains MSW7^T and MSW13^T are motile and non-motile rods, respectively. Strain MSW7^T optimally grew at 25 °C and pH 7.0 and in the presence of 3 % (w/v) NaCl, whereas strain MSW13^T optimally grew at 25 °C and pH 6.0-7.0 and in the presence of 2 % NaCl. As the sole respiratory quinone and the major fatty acids and polar lipids, strain MSW7^T contained ubiquinone-8, C_16 : 0, C_15 : 1  ω8c, C_17 : 1  ω8c and summed feature 3 (C_16 : 1  ω7c and/or C_16 : 1  ω6c), and phosphatidylethanolamine and phosphatidylglycerol, respectively, whereas strain MSW13^T contained menaquinone-6, C_15 : 1  ω6c, iso-C_15 : 0, anteiso-C_15 : 0, and iso-C_15 : 0 3-OH, and phosphatidylethanolamine, respectively. The DNA G+C contents of strains MSW7^T and MSW13^T were 37.3 and 29.9 %, respectively. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains MSW7^T and MSW13^T were most closely related to Colwellia echini A3^T and Polaribacter atrinae WP25^T with 98.8 and 98.1 % sequence similarities, respectively. The average nucleotide identity and digital DNA-DNA hybridization values between strain MSW7^T and C. echini A3^T and between strain MSW13^T and P. atrinae KACC 17473^T were 73.6 and 22.6 % and 80.4 and 23.8 %, respectively. Based on phenotypic, chemotaxonomic and phylogenetic data, strains MSW7^T and MSW13^T represent novel species of the genera Colwellia and Polaribacter, respectively, for which the names Colwellia maritima sp. nov. and Polaribacter marinus sp. nov. are proposed, respectively. The type strains of C. maritima sp. nov. and P. marinus sp. nov. are MSW7^T (=KACC 22339^T=JCM 35001^T) and MSW13^T (=KACC 22341^T=JCM 35021^T), respectively.

Polaribacter septentrionalilitoris sp. nov., isolated from the biofilm of a stone from the North Sea

A new member of the family Flavobacteriaceae was isolated from the biofilm of a stone at Nordstrand, a peninsula at the German North Sea shore. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain ANORD1^T was most closely related to the validly described type strains Polaribacter porphyrae LNM-20^T (97.0 %) and Polaribacter reichenbachii KMM 6386^T (96.9 % 16S rRNA gene sequence similarity) and clustered with Polaribacter gangjinensis K17-16^T (96.0 %). Strain ANORD1^T was determined to be mesophilic, Gram-negative, non-motile and strictly aerobic. Optimal growth was observed at 20-30 °C, within a salinity range of 2-7 % sea salt and from pH 7-10. Like other type strains of the genus Polaribacter, ANORD1^T was tested negative for flexirubin-type pigments, while carotenoid-type pigments were detected. The DNA G+C content of strain ANORD1^T was 30.6 mol%. The sole respiratory quinone detected was menaquinone 6 (MK-6). The major fatty acids identified were C_15 : 0, iso-C_15 : 0, C_15 : 1 ω6c and iso-C_15 : 0 3-OH. Based on the polyphasic approach, strain ANORD1^T represents a novel species in the genus Polaribacter, with the name Polaribacter septentrionalilitoris sp. nov. being proposed. The type strain is ANORD1^T (=DSM 110039^T=NCIMB 15081^T=MTCC 12685^T).

Characterization of Gut Microbiome in the Mussel Mytilus galloprovincialis in Response to Thermal Stress

The gut microbiota is essential for utilization of energy and nutrition and may have a role in host immunity in response to environmental shifts. The present study evaluated the temperature stress (increasing from 21 to 27°C) on gut microbiome and dynamics of the mussel Mytilus galloprovincialis by 16S rRNA gene sequencing with the aim of discovering the gut microbiome resilience to warming. Exposure to high temperature of 27°C significantly reduced the survival of M. galloprovincialis associated with increased microbial diversity of gut. The microbial communities were shifted with elevated temperature (from 21 to 27°C) and different exposure time (from day 0 to day 7) by principal coordinate analysis (PCoA). Linear discriminant analysis effect size (LEfSe) revealed that the relative abundance of Vibrio and Arcobacter presented in live animals as the top genus-level biomarkers during the initial exposure to 27°C and followed by microbiomes fluctuation with increasing exposure time at day 4 and day 7. The proliferation of opportunistic pathogens such as genus Vibrio and Arcobacter might increase host susceptibility to disease and contributed greatly to mortality. The results obtained in this study provide the knowledge on ecological adaptation for south domestication of M. galloprovincialis and host-bacteria interaction during temperature stress (27°C).

