Pseudoalteromonas arabiensis sp. nov., a marine polysaccharide-producing bacterium

Genome-Based Classification of Strain 16-SW-7, a Marine Bacterium Capable of Converting B Red Blood Cells, as Pseudoalteromonas distincta and Proposal to Reclassify Pseudoalteromonas paragorgicola as a Later Heterotypic Synonym of Pseudoalteromonas distincta

A strictly aerobic, Gram-stain-negative, rod-shaped, and motile bacterium, designated strain 16-SW-7, isolated from a seawater sample, was investigated in detail due to its ability to produce a unique α-galactosidase converting B red blood cells into the universal type blood cells. The phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain 16-SW-7 is a member of the Gammaproteobacteria genus Pseudoalteromonas. The closest relatives of the environmental isolate were Pseudoalteromonas distincta KMM 638^T and Pseudoalteromonas paragorgicola KMM 3548^T, with the plural paralogous 16S rRNA genes of 99.87-100% similarity. The strain 16-SW-7 grew with 1-10% NaCl and at 4-34°C, and hydrolyzed casein, gelatin, tyrosine, and DNA. The genomic DNA G+C content was 39.3 mol%. The prevalent fatty acids were C_16:1 ω7c, C_16:0, C_17:1 ω8c, C_18:1 ω7c, C_17:0, and C_12:0 3-OH. The polar lipid profile was characterized by the presence of phosphatidylethanolamine, phosphatidylglycerol, two unidentified amino lipids, and three unidentified lipids. The major respiratory quinone was Q-8. The finished genome of the strain 16-SW-7 (GenBank assembly accession number: GCA_005877035.1) has a size of 4,531,445 bp and comprises two circular chromosomes L1 and S1, deposited in the GenBank under the accession numbers CP040558 and CP040559, respectively. The strain 16-SW-7 has the ANI values of 98.2% with KMM 638^T and KMM 3548^T and the DDH values of 84.4 and 83.5%, respectively, indicating clearly that the three strains belonged to a single species. According to phylogenetic evidence and similarity for the chemotaxonomic and genotypic properties, the strain 16-SW-7 (= KCTC 52772 = KMM 701) represents a novel member of the species Pseudoalteromonas distincta. Also, we have proposed to reclassify Pseudoalteromonas paragorgicola as a later heterotypic synonym of P. distincta based on the rules of priority with the emendation of the species.

Degradation and Utilization of Alginate by Marine Pseudoalteromonas: a Review

Alginate, which is mainly produced by brown algae and decomposed by heterotrophic bacteria, is an important marine organic carbon source. The genus Pseudoalteromonas contains diverse forms of heterotrophic bacteria that are widely distributed in marine environments and are an important group in alginate degradation. In this review, the diversity of alginate-degrading Pseudoalteromonas is introduced, and the characteristics of Pseudoalteromonas alginate lyases, including their sequences, enzymatic properties, structures, and catalytic mechanisms, and the synergistic effect of Pseudoalteromonas alginate lyases on alginate degradation are introduced. The acquisition of the alginate degradation capacity and the alginate utilization pathways of Pseudoalteromonas are also introduced. This paper provides a comprehensive overview of alginate degradation by Pseudoalteromonas, which will contribute to the understanding of the degradation and recycling of marine algal polysaccharides driven by marine bacteria.

Variation of Microbial Diversity in Catastrophic Oil Spill Area in Marine Ecosystem and Hydrocarbon Degradation of UCMs (Unresolved Complex Mixtures) by Marine Indigenous Bacteria

The study targeted an assessment of microbial diversity during oil spill in the marine ecosystem (Kaohsiung port, Taiwan) and screened dominant indigenous bacteria for oil degradation, as well as UCM weathering. DO was detected lower and TDS/conductivity was observed higher in oil-spilled area, compared to the control, where a significant correlation (R² = 1; P < 0.0001) was noticed between DO and TDS. The relative abundance (RA) of microbial taxa and diversities (> 90% similarity by NGS) were found higher in the boundary region of spilled-oily-water (site B) compared to the control (site C) and center of the oil spill area (site A) (B_RA/diversity > C_RA/diversity > A_RA/diversity). The isolated indigenous bacteria, such as Staphylococcus saprophyticus (CYCTW1), Staphylococcus saprophyticus (CYCTW2), and Bacillus megaterium (CYCTW3) degraded the C₁₀-C₃₀ including UCM of oil, where Bacillus sp. are exhibited more efficient, which are applicable for environmental cleanup of the oil spill area. Thus, the marine microbial diversity changes due to oil spill and the marine microbial community play an important role to biodegrade the oil, besides restoring the catastrophic disorders through changing their diversity by ecological selection and adaptation process.

