Peculiarities of Alteromonas macleodii strains reflects their deep/surface habitation rather than geographical distribution

The phenotypic, chemotaxonomic and genetic peculiarities of 5 deep strains of Alteromonas macleodii (isolated from Adriatic and Ionian Sea water from a depth of 1,000-3,500 m) and 5 strains of the same species isolated from the surface layer of Aegean, Andaman, Black Sea and Atlantic Ocean water near the British shore have been studied. Electron microscopy has shown that the deep strains' cells were, on average, two times longer (2.1±0.2×0.7±0.1 μm) than the surface strains' (1.1±0.1×0.6±0.1 μm). Using fatty acid analysis (particularly the mono-unsaturated C16:1 and C18:1 fatty acids contents) the deep and surface isolates were clearly separated into two clusters. Distinctions between them were also found in different lectin binding capacity, which is probably determined by the structure of their extracellular polysaccharide matrix. Analysis of the results of PCR with primers to repeated nucleotide sequences revealed a higher level of genetic polymorphism in surface strains in comparison with the deep isolates. This division was confirmed by the cluster analysis method though it was not as clear as in the fatty acids analysis. The described peculiarities are probably reflective of specific conditions in which A. macleodii strains live on the surface or in the depth of the world's oceans.     

Diversity of 746 heterotrophic bacteria isolated from microbial mats from ten Antarctic lakes

Microbial mats, growing in Antarctic lakes constitute unique and very diverse habitats. In these mats microorganisms are confronted with extreme life conditions. We isolated 746 bacterial strains from mats collected from ten lakes in the Dry Valleys (lakes Hoare and Fryxell), the Vestfold Hills (lakes Ace, Druzhby, Grace, Highway, Pendant, Organic and Watts) and the Larsemann Hills (lake Reid), using heterotrophic growth conditions. These strains were investigated by fatty acid analysis, and by numerical analysis, 41 clusters, containing 2 to 77 strains, could be delineated, whereas 31 strains formed single branches. Several fatty acid groups consisted of strains from different lakes from the same region, or from different regions. The 16S rRNA genes from 40 strains, representing 35 different fatty acid groups were sequenced. The strains belonged to the alpha, beta and gamma subclasses of the Proteobacteria, the high and low percent G+C Gram-positives, and to the Cytophaga-Flavobacterium-Bacteroides branch. For strains representing 16 fatty acid clusters, validly named nearest phylogenetic neighbours showed pairwise sequence similarities of less than 97%. This indicates that the clusters they represent, belong to taxa that have not been sequenced yet or as yet unnamed new taxa, related to Alteromonas, Bacillus, Clavibacter, Cyclobacterium, Flavobacterium, Marinobacter, Mesorhizobium, Microbacterium, Pseudomonas, Saligentibacter, Sphingomonas and Sulfitobacter.     

Computer-aided comparison of protein electrophoretic patterns for grouping and identification of heterotrophic bacteria from mineral water

The microflora of a natural mineral water was studied immediately after bottling (T0) and after 7 d storage (T7) during 6 months, and isolates were clustered by SDS-PAGE of wholecell protein profiles. Isolates from each cluster were further characterized by API 20NE, fatty acid composition and quinone profiles. The numerical analysis of the electrophoregrams of all bacteria isolated from the mineral water formed 15 clusters and five unclustered strains. Except for five minor clusters, all clusters were composed of strains isolated over several months. The numerical analysis of the electrophoregrams of bacteria isolated immediately after bottling formed 15 clusters while after 7 d storage only four of these populations could be isolated, indicating that populations present in the mineral water were stable and that changes occurring after bottling probably resulted from a selection process. Only one unclustered strain was identified simultaneously by all the systems, as Sphingomonas paucimobilis. The monitoring of the aquifer and the bottling system, and the construction of a large database with bacteria of the autochthonous flora allows the detection of alterations in the aquifer by changes in the microflora.     