Ulvibacterium marinum gen. nov., sp. nov., a novel marine bacterium of the family Flavobacteriaceae, isolated from a culture of the green alga Ulva prolifera

A Gram-stain negative, aerobic, rod-shaped, and non-motile bacterium, designated strain CCMM003^T, was isolated from a culture of the green alga Ulva prolifera. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CCMM003^T belongs to the family Flavobacteriaceae and exhibits a close relationship to Pseudozobellia thermophila DSM 19858^T (92.5%). Optimal growth occurred in the presence of 4% (w/v) NaCl, at pH 7.0 and 30 °C. The polar lipids of strain CCMM003^T consisted of phosphatidylethanolamine and six unidentified lipids. The predominant isoprenoid quinone was MK-6. The major fatty acids were iso-C_15:0, iso-C_15:1 G, iso-C_17:0 3-OH and summed feature 3 (C_16:1ω7c and/or iso-C_15:0 2-OH). The DNA G + C content of strain CCMM003^T calculated on the basis of the genome sequence was 41.2 mol% and the genome size was 5.9 Mbp. On the basis of data from this polyphasic study, strain CCMM003^T is considered to represent a novel genus and species of the family Flavobacteriaceae, for which the name Ulvibacterium marinum gen. nov., sp. nov. is proposed. The type strain is CCMM003^T (= MCCC 1K03244^T =KCTC 52639^T).

Repeated evolutionary transitions of flavobacteria from marine to non-marine habitats

The taxonomy of marine and non-marine organisms rarely overlap, but the mechanisms underlying this distinction are often unknown. Here, we predicted three major ocean-to-land transitions in the evolutionary history of Flavobacteriaceae, a family known for polysaccharide and peptide degradation. These unidirectional transitions were associated with repeated losses of marine signature genes and repeated gains of non-marine adaptive genes. This included various Na⁺ -dependent transporters, osmolyte transporters and glycoside hydrolases (GH) for sulfated polysaccharide utilization in marine descendants, and in non-marine descendants genes for utilizing the land plant material pectin and genes facilitating terrestrial host interactions. The K⁺ scavenging ATPase was repeatedly gained whereas the corresponding low-affinity transporter repeatedly lost upon transitions, reflecting K⁺ ions are less available to non-marine bacteria. Strikingly, the central metabolism Na⁺ -translocating NADH: quinone dehydrogenase gene was repeatedly gained in marine descendants, whereas the H⁺ -translocating counterpart was repeatedly gained in non-marine lineages. Furthermore, GH genes were depleted in isolates colonizing animal hosts but abundant in bacteria inhabiting other non-marine niches; thus relative abundances of GH versus peptidase genes among Flavobacteriaceae lineages were inconsistent with the marine versus non-marine dichotomy. We suggest that phylogenomic analyses can cast novel light on mechanisms explaining the distribution and ecology of key microbiome components.

Evaluation of the effects of different stocking densities on the sediment microbial community of juvenile hybrid grouper (♀Epinephelus fuscoguttatus × ♂ Epinephelus lanceolatus) in recirculating aquaculture systems