Antimicrobial-producing Pseudoalteromonas from the marine environment of Panama shows a high phylogenetic diversity and clonal structure

Pseudoalteromonas is a genus of marine bacteria often found in association with other organisms. Although several studies have examined Pseudoalteromonas diversity and their antimicrobial activity, its diversity in tropical environments is largely unexplored. We investigated the diversity of Pseudoalteromonas in marine environments of Panama using a multilocus phylogenetic approach. Furthermore we tested their antimicrobial capacity and evaluated the effect of recombination and mutation in shaping their phylogenetic relationships. The reconstruction of clonal relationships among 78 strains including 15 reference Pseudoalteromonas species revealed 43 clonal lineages, divided in pigmented and non-pigmented strains. In total, 39 strains displayed moderate to high activity against Gram-positive and Gram-negative bacteria and fungi. Linkage disequilibrium analyses showed that the Pseudoalteromonas strains of Panama have a highly clonal structure and that, although present, recombination is not frequent enough to break the association among alleles. This clonal structure is in contrast to the high rates of recombination generally reported for aquatic and marine bacteria. We propose that this structure is likely due to the symbiotic association with marine invertebrates of most strains analyzed. Our results also show that there are several putative new species of Pseudoalteromonas in Panama to be described.

Seafood spoilage microbiota and associated volatile organic compounds at different storage temperatures and packaging conditions

Seafood comprising of both vertebrate and invertebrate aquatic organisms are nutritious, rich in omega-3 fatty acids, essential vitamins, proteins, minerals and form part of healthy diet. However, despite the health and nutritional benefits, seafood is highly perishable. Spoilage of seafood could be as a result of microbial activity, autolysis or chemical oxidation. Microbial activity constitutes more spoilage than others. Spoilage bacteria are commonly Gram negative and produce off odours and flavours in seafood as a result of their metabolic activities. Storage temperature, handling and packaging conditions affect microbial growth and thus the shelf-life of seafood. Due to the complexity of the microbial communities in seafood, culture dependent methods of detection may not be useful, hence the need for culture independent methods are necessary to understand the diversity of microbiota and spoilage process. Similarly, the volatile organic compounds released by spoilage bacteria are not fully understood in some seafood. This review therefore highlights current knowledge and understanding of seafood spoilage microbiota, volatile organic compounds, effects of storage temperature and packaging conditions on quality of seafood.

Physiological and genomic features of a novel violacein-producing bacterium isolated from surface seawater

Strains JW1^T and JW3, isolated from surface seawater of the Arabian Sea, were subjected to polyphasic taxonomic analysis. Cells of both strains were Gram-stain-negative, aerobic, and rod-shaped. They formed violet pigment and produced violacein. On the basis of 16S rRNA gene sequence analysis, strains JW1^T and JW3 showed high 16S rRNA gene sequence similarity with Pseudoalteromonas byunsanensis JCM12483^T (98.2%), P. shioyasakiensis SE3^T (97.8%), P. arabiensis JCM 17292^T (97.3%), and P. gelatinilytica NH153^T (97.1%). The 16S rRNA gene sequence similarity between JW1^T and JW3 was 100%. Phylogenetic analyses revealed that both strains fell within the cluster of the genus Pseudoalteromonas and represented an independent lineage. The average nucleotide identity and in silico DNA-DNA hybridization values between JW1^T and type strains of the closely related Pseudoalteromonas species were 70.9–83.3% and 20.0–26.4%, respectively. The sole respiratory quinone in both strains is ubiquinone 8 (Q-8). The principal fatty acids are summed feature 3 (C_16:1ω7c and/or iso-C_15:0 2OH), C_18:1ω7c, and C_16:0. The major polar lipids are phosphatidylethanolamine, phosphatidylglycerol, one unidentified glycolipid, one unidentified aminolipid, and one unidentified phospholipid. The DNA G+C content was 43.3 mol%. Differential phylogenetic distinctiveness, chemotaxonomic differences, and phenotypic properties indicated that strains JW1^T and JW3 could be differentiated from the Pseudoalteromonas species with validly published names. Therefore, it is proposed that strains JW1^T and JW3 represent a novel species of the genus Pseudoalteromonas, for which the name Pseudoalteromonas amylolytica sp. nov. (type strain, JW1^T = CGMCC 1.15681^T = KCTC 52406^T = MCCC 1K02162^T) is proposed.