Characterisation of Antarctic cyanobacteria and comparison with New Zealand strains

Cyanobacterial mats are common in Antarctic lakes, ponds and on moist soils. The species comprising these mats have adapted to tolerate extreme conditions (e.g. high salinities and UV radiation, freezing and extended periods of darkness). In this study, cyanobacterial mats were collected from shallow melt-water ponds in Pyramid Trough in Southern Victoria Land, Antarctica. Eight strains were isolated and characterised by morphological and molecular (16S rRNA gene sequences) techniques and their fatty acid methyl ester (FAME) and lipid class profiles determined. These data were compared to parallel information obtained from cyanobacterial cultures isolated from New Zealand. In general, the morphological and molecular characterisation complemented each other, and the Antarctic strains identified belonged to the orders: Oscillatoriales (six), Nostocales (one) and Chroococcales (one). Two of the Antarctic strains (CYN67 and CYN68) showed low similarity (<96% 16S rRNA gene sequence) when compared to other cultured cyanobacteria. The fatty acid (FA) profiles from the Antarctic and New Zealand strains shared many similarities with palmitic (C16:0), stearic (C18:0) and oleic acid (C18:1n-9) most abundant. In contrast, the lipid class analysis differed among geographic locations with Antarctic strains containing higher amounts of hydrocarbons and eicosapentaenoic and hexadecatrienoic acids.     

Relationships between Arctic and Antarctic Shewanella strains evaluated by a polyphasic taxonomic approach

As a result of the recent application of DNA-based technologies to investigate bacterial diversity in the polar marine environment, bacterial strains sharing significant 16S rRNA gene sequence similarities were isolated from both the Arctic and the Antarctic sea waters. Three selected marine bacterial isolates (BSw20248, BSw20661 and BSw10166) from two Arctic regions (the Greenland Sea and Canada Basin) and from Antarctica (Prydz Bay) were studied to determine their evolutionary relationships and phylogenetic position using a polyphasic taxonomic approach, including phenotypic characterization and genotypic analyses. These bacterial isolates proved to belong to the same species and were identified as Shewanella frigidimarina. Differences in phenotypic properties observed among them revealed a diversity of ecotypes for adaptation to the changing ecological or geographical conditions. It provided the evidence that Shewanella frigidimarina has a bipolar, or even global, distribution in the marine environment.     

Evolutionary relationships of superoxide dismutases and glutamine synthetases from marine species of Alteromonas,Oceanospirillum, Pseudomonas and Deleya

Evolutionary relationships among marine species assigned to the genera Alteromonas, Oceanospirillum, Pseudomonas, and Alcaligenes were determined by an immunological study of their Fe-containing superoxide dismutases (FeSOD) and glutamine synthetases (GS), two enzymes with differentially conserved amino acid sequences which are useful for determining intermediate and distant relationships, respectively. Five reference antisera were prepared against the FeSODs from Alteromonas macleodii, A. haloplanktis, Oceanospirillum commune, Pseudomonas stanieri, and Deleya pacifica. For GS, a previously prepared antiserum to the enzyme from Escherichia coli was employed. Amino acid sequence similarities for both enzymes were determined by the quantitative microcomplement fixation technique and the Ouchterlony double diffusion procedure. Six evolutionary groups were detected by FeSOD sequence similarities: three subgroups within the genus Alteromonas, the genera Oceanospirillum and Pseudomonas, and a new genus, Deleya (to accommodate marine Alcaligenes). Only four groupings were delineated by the GS data: the latter three genera and one group composed of all the species of Alteromonas. Evidence that all of these subgroups are derived from the evolutionary lineage defined by the purple sulfur photosynthetic bacteria is presented.Abbreviations Alt Alteromonas - anti-Amac, anti-Ahal, anti-Ocom, anti-Psta, anti-Dpac antisera to the Fe-containing superoxide dismutases from Alteromonas macleodii 107, Alteromonas haloplanktis 121, Oceanospirillum commune 8, Pseudomonas stanieri 146, Deleya pacifica 62 - FeSOD Fe-containing superoxide dismutase - G+C guanine plus cytosine - GS glutamine synthetase - ImD immunological distance - MnSOD Mn-containing superoxide dismutase - Oce Oceanospirillum - Pse Pseudomonas - Rm relative mobility - rRNA ribosomal RNA - SOD superoxide dismutase Dedicated to the memory of Professor Roger Y. Stanier     