Aquatic microorganisms are an important part of aquatic ecosystems because they are involved in nutrient cycling and water quality, eventually influencing fish productivity. However, at present, reports on the effect of stocking density on microorganisms in sediment samples in recirculating aquaculture systems (RAS) are relatively rare. In this study, the changes in the microbial community in an RAS were investigated under different stocking densities of juvenile hybrid grouper (♀Epinephelus fuscoguttatus × ♂Epinephelus lanceolatus). Total DNA was extracted from the sediment samples, the 16S rDNA gene was amplified, and the bacterial community was analysed by Illumina high-throughput sequencing. We identified 741 OTUs from a total of 409,031 reads. Based on the analysis of bacterial composition, richness, diversity, bacterial 16S and rDNA gene abundance; sediment sample comparisons; and the existence of specific bacterial taxa within four densities, we concluded that the dominant phyla in all samples were similar and included: Proteobacteria, Bacteroidetes, Nitrospirae, Planctomycetes, Verrucomicrobia, and Chloroflexi. However, their relative distributions differed at different fish densities. Linear discriminant analysis further indicated that the stocking treatment influenced the sediment bacterial community. This study indicates that under RAS aquaculture, mode density is a factor regulating the microbial community, which provides insights into microbe management in RAS culture.

Taxonomic profiles in metagenomic analyses of free-living microbial communities in the Ofunato Bay

The Ofunato Bay in Iwate Prefecture, Japan is a deep coastal bay located at the center of the Sanriku Rias Coast and considered an economically and environmentally important asset. Here, we describe the first whole genome sequencing (WGS) study on the microbial community of the bay, where surface water samples were collected from three stations along its length to cover the entire bay; we preliminarily sequenced a 0.2 μm filter fraction among sequentially size-fractionated samples of 20.0, 5.0, 0.8 and 0.2 μm filters, targeting the free-living fraction only. From the 0.27-0.34 Gb WGS library, 0.9 × 10⁶-1.2 × 10⁶ reads from three sampling stations revealed 29 bacterial phyla (~80% of assigned reads), 3 archaeal phyla (~4%) and 59 eukaryotic phyla (~15%). Microbial diversity obtained from the WGS approach was compared with 16S rRNA gene results by mining WGS metagenomes, and we found similar estimates. The most frequently recovered bacterial sequences were Proteobacteria, predominantly comprised of 18.0-19.6% Planktomarina (Family Rhodobacteraceae) and 13.7-17.5% Candidatus Pelagibacter (Family Pelagibacterales). Other dominant bacterial genera, including Polaribacter (3.5-6.1%), Flavobacterium (1.8-2.6%), Sphingobacterium (1.4-1.6%) and Cellulophaga (1.4-2.0%), were members of Bacteroidetes and likely associated with the degradation and turnover of organic matter. The Marine Group I Archaea Nitrosopumilus was also detected. Remarkably, eukaryotic green alga Bathycoccus, Ostreococcus and Micromonas accounted for 8.8-15.2%, 3.6-4.9% and 2.1-3.1% of total read counts, respectively, highlighting their potential roles in the phytoplankton bloom after winter mixing.

Large-scale seaweed cultivation diverges water and sediment microbial communities in the coast of Nan'ao Island, South China Sea

Seaweed cultivation not only provides economy benefits, but also remediates the environment contaminated by mariculture of animals (e.g., fish, shrimps). However, the response of microbial communities to seaweed cultivation is poorly understood. In this study, we analyzed the diversity, composition, and structure of water and sediment microbial communities at a seaweed, Gracilaria lemaneiformis, cultivation zone and a control zone near Nan'ao Island, South China Sea by MiSeq sequencing of 16S rRNA gene amplicons. We found that large-scale cultivation of G. lemaneiformis increased dissolved oxygen (DO) and pH but decreased inorganic nutrients, possibly due to nutrient uptake, photosynthesis and other physiological processes of G. lemaneiformis. These environmental changes significantly (adonis, P<0.05) shifted the microbial community composition and structure of both water column and sediment samples in the G. lemaneiformis cultivation zone, compared to the control zone. Also, certain microbial taxa associated with seaweed, such as Arenibacter, Croceitalea, Glaciecola, Leucothrix and Maribacter were enriched at the cultivation zone. In addition, we have proposed a conceptual model to summarize the results in this study and guide future studies on relationships among seaweed processes, microbial communities and their environments. Thus, this study not only provides new insights into our understanding the effect of G. lemaneiformis cultivation on microbial communities, but also guides future studies on coastal ecosystems.

