Vertical distribution of bacterial and archaeal communities along discrete layers of a deep-sea cold sediment sample at the East Pacific Rise (similar to 13 degrees N)

The community structure and vertical distribution of prokaryotes in a deep-sea (ca. 3,191 m) cold sediment sample (ca. 43 cm long) collected at the East Pacific Rise (EPR) similar to 13 degrees N were studied with 16SrDNA-based molecular analyses. Total community DNA was extracted from each of four discrete layers EPRDS-1, -2, -3 and -4 (from top to bottom) and 16S rDNA were amplified by PCR. Cluster analysis of DGGE profiles revealed that the bacterial communities shifted sharply between EPRDS-1 and EPRDS-2 in similarity coefficient at merely 49%. Twenty-three sequences retrieved from DGGE bands fell into 11 groups based on BLAST and bootstrap analysis. The dominant groups in the bacterial communities were Chloroflexi, Gamma proteobacteria, Actinobacterium and unidentified bacteria, with their corresponding percentages varying along discrete layers. Pairwise Fst (F-statistics) values between the archaeal clone libraries indicated that the archaeal communities changed distinctly between EPRDS-2 and EPRDS-3. Sequences from the archaeal libraries were divided to eight groups. Crenarchaea Marine Group I (MGI) was prevalent in EPRDS-1 at 83%, while Uncultured Crenarchaea group II B (UCII B) abounded in EPRDS-4 at 61%. Our results revealed that the vertically stratified distribution of prokaryotic communities might be in response to the geochemical settings and suggested that the sampling area was influenced by hydrothermalism. The copresence of members related to hydrothermalism and cold deep-sea environments in the microbial community indicated that the area might be a transitional region from hydrothermal vents to cold deep-sea sediments.

Broader pattern of tandem repeats in the mitochondrial control region of Perciformes

Perciformes, the largest order of vertebrates with 20 suborders, is the most diverse fish order that dominates vertebrate ocean life. The complete mitochondrial control region (CR) of Trichiurus japonicus (Trichiuridae, Scombroidei) and Pampus sp. (Stromateidae, Stromateoidei) were amplified and sequenced. Together with data from GenBank, the tandem repeats in the mitochondrial CR from 48 species, which covered nine suborders of Perciformes, are reported in this study. The tandem repeats tend to be long in the suborder Percoidei and Stromateoidei. The identical repeats in 21 species of Cichlidae suggest a common origin and have existed before species divergence. Larimichthys crocea shows tandem repeats instead of the typical structure of the central conserved sequence blocks, which was first reported in Perciformes and vertebrates. This might have resulted from interruption of the polymerase activity during the H-strand synthesis. The four broader patterns presented here for the tandem repeats, including those in both the 5' and 3' ends, only in the either 5' or 3' end, and in the central conserved domain of the control region, will be useful for understanding the evolution of species.

Ulva and Enteromorpha (Ulvaceae, Chlorophyta) from two sides of the Yellow Sea: analysis of nuclear rDNA ITS and plastid rbcL sequence data

Ulvacean green seaweeds are common worldwide; they formed massive green tides in the Yellow Sea in recent years, which caused marine ecological problems as well as a social issue. We investigated two major genera of the Ulvaceae, Ulva and Enteromorpha, and collected the plastid rbcL and nuclear ITS sequences of specimens of the genera in two sides of the Yellow Sea and analyzed them. Phylogenetic trees of rbcL data show the occurrence of five species of Enteromorpha (E. compressa, E. flexuosa, E. intestinalis, E. linza and E. prolifera) and three species of Ulva (U. pertusa, U. rigida and U. ohnoi). However, we found U. ohnoi, which is known as a subtropical to tropical species, at two sites on Jeju Island, Korea. Four ribotypes in partial sequences of 5.8S rDNA and ITS2 from E. compressa were also found. Ribotype network analysis revealed that the common ribotype, occurring in China, Korea and Europe, is connected with ribotypes from Europe and China/Japan. Although samples of the same species were collected from both sides of the Yellow Sea, intraspecific genetic polymorphism of each species was low among samples collected worldwide.

Source of a floating dust episode over the Qingdao region and dust throughput to the ocean

A floating dust weather happened on March 11-12, 1995 over the Qingdao region. Its sources and throughput to the ocean were studied. The result indicated that the floating dust was caused by the dust storm that starred in northwestern China and developed in northern China. 21 x 10(6)t fine soil particles were carried to the ocean during the episode.

Carbonate cycle and its control factors in Kuroshio source region during the last 190ka BP

Two deep sea cores (Ph05-5, 16.05 degrees N, 124.34 degrees E, water depth 3382m and WP3: 22.15 degrees N, 122.95 degrees E, water depth 2700m) retrieved from the Kuroshio source region of the western Philippine Sea were selected to carry out the CaCO3 and calcareous nannofossil faunas study. Based on AMS(14)C data and comparing tire oxygen isotope curve with SPECMAP delta O-18 (Martinson et al., 1987) a stratigraphy was established. And, combining the changes of primary productivity and dissolution index of carbonate, the carbonate cycle and its control factors were analyzed in this region during the last 190ka BP. The carbonate contents showed higher values in the glacial periods and lower values during the interglacial and Holocene periods, which characteristics was similar to the tendency of "Pacific Type" carbonate cycle. However, there were high carbonate contents in the warm period and low values during the cold interval, which displayed the same tendency with the "Atlantic Type" carbonate cycle during the last glacial period (MIS4-2) in the east of Phillipines. The variations of primary productivity and carbonate dissolution index indicated that the carbonate dissolution was a major factor controlling the carbonate content in tire cast of Philippines, and the variations in carbonate contents were mainly affected by the productivity of calcareous organism in the Southeast of Taiwan. The "Atlantic Type" carbonate cycle in the cast of Phillipines during the last glacial period (MIS4-2) was an effect of the process of dissolution combined with the change of primary productivity.