第六次北极科学考察海洋沉积物可培养细菌的多样性分析

【目的】研究北极海洋沉积物可培养细菌的菌种资源多样性。【方法】采用海水Zobell2216E培养基和涂布平板法对第六次北极科学考察获得的海洋沉积物开展细菌分离培养,通过16S rRNA基因系统发育分析了解可培养细菌的多样性。【结果】根据菌落形态特征,从40个站位的北极海洋沉积物样品中共分离并获得16S rRNA基因有效序列的细菌达445株;基于16S rRNA基因的相似性分析与系统发育研究结果表明,分离获得的细菌分属于细菌域的4个门、6个纲、13个目、28个科、49个属、91个种,其中γ-Proteobacteria占大多数;有12株与模式菌株的16S rRNA基因序列相似性小于97%,可能代表了6个潜在的细菌新物种;此次获得的细菌种类组成与以往第五次北极科考获得的相比,在属水平上差异较大。【结论】北极海洋沉积物中存在着丰富的微生物菌种资源,具有很多新型微生物仍未被发现,是亟待开发的微生物资源宝库。     

16S rDNA sequence analysis of bacterial isolates from biodeteriorated mural paintings in the Servilia tomb (Necropolis of carmona, Seville, Spain)

Bacteria were isolated from damaged mural paintings of the Servilia tomb (necropolis of Carmona, Seville, Spain). Selected strains, representative for different clusters of isolates with similar fatty acid profiles, were analysed by 16S rDNA sequence analysis. Bacillus is the dominant genus among the isolates: members of the rRNA species complexes of B. megaterium, B. pumilus and B. firmus were found as well as several other Bacillus species. One group of halotolerant isolates falls in the Bacillus sensu lato group, with closest relatedness to the genera Salibacillus and Virgibacillus. Other genera found are Artbrobacter, Micrococcus, Streptomyces, Sphingomonas, Paenibacillus, and a genus closely related to Paracraurococcus. Many isolates showed low 16S rDNA sequence similarities with the closest related database entries, a strong indication for the presence of several new species among the isolates.     

Lipid composition of novel Shewanella species isolated from far Eastern seas

A comparative study of the lipid composition of 26 strains (including type strains) of marine Gammaproteobacteria belonging to the genera Shewanella, Alteromonas, Pseudoalteromonas, Marinobacterium, Microbulbifer, and Marinobacter was carried out. The bacteria exhibited genus-specific profiles of ubiquinones, phospholipids, and fatty acids, which can serve as reliable chemotaxonomic markers for tentative identification of new isolates. The studied species of the genus Shewanella were distinguished by the presence of two types of isoprenoid quinones, namely, ubiquinones Q-7 and Q-8 and menaquinones MK-7 and MMK-7; five phospholipids typical of this genus, namely, phosphatidylethanolamine (PE), phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), lyso-PE, and acyl-PG; and the fatty acids 15:0, 16:0, 16:1 (n-7), 17:1 (n-8), i-13:0, and i-15:0. The high level of branched fatty acids (38-45%) and the presence of eicosapentaenoic acid (4%) may serve as criteria for the identification of this genus. Unlike Shewanella spp., bacteria of the other genera contained a single type of isoprenoid quinone: Q-8 (Alteromonas, Pseudoalteromonas, Marinobacterium, and Microbulbifer) or Q-9 (Marinobacter). The phospholipid compositions of these bacteria were restricted to three components: two major phospholipids (PE and PG) and a minor phospholipid, bisphosphatidic acid (Alteromonas and Pseudoalteromonas) or DPG (Marinobacterium, Microbulbifer, and Marinobacter). The bacteria exhibited genus-specific profiles of fatty acids.     