Polaribacter insulae sp. nov., isolated from a tidal flat

A Gram-stain-negative, aerobic, non-motile and ovoid or rod-shaped bacterial strain, designated OITF-22^T, was isolated from a tidal flat of Oido, an island of South Korea, and subjected to a polyphasic taxonomic study. Strain OITF-22^T grew optimally at 25 °C, at pH 7.0-8.0 and in the presence of 2.0-3.0 % (w/v) NaCl. The phylogenetic trees based on 16S rRNA gene sequences showed that strain OITF-22^T fell within the clade comprising the type strains of Polaribacter species. Strain OITF-22^T exhibited 16S rRNA gene sequence similarity values of 97.2-99.4 % to the type strains of Polaribacter vadi, P. haliotis, P. atrinae, P. dokdonensis, P. litorisediminis,P. reichenbachii, P. irgensii and P. marinaquae, and of 93.0-96.9 % to the type strains of the other Polaribacter species. Strain OITF-22^T contained MK-6 as the predominant menaquinone and iso-C15 : 0 and iso-C15 : 0 3-OH as the major fatty acids. The major polar lipids detected in strain OITF-22^T were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content of strain OITF-22^T was 32.3 mol% and its DNA-DNA relatedness values with the type strains of the eight phylogenetically most closely related Polaribacter species were 9-32 %. Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, revealed that strain OITF-22^T is separated from recognized species of the genus Polaribacter. On the basis of the data presented, strain OITF-22^T is considered to represent a novel species of the genus Polaribacter, for which the name Polaribacter insulae sp. nov. is proposed. The type strain is OITF-22^T (=KCTC 52658^T=NBRC 112706^T).

Polaribacter pacificus sp. nov., isolated from a deep-sea polymetallic nodule from the Eastern Pacific Ocean

A Gram-staining-negative, yellow-colony-forming, rod-shaped, non-flagellated and facultatively aerobic strain, designed HRA130-1T, was isolated from a deep-sea polymetallic nodule from the Pacific Clarion-Clipperton Fracture Zone (CCFZ). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain HRA130-1T belonged to the genus Polaribacter (96.3-93.2 % 16S rRNA gene sequence similarity), and exhibited 94 % 16S rRNA gene sequence similarity to Polaribacter filamentus KCTC 23135T (type species) and the highest sequence similarity to Polaribacter huanghezhanensis KCTC 32516T (96.3 %). Optimal growth occurred in the presence of 4 % (w/v) NaCl, at pH 7.0 and 16 °C. The DNA G+C content of strain HRA130-1T was 35.9 mol%. The major fatty acid was iso-C15 : 0. The predominant respiratory quinone was menaquinone-6 (MK-6). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, one unidentified phospholipid and an unidentified aminolipid. On the basis of data from the present taxonomic study using a polyphasic approach, strain HRA130-1T represents a novel species of the genus Polaribacter, for which the name Polaribacter pacificus sp. nov. is proposed. The type strain is HRA130-1T (=KCTC 52370T=MCCC 1K03199T=JCM 31460T=CGMCC 1.15763T).

Polaribacter litorisediminis sp. nov., isolated from a tidal flat

A Gram-stain-negative, aerobic, non-motile and ovoid or rod-shaped bacterial strain, designated OITF-11T, was isolated from a tidal flat in Oido, an island of South Korea, and subjected to a polyphasic taxonomic study. Strain OITF-11T grew optimally at 25 °C, at pH 7.0-8.0 and in the presence of 2.0 % (w/v) NaCl. The phylogenetic trees based on 16S rRNA gene sequences showed that strain OITF-11T belonged to the genus Polaribacter. Strain OITF-11T exhibited 16S rRNA gene sequence similarity values of 97.4-98.1 % to Polaribacter haliotis RA4-7T, Polaribacter atrinae KACC 17473T, Polaribacter dokdonensis DSW-5T and Polaribacter marinaquae KCTC 42664T, and of 94.1-96.9 % to the type strains of the other Polaribacter species. Strain OITF-11T contained menaquinone MK-6 as the predominant menaquinone and iso-C15 : 0, iso-C15 : 1 G, iso-C15 : 0 3-OH, iso-C17 : 0 3-OH and C15 : 1ω6c as the major fatty acids. The major polar lipids detected in strain OITF-11T were phosphatidylethanolamine, phosphatidylmonomethylethanolamine and one unidentified lipid. The DNA G+C content of strain OITF-11T was 32.2 mol% and its DNA-DNA relatedness values with the type strains of P. haliotis, P. atrinae, P. dokdonensis and P. marinaquae were 14-33 %. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain OITF-11T is separated from recognized species of the genus Polaribacter. On the basis of the data presented, strain OITF-11T is considered to represent a novel species of the genus Polaribacter, for which the name Polaribacter litorisediminis sp. nov. is proposed. The type strain is OITF-11T (=KCTC 52500T=NBRC 112457T).

