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Four long-spined sea urchin species in the genus Diadema are known to occur around the Japanese Archipelago. Three species (D. savignyi, D. setosum, and D. paucispinum) are widely distributed in the Indo-Pacific Ocean. The fourth species was detected by DNA analysis among samples originally collected as D. savignyi or D. setosum in Japan and the Marshall Islands and tentatively designated as Diadema-sp, remaining an undescribed species. We analyzed nucleotide sequences of the cytochrome oxidase I (COI) gene in the "D. savignyi-like" samples, and found all 17 individuals collected in the mainland of Japan (Sagami Bay and Kyushu) to be Diadema-sp, but all nine in the Ryukyu Archipelago (Okinawa and Ishigaki Islands) to be D. savignyi, with large nucleotide sequence difference between them (11.0%±1.7 SE). Diadema-sp and D. savignyi shared Y-shaped blue lines of iridophores along the interambulacrals, but individuals of Diadema-sp typically exhibited a conspicuous white streak at the fork of the Y-shaped blue iridophore lines, while this feature was absent in D. savignyi. Also, the central axis of the Y-shaped blue lines of iridophores was approximately twice as long as the V-component in D. savignyi whereas it was of similar length in Diadema-sp. Two parallel lines were observed to constitute the central axis of the Y-shaped blue lines in both species, but these were considerably narrower in Diadema-sp. Despite marked morphological and genetic differences, it appears that Diadema-sp has been mis-identified as D. savignyi for more than half a century.

Gram-stain-negative, aerobic, halophilic bacteria, designated SCM-1(T), LCM10-1 and CTBL-B-147, were isolated from modified half-strength SWM-III medium, PES medium and thalli after laboratory cultivation of a red alga, Porphyra yezoensis. Phylogenetic analysis of 16S rRNA gene sequences indicated that the new isolates were affiliated to the genus Sulfitobacter of the class Alphaproteobacteria, and the 16S rRNA gene sequence similarity of the new isolates with the closest related species, Sulfitobacter mediterraneus CH-B427(T), was 98.8%. The DNA G+C contents of the new isolates were in the range of 61.4-62.3 mol%. DNA-DNA relatedness values of strain SCM-1(T) with other type strains of the genus Sulfitobacter were less than 15.9%. The new isolates contained Q-10 as the predominant ubiquinone, phosphatidylcholine, phosphatidylglycerol, an unidentified amino lipid and an unidentified lipid as the main polar lipids, and C(18 : 1)ω7c, C(19 : 1)ω7c and C(16 : 0) as the major fatty acids (>10% of the total). Strain SCM-1(T) could be differentiated from Sulfitobacter mediterraneus JCM 21792(T) by 35 morphological and phenotypic characteristics. On the basis of the phylogenetic, genetic and phenotypic properties of the new isolates, the name Sulfitobacter porphyrae sp. nov. is proposed, with strain SCM-1(T) ( = LMG 27110(T) = NBRC 109054(T)) as the type strain.

Three strains (14A-2-7(T), 14A-3-1 and 14A-3) of Gram-stain-negative, prosthecate, motile bacteria were isolated from an algal medium supplemented with 10 mg ampicillin l(-1) (w/v), in which the red alga Porphyra yezoensis had been cultured. Based on the 16S rRNA gene sequence analysis, the three isolates formed a cluster with the genus Algimonas of the family Hyphomonadaceae. The sequences of the three isolates had high similarity with those of Algimonas porphyrae 0C-2-2(T) (97.6 % similarity) and Litorimonas taeanensis G5(T) (95.6 % similarity). The DNA G+C contents of the three isolates ranged from 54.3 to 55.0 mol%, which were more similar to that of A. porphyrae 0C-2-2(T) (58.5 mol%) than to that of L. taeanensis G5(T) (47.1 mol%). The DNA-DNA relatedness showed that the three isolates were representatives of the same species (88.1-94.0 % relatedness) and that strain 14A-2-7(T) was a representative of a different species from A. porphyrae 0C-2-2(T) and L. taeanensis G5(T) (1.2-8.6 % relatedness). The phenotypic characteristics of strain 14A-2-7(T) differed by 20 results and 30 results from A. porphyrae 0C-2-2(T) and L. taeanensis G5(T), respectively. The three isolates contained ubiquinone-10 as the predominant quinone and C18 : 1ω7c as the major fatty acid. Based on the polyphasic taxonomic analysis, the three isolates represent a novel species of the genus Algimonas, for which the name Algimonas ampicilliniresistens sp. nov. is proposed. The type strain is 14A-2-7(T) ( = LMG 26421(T) = NBRC 108219(T)). An emended description of the genus Algimonas is also proposed.

