Olga I. Nedashkovskaya

Genome analysis of the proteorhodopsin-containing marine bacterium Polaribacter sp. MED152 (Flavobacteria)

Analysis of marine cyanobacteria and proteobacteria genomes has provided a profound understanding of the life strategies of these organisms and their ecotype differentiation and metabolisms. However, a comparable analysis of the Bacteroidetes, the third major bacterioplankton group, is still lacking. In the present paper, we report on the genome of Polaribacter sp. strain MED152. On the one hand, MED152 contains a substantial number of genes for attachment to surfaces or particles, gliding motility, and polymer degradation. This agrees with the currently assumed life strategy of marine Bacteroidetes. On the other hand, it contains the proteorhodopsin gene, together with a remarkable suite of genes to sense and respond to light, which may provide a survival advantage in the nutrient-poor sun-lit ocean surface when in search of fresh particles to colonize. Furthermore, an increase in CO2 fixation in the light suggests that the limited central metabolism is complemented by anaplerotic inorganic carbon fixation. This is mediated by a unique combination of membrane transporters and carboxylases. This suggests a dual life strategy that, if confirmed experimentally, would be notably different from what is known of the two other main bacterial groups (the autotrophic cyanobacteria and the heterotrophic proteobacteria) in the surface oceans. The Polaribacter genome provides insights into the physiological capabilities of proteorhodopsin-containing bacteria. The genome will serve as a model to study the cellular and molecular processes in bacteria that express proteorhodopsin, their adaptation to the oceanic environment, and their role in carbon-cycling.

Arenibacter gen. nov., new genus of the family Flavobacteriaceae and description of a new species, Arenibacter latericius sp. nov

Five dark-orange-pigmented, Gram-negative, rod-shaped, non-motile, aerobic bacterial strains were isolated from sandy sediment samples collected in the South China Sea in the Indian Ocean, from a holothurian, Apostichopus japonicus, in the Sea of Japan and from a brown alga, Chorda filum, from the Sea of Okhotsk in the Pacific Ocean. Phenotypic data were collected, demonstrating that the bacteria are chemo-organotrophic and require seawater-based media for growth. Polar lipids were analysed and 27% of the total extract comprised phosphatidylethanolamine as the major component. The predominant cellular fatty acids were branched-chain saturated and unsaturated [i-C15:0, i-C15:1, a-C15:0, C15:0, C16:1(n-7)]. The DNA base composition was 37.5-38.2 mol % G+C. The level of DNA homology of the five isolates was 83-94%, indicating that these isolates belong to the same species. A 16S rDNA sequence of the type strain KMM 426T was determined and phylogenetic analysis, based on neighbour-joining and Fitch-Margoliash methods, revealed that the type strain formed a distinct phyletic line in a clade corresponding to the family Flavobacteriaceae and represented a new genus. From the results of this polyphasic taxonomic analysis, it is proposed that the bacterial strains be classified in a new genus, Arenibacter gen. nov., and species, Arenibacter latericius sp. nov. The type strain is KMM 426T (VKM B 2137DT = LMG 19694T = CIP 106861T).

Degradation of fucoidan by the marine proteobacterium Pseudoalteromonas citrea

It was found that Pseudoalteromonas citrea strains KMM 3296 and KMM 3298 isolated from the brown algae Fucus evanescens and Chorda filum, respectively, and strain 3297 isolated from the sea cucumber Apostichopus japonicus are able to degrade fucoidans. The fucoidanases of these strains efficiently degraded the fucoidan of brown algae at pH 6.5–7.0 and remained active at 40–50°C. The endo-type hydrolysis of fucoidan resulted in the formation of sulfated α-L-fucooligosaccharides. The other nine strains of P. citrea studied (including the type strain of this species), which were isolated from other habitats, were not able to degrade fucoidan.