Phylogenetic diversity of culturable bacteria from Antarctic sandy intertidal sediments

The diversity of culturable bacteria associated with sandy intertidal sediments from the coastal regions of the Chinese Antarctic Zhongshan Station on the Larsemann Hills (Princess Elizabeth Land, East Antarctica) was investigated. A total of 65 aerobic heterotrophic bacterial strains were isolated at 4°C. Microscopy and 16S rRNA gene sequence analysis indicated that the isolates were dominated by Gram-negative bacteria, while only 16 Gram-positive strains were isolated. The bacterial isolates fell in five phylogenetic groups: Alpha- and Gammaproteobacteria, Bacteroidetes, Actinobacteria and Firmicutes. Based on phylogenetic trees, all the 65 isolates were sorted into 29 main clusters, corresponding to at least 29 different genera. Based on sequence analysis (<98% sequence similarity), the Antarctic isolates belonged to at least 37 different bacterial species, and 14 of the 37 bacterial species (37.8%) represented potentially novel taxa. These results indicated a high culturable diversity within the bacterial community of the Antarctic sandy intertidal sediments.     

Cultivatable microbial biodiversity: gnawing at the Gordian knot

Rapid and inexpensive sorting of bacterial isolates may be achieved using Fourier transform infrared spectroscopy (FT-IR), a method that has hitherto been applied to identification and classification. The comprehensive characterization of environmental samples requires the isolation of large numbers of isolates using different growth media and growth conditions. In such cases, sorting the isolates is critical before isolates are subjected to more detailed studies. Using FT-IR, isolates are grown under standardized conditions, and 100 strains can be tested within less than 8 h. Chemotaxonomic and molecular characterization of members of clusters emerging from FT-IR analysis either at a level of spectral distance values below 20–30 (analysis of region 600–800 cm⁻¹, average linkage algorithm) or at spectral heterogeneity values below 75 (regions 1200–900, 3000–2798 and 901–698, scaling to first region, Ward's algorithm) reveals great similarities in fatty acids and 16S rDNA sequences. As judged from riboprinting analyses and fatty acid analyses, FT-IR analysis is able to unravel intraspecific subclustering. The example used in this study of 100 isolates from a mat system, Lake Fryxell, Dry Valleys, Antarctica, selected from a larger number of isolates, picked mainly on the basis of colony pigmentation and form, reveals the utility of the method for identifying the number of putative species quickly. The method described is able to select strains rapidly that represent clusters at the specific and intraspecific level for subsequent characterization.     

A polyphasic taxonomic study of thermophilic bacilli from shallow, marine vents

Eighty-seven thermophilic, aerobic, spore-forming bacteria were isolated from shallow, marine, thermal vents of the Eolian Islands (Italy) and tested for a broad spectrum of phenotypic characteristics. A numerical taxonomy study was performed on these isolates and 8 thermophilic Bacillus and Geobacillus reference strains by 89 selected features. Results from cluster analysis showed the formation of nine clusters. Most of the isolates (83%) fell into several phenetically well distinguished clusters, loosely related to Geobacillus thermodenitrificans. The remaining isolates grouped together with different reference strains. Eighteen isolates, representative of the different clusters, were selected for subsequent genotypic characterisation, including partial 16S rDNA sequence analysis of 18 strains and almost complete 16S rDNA sequences of 9 strains. Subsequent DNA/DNA reassociation studies and determination of the base composition of DNA identified seven isolates as Geobacillus thermodenitrificans, two isolates as G. thermoleovorans and one isolate as Bacillus pallidus. Four isolates represented two novel species of Bacillus. The remaining four represented novel Geobacillus species, one of which has recently been described as Bacillus vulcani DSMZ 13174 T.     

