Development and evaluation of specific PCR primers targeting the ribosomal DNA-internal transcribed spacer(ITS) region of peritrich ciliates in environmental samples

Peritrich ciliates are highly diverse and can be important bacterial grazers in aquatic ecosystems. Morphological identifi cations of peritrich species and assemblages in the environment are time-consuming and expertise-demanding. In this study, two peritrich-specifi c PCR primers were newly designed to amplify a fragment including the internal transcribed spacer(ITS) region of ribosomal rDNA from environmental samples. The primers showed high specifi city in silico, and in tests with peritrich isolates and environmental DNA. Application of these primers in clone library construction and sequencing yielded exclusively sequences of peritrichs for water and sediment samples. We also found the ITS1, ITS2, ITS, D1 region of 28 S rDNA, and ITS+D1 region co-varied with, and generally more variable than, the V9 region of 18 S rDNA in peritrichs. The newly designed specifi c primers thus provide additional tools to study the molecular diversity, community composition, and phylogeography of these ecologically important protists in dif ferent systems.     

Sequence analysis of the ITS region and 5.8S rDNA of <Emphasis Type="Italic">Porphyra haitanensis</Emphasis>

The sequences of the ITS(internal transcribed spacer) and 5.8S rDNA of three cultivated strains of Porphyra haitanensis thalli(NB,PT and ST) were amplified,sequenced and analyzed.In addition,the phylogenic relationships of the sequences identified in this study with those of other Porphyra retrieved from GenBank were evaluated.The results are as follows:the sequences of the ITS and 5.8S rDNA were essentially identical among the three strains.The sequences of ITS1 were 331 bp to 334 bp,while those of the 5.8...     

Morphology and molecular phylogeny of three black corals(Antipatharia,Schizopathidae) from seamounts in the Western Pacific Ocean,with description of a new species

Three deep-sea black corals belonging to the family Schizopathidae,are reported from two seamounts on the Caroline Ridge in the tropical Western Pacific:Umbellapathes parva sp.nov.with depth of 1 488-1 766 m,Telopathes cf.magna MacIsaac Best,2013 with depth of 937-1 016 m,and Stauropathes cf.punctata(Roule,1905) with depth of 942-1 353 m.The latter two species are the first records in the Western Pacific Ocean.U.parva sp.nov.is characterized by monopodial corallum,relatively long unpinnulated stalk with complex pinnulated branche s developing from the lowermost primary pinnules and small spine s.It differs from two known congeners by much smaller spine s and the present of secondary pinnules.T.cf.magna MacIsaac Best,2013 has sparsely branched corallum,relatively long and simple pinnules arranged in subopposite or alternate pairs.S.cf.punctata(Roule,1905) is characterized by the corallum with almost planar pinnulated branches,and pinnules arranged in subopposite pairs.Our results indicate that the corallum size and shape are variable in conspecific specimens particularly those at different growth stages.By contrast,the size of the polypar spines as well as the abpolypar spines have little variation and can be served as a main differing feature for schizopathid species.The phylogenetic analyses using nuclear internal transcribed spacer region(spanning partial 18 S rDNA,ITS 1,5.8 S,ITS2,and partial 28 S rDNA) and two mitochondrial fragments cox3-IGR-coxl(COI) and trnW-IGR-nad2(NAD2) showed Telopathes,Stau ropathes,and Bathypathes had close relationships,and Umbellapathes formed a sister clade with Alternatipathes.     

Molecular diversity of Enteromorpha from the coast of Yantai: a dual-marker assessment

We collected nine Enteromorpha specimens from the coast of Yantai and evaluated their diversity based on analyses of their ITS （internal transcribed spacer） and 5S rDNA NTS （non-transcribed spacer） sequences. The ITS sequences showed slight nucleotide divergences between Enteromorpha linza and Enteromorpha prolifera. In contrast, multiple highly variable regions were found in the ITS region of Enteromorpha flexuosa. In general, there were more variable sites in the NTS region than in the ITS region in the three species. The variations in 5S rDNA NTS sequences indicated that the molecular diversity of Enteromorpha from the coast of Yantai is very high. However, a phylogenetic tree constructed using 5S rDNA NTS sequence data indicated that genetic differences were not directly related to geographical distribution.     