Three Gram-negative, non-motile, strictly aerobic strains, designated LNM-20(T), LCM-1 and LAM-13, were isolated from thalli of the marine red alga Porphyra yezoensis. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolates were associated with the genus Polaribacter in the family Flavobacteriaceae and were most closely related to Polaribacter dokdonensis DSW-5(T) (96.2 % 16S rRNA gene sequence similarity) and Polaribacter gangjinensis K17-16(T) (95.0 %). The DNA G+C content of the isolates was 28.6-29.2 mol%. DNA-DNA hybridization analysis showed that the isolates belonged to a single species distinct from both of their closest relatives. The only isoprenoid quinone detected was menaquinone-6. The main polar lipids were phosphatidylethanolamine, two unidentified aminolipids and two unidentified lipids. The major fatty acids were iso-C15 : 0, iso-C15 : 1ω10c and iso-C15 : 0 3-OH. The phenotypic features of strain LNM-20(T) differed from those of their closest relatives in several regards (colony colour, growth with 1 % NaCl and on TSA plus 2.5 % NaCl, hydrolysis of Tweens 40 and 80, and oxidization of five carbon compounds). On the basis of phylogenetic, chemotaxonomic and phenotypic analysis, the isolates represent a novel species in the genus Polaribacter, for which the name Polaribacter porphyrae sp. nov. is proposed. The type strain is LNM-20(T) ( = LMG 26671(T)  = NBRC 108759(T)). Emended descriptions of the genus Polaribacter and P. dokdonensis and P. gangjinensis are also proposed.

Three Gram-negative, stalked, motile bacteria, designated 0C-2-2(T), 0C-17 and LNM-3, were isolated from the red alga Porphyra yezoensis. 16S rRNA gene sequence analysis revealed that the three novel strains belonged to the family Hyphomonadaceae, and were closely related to Litorimonas taeanensis G5(T) (96.5 % 16S rRNA gene sequence similarity) and Hellea balneolensis 26III/A02/215(T) (94.3 %). The DNA G+C contents of the novel isolates (58.5-60.2 mol%) were clearly distinguished from those of L. taeanensis G5(T) (47.1 mol%) and H. balneolensis DSM 19091(T) (47.9 mol%). The G+C content of L. taeanensis G5(T) obtained in this study was quite different from a previous report (63.6 mol%). DNA-DNA hybridization experiments showed that the novel strains constituted a single species. Eleven phenotypic features of the three isolates differed from those of both related genera. The predominant respiratory quinone was ubiquinone-10 and the major fatty acid was C(18 : 1)ω7c. On the basis of this polyphasic taxonomic analysis, the novel strains represent a novel genus and species, for which the name Algimonas porphyrae gen. nov., sp. nov. is proposed. The type strain of Algimonas porphyrae is 0C-2-2(T) (= LMG 26424(T) = NBRC 108216(T)).

We constructed ammonia monooxygenase alpha subunit (amoA) gene clone libraries of ammonia-oxidizing archaea (AOA) and bacteria (AOB) from three biofiltration tanks used for closed marine fish culture systems. The number of operational taxonomic units (OTUs) found in any one place was 76%-80% of the total OTUs in each tank for AOA and 100% for AOB when OUTs were defined on the basis of a 5% nucleotide difference. In a phylogenetic tree, all of the AOA amoA sequences fell into a cluster, which contained Candidatus Nitrosopumilus maritimus. All of the AOB amoA sequences were related to the Nitrosospira lineage. These results indicated that different ammonia oxidizers were present in different tanks, but that the dominant phylogenetic types were stable. In a biofiltration tank to which a high concentration of ammonium chloride was added periodically to condition the biofilter materials, most of the AOA amoA sequences were different from the dominant one observed in the fish culture tanks. The AOB amoA sequences were also different, and were similar to those of Nitrosomonas aestuarii. These findings suggest that high concentration ammonia loads have a considerable affect on ammonia-oxidizer community composition., (Copyright © 2012 Elsevier B.V. All rights reserved.)