Pseudotenacibaculum haliotis gen. nov., sp. nov., a new member within the Tenacibaculum-Polaribacter clade of the family Flavobacteriaceae, isolated from the intestine of adult abalones, Haliotis diversicolor and H. discushannai

Two rod-shaped marine bacterial strains named FDZSB0410T and FDZWPB0420, were isolated from the intestine of two adult abalone species, Haliotis diversicolor and Haliotis discushannai, respectively. The strains were non-flagellated, motile by gliding, oxidase-positive but catalase-negative, and agar-degrading. The two strains had identical 16S rRNA gene sequences with the highest sequence similarity less than 96.0 % with species of the genera Tenacibaculumand Polaribacter within the family Flavobacteriaceae. Phylogenetic analysis indicated the strains represented an independent cluster neighbouring with the species of the genera Tenacibaculum and Polaribacter. Strain FDZSB0410T can grow under conditions at 15 to 37 °C with optimum of 30 °C, salinity range from 3 to 4 % (NaCl, w/v) with optimum of 3 %, and pH range from 7 to 8 with optimum of pH 7. The predominant fatty acids of strain FDZSB0410T consisted of iso-C15 : 0, iso-C15 :1 G, summed feature 3 (comprising C16 : 1ω7c/C16 : 1ω6c), iso-C13 : 0, iso-C17 : 0 3-OH, and iso-C15 : 0 3-OH. The ubiquinone system detected was MK-6. The flexirubin pigment was absent, but the carotenoid was present. The polar lipids were identified as aminolipid, glycolipid, phosphatidylglycerol, an unknown phospholipid and four unknown lipids. The DNA G+C content was 35.3 mol%. On the basis of the genotypic and phenotypic characterizations, strain FDZSB0410T and strain FDZWPB0420 represent a novel species of a new genus in the family Flavobacteriaceae, for which the name Pseudotenacibaculum haliotis gen. nov., sp. nov. is proposed. The type strain of the type species is FDZSB0410T (=KCTC 52127T=MCCC 1A01897T).

Spongiiferula fulva gen. nov., sp. nov., a Bacterium of the Family Flavobacteriaceae Isolated from a Marine Sponge

A Gram stain-negative, strictly aerobic, brown-pigmented, non-motile, rod-shaped, chemoheterotrophic bacterial strain-designated A6F-119(T) was isolated from a marine sponge (Rhabdastrella sp.). Phylogenetic analyses based on the 16S rRNA gene sequence revealed that the new strain represented a member of the family Flavobacteriaceae of the phylum Bacteroidetes and that it showed highest sequence similarity (93 %) to Tenacibaculum maritimum NBRC 15946(T). The strain could be differentiated phenotypically from the recognized members of the family Flavobacteriaceae. The DNA G + C content of strain A6F-119(T) was determined to be 30.8 mol%; MK-6 was identified as the major menaquinone; and the presence of iso-C15:0, iso-C17:0 3-OH, and C16:1 ω7c and/or C16:1 ω6c as the major (>10 %) cellular fatty acids. A polar lipid profile was present consisting of phosphatidylethanolamine, an unidentified aminolipid, and three unidentified lipids. From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain is considered to represent a novel genus for which the name Spongiiferula fulva gen. nov., sp. nov. is proposed. The type strain of S. fulva is A6F-119(T) (= KCTC 42752(T) = NBRC 111402(T)).