Phylogenetic analyses of four species of Ulva and Monostroma grevillei using ITS, rbc L and 18S rDNA sequence data

Chlorophyta species are common in the southern and northern coastal areas of China. In recent years, frequent green tide incidents in Chinese coastal waters have raised concerns and attracted the attention of scientists. In this paper, we sequenced the 18S rDNA genes, the internal transcribed spacer (ITS) regions and the rbcL genes in seven organisms and obtained 536-566 bp long ITS sequences, 1 377-1 407 bp long rbcL sequences and 1 718-1 761 bp long partial 18S rDNA sequences. The GC base pair content was highest in the ITS regions and lowest in the rbcL genes. The sequencing results showed that the three Ulva prolifera (or U. pertusa) gene sequences from Qingdao and Nan’ao Island were identical. The ITS, 18S rDNA and rbcL genes in U. prolifera and U. pertusa from different sea areas in China were unchanged by geographic distance. U. flexuosa had the least evolutionary distance from U. californica in both the ITS regions (0.009) and the 18S rDNA (0.002). These data verified that Ulva and Enteromorpha are not separate genera.     

Molecular phylogenetic analysis of dinoflagellate Scrippsiella trochoidea isolated from the East Asian waters

Previous studies found intraspecific diversity in Scrippsiella trochoidea A. R. Loeblich III, a widely distributed calcareous cyst-producing dinoflagellate. In this study, three strains (ST-1, ST-D6 and ST-K) of S. trochoidea isolated from the East Asian waters were studied, together with other geographical strains, to resolve their phylogenetic relationships. For the three East Asian isolates, two highly diverse regions of nuclear-encoded ribosomal DNA (rDNA), the 5.8S rDNA and its flanking internal transcribed spacers 1 and 2, and the 5′ portion of the large-subunit rDNA (encompassing the “D1“ and “D2” domains) were sequenced. Homologous sequences from other geographical isolates were selected from the GenBank database and the phylogenetic relationships were inferred from the molecular data of these strains. Strains of S. trochoidea were found to cluster into three major clades (STR1, STR2 and STR3), as reported in previous studies. Two of the three strains ST-1 and ST-K, were grouped in clade STR2, the other strain, ST-D6, belonged to clade STR3. The intraspecific diversity of S. trochoidea in East Asian waters makes it necessary to carry out phylogenetic investigations in combination with data of biogeography, population dynamics, and life cycle on the ecophysiology of a region.     

Preliminary Identification of Three New Isolates in Genus Alexandrium (Dinophyceae) from China Sea Area

1 Introduction Dinoflagellate Alexandrium has received intensive at-tention in recent years, as it is a valuable bioactive com-pound resource and related to harmful algal bloom (HAB)which has negative impact on marine ecology systemaquiculture, human health and tourism (Hallegraeff andBolch, 1992; Smayda, 1997; Vale and Antonia de MSampayo, 2001). However, not all of the species in genusAlexandrium produce toxin (Wendy et al., 2001), so rapididentification and clarification of the phyloge…     

Primary species recognitionand phylogeny of Chondrus （Gigartinales, Rhodophyta） using 18S rDNA sequence data

The nuclear-encoded small subunit ribosomal RNA gene (18S rDNA) of 16 isolates of Chondrus from 8 countries were sequenced. A total of 1796 nucleotides were obtained and aligned with the phylogenetic analysis conducted. The results suggest that the entity from Dalian, China, regarded as C. sp1 is C. pinnulatus. The C. sp2 previously depicted as C. yendoi or Mazzaella japonica may belong to genus Chondrus. So, 4 Chondrus species, i.e. C. ocellatus, C. nipponicus, C. armatus, and C. pinnulatus are distributed in China. However, the entity from Connemara, Ireland, named C. crispus, is not a Chondrus species but that of Mastocarpus stellatus, although it is morphologically similar to C. crispus. Phylogenetic analysis based on complete 18S rDNA sequence data shows that genus Chondrus includes 3 main lineages: the Northern Pacific lineage, containing C. ocellatus, C. yendoi, and C. nipponicus; C. armatus, and C. pinnulatus form the sub-North Pacific lineage; and the Northern Atlantic Ocean lineage, comprising samples of C. crispus from Canada, Portugal, Ireland, Germany and France. The phylogenetic relationships indicate that genus Chondrus might have a North Pacific ancestral origin, radiated to North Atlantic area, and then formed the species C. crispus.     