The variation of upper ocean structure and paleoproductivity in the Kuroshio source region during the last 200 kyr

A core from the source region of the Kuroshio warm current (east of the Luzon Island) was analyzed using several proxies in order to study the variability of the Western Pacific Warm Pool (WPWP) during the last two glacial-interglacial cycles. Primary productivity (PP) variations were deduced from variations in the coccolith flora. Primary productivity was higher during glacial periods (the end of Marine Isotope Stage [MIS] 3, some periods in MIS 2 and 6), and decreased during interglacial periods (MIS 7, MIS Se and probably MIS 5c-5d), with the lowest PP in MIS 5e. variations in the delta C-13 difference in benthic and bulk carbonate, thus in the vertical gradient of delta C-13 in dissolved inorganic carbon (Delta delta C-13(c). (wuellerstorfi-N. dutertrei) and Delta delta C-13(c.) (wuellerstorfi-coccolith)) Coincided With the PP Changes, showing that export productivity was low during interglacial periods (MIS 7, MIS 5e and Holocene) and high during glacial periods (MIS 6, probably MIS 5c-5d, late MIS 4 and late MIS 3). Comparison of foraminiferal carbonate dissolution indicators and PP changes reveals that nannofossil assemblage in core Ph05-5 is not sensitive to carbonate dissolution intensity. The depth of the thermocline (DOT) was estimated from planktonic forminiferal assemblages, and was relatively greater during interglacial periods (MIS 7, MIS 5e, probably MIS 5c and Holocene) than during glacials (middle MIS 6, probably MIS 5b and 5d, some periods in MIS 4, MIS 3 and MIS 2). Good coherence between the paleoproductivity records and the DOT suggests that the DOT changes could be the primary control factor in changes of paleoproductivity, and the glacial high productivity in the Kuroshio source region could be associated with a global increase of nutrient concentration in the intermediate waters that upwelled into the photic zone. The low CO2 values derived for intervals of high productivity and a relatively shallow DOT suggest that the changes in biological productivity and DOT in the equatorial Pacific could have modified atmospheric CO2 concentrations. High Sea Surface Temperatures (SSTs) during the warm MIS 5e in combination with intensified monsoonal rain fall could have resulted in a more intense stratification of the upper waters, resulting in low nutrient supply to the surface waters and a resulting decrease in productivity. (C) 2010 Elsevier B.V. All rights reserved.

Living planktonic foraminifera from the northwestern Pacific Ocean: SSU rDNA sequences and their paleoceanographic significance

Living planktonic foraminifera (PF) samples from the Okinawa Trough of the northwestern Pacific Ocean were taken for DNA analysis. The SSU rDNA sequences of two PF species, Globigerina sp. and Pulleniatina obliquiloculata collected at Station WP01, were obtained and compared with those from the southwestern Pacific Ocean. Only small differences (< 0.7%-1.2% for P. obliquiloculata, and 0.3% for Globigerina sp.) were found between samples from the north- and south-western Pacific Ocean areas and this molecular evidence supported that these micropaleontological species are the same species, which implies that the West Pacific Ocean circulation system influences the planktonic foraminiferal gene communication.

Identification and assessing the cultivars of Laminaria Lamx. (phaeophyceae) with molecular markers

Molecular markers were used to identify and assess cultivars of Laminaria Lamx. and to delineate their phylogenetic relationships. Random amplified polymorphic DNA (RAPD) analysis was used for detection. After screening, 11 primers were selected and they yielded 133 bands in all, of which approximately 99.2% were polymorphic. The genetic distances between gametophytes ranged from 0.412 to 0.956. Two clusters were formed with the unweighted pair group method with arithmetic mean (UPGMA) dendrogram based on the simple matching coefficient. All cultivars of Laminaria japonica Aresch. used for breeding in China fell into one cluster. L. japonica from Japan, L. saccharina (L.) Lam., and L. angustata Kjellm. formed the other cluster and showed higher genetic variation than L. japonica from China. Nuclear ribosomal DNA (rDNA) sequences, including internal transcribed spacers (ITS1 and ITS2) were studied and aligned. The nucleotides of the sequences ranged from 634 to 668, with a total of 692 positions including TTS1, ITS2, and the 5.8S coding region. The phylogenetic tree obtained by the neighbor-joining method favored, to some extent, the results revealed by RAPD analysis. The present study indicates that RAPD and ITS analyses could be used to identify and assess Laminaria germplasm and to distinguish some species and, even intraspecies, in Laminaria.

Traveling wave front for the Fisher equation on an infinite band region

Instead of discussing the existence of a one-dimensional traveling wave front solution which connects two constant steady states, the present work deals with the case connecting a constant and a nonhomogeneous steady state on an infinite band region. The corresponding model is the well-known Fisher equation with variational coefficient and Dirichlet boundary condition. (c) 2006 Elsevier Ltd. All rights reserved.

几种赤潮微藻的形态和系统进化分析及荧光原位杂交检测

赤潮也称红潮，通常是指由于一些海洋浮游生物在水体中过度繁殖或聚集而使海水变色的现象。赤潮特别是有害赤潮造成了严重的生态环境问题，给水产养殖业和滨海旅游业造成了巨大损失，并可直接危害人类健康。研究赤潮，进而预防和