香樟产芽孢内生细菌的系统发育多样性

为了解香樟产芽孢内生细菌的多样性,采用改良的NA培养基分离、去除冗余及芽孢染色,得到40株产芽孢内生细菌,占分离所得内生细菌总数的29.9%,其中根、茎、叶中分别分离到25、5和10株。16SrRNA序列系统发育分析结果表明,这40株菌分属于Bacillus、Lysinibacillus、Paenibacillus和Brevibacillus属的12个种;7株菌的16SrRNA部分序列与数据库中模式菌株对应序列相似性小于97%,代表着潜在新类群的存在。同时,3个部位分离出的产芽孢内生细菌既呈现出一定程度的细菌区系相似性,又表现出细菌区系的器官特异性。     

Chitinophaga soli sp. nov. and Chitinophaga terrae sp. nov., isolated from soil of a ginseng field in Pocheon Province, Korea

Two novel strains of the Cytophaga-Flexibacter-Bacteroides (CFB) group, designated Gsoil 219" and Gsoil 2381, were isolated from soil of a ginseng field of Pocheon Province in Korea. Both strains were Gram-negative, aerobic, nonmotile, nonspore-forming, and rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences indicated that both isolates belong to the genus Chitinophaga but were clearly separated from established species of this genus. The sequence similarities between strain Gsoil 219T and type strains of the established species and between strain Gsoil 238T and type strains of the established species ranged from 91.4 to 94.7% and 91.6 to 94.2%, respectively. Phenotypic and chemotaxonomic data (major menaquinone, MK-7; major fatty acids, iso-C15:0 and C(16:1) omega5c; major hydroxy fatty acid, iso-C(17:0) 3-OH; major polyamine, homospermidine) supported the affiliation of both strains Gsoil 219T and Gsoil 238T to the genus Chitinophaga. Furthermore, the results of physiological and biochemical tests allowed genotypic and phenotypic differentiation of both strains from the other validated Chitinophaga species. Therefore, the two isolates represent two novel species, for which the name Chitinophaga soli sp. nov. (type strain, Gsoil 219T=KCTC 12650T=DSM 18093T) and Chitinophaga terrae sp. nov. (type strain, Gsoil 238T=KCTC 12651T=DSM 18078T) are proposed.     

南极交替单胞菌R11-5产卡拉胶酶的发酵条件优化

【背景】极地寒冷环境中发现了大量具有潜在应用前景的冷适应酶,同时也存在种类繁多的海藻多糖降解菌,因此极端环境微生物是筛选获得新颖、高效多糖降解酶的重要新源泉。由于筛选培养基通常并非野生菌发酵产酶的最优条件,为了使野生菌的产酶效率达到最高,需要对其培养条件进行优化,从而为其深入研究及开发利用提供依据。【目的】对一株产卡拉胶酶的南极菌株进行种属鉴定,并采用响应面法对该菌的发酵产酶条件进行优化。【方法】通过16SrRNA基因对产卡拉胶酶的南极菌株进行种属鉴定,采用响应面法优化南极菌株产酶发酵条件。【结果】该南极菌属于交替单胞菌属(Alteromonas),命名为交替单胞菌R11-5。发酵条件优化结果显示,7个环境因子影响交替单胞菌R11-5的产酶量。利用Design-Expert软件中的Plackett-Burman设计实验,筛选出影响交替单胞菌R11-5产酶量的4个主要因素分别为培养温度、牛肉膏浓度、卡拉胶浓度和Ca~(2+)浓度。通过Box-Behnken设计和响应面分析得到交替单胞菌R11-5最佳产酶发酵条件为:温度15.0°C,牛肉膏浓度11.0 g/L,卡拉胶浓度3.0 g/L,Ca~(2+)浓度5.0 mmol/L。优化后发酵上清液酶产量达到87.193 U/mL,与优化前相比提高了1.8倍。【结论】响应面法提高了南极交替单胞菌R11-5卡拉胶酶的产量,为其开发应用提供了科学依据。     

