Properties of Bacteria Isolated from Deep-Sea Sediments

Thirty-eight isolates were subjected to taxonomic analysis by computer. Of the 38 isolates, 31 were from sediment samples collected at depths from 9,400 to 10,400 meters in the Philippine and Marianas Trenches of the Pacific Ocean, and 7 cultures were from seawater samples collected at various depths from surface to 4,000 meters and from several locations in the Pacific Ocean. A total of 116 characteristics were determined for each isolate, coded, and transferred to punch cards. Similarity values were obtained by computer analysis, with the use of two recently developed computer programs. Five distinct phenetic clusters were observed from the numerical analyses. Four of the clusters were identified as species of the genus Pseudomonas, and one, as an aerogenic species of Aeromonas. Group IV was identified as pigmented Pseudomonas fluorescens, and the major cluster, consisting of groups I and II, which merged at a species level of similarity, was treated as a new species of Pseudomonas. The 38 strain data were compared with data for 132 marine and nonmarine strains previously subjected to computer taxonomic analysis. The barotolerant deep-sea strains, with the exception of the deep-sea P. fluorescens isolates, clustered separately from all other marine strains.     

Presence of Erwinia carotovora in surface water in North America

Erwinia carotovora was frequently isolated from samples of surface water collected from 66 rivers, springs, creeks, streams, lakes, reservoirs and ponds in 16 states in the US but was not found in the single fresh water sample collected in Canada. The organism was also isolated from water collected from the Pacific Ocean and the Gulf of Mexico. In Colorado and Wyoming, E. carotovora was isolated from water samples nearly every month of the year when monthly samples were collected from several streams. Erwinia carotovora subsp. carotovora represented 98–8% of the strains recovered from the water samples; E. carotovora subsp. atroseptica made up the remainder of the strains; E. chrysanthemi was not found.     

First record of the firebrow lanternfish Diaphus adenomus (Myctophiformes: Myctophidae) from the South Atlantic

The myctophid Diaphus adenomus is recorded for the first time in the South Atlantic Ocean based on 139 specimens (83–203 mm standard length) collected from eight trawl stations off eastern Brazil, between 13 and 16° S at 38 and 39° W, at depths from 233 to 1275 m.     

DNA base composition of planktonic species of Anabaena (Cyanobacteria) and its taxonomic value

Fifty axenic strains of planktonic Anabaena, including 24 strains of the straight form and 26 strains of the coiled form, were examined for their DNA base composition (GC content). The taxonomic value of their GC content at species level was evaluated by comparing their morphological, physiological and biochemical properties. The DNA base composition determined for all fifty strains ranged from 35.9 to 56.4 mol% GC. The straight-form strains were in the range of 35.9-56.4 mol% GC, while coiled forms were in the range of 38.1-50.3 mol% GC. In general, strains assigned to the same species showed similar DNA base composition. However, of three strains of A. affinis Lemmermann that were separated into two categories, two had 40.6-40.9 mol% GC, and the third strain 45.6 mol% GC. It is noteworthy that the DNA base composition of the newly established species A. eucompacta Li et Watanabe was 45.5 mol% GC, which differed from 39.5 mol% GC of the morphologically close species, A. compacta (Nygarrd) Hickel.     

Actinomycetal Community Structures in Seawater and Freshwater Examined by DGGE Analysis of 16S rRNA Gene Fragments

The actinomycetal community structures in marine and freshwater environments (the Pacific Ocean, East China Sea, Tokyo Bay, and Arakawa River) were investigated by a culture-independent molecular method to clarify spatial and seasonal distributions. Deoxyribonucleic acid (DNA) was extracted from environmental water samples, and a community analysis was carried out on polymerase chain reaction-amplified 16S ribosomal DNA. The amplified DNA fragments were analyzed by denaturing gradient gel electrophoresis (DGGE) and nonmetric multidimensional scaling analysis, followed by sequencing analysis. The actinomycetal community structures were different at each station in the Pacific Ocean, the East China Sea, Tokyo Bay, and Arakawa River, and different populations predominated in each area. There were vertical variations in actinomycetal communities in the Pacific Ocean and East China Sea between the surface and 100-m depth, but communities were similar from 200- to 1,000-m depths. There were also distinct seasonal variations in communities in Tokyo Bay. Phylogenetic analysis of DNA fragments recovered from DGGE bands revealed that most of the predominant actinomycetal strains were uncultured and were quite different from well known culturable strains, such as the Streptomyces, Micromonospora, Microbispora, Salinispora, and Actinoplanes groups. These results suggest that the marine environment is an attractive target for discovering new actinomycetal populations producing bioactive compounds and that sampling depth and season are important considerations for isolating various populations effectively.     

Ammonia-oxidizing Archaea in the Arctic Ocean and Antarctic coastal waters

We compared abundance, distributions and phylogenetic composition of Crenarchaeota and ammonia-oxidizing Archaea (AOA) in samples collected from coastal waters west of the Antarctic Peninsula during the summers of 2005 and 2006, with samples from the central Arctic Ocean collected during the summer of 1997. Ammonia-oxidizing Archaea and Crenarchaeota abundances were estimated from quantitative PCR measurements of amoA and 16S rRNA gene abundances. Crenarchaeota and AOA were approximately fivefold more abundant at comparable depths in the Antarctic versus the Arctic Ocean. Crenarchaeota and AOA were essentially absent from the Antarctic Summer Surface Water (SSW) water mass (0–45 m depth). The ratio of Crenarchaeota 16S rRNA to archaeal amoA gene abundance in the Winter Water (WW) water mass (45–105 m depth) of the Southern Ocean was much lower (0.15) than expected and in sharp contrast to the ratio (2.0) in the Circumpolar Deep Water (CDW) water mass (105–3500 m depth) immediately below it. We did not observe comparable segregation of this ratio by depth or water mass in Arctic Ocean samples. A ubiquitous, abundant and polar-specific crenarchaeote was the dominant ribotype in the WW and important in the upper halocline of the Arctic Ocean. Our data suggest that this organism does not contain an ammonia monooxygenase gene. In contrast to other studies where Crenarchaeota populations apparently lacking amoA genes are found in bathypelagic waters, this organism appears to dominate in well-defined, ammonium-rich, near-surface water masses in polar oceans.     

Classification of the genus Humicola Traaen: II. The DNA base composition of some strains within the genus

The base composition of DNA (GC content) of 25 strains, morphologically referred to the genusHumicola Traaen, is studied. The range of GC% variation is about 23 % (from 28,5 % to 51,6). Two prominent groups of strains with similar GC content may be distinguished: one ranging from 28 % to 37 % and the other ranging from 40 % to 49 %. The aleuriospore size is not related to the DNA base composition, but a group of strains with prevalently coloured hyphae, with aleuriospores of similar size and with high GC content is recognized. Several previous literature reports on the taxonomy ofHumicola are discussed.     

DNA restriction endonuclease cleavage patterns,DNA sequence similarity and phenotypical characteristics in some strains of Lactobacillus helveticus and Lactobacillus jugurti

Physiological characteristics, deoxyribonucleic acid (DNA) base composition (% guanine + cytosine; % GC), DNA sequence similarity (% DNA-DNA hybridization) and DNA restriction endonuclease cleavage patterns of two strains of Lactobacillus helveticus and four strains of Lactobacillus jugurti were examined.All the strains investigated were closely related genetically, having DNA-DNA hybridization values ranging from 89–100%. Nevertheless, these strains can be differentiated from one another on the basis of the digestion of their DNA by specific restriction endonucleases, such as Bam HI, Eco RI and Hind III. The DNA of these strains shows clear, reproducible and distinct cleavage patterns. Cleavage patterns of DNA from strains L. jugurti S.35.19 and S.36.2 were found to be similar. These findings suggest that fingerprinting of DNA by restriction endonuclease cleavage might provide, in addition to the conventional methods, a useful tool for the characterization of closely related microorganisms at the strain level.     

A mitochondrial phylogeography of Brachidontes variabilis (Bivalvia: Mytilidae) reveals three cryptic species

This study examined genetic variation across the range of Brachidontes variabilis to produce a molecular phylogeography. Neighbour joining (NJ), minimum evolution (ME) and maximum parsimony (MP) trees based on partial mitochondrial DNA sequences of 16S-rDNA and cytochrome oxidase (COI) genes revealed three monophyletic clades: (1) Brachidontes pharaonis s.l. from the Mediterranean Sea and the Red Sea; (2) B. variabilis from the Indian Ocean; (3) B. variabilis from the western Pacific Ocean. Although the three clades have never been differentiated by malacologists employing conventional morphological keys, they should be ascribed to the taxonomic rank of species. The nucleotide divergences between Brachidontes lineages (between 10.3% and 23.2%) were substantially higher than the divergence between congeneric Mytilus species (2.3–6.7%) and corresponded to interspecific divergences found in other bivalvia, indicating that they should be considered three different species. Analysis of the 16S-rDNA sequences revealed heteroplasmy, indicating dual uniparental inheritance (DUI) of mtDNA in the species of Brachidontes collected in the Indian Ocean, but not in the species in the Pacific nor in the species in the Red Sea and the Mediterranean Sea. When we employed the conventional estimate of the rate of mitochondrial sequence divergence (2% per million years), the divergence times for the three monophyletic lineages were 6–11 Myr for the Indian Ocean and Pacific Ocean Brachidontes sp. and 6.5–9 Myr for the Red Sea and Indian Ocean Brachidontes sp . Thus, these species diverged from one another during the Miocene (23.8–5.3 Myr). We infer that a common ancestor of the three Brachidontes species probably had an Indo-Pacific distribution and that vicariance events, linked to Pleistocene glaciations first and then to the opening of the Red Sea, produced three monophyletic lineages.     

Cultivable Fungal Diversity in Deep-Sea Sediment of the East Pacific Ocean

The diversity of fungi in the marine environment has been extensively studied, but their denitrification activity has rarely been reported to date. In the present study, we used six different media to isolate fungi from 10 sediment samples collected at five different locations of the East Pacific Ocean with water depths ranging from 4545 to 7068?m. Fungal identification and phylogenetic diversity analysis were conducted based on morphological characteristics and internal transcribed spacers of ribosomal DNA (ITS-rRNA) sequencing. A total of 106 fungal isolates, belonging to 12 genera, including Aspergillus (five strains), Aureobasidium (three strains), Candida (two strains), Cladosporium (56 strains), Cystobasidium (one strain), Devriesia (nine strains), Knufia (one strain), Nigrospora (three strains), Penicillium (18 strains), Rhodotorula (four strains), Sarocladium (three strains), and unclassified Xylariales (one strain) were obtained. The most dominant culturable genus was Cladosporium. One possible novel fungal strains showed less than 97% similarity to their closest matches of unclassified Xylariales in the Genbank. In addition, we used nirK gene as the molecular marker to detect denitrifying fungi among the cultivable fungal isolates. The nirK gene was detected in Aspergillus niger and Penicillium chrysogenum. Our research indicated that diverse fungi from the deep sea sediments of the East Pacific Ocean and highlighted the involvement of these fungi in denitrification process.     

DNA base composition of some sheathed bacteria

The DNA base composition of five recently isolated Haliscomenobacter hydrossis strains were compared with those of Sphaerotilus natans, Leptothrix cholodnii and Leptothrix discophora. The DNA base composition of H. hydrossis strains ranged from 48.3 to 49.7% GC, whereas the % GC values of S. natans, L. cholodnii and L. discophora were found to be 69.7, 69.6 and 71.2, respectively. These results indicate that Haliscomenobacter species and the microorganisms of the Sphaerotilus-Leptothrix group should not be classified into the same genus, as they are genetically at best remotely related.The reallocation of some Leptothrix species into the genus Sphaerotilus is not in contradiction with their DNA base composition.     

Deoxyribonucleic Acid Base Composition of Some Members of the Subgenera Betabacterium and Streptobacterium

The base composition of deoxyribonucleic acid (DNA) prepared from four Betabacterium strains and four Streptobacterium strains was determined. Per cent GC values (guanine + cytosine/total bases) of the DNA were evaluated from the “melting-temperatures” (Tm) of the nucleic acids. For the Betabacterium strains, these values ranged from 44 to 51.5% GC, and those for the Streptobacterium strains ranged from 43 to 47.5% GC. The taxonomic division into these two subgenera is not, therefore, supported by these findings.     

Bacteriophage sensitivity patterns among bacteria isolated from marine waters

Phage-host cross-reaction tests were performed with 774 bacterial strains and 298 bacteriophages. The bacteria (bacteriophages) were isolated at different times from water samples collected in the Atlantic Ocean between the European continental shelf and the Sargasso Sea: 733 (258) strains; in the North Sea near Helgoland: 31 (31) strains; and in the Bay of Biscay: 10 (9) strains. Of the Atlantic Ocean bacteria 326 were found to be susceptible to one or more Atlantic Ocean bacteriophage(s). The bacteriophage sensitivity patterns of these bacteria vary considerably, placing 225 of them in two large clusters of bacteriophage-host systems. Taking all into account, 250 of the 326 Atlantic Ocean bacteria are different from each other. This high degree of variation among the bacteria distinguishes microbial populations derived from widely separated eastern and western regions of the Atlantic Ocean. It also sets apart from each other the populations derived from samples collected at successive stations some 200 miles apart, although to a lesser degree. With bacterial populations found from samples collected on the way back and forth between Europe and the Sargasso Sea a gradual change was observed from "western" phage sensitivity patterns to "eastern" ones. Sixty-nine Atlantic Ocean bacteria are sensitive to bacteriophages isolated from the North Sea and the Bay of Biscay; of these only 26 strains are also susceptible to Atlantic Ocean phages. The interpretation of the results is based on the hydrographical conditions prevailing in the northern Atlantic Ocean including the North Sea, and on the assumption that the microbial populations investigated have undergone genetic changes while being transported within water masses from west to east.     

Ancient Divergence in the Trans-Oceanic Deep-Sea Shark Centroscymnus crepidater

Unravelling the genetic structure and phylogeographic patterns of deep-sea sharks is particularly challenging given the inherent difficulty in obtaining samples. The deep-sea shark Centroscymnus crepidater is a medium-sized benthopelagic species that exhibits a circumglobal distribution occurring both in the Atlantic and Indo-Pacific Oceans. Contrary to the wealth of phylogeographic studies focused on coastal sharks, the genetic structure of bathyal species remains largely unexplored. We used a fragment of the mitochondrial DNA control region, and microsatellite data, to examine genetic structure in C. crepidater collected from the Atlantic Ocean, Tasman Sea, and southern Pacific Ocean (Chatham Rise). Two deeply divergent (3.1%) mtDNA clades were recovered, with one clade including both Atlantic and Pacific specimens, and the other composed of Atlantic samples with a single specimen from the Pacific (Chatham Rise). Bayesian analyses estimated this splitting in the Miocene at about 15 million years ago. The ancestral C. crepidater lineage was probably widely distributed in the Atlantic and Indo-Pacific Oceans. The oceanic cooling observed during the Miocene due to an Antarctic glaciation and the Tethys closure caused changes in environmental conditions that presumably restricted gene flow between basins. Fluctuations in food resources in the Southern Ocean might have promoted the dispersal of C. crepidater throughout the northern Atlantic where habitat conditions were more suitable during the Miocene. The significant genetic structure revealed by microsatellite data suggests the existence of present-day barriers to gene flow between the Atlantic and Pacific populations most likely due to the influence of the Agulhas Current retroflection on prey movements.     

New Method for Isolating Barophiles from Intestinal Contents of Deep-Sea Fishes Retrieved from the Abyssal Zone

We devised a new method (the dorayaki method) using marine agar under in situ pressures to isolate barophilic bacteria from the intestinal contents of three deep-sea fishes (two Coryphaenoides yaquinae samples and one Ilyophis sp. sample) retrieved from depths of 4,700 to 6,100 m in the Northwest Pacific Ocean. All 10 strains isolated from one sample (C. yaquinae) were obligately barophilic. One of the 10 strains did not grow at atmospheric pressure and 103.4 MPa but did grow well between 20.7 and 82.7 MPa, with optimal growth at 41.4 MPa. This method is useful for isolating psychrophilic and barophilic deep-sea bacteria.     

Resurrection of New Caledonian maskray Neotrygon trigonoides (Myliobatoidei: Dasyatidae) from synonymy with N. kuhlii, based on cytochrome-oxidase I gene sequences and spotting patterns

The maskray from New Caledonia, Neotrygon trigonoides Castelnau, 1873, has been recently synonymized with the blue-spotted maskray, N. kuhlii (Müller and Henle, 1841), a species with wide Indo-West Pacific distribution, but the reasons for this are unclear. Blue-spotted maskray specimens were collected from the Indian Ocean (Tanzania, Sumatra) and the Coral Triangle (Indonesia, Taiwan, and West Papua), and N. trigonoides specimens were collected from New Caledonia (Coral-Sea). Their partial COI gene sequences were generated to expand the available DNA-barcode database on this species, which currently comprises homologous sequences from Ningaloo Reef, the Coral Triangle and the Great Barrier Reef (Coral-Sea). Spotting patterns were also compared across regions. Haplotypes from the Coral-Sea formed a haplogroup phylogenetically distinct from all other haplotypes sampled in the Indo-West Pacific. No clear-cut geographic composition relative to DNA-barcodes or spotting patterns was apparent in N. kuhlii samples across the Indian Ocean and the Coral Triangle. The New Caledonian maskray had spotting patterns markedly different from all the other samples. This, added to a substantial level of net nucleotide divergence (2.6%) with typical N. kuhlii justifies considering the New Caledonian maskray as a separate species, for which we propose to resurrect the name Neotrygon trigonoides.     

Genetic heterogeneity among Lactobacillus acidophilus strains

Physiological characteristics, DNA base composition (% GC) and DNA-DNA reassociation values were determined for 138 Lactobacillus acidophilus strains. Twenty seven strains were received from various culture collections and 111 strains were freshly isolated during a study on the composition of the intestinal lactic microflora of piglets and suckling calves.All strains had physiological characteristics which were substantially similar. The strains isolated from pigs were unable to ferment trehalose. The % GC ranged from 35.8 to 43.4.On the basis of the results of DNA-DNA hybridization the strains were divided into four genetic groups.This study was partially supported by grants from the Consiplio Nazionale Ricerche (C.N.R.).     

Geographic distribution of the bathypelagic genus paraeuchaeta (Copepoda,Calanoida)

The geographic distribution of the bathypelagic calanoid genus Paraeuchaeta was investigated by examining midwater trawl and plankton net samples collected mostly from depths exceeding 1000 m throughout the world's oceans. Of the 81 species referred to Paraeuchaeta, the geographic ranges of about 50 species could be defined with reasonable certainty. Contrary to early authors, the number of species having a worldwide distribution was surprisingly small (12 species or 15% of the 81 species of the genus) as compared to common species endemic to various geographic regions (34 species or 42% of the total of 81). Almost twice as many species were found in the Indo-Pacific Ocean as in either the Atlantic or the Southern Ocean. Faunistically, the northern Atlantic, mid-Atlantic, northern Pacific, East Pacific, Indo-West Pacific, and Southern Ocean were distinct in terms of endemic species. A number of species were found to be endemic to highly productive areas, where they were usually very abundant. Rare species, on the other hand, were generally found to be widely distributed, although some were too rare for their range to be determined with certainty. To explain these findings, the following hypothesis is proposed: Bathypelagic calanoids endemic to and abundant in eutrophic areas are those adapted to eutrophic conditions of their habitats and therefore cannot expand their ranges into contiguous oligotrophic waters even if the other environmental conditions are favorable. Other species, on the other hand, generally have extensive geographic ranges because of their survival ability in widely expanding oligotrophic conditions and the absence of physicochemical barriers at bathypelagic depths of the world's oceans.     

Biochemical properties of Fusobacterium naviforme and phenotypically similar isolates

Three strains which resemble the type strain of Fusobacterium naviforme (ATCC 25832) by morphological and physiological criteria were isolated from human clinical specimens. All were non-fermentative, produced indole and, in common with other members of the genus Fusobacterium , butyrate was a major end-product of metabolism. Glutamate dehydrogenase and 2-oxoglutarate reductase were present in both taxa, but the enzymes of the test strains migrated to only about half the distance of that of strain ATCC 25832. The latter contained meso -diaminopimelic acid as its peptidoglycan dibasic amino acid whereas the test strains possessed meso -lanthionine. The wide divergence in DNA base composition between strain ATCC 25832 (49 mol% G + C) and the clinical isolates ( ca 30–31 mol% G + C) was reflected in their low DNA-DNA homology ( ca 5–15%). The present study therefore revealed major differences between F. naviforme (ATCC 25832) and the new isolates and indicate that the latter may belong to a hitherto undescribed taxon within the genus Fusobacterium.     

Records of anglerfishes (Lophiiformes: Lophiidae) from the western South Pacific Ocean, with descriptions of two new species

Species of Lophiidae collected from the western South Pacific Ocean are examined. Nine nominal species are recognized, all but one species with their distributions extended eastwards and southwards from the western Pacific Ocean. Two new species are described from Polynesia. Lophiodes iwamotoi n. sp. is described from five specimens collected from Savannah Seamount. It is characterized by a relatively long third dorsal-fin spine (56.9-70.8% standard length, L(S)) that extends (when retracted) to between the end of the soft dorsal fin and caudal-fin base; a relatively short fifth dorsal-fin spine (10.5-13.1% L(S)); a relatively short and narrow head; 19-20 pectoral-fin rays. Lophiodes maculatus n. sp. is described from 20 specimens collected from Marquesas Islands. It is characterized by an extremely long third dorsal-fin spine (71.9-87.2% L(S)), extending well beyond the caudal-fin base; a relatively short fifth dorsal-fin spine (11.4-16.5% L(S)); 17-18 pectoral-fin rays. A key to the lophiids in the western South Pacific Ocean is provided.