Pseudoalteromonas profundi sp. nov., isolated from a deep-sea seamount

A Gram-stain-negative, rod-shaped, strictly aerobic, motile bacterial strain, designated TP162T, was isolated from a seamount near the Yap Trench in the tropical western Pacific. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain TP162T was related to the genus Pseudoalteromonas and had highest 16S rRNA gene sequence similarities with the type strains Pseudoalteromonas shioyasakiensis SE3T (98.2 %), Pseudoalteromonas lipolytica LMEB 39T (97.7 %), Pseudoalteromonas arabiensis k53T (97.4 %) and Pseudoalteromonas aliena KMM 3562T (97.2 %). The predominant cellular fatty acids were summed feature 3 (composed of iso-C15 : 0 2-OH and/or C16 : 1ω7c), C17 : 1ω8c and C16 : 0. The quinone system for strain TP162T comprised predominantly ubiquinone-8, and the polar lipid profile contained phosphatidylethanolamine, phosphatidylglycerol, one unidentified phospholipid and four unidentified lipids. The genomic DNA G+C content of strain TP162T was 46.7 mol%. Strain TP162T shared 28 % DNA-DNA relatedness with P.shioyasakiensis JCM 18891T, 21 % with P. lipolytica JCM 15903T, 35 % with P.arabiensis JCM 17292T and 18 % with P.aliena LMG 22059T. Combined data from phenotypic, chemotaxonomic, phylogenetic and DNA-DNA relatedness studies demonstrated that strain TP162T is a representative of a novel species of the genus Pseudoalteromonas, for which we propose the name Pseudoalteromonas profundi sp. nov. (type strain TP162T=KACC 18554T=CGMCC 1.15394T).

Pseudoalteromonas gelatinilytica sp. nov., isolated from surface seawater

Three Gram-stain-negative, rod-shaped bacteria, designated strains NH153T, F-2-11 and M-1-78, were isolated from surface seawater of the South China Sea and the East China Sea. The three isolates were able to grow at 15-45 °C (optimum 28-37 °C), but no growth occurred at 4 or 50 °C. The pH range for growth was pH 5.5-9.5 (optimum pH 7.5-8.5). The isolates required sea salts for growth and growth occurred in the presence of 0-10 % (w/v) NaCl (optimum 3-5 %); no growth occurred in the presence of 12.0, 15.0 or 20.0 % (w/v) NaCl. They were positive for hydrolysis of gelatin and Tween 80. The sole respiratory quinone was ubiquinone-8 (Q-8). The major cellular fatty acids (>10 %) were C16 : 0, C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The major polar lipid components were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified glycolipid, one unidentified phospholipid and one unidentified lipid. The genomic DNA G+C content of strain NH153T was 41.4 mol%. Based on 16S rRNA gene sequence analysis, the isolates were closely related to the type strain of Pseudoalteromonas shioyasakiensis (98.0-98.6 % sequence similarity). The 16S rRNA gene sequence similarities between the three isolates were 98.8-99.7 %. Phylogenetic analysis indicated that they formed a distinct lineage and clustered with P. shioyasakiensis and Pseudoalteromonas arabiensis. The level of DNA-DNA relatedness among the three isolates was 78.0-85.5 %. Strain NH153T exhibited average nucleotide identity values of 93.4 and 84.2 % with respect to P. shioyasakiensisJCM 18891T and P. arabiensisJCM 17292T, respectively. The genome-to-genome distance analysis revealed that strain NH153T shared 52.4 % DNA relatedness with P. shioyasakiensisJCM 18891T and 28.1 % with P. arabiensisJCM 17292T. On the basis of the phenotypic, genotypic and chemotaxonomic characterizations, as well as phylogenetic inference obtained in this study, strains NH153T, F-2-11 and M-1-78 represent a novel species within the genus Pseudoalteromonas, for which the name Pseudoalteromonasgelatinilytica sp. nov. is proposed. The type strain is NH153T (=CGMCC 1.15370T=DSM 100951T), and F-2-11 (=CGMCC 1.15364=DSM 100953) and M-1-78 (=CGMCC 1.15365=DSM 100952), are additional strains of the species.