Southern ocean SST variability and its relationship with ENSO on inter-decadal time scales

Empirical orthogonal function (EOF) analysis reveals a co-variability of Sea surface temperatures (SSTs) in the Southern Hemisphere (0°-60°S). In the South Indian and Atlantic Oceans, there is a subtropical dipole pattern slanted in the southwest- north-east direction. In the South Pacific Ocean, a meridional tripole structure emerges, whose middle pole co-varies with the dipoles in the South Indian and Atlantic Oceans and is used in this study to track subtropical Pacific variability. The South Indian and Atlantic Ocean dipoles and the subtropical Pacific variability are phase-locked in austral summer. On the inter-decadal time scales, the dipoles in the South Indian and Atlantic Oceans weaken in amplitude after 1979/1980. No such weakening is found in the subtropical South Pacific Ocean. Interestingly, despite the reduced amplitude, the correlation of the Indian Ocean and Atlantic dipoles with El Nio and Southern Oscillation (ENSO) are enhanced after 1979/1980. The same increase in correlation is found for subtropical South Pacific variability after 1979/1980. These inter-decadal modulations imply that the Southern Hemisphere participates in part of the climate shift in the late 1970s. The correlation between Southern Hemisphere SST and ENSO reduces after 2000.     

Morphology and phylogeny of Chrysogorgia pinniformis sp.nov.and C.varians sp.nov.,two golden corals from the Caroline seamounts in the tropical Western Pacific Ocean

Two new species of Chrysogorgia Duchassaing Michelotti,1864 collected from the Caroline seamounts in the tropical Western Pacific Ocean are described.Chrysogorgia pinniformis sp.nov.belongs to Versluys' group C(Squamosae typicae) with only scales in polyp body wall and tentacles.C.pinniformis sp.nov.is characterized by large branches pinnately branched and forming multiple fans with its small branches regularly and quasi-dichotomous branched,and scales and rods present in the polyp mouth area.It is most similar to C.pinnata Cairns,2007 by the pinnate trait,but differs from the latter by its group C pattern(vs.group A,Spiculosae) and having sclerites present in the polyp mouth area(vs.absent).Chrysogorgia varians sp.nov.belongs to the Chrysogorgia group A(Spiculosae) with rods distributed in the polyp body wall and tentacles.It is characterized by warty rods and elongated scales in the tentacles,many warts and ridges on the scales,conspicuously toothed margins at the rounded ends in the pinnules,and small rods with ridge-like warts in the polyp mouth area.This species was frequent and abundant in the Caroline seamounts during our cruises and its morphological variability in growth period was obvious.The phylogenetic analyses based on mtMutS and 28 S rDNA regions supported the assignment of the new species to the genus Chrysogorgia.However,the mtMutS marker showed very limited usefulness for species delimitation and inner relationship inference of Chrysogorgia.In contrast,the 28 S rDNA showed much higher level of genetic variation,and it may be a potential barcode for this genus.In the 28 S rDNA trees,the two new species clustered together.Additionally,compilation of our data showed that 42 of 78(ca.54%) Chrysogorgia species were found in the Indo-West Pacific convergent region,indicating that this area may be a hotspot of deep-water Chrysogorgia species.     

关于地壳板块成因的猜想

地壳板块的形成,是由于外来星球的撞击而造成的。太平洋就是巨大的撞击坑,大西洋则是撞击产生的地球背面的S形裂谷。地球上的水,也很有可能主要来源于这次撞击。     

Global distribution of thermosteric contribution to sea level rising trend

The sea level derived from TOPEX/Poseidon(T/P) altimetry data shows prominent long term trend and inter-annual variability.The global mean sea level rising rate during 1993-2003 was 2.9 mm a-1.The T/P sea level trend maps the geographical variability.In the Northern Hemisphere(15°-64°N),the sea level rise is very fast at the mid-latitude(20°-40°N) but much slower at the high-latitude,for example,only 0.5 mm a-1 in the latitude band 40°-50°N.In the Southern Hemisphere,the sea level shows high rising rate both in mid-latitude and high-latitude areas,for example,5.1 mm a-1 in the band 40°-50°S.The global thermosteric sea level(TSL) derived from Ishii temperature data was rising during 1993-2003 at a rate of 1.2 mm a-1 and accounted for more than 40% of the global T/P sea level rise.The contributions of the TSL distribution are not spatially uniform;for instance,the percentage is 67% for the Northern Hemisphere and only 29% for the Southern Hemisphere(15°-64°S) and the maximum thermosteric contribution appears in the Pacific Ocean,which contributes more than 60% of the global TSL.The sea level change trend in tropical ocean is mainly caused by the thermosteric effect,which is different from the case of seasonal variability in this area.The TSL variability dominates the T/P sea level rise in the North Atlantic,but it is small in other areas,and shows negative trend at the high-latitude area(40°-60°N,and 50°-60°S).The global TSL during 1945-2003 showed obvious rising trend with the rate of about 0.3 mm a-1 and striking inter-annual and decadal variability with period of 20 years.In the past 60 years,the Atlantic TSL was rising continuously and remarkably,contributing 38% to the global TSL rising.The TSL in the Pacific and Indian Ocean rose with significant inter-annual and decadal variability.The first EOF mode of the global TSL from Ishii temperature data was the ENSO mode in which the time series of the first mode showed steady rising trend.Among the three oceans,the first mode of the Pacific TSL presented the ENSO mode;there was relatively steady rising trend in the Atlantic Ocean,and no dominant mode in the Indian Ocean.     