Evaluation of arabinofuranosidase and xylanase activities of Geobacillus spp. isolated from some hot springs in Turkey

Some hot springs located in the west of Turkey were investigated with respect to the presence of thermophilic microorganisms. Based on phenotyping characteristics and 16S rRNA gene sequence analysis, 16 of the isolates belonged to the genus Geobacillus and grew optimally at about 60 degrees C on nutrient agar. 16S rRNA gene sequence analysis showed that these isolates resembled Geobacillus species by > or = 97%, but SDS-PAGE profiles of these 16 isolates differ from some of the other species of the genus Geobacillus. However, it is also known that analysis of 16S rRNA gene sequences may be insufficient to distinguish between some species. It is proposed that recN sequence comparisons could accurately measure genome similarities for the Geobacillus genus. Based on recN sequence analysis, isolates 11, IT3, and 12 are strains of G stearothermophilus; isolate 14.3 is a strain of G thermodenitrificans; isolates 9.1, IT4.1, and 4.5 are uncertain and it is required to make further analysis. The presence of xylanase and arabinofuranosidase activities, and their optimum temperature and pH were also investigated. These results showed that 7 of the strains have both xylanase and arabinofuranosidase activities, 4 of them has only xylanase, and the remaning 5 strains have neither of these activities. The isolates 9.1, 7.1, and 3.3 have the highest temperature optima (80 degrees C), and 7.2, 9.1, AO4, 9.2, and AO17 have the highest pH optima (pH 8) of xylanase. Isolates 7.2, AO4, AC15, and 12 have optimum arabinofuranosidase activities at 75 degrees C, and only isolate AC 15 has the lowest pH of 5.5.     

北极高维度海域海冰嗜冷菌系统发育多样性及其低温水解酶分析

应用样品直接稀释涂布平板、-1℃富集培养和-20℃冷冻24h后富集培养等3种方法,从北极加拿大海盆和格陵兰海的高纬度海域(77°30′N~81°12′N)海冰中分离到37株嗜冷菌。根据其16S rDNA全长序列所进行的系统发育分析表明,分离菌株分属于γ_变形细菌群(γ_Proteobacteria)的Colwellia、Marinobacter、Shewanella、Thalassomonas、Glaciecola、Marinomonas、Pseudoalteromonas和嗜纤维菌_曲挠杆菌_拟杆菌群(Cytophaga_Flexibacter_Bacteroide,CFB)的Flavobacterium、Psychroflexus等9个属。其中有9株菌的16S rDNA序列与已明确鉴定种的相似性在93.4%~96.9%,为潜在的新种。北极加拿大海盆海冰细菌BSi20002与南极威德尔海海冰细菌Marinobactersp.ANT8277的16S rDNA序列相似性为100%,表明在种水平上南、北两极也存在相同的细菌。分离的嗜冷菌在4℃条件下能产生多种大分子物质水解酶类,其中62.6%、51.4%和40.5%的菌株分别能水解Tween_80、明胶和淀粉。     