Aurantivirga profunda gen. nov., sp. nov., isolated from deep-seawater, a novel member of the family Flavobacteriaceae

A Gram-stain-negative, aerobic, proteorhodopsin-containing, orange, rod-shaped bacterium, designated SAORIC-234T, was isolated from deep seawater in the Pacific Ocean. 16S rRNA gene sequence analysis revealed that the strain could be affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes and shared less than 94.6 % similarity with other species of the family with validly published names. The phenotypic characteristics of this novel isolate, such as growth properties and enzyme activities, could be differentiated from those of other species. The strain was non-motile, oxidase-positive and catalase-negative. The G+C content of the genomic DNA was determined to be 34.8 mol% and menaquinone-6 (MK-6) was the predominant isoprenoid quinone. The predominant fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C16 : 0 3-OH, iso-C17 : 0 3-OH and iso-C15 : 0 3-OH. The major polar lipids comprised phosphatidylethanolamine, three unknown aminolipids and three unknown lipids. On the basis of the taxonomic data collected in this study, it was concluded that strain SAORIC-234T represents a novel genus and species in the family Flavobacteriaceae, for which the name Aurantivirga profunda gen. nov., sp. nov. is proposed. The type strain of the type species, Aurantivirga profunda sp. nov., is SAORIC-234T ( = NBRC 110606T = KACC 18400T).

Polaribacter undariae sp. nov., isolated from a brown alga reservoir

A Gram-stain-negative, non-flagellated, non-gliding, aerobic and rod-shaped or ovoid bacterial strain, designated W-BA7(T), was isolated from a brown alga reservoir on the South Sea in South Korea. This strain grew optimally at 25 °C, at pH 7.0-8.0 and in the presence of approximately 2.0% (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain W-BA7(T) belonged to the genus Polaribacter, clustering coherently with the type strain of Polaribacter sejongensis, showing 99.3% sequence similarity. Strain W-BA7(T) exhibited 16S rRNA gene sequence similarity of 93.4-98.6% to the type strains of the other species of the genus Polaribacter. Strain W-BA7(T) contained MK-6 as the predominant menaquinone and iso-C15 : 0 3-OH and anteiso-C15 : 0 as the major fatty acids. The major polar lipids of strain W-BA7(T) were phosphatidylethanolamine, three unidentified lipids, one unidentified glycolipid, one unidentified aminolipid and one unidentified aminophospholipid. The DNA G+C content of strain W-BA7(T) was 31.9 mol%, and the mean DNA-DNA relatedness with the type strains of four phylogenetically related species of the genus Polaribacter was 12-27%. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain W-BA7(T) is separated from recognized species of the genus Polaribacter. On the basis of the data presented, strain W-BA7(T) is considered to represent a novel species of the genus Polaribacter, for which the name Polaribacter undariae sp. nov. is proposed. The type strain is W-BA7(T) ( =KCTC 42175(T) =CECT 8670(T)).

Niches of two polysaccharide-degrading Polaribacter isolates from the North Sea during a spring diatom bloom

Members of the flavobacterial genus Polaribacter thrive in response to North Sea spring phytoplankton blooms. We analyzed two respective Polaribacter species by whole genome sequencing, comparative genomics, substrate tests and proteomics. Both can degrade algal polysaccharides but occupy distinct niches. The liquid culture isolate Polaribacter sp. strain Hel1_33_49 has a 3.0-Mbp genome with an overall peptidase:CAZyme ratio of 1.37, four putative polysaccharide utilization loci (PULs) and features proteorhodopsin, whereas the agar plate isolate Polaribacter sp. strain Hel1_85 has a 3.9-Mbp genome with an even peptidase:CAZyme ratio, eight PULs, a mannitol dehydrogenase for decomposing algal mannitol-capped polysaccharides but no proteorhodopsin. Unlike other sequenced Polaribacter species, both isolates have larger sulfatase-rich PULs, supporting earlier assumptions that Polaribacter take part in the decomposition of sulfated polysaccharides. Both strains grow on algal laminarin and the sulfated polysaccharide chondroitin sulfate. For strain Hel1_33_49, we identified by proteomics (i) a laminarin-induced PUL, (ii) chondroitin sulfate-induced CAZymes and (iii) a chondroitin-induced operon that likely enables chondroitin sulfate recognition. These and other data suggest that strain Hel1_33_49 is a planktonic flavobacterium feeding on proteins and a small subset of algal polysaccharides, while the more versatile strain Hel1_85 can decompose a broader spectrum of polysaccharides and likely associates with algae.