Winogradskyella echinorum sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from the sea urchin Strongylocentrotus intermedius

The taxonomic position of a novel marine, yellow-pigmented bacterium, designated strain KMM 6211(T), was examined by using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain KMM 6211(T) is a member of the family Flavobacteriaceae, phylum Bacteroidetes. The closest relative of strain KMM 6211(T) was Winogradskyella eximia KMM 3944(T), the sequence similarity being 97.1 %. The DNA G+C content of KMM 6211(T) was 33.6 mol%. The strain was motile by gliding and grew with 1-6 % NaCl and at 4-37 degrees C. Aesculin, casein and gelatin were hydrolysed, but agar, starch, DNA and chitin were not degraded. On the basis of phylogenetic data and phenotypic differences between the isolate and recognized Winogradskyella species, strain KMM 6211(T) represents a novel species of the genus Winogradskyella, for which the name Winogradskyella echinorum sp. nov. is proposed. The type strain is KMM 6211(T) (=KCTC 22026(T)=LMG 24757(T)).

Polaribacter butkevichii sp. nov., a Novel Marine Mesophilic Bacterium of the Family Flavobacteriaceae

A novel heterotrophic, yellow pigmented, aerobic, Gram-negative, nonmotile, oxidase- and catalase-positive bacterium KMM 3938T was isolated from sea water collected in the Sea of Japan, Russia. The strain grew at mesophilic temperature range, and required the presence of NaCl for growth. 16S rRNA gene sequence analysis revealed that strain KMM 3938T is a member of the family Flavobacteriaceae. The predominant fatty acids were C13:0 iso, C14:0 iso, C15:0 iso, C15:0, C15:1Δ6, 3OH-C15:0:3 iso, and 3OH-C15:0. The G + C content of the DNA of KMM 3938T was 32.4 mol%. On the basis of phenotypic, chemotaxonomic, genotypic, and phylogenetic characteristics, the novel bacterium was assigned to the genus Polaribacter as Polaribacter butkevichii sp. nov. The type strain is KMM 3938T (= KCTC 12100T = CCUG 48005T).

Distribution of intracellular fucoidan hydrolases among marine bacteria of the family Flavobacteriaceae

A search for fucoidan-degrading enzymes and other O-glycosylhydrolases has been performed among 51 strains of marine bacteria of the family Flavobacteriaceae isolated from red, green, and brown algae, as well as from the sea urchin Strongylocentrotus intermedius and the holothurian Apostichopus japonicus. Over 40% of the studied strains synthesized fucoidanases. The marine bacteria Mesonia algae KMM 3909T (an isolate from green alga Acrosiphonia sonderi), as well as Maribacter sp. KMM 6211 and Gramella sp. KMM 6054 (associants of the sea urchin S. intermedius), were the best producers of fucoidanases. Xylose effectively induced the biosynthesis of fucoidanases in these strains. None of the 15 strains of marine bacteria belonging to the genus Arenibacter produced polysaccharide hydrolases.

Maribacter stanieri sp. nov., a marine bacterium of the family Flavobacteriaceae

The taxonomic status of two novel heterotrophic, Gram-negative, gliding and yellow pigmented bacterial strains was established in this study. Phylogenetic analysis based on 16S rRNA gene sequencing revealed that the strains formed a distinct lineage within the genus Maribacter, a member of the family Flavobacteriaceae, with sequence similarities of 96.3-98.5 % to recognized species of the genus Maribacter. The maximum growth temperature of the strains was 35 degrees C and they required NaCl or seawater for growth. They hydrolysed aesculin and gelatin, reduced nitrates to nitrites and produced acid from carbohydrates. The DNA G+C contents of strains KMM 6025 and KMM 6046(T) were 36-37 mol%. On the basis of phenotypic, genotypic and phylogenetic characteristics, it is suggested that the new isolates represent a novel species of the genus Maribacter, for which the name Maribacter stanieri sp. nov. is proposed. The type strain is KMM 6046(T) (=KCTC 22023(T)=LMG 22581(T)).