Phylogenetic composition of bacterioplankton assemblages from the Arctic Ocean

We analyzed the phylogenetic composition of bacterioplankton assemblages in 11 Arctic Ocean samples collected over three seasons (winter-spring 1995, summer 1996, and summer-fall 1997) by sequencing cloned fragments of 16S rRNA genes. The sequencing effort was directed by denaturing gradient gel electrophoresis (DGGE) screening of samples and the clone libraries. Sequences of 88 clones fell into seven major lineages of the domain Bacteria: alpha(36%)-, gamma(32%)-, delta(14%)-, and epsilon(1%)-Proteobacteria; Cytophaga-Flexibacter-Bacteroides spp. (9%); Verrucomicrobium spp. (6%); and green nonsulfur bacteria (2%). A total of 34% of the cloned sequences (excluding clones in the SAR11 and Roseobacter groups) had sequence similarities that were <94% compared to previously reported sequences, indicating the presence of novel sequences. DGGE fingerprints of the selected samples showed that most of the bands were common to all samples in all three seasons. However, additional bands representing sequences related to Cytophaga and Polaribacter species were found in samples collected during the summer and fall. Of the clones in a library generated from one sample collected in spring of 1995, 50% were the same and were most closely affiliated (99% similarity) with Alteromonas macleodii, while 50% of the clones in another sample were most closely affiliated (90 to 96% similarity) with Oceanospirillum sp. The majority of the cloned sequences were most closely related to uncultured, environmental sequences. Prominent among these were members of the SAR11 group. Differences between mixed-layer and halocline samples were apparent in DGGE fingerprints and clone libraries. Sequences related to alpha-Proteobacteria (dominated by SAR11) were abundant (52%) in samples from the mixed layer, while sequences related to gamma-proteobacteria were more abundant (44%) in halocline samples. Two bands corresponding to sequences related to SAR307 (common in deep water) and the high-G+C gram-positive bacteria were characteristic of the halocline samples.     

Automated Systems for Identification of Heterotrophic Marine Bacteria on the Basis of Their Fatty Acid Composition

The fatty acid methyl ester composition of a total of 71 marine strains representing the genera Alteromonas, Deleya, Oceanospirillum, and Vibrio was determined by gas-liquid chromatographic analysis. Over 70 different fatty acids were found. The predominant fatty acids were 16:0, 16:1 cis 9, summed-in-feature (SIF) 4 (15:0 iso 2OH and/or 16:1 trans 9) and SIF 7 (18:1 cis 11, 18:1 trans 9, and/or 18:1 trans 6) for all the strains considered, but minor quantitative variations could be used to distinguish the different genera. In addition to a conventional statistical processing method to analyze the data and draw comparison between species and genera, an approach involving neutral network-based elaboration is applied. The statistical analysis and dendrogram representation gave a comparison of the species considered, while the neural network computation provided a more accurate assignment of species to their genera. Moreover, by using neural networks, it was possible to conclude that only 22 fatty acids were important for the identification of the marine genera considered. A database of Alteromonas, Deleya, Oceanospirillum, and Vibrio fatty acid methyl ester profiles was generated and is now routinely used to identify fresh marine isolates.     

A preliminary report of phylogenetic diversity of bacterial strains isolated from marine creatures

Bacterial diversity among marine creatures, especially molluscs, as a source for searching out novel lineages of bacteria, was studied. Marine creatures were collected at the coasts of the Kanto area in Japan. A total of 116 strains of bacteria were isolated from the intestines of 19 species of marine creatures includings molluscs, pisces and protochordata. Partial sequencing of 16S rDNA revealed that most of the isolates belonged to the gamma subclass of the Proteobacteria and Cytophaga-Flavobacterium-Bacteroides group. The BLAST searches revealed that the complete 16S rDNA sequence of 17 strains out of 116 isolates showed less than 94% similarity with 16S rDNA sequences deposited in the database. Four strains out of the 17 isolates belonged to the Rhodobacter group, 8 strains to the Alteromonas group, and the remaining 5 strains to the Cytophaga-Flavobacterium-Bacteroides group. Phylogenetic positions of 6 strains belonging to the Alteromonas group, which were isolated from different marine creatures, were close to each other, and represented a novel 16S rDNA lineage within the gamma subclass of Proteobacteria. Therefore, it may be inferred that these 6 strains belong to a new genus of Proteobacteria. Phylogenetic positions of the other strains are also independent from neighboring taxa, and they were suggested to respectively form a novel lineage. From these results, it is clear that the biodiversity of bacteria in marine creatures is much wider than was previously thought, and unknown microbiological resources are buried in these organisms.