Pseudoalteromonas fenneropenaei sp. nov., a marine bacterium isolated from sediment of a Fenneropenaeus chinensis pond

A novel Gram-stain-negative, motile, oxidase- and catalase-positive, non-spore-forming, non-pigmented, aerobic bacterium, designated rzy34^T, was isolated from the sediment of a pond containing farmed Fenneropenaeus chinensis Rizhao, China. The strain was able to grow at pH 6-10 (optimum pH 7), 20-40 °C (optimum 30 °C) and in the presence of 1.0-6.0 % NaCl (optimum 1.0-2.0 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that the nearest relative of strain rzy34^T was Pseudoalteromonas xiamenensis Y2^T, with the highest sequence similarity of 96.09 %. Within the genus Pseudoalteromonas, it showed the lowest similarity of 92.7 % to Pseudoalteromonas donghaensis. The G+C content of the chromosomal DNA of strain rzy34^T was 45.3 mol%. The predominant cellular fatty acids were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0, C17 : 1ω8c and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c). The major respiratory quinone was Q-8. Polar lipid analysis indicated the presence of phosphatidylethanolamine and phosphatidylcholine. On the basis of the phenotypic and phylogenetic characteristics, strain rzy34^T represents a novel species of the genus Pseudoalteromonas, for which the name Pseudoalteromonas fenneropenaei sp. nov. is proposed. The type strain is rzy34^T (=CGMCC 1.15325^T=KCTC 42730^T).

MALDI-TOF Mass Spectrometry Discriminates Known Species and Marine Environmental Isolates of Pseudoalteromonas

The genus Pseudoalteromonas constitutes an ecologically significant group of marine Gammaproteobacteria with potential biotechnological value as producers of bioactive compounds and of enzymes. Understanding their roles in the environment and bioprospecting for novel products depend on efficient ways of identifying environmental isolates. Matrix Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) biotyping has promise as a rapid and reliable method of identifying and distinguishing between different types of bacteria, but has had relatively limited application to marine bacteria and has not been applied systematically to Pseudoalteromonas. Therefore, we constructed a MALDI-TOF MS database of 31 known Pseudoalteromonas species, to which new isolates can be compared by MALDI-TOF biotyping. The ability of MALDI-TOF MS to distinguish between species was scrutinized by comparison with 16S rRNA gene sequencing. The patterns of similarity given by the two approaches were broadly but not completely consistent. In general, the resolution of MALDI-TOF MS was greater than that of 16S rRNA gene sequencing. The database was tested with 13 environmental Pseudoalteromonas isolates from UK waters. All of the test strains could be identified to genus level by MALDI-TOF MS biotyping, but most could not be definitely identified to species level. We conclude that several of these isolates, and possibly most, represent new species. Thus, further taxonomic investigation of Pseudoalteromonas is needed before MALDI-TOF MS biotyping can be used reliably for species identification. It is, however, a powerful tool for characterizing and distinguishing among environmental isolates and can make an important contribution to taxonomic studies.

Psychrobacter oceani sp. nov., isolated from marine sediment

A novel marine bacterium, designated strain 4k5T, was isolated from a sediment sample of the Pacific Ocean. The strain was Gram-stain-negative, strictly aerobic, non-motile, oxidase-positive and catalase-positive and required Na+ for growth. Its major isoprenoid quinone was ubiquinone 8 (Q-8), and its cellular fatty acid profile consisted mainly of C18 : 1v9c (71.4 %), C16 : 1v7c (9.1 %) and C18 : 0. The DNA G+C content was 45.3 mol%. 16S rRNA gene sequence analysis suggested that strain 4k5T is a member of the genus Psychrobacter . Strain 4k5T exhibited the closely phylogenetic affinity to Psychrobacter pacificensis IFO 16270T (99.4 % 16S rRNA gene sequence similarity), P. piscatorii T-3-2T (97.7 %), P. nivimaris 88/2-7T (97.7 %), P. celer SW-238T (97.7 %), P. aestuarii SC35T (97.6 %) and P. vallis CMS39T (97.6 %). DNA–DNA hybridization between strain 4k5T and P. pacificensis NBRC 103191T, P. piscatorii JCM 15603T. P. nivimaris DSM 16093T, P. celer JCM 12601T, P. aestuarii JCM 16343T and P. vallis DSM 15337T was 42.5, 47.0, 38.1, 23.7, 9.0 and 27.4 %, respectively. Owing to the significant differences in phenotypic and chemotaxonomic characteristics, phylogenetic analysis based on the 16S rRNA gene sequence and DNA–DNA relatedness data, the isolate merits classification within a novel species, for which the name Psychrobacter oceani sp. nov. is proposed. The type strain is 4k5T ( = JCM 30235T = NCIMB 14948T).