Isolation of hyphomonas strains that induce normal morphogenesis in protoplasts of the marine red alga Pyropia yezoensis

Marine macroalgae cannot develop normal morphology under axenic conditions although normal morphogenesis can be sustained when certain bacteria are present. In this study, bacteria that induced normal morphogenesis in the red alga Pyropia yezoensis (Nori) were identified. The bacteria were isolated from algal media, thalli, tissue debris, and purified protoplasts during protoplast isolation from P. yezoensis laboratory cultures. 16S rRNA gene sequence analysis showed these bacterial isolates belonged to α-Proteobacteria (12 groups), γ-Proteobacteria (3 groups), and Flavobacteria (2 groups). Axenic protoplasts of P. yezoensis generated by removing epiphytic bacteria were co-cultured along with the bacterial isolates. Most axenic protoplasts showed irregular morphogenetic and anaplastic cells; cells with normal morphology were scarce. However, inoculation with 11 strains of Hyphomonas (α-Proteobacteria) led to significantly higher normal morphogenetic rates (4.5-7.3 %, P < 0.01 or 0.05) compared to axenic protoplasts (0.06 %). These Hyphomonas strains were recovered from all experiments; thus, certain Hyphomonas strains can induce normal morphogenesis in P. yezoensis protoplasts. Direct inoculation of the Hyphomonas strain exhibited higher morphogenetic activity than inoculation of its extracellular and intracellular products. This is the first study demonstrating the influence of specific bacteria on protoplast morphology in marine macroalgae.

Polaribacter atrinae sp. nov., isolated from the intestine of a comb pen shell, Atrina pectinata

A novel Gram-staining-negative, aerobic, non-motile, yellow-to-orange carotenoid-type-pigmented and rod-shaped bacterium, designated strain WP25T, was isolated from the intestine of a comb pen shell, Atrina pectinata, which was collected from the South Sea near Yeosu in Korea. The isolate grew optimally at 20 °C, at pH 7 and with 2 % (w/v) NaCl. 16S rRNA gene sequence analysis showed that strain WP25T belonged to the genus Polaribacter in the family Flavobacteriaceae and the highest sequence similarity was shared with the type strain of Polaribacter sejongensis (98.5 %). The major cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, C15 : 1ω6c and iso-C15 : 0 3-OH. The main respiratory quinone was menaquinone MK-6. The polar lipids of strain WP25T were phosphatidylethanolamine, two unidentified aminolipids, an unidentified phospholipid and four unidentified lipids. The genomic DNA G+C content was 31.2 mol%. DNA–DNA hybridization experiments indicated <12.6 % genomic relatedness with closely related strains. Based on phylogenetic, phenotypic and genotypic analyses, strain WP25T represents a novel species in the genus Polaribacter , for which the name Polaribacter atrinae sp. nov. is proposed, with the type strain WP25T ( = KACC 17473T = JCM 19202T).

Wenyingzhuangia marina gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from a recirculating mariculture system

A Gram-stain-negative, strictly aerobic and heterotrophic bacterial strain, designed strain D1T, was isolated from a recirculating mariculture system in Tianjin, China. Its taxonomic position was determined using a polyphasic approach. Cells of strain D1T were non-flagellated short rods, 0.3–0.5 µm wide and 0.5–1.0 µm long. Growth was observed at 15–30 °C (optimum, 25 °C), at pH 5.5–9.0 (optimum, pH 6.5–7.0) and in the presence of 1–8 % (w/v) NaCl (optimum, 2–3 %). Cells contained carotenoid pigments but not flexirubin-type pigments. Strain D1T contained MK-6 as the sole menaquinone and phosphatidylethanolamine (PE) as the sole phospholipid and four unidentified lipids. The major cellular fatty acids (>10 %) were iso-C15 : 0 (23.2 %), iso-C17 : 0 3-OH (15.2 %), C16 : 1ω7c/C16 : 1ω6c (14.3 %), iso-C15 : 0 3-OH (13.5 %) and iso-C15 : 1 G (10.8 %). 16S rRNA gene sequence analyses indicated that strain D1T belonged to the family Flavobacteriaceae and showed closest phylogenetic relationship to the genus Lutibacter , with highest sequence similarity to Lutibacter aestuarii MA-My1T (92.2 %). The DNA G+C content of strain D1T was 35.9 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain D1T was considered to represent a novel species in a new genus of the family Flavobacteriaceae , for which the name Wenyingzhuangia marina gen. nov., sp. nov. is proposed. The type strain of the type species is D1T ( = CGMCC 1.12162T = JCM 18494T).