Winogradskyella rapida sp. nov., isolated from protein-enriched seawater

Flavobacteria are emerging as an important group of organisms associated with the degradation of complex organic matter in aquatic environments. A novel Gram-reaction-negative, heterotrophic, rod-shaped, aerobic, yellow-pigmented and gliding bacterium, strain SCB36T, was isolated from a protein-enriched seawater sample, collected at Scripps Pier, Southern California Bight (Eastern Pacific). Analysis of the 16S rRNA gene sequence showed that the bacterium was related to members of the genus Winogradskyella within the family Flavobacteriaceae, phylum Bacteroidetes. 16S rRNA gene sequence similarity to the other Winogradskyella species was 94.5-97.1%. DNA-DNA relatedness between strain SCB36T and Winogradskyella thalassocola KMM 3907T, its closest relative in terms of 16S rRNA gene sequence similarity, was 20%. On the basis of the phylogenetic and phenotypic data, strain SCB36T represents a novel species of the genus Winogradskyella, for which the name Winogradskyella rapida sp. nov. is proposed. The type strain is SCB36T (=CECT 7392T=CCUG 56098T).

Lacinutrix algicola sp. nov. and Lacinutrix mariniflava sp. nov., two novel marine alga- associated bacteria and emended description of the genus Lacinutrix

Two heterotrophic, aerobic, yellow-pigmented, Gram-negative, non-gliding bacteria, designated AKS293(T) and AKS432(T), isolated from a red alga, were analysed using a polyphasic taxonomic approach. 16S rRNA gene sequence analysis revealed that the novel strains were affiliated to the genus Lacinutrix, a member of the family Flavobacteriaceae, showing sequence similarities of 96.1-96.4 % with respect to the type strain of Lacinutrix copepodicola. The two novel isolates shared 99.5 % 16S rRNA gene sequence similarity and 55.0 % DNA-DNA relatedness. They grew optimally at 17.5 degrees C and pH 6.5. The main cellular fatty acids of strain AKS293(T) were iso-C(15 : 0), iso-C(15 : 0) 3-OH and iso-C(16 : 0) 3-OH, while those of strain AKS432(T) were anteiso-C(15 : 0), iso-C(15 : 0), iso-C(15 : 1) and iso-C(15 : 0) 3-OH. In both cases, the major isoprenoid quinone was MK-6. The DNA G+C contents were 34.7 and 37.0 mol% for strains AKS293(T) and AKS432(T), respectively. The phylogenetic evidence, phenotypic data and DNA-DNA hybridization results support the differentiation of strains AKS293(T) and AKS432(T) from each other and from their closest relative, L. copepodicola DJ3(T). Therefore, strains AKS293(T) and AKS432(T) represent two novel species, for which the names Lacinutrix algicola sp. nov. and Lacinutrix mariniflava sp. nov. are proposed, respectively. The type strain of L. algicola sp. nov. is AKS293(T) (=KCCM 42313(T)=JCM 13825(T)) and the type strain of L. mariniflava sp. nov. is AKS432(T) (=KCCM 42306(T)=JCM 13824(T)). An emended description of the genus Lacinutrix is also proposed.

Ecophysiological variabilities in Ectohydrolytic enzyme activities of some Pseudoalteromonas species, P. citrea, P. issachenkonii, and P. nigrifaciens

The ecophysiological variabilities in the ectohydrolytic enzyme profiles of the three species of Pseudoalteromonas, P. citrea, P. issachenkonii, and P. nigrifaciens, have been investigated. Forty-one bacteria isolated from several invertebrates, macroalgae, sea grass, and the surrounding water exhibited different patterns of hydrolytic enzyme activities measured as the hydrolysis of either native biopolymers or fluorogenic substrates. The activities of the following enzymes were assayed: proteinase, tyrosinase, lipase, amylase, chitinase, agarase, fucoidan hydrolase, laminaranase, alginase, pustulanase, cellulase, β-glucosidase, α- and β-galactosidases, β-N-acetylglucosaminidase, β-glucosaminidase, β-xylosidase, and α-mannosidase. The occurrence and cell-specific activities of all enzymes varied over a broad range (from 0 to 44 μmol EU per hour) and depended not only on taxonomic affiliation of the strain, but also on the source/place of its isolation. This suggests ‘specialization’ of different species for different types of polymeric substrates as, for example, all strains of P. citrea and P. issachenkonii hydrolyzed alginate and laminaran, while strains of P. nigrifaciens were lacking the ability to hydrolyze most of the algal polysaccharides. The incidence of certain enzymes such as fucoidan hydrolases, alginate lyases, agarases, and α-galactosidases might be strain specific and reflect its particular ecological habitat.