Alteromonas gracilis sp. nov., a marine polysaccharide-producing bacterium

A novel exopolysaccharide-producing bacterium, designated strain 9a2T, was isolated from Pacific Ocean sediment. The strain was Gram-stain-negative, motile, strictly aerobic, oxidase- and catalase-positive, and required NaCl for growth. Its major isoprenoid quinone was ubiquinone-8 (Q-8), and its cellular fatty acid profile consisted mainly of C16 : 1ω7c, C18 : 1ω9c and C16 : 0. The DNA G+C content was 46.6 mol%. 16S rRNA gene sequence analysis suggested that strain 9a2T is a member of the genus Alteromonas . Strain 9a2T exhibited closest phylogenetic affinity to Alteromonas macleodii NBRC 102226T (99.3 % 16S rRNA gene sequence similarity), A. marina SW-47T (99.3 %), A. litorea TF-22T (99.0 %), A. australica H17T (98.7 %), A. simiduii BCRC 17572T (98.5 %), A. stellipolaris LMG 21861T (98.3 %) and A. hispanica F-32T (98.2 %). The DNA–DNA reassociation values between strain 9a2T and A. macleodii JCM 20772T, A. marina JCM 11804T, A. litorea JCM 12188T, A. australica CIP 109921T, A. simiduii JCM 13896T, A. stellipolaris LMG 21861T and A. hispanica LMG 22958T were below 70 %. Strain 9a2T contained phosphatidylethanolamine, phosphatidylglycerol and an unidentified polar lipid. Owing to differences in phenotypic and chemotaxonomic characteristics, phylogenetic analysis based on 16S rRNA gene sequences and DNA–DNA relatedness data, the isolate merits classification as representing a novel species, for which the name Alteromonas gracilis sp. nov. is proposed. The type strain of this species is 9a2T ( = JCM 30236T = NCIMB 14947T).

Pseudoalteromonas xiamenensis sp. nov., a marine bacterium isolated from coastal surface seawater

A Gram-negative, oxidase- and catalase-positive, rod-shaped, non-spore-forming, motile, aerobic bacterium, designated Y2(T), was isolated from surface seawater of Yundang Lake, Xiamen, China. The strain was able to grow in the presence of 0.5-6.0% NaCl (optimum 1.0-1.5%), at pH 5-10 (optimum pH 8) and at 10-40 °C (optimum 25 °C). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain Y2(T) belongs to the genus Pseudoalteromonas, with the highest sequence similarity of 94.9% to Pseudoalteromonas tunicata D2(T); within the genus Pseudoalteromonas, it showed the lowest similarity of 92.8% to Pseudoalteromonas denitrificans ATCC 43337(T). The G+C content of the chromosomal DNA of strain Y2(T) was 45.1 mol%. The predominant fatty acids were summed feature 3 (C(16 : 1)ω6c and/or C(16 : 1)ω7c), C(16 : 0), C(12 : 0) 3-OH and summed feature 8 (C(18 : 1)ω6c and/or C(18 : 1)ω7c). The only respiratory quinone detected was Q-8. Based on the phylogenetic and phenotypic characteristics, strain Y2(T) represents a novel species of the genus Pseudoalteromonas, for which the name Pseudoalteromonas xiamenensis sp. nov. is proposed; the type strain is Y2(T) ( = CGMCC 1.12157(T) = JCM 18779(T)).

Pseudoalteromonas shioyasakiensis sp. nov., a marine polysaccharide-producing bacterium

A novel exopolysaccharide-producing bacterium, designated strain SE3(T), was isolated from Pacific Ocean sediment. The strain was Gram-stain-negative, motile, strictly aerobic, oxidase-positive and catalase-positive, and required Na(+) for growth. Its major isoprenoid quinone was ubiquinone-8 (Q-8), and its cellular fatty acid profile mainly consisted of C16 : 1ω7c, C16 : 0 and C18 : 1ω7c. The DNA G+C content was 46.9 mol%. 16S rRNA gene sequence analysis suggested that strain SE3(T) is a member of the genus Pseudoalteromonas. Strain SE3(T) exhibited close phylogenetic affinity to Pseudoalteromonas arabiensis JCM 17292(T) (99.0 % 16S rRNA gene sequence similarity), Pseudoalteromonas lipolytica LMEB 39(T) (98.39 %) and Pseudoalteromonas donghaensis HJ51(T) (97.65 %). The DNA-DNA reassociation values between strain SE3(T) and P. arabiensis JCM 17292(T), P. lipolytica JCM 15903(T) and P. donghaensis LMG 24469(T) were 31, 26 and 44 %, respectively. Owing to the significant differences in phenotypic and chemotaxonomic characteristics, phylogenetic analysis based on 16S rRNA gene sequences and DNA-DNA relatedness data, the new isolate merits classification as a representative of novel species, for which the name Pseudoalteromonas shioyasakiensis is proposed. The type strain is SE3(T) ( = JCM 18891(T) = NCIMB 14852(T)).