Polaribacter huanghezhanensis sp. nov., isolated from Arctic fjord sediment, and emended description of the genus Polaribacter

A Gram-negative, orange-colony-forming, aerobic and non-flagellated bacterium, designated strain SM1202(T), was isolated from marine sediment of Kongsfjorden, Svalbard. Analysis of 16S rRNA gene sequences revealed that strain SM1202(T) was phylogenetically closely related to the genus Polaribacter. It shared the highest 16S rRNA gene sequence similarity with the type strain of Polaribacter dokdonensis (94.2 %) and 92.7-93.9 % sequence similarity with type strains of other known species of the genus Polaribacter. The strain grew at 4-35 °C and with 1.0-5.0 % (w/v) NaCl. It contained iso-C15 : 0, iso-C15 : 0 3-OH, iso-C13 : 0, C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH and C15 : 1ω6c as predominant cellular fatty acids and menaquinone-6 (MK-6) as the major respiratory quinone. The polar lipids of strain SM1202(T) were phosphatidylethanolamine, one unidentified lipid, two unidentified aminophospholipids and one unidentified aminolipid. The genomic DNA G+C content of strain SM1202(T) was 36.4 mol%. On the basis of the data from this polyphasic taxonomic study, strain SM1202(T) represents a novel species in the genus Polaribacter of the family Flavobacteriaceae, for which the name Polaribacter huanghezhanensis sp. nov. is proposed. The type strain of Polaribacter huanghezhanensis is SM1202(T) ( = CCTCC AB 2013148(T) = KCTC 32516(T)). An emended description of the genus Polaribacter is also presented.

Polaribacter sejongensis sp. nov., isolated from Antarctic soil, and emended descriptions of the genus Polaribacter , Polaribacter butkevichii and Polaribacter irgensii

A Gram-staining-negative, catalase- and oxidase-positive, non-motile bacterium, designated strain KOPRI 21160T, was isolated from Antarctic soil. Based on 16S rRNA gene sequence analysis, strain KOPRI 21160T was found to belong to the genus Polaribacter . Sequence similarity between strain KOPRI 21160T and the type strains of species of the genus Polaribacter was 94.2–98.3 %. The nearest phylogenetic neighbours of strain KOPRI 21160T were Polaribacter butkevichii KCTC 12100T (98.3 % similarity) and Polaribacter irgensii KCTC 23136T (97.5 %). DNA–DNA relatedness was 50.6 %, between strain KOPRI 21160T and P. butkevichii KCTC 12100T, and 45.2 % between strain KOPRI 21160T and P. irgensii KCTC 23136T. Strain KOPRI 21160T grew at 4–37 °C and at pH 7.0–8.5. It could hydrolyse DNA, starch and Tweens 20, 40, 60 and 80. Menaquinone-6 (MK-6) was the only respiratory quinone, and iso-C15 : 0, iso-C15 : 0 3-OH and C15 : 1ω6c were the major cellular fatty acids. The major polar lipids were phosphatidylethanolamine, two unidentified aminolipids and one unidentified lipid. The DNA G+C content was 30.0 mol%. Based on data from our polyphasic study, the organism is considered to represent a novel species of the genus Polaribacter , for which we propose the name Polaribacter sejongensis sp. nov. The type strain is KOPRI 21160T ( = KCTC 23670T = JCM 18092T). Emended descriptions of the genus Polaribacter , Polaribacter butkevichii Nedashkovskaya et al. 2005 and Polaribacter irgensii Gosink et al. 1998 are also proposed.