Preliminary identification of three new isolates in genus Alexandrium (Dinophyceae) from China sea area

The 5.8S ribosomal DNA sequences (5.8S rDNA) and their flanking regions, internal transcribed spacer 1 and spacer 2 (ITS1 and ITS2) of three new isolates in genus Alexandrium (Alexandrium sp. qd1, Alexandrium sp. qd2, Alexandrium sp. gz) from China were amplified, sequenced, and subjected to phylogenetic analysis. Alexandrium sp. gz and Alexandrium sp. qd1 were grouped with high bootstrap values with four strains/species, i.e., A. catenella South Korea strain, A. catenella Japan strain, and two from China, Alexandrium sp. AC03 and Alexandrium sp. AN01 being proposed to be A. catenalla in a previous study. Then Alexandrium sp. gz and Alexandrium sp. qd1 were identified as Alexandrium catenella. As A. catenella was isolated from Qingdao and Guangzhou sea areas, it supposedly distributed at least in these two areas and was genetically different. Alexandrium sp. qd2 differed greatly from species in Alexandrium. It clustered with Symbiodinium californium, Symbiodinium sp. G15 and Gymnodinium sp. Zhao 01 with 100% bootstrap value; so Alexandrium sp. qd2 affiliates to genus Symbiodinium, and is probably a free-living Symbiodinium species.     

Molecular identification based on ITS sequences for Kappaphycus and Eucheuma cultivated in China

The systematic classification of the Eucheumatoideae is difficult because of their variable morphology and interpretation of reproductive structures. Kappaphycus and Eucheuma specimens cultivated on the Hainan and Fujian coast of China were introduced from Vietnam, the Philippines and Indonesia. Combined with morphological characteristics, all Kappaphycus and Eucheuma cultivated strains were identified by internal transcribed spacer (ITS) sequences. The phylogenetic tree was constructed using neighbor-joining and maximum likelihood methods. The results indicate that different ITS sequence lengths occurred in the different genera and species. An obvious difference in morphology could be found in the protuberance shape between Kappaphycus and Eucheuma. The protuberance in Eucheuma was thorn-like and in Kappaphycus was wartlike or papillate. Their ITS sequence lengths differed significantly in nucleotide variation rates up to 58.55%-63.90%. All nucleotide variations occurred in the ITS1 and ITS2 regions except for five nucleotide transversions in the 5.8S rDNA region. In addition, the difference was at the branches among congeneric species. Kappaphycus sp. had branches with small buds, while K. alvarezii did not have such a feature. The nucleotide variation rates varied from 7.02% to 7.48% among species; within the same species of the clades it was <1.20%. Eucheumatoideae algae cultivated in China consisted of three clades, K. alvarezii, Kappaphycus sp., and E. denticulatum. The results indicate that ITS sequence analysis was an effective way for identification of interspecies and intraspecies phylogenetic relationships and might provide a clue for molecular identification of algal Eucheumatoideae.     