To clarify the natural diet of phyllosoma larvae of the Japanese spiny lobster Panulirus japonicus, the sources of 18S rDNA clones obtained from the hepatopancreas were investigated. Of a total of 1537 clones examined, 160 had different restriction profiles from the host larvae, in which 21 restriction types were observed. Nucleotide sequences of 16 of 21 restriction types were successfully determined and their assignments were investigated by homology search and phylogenetic analysis. From seven late-stage larvae collected in spring to early summer, eukaryote DNA molecules of Teleostei, Oomycetes, Mycetozoa, and Fungi were identified. Exogenous DNA from four younger phyllosoma larvae collected in late autumn could not be recovered. A previous study identified DNAs of cnidarians and urochordates in late-stage phyllosoma larvae of a closely related species collected in winter. This indicates that the phyllosoma larvae are opportunistic carnivores, whose diets correlate with the relative abundance of prey organisms in the ambient water.

Fishes of the order Cypriniformes are almost completely restricted to freshwater bodies and number > 3400 species placed in 5 families, each with poorly defined subfamilies and/or tribes. The present study represents the first attempt toward resolution of the higher-level relationships of the world's largest freshwater-fish clade based on whole mitochondrial (mt) genome sequences from 53 cypriniforms (including 46 newly determined sequences) plus 6 outgroups. Unambiguously aligned, concatenated mt genome sequences (14,563 bp) were divided into 5 partitions (first, second, and third codon positions of the protein-coding genes, rRNA genes, and tRNA genes), and partitioned Bayesian analyses were conducted, with protein-coding genes being treated in 3 different manners (all positions included; third codon positions converted into purine [R] and pyrimidine [Y] [RY-coding]; third codon positions excluded). The resultant phylogenies strongly supported monophyly of the Cypriniformes as well as that of the families Cyprinidae, Catostomidae, and a clade comprising Balitoridae + Cobitidae, with the 2 latter loach families being reciprocally paraphyletic. Although all of the data sets yielded nearly identical tree topologies with regard to the shallower relationships, deeper relationships among the 4 major clades (the above 3 major clades plus Gyrinocheilidae, represented by a single species Gyrinocheilus aymonieri in this study), were incongruent depending on the data sets. Treatment of the rapidly saturated third codon-position transitions appeared to be a source of such incongruities, and we advocate that RY-coding, which takes only transversions into account, effectively removes this likely "noise" from the data set and avoids the apparent lack of signal by retaining all available positions in the data set.

This report deals with an unusual mode of mitochondrial gene introgression between Cobitis hankugensis (C. sinensis) and C. longicorpus which is mediated by a unisexual hybridogenetic system of diploid-triploid C. hankugensis-longicorpus complex. Mitochondrial DNA sequences of 3329-3330bp encompassing from upstream ND6 to 12S rDNA indicated that mitochondrial genomes from the diploid hybrids, triploid hybrids, and their parental species are almost identical. Because triploid hybrids produce haploid ova with C. hankugensis chromosome set, normal diploid C. hankugensis regenerates upon insemination with C. hankugensis sperm. If the hybrid carries C. longicorpus mitochondrial genome, the regenerated C. hankugensis is a nucleo-cytoplasmic hybrid, thus accomplishing the unusual mode of mitochondrial gene introgression.

Ostariophysi is the second largest superorder within Teleostei. It contains five orders: Gonorynchiformes, Cypriniformes, Characiformes, Siluriformes, and Gymnotiformes. Resolving the higher-level relationships among ostariophysan and related fishes will aid in resolving basal teleostean divergence and provide basis to historical biogeographic analysis of major freshwater fish groups. In this study, we report the complete mitochondrial (mt) DNA sequences for eleven ostariophysan fishes and the results of phylogenetic analyses including these species plus four other ostariophysan and nine non-ostariophysan teleostean fishes. Maximum likelihood and maximum parsimony analyses reconfirmed clupeiforms as the closest relatives of ostariophysans. However, gonorynchiforms were closer to clupeiforms than to otophysans (ostariophysan groups excluding gonorynchiforms), thus raising a question over the current definition of Ostariophysi. The lack of clarity in otocephalan (ostariophysans + clupeiforms) basal relationships implies that such divergence took place over a short period of time. The monophyly of cypriniforms, characiphysans (characiforms, siluriforms, and gymnotiforms), and orders or superorders outside the ostariophysans examined here were conceivably reconstructed. The phylogenetic hypothesis suggests a Pangean origin of otophysans. Within characiphysans, gymnotiforms and siluriforms have independent evolutionary origins and evolutionary histories comparable to or older than that of characiforms. This helps to explain the present geographic distribution of characiphysans.