Construction of Porphyra yezoensis Pure Line from Protoplasts and Its 18S rDNA Sequence Determination

1　Introduction　PorphyraisthemainobjectforalgafarmingandplaysaveryimportantroleinChinesemarineindus tries.Recently ,therehasbeenagreatlossinPor phyracultivationduetothedegenerationoftheculti var,sothereisanincreasingdemandforgoodPor phyracultivars .Theprerequisiteofthetraditionalbreed ingandbioengineeringresearchofPorphyraistheconstructionofpurelines .Traditionally ,theclassifi cationofPorphyrawasaccordingtotheirmorphologi calcharacteristics .However ,mostmorphologicalfea turesofPorphyraar…     

First record of Biecheleria cincta (Dinophyceae) from Chinese coasts, with morphological and molecular characterization of the strains

The presence of Biecheleria cincta (=Woloszynskia cincta) in the Chinese coasts is reported for the first time. In scanning electron microscope, three to five series of vesicles and an elongated apical vesicle (EAV) were visible in the epicone, and both the hypocone and the cingulum had three series of vesicles each. Thin sections revealed that B. cincta possesses stalked pyrenoids and an unusual eyespot consisting of a stack of cisternae with brick-like materials (type E), thus supporting its transfer from Woloszynskia to Biecheleria. Spiny cysts formed spontaneously in culture, with an encystment rate of around 20%. Both large subunit ribosomal DNA (LSU rDNA) and internal transcribed spacer region (ITS) sequences in 12 strains from the Chinese coasts were determined. Phylogenetic analyses based on LSU rDNA and ITS sequences using Bayesian inference and maximum likelihood revealed two distinct ribotypes (referred to as ribotype A and B) in B. cincta. ITS region pairwise distances within B. cincta ranged from 0.024 to 0.072, suggesting the existence of a complex of cryptic species.     

20世纪80年代初以来北太平洋海温变化特征

应用1979.1-2006.12北太平洋海表温度（SST）资料,采用一元线性回归、功率谱等统计方法对该区SST的变化特征进行分析,结果表明：（1）北太平洋SST年际变化较为显著,尤其在靠近亚洲大陆一带洋面、北太平洋中部中纬度海域及赤道中、东太平洋;（2）北太平洋西部和中部SST1-12月均呈上升趋势,靠近亚洲大陆的日本海一带和我国大陆以东洋面升温最快。除我国以东洋面升温中心在冬季外,其余海域升温均在夏秋季更迅速,20世纪90年代初以来尤为明显;北美海岸山脉以西及赤道中、东太平洋SST则呈弱的下降趋势;（3）赤道中、东太平洋春夏季存在显著5a和3.5a左右的年际变化;北太平洋中部30°N一带冬春季存在5-6a左右的年际变化和约14a的年代际变化;（4）除北太平洋中部（西风漂流区）外,各个海域大部分月份SST高值年和低值年分别与厄尔尼诺年和拉尼娜年对应,西风漂流区SST高值年均出现在20世纪末21世纪初,低值年与厄尔尼诺年对应。     

Analysis of the global swell distributions using ECMWF Re-analyses wind wave data

The existence of three well-defined tongue-shaped zones of swell dominance, termed as ‘swell pools’, in the Pacific, the Atlantic and the Indian Oceans, was reported by Chen et al. (2002) using satellite data. In this paper, the ECMWF Re-analyses wind wave data, including wind speed, significant wave height, averaged wave period and direction, are applied to verify the existence of these swell pools. The swell indices calculated from wave height, wave age and correlation coefficient are used to identify swell events. The wave age swell index can be more appropriately related to physical processes compared to the other two swell indices. Based on the ECMWF data the swell pools in the Pacific and the Atlantic Oceans are confirmed, but the expected swell pool in the Indian Ocean is not pronounced. The seasonal variations of global and hemispherical swell indices are investigated, and the argument that swells in the pools seemed to originate mostly from the winter hemisphere is supported by the seasonal variation of the averaged wave direction. The northward bending of the swell pools in the Pacific and the Atlantic Oceans in summer is not revealed by the ECMWF data. The swell pool in the Indian Ocean and the summer northward bending of the swell pools in the Pacific and the Atlantic Oceans need to be further verified by other datasets.     

A new species of Macandrewia(Demospongiae,Tetractinellida,Macandrewiidae) from a seamount in the Western Pacific Ocean

A new species of Macandrewia Gray from a seamount near Yap Trench in the Western Pacific Ocean was described.Macandrewia yapensis sp.nov.is distinct from its congeners by possessing a foliate shape with contorted lamellae,tuberculiform terminations of desmas,and unique size of spicules.This is the third species of Macandrewia described from the Pacific Ocean.In addition a partial sequence of COI gene was obtained from the new specimen and then it submitted to GenBank.Phylogenetic tree constructed with the partial COI sequences appears to exhibit a more congruent relationship with morphological data of macandrewiid species compared to 28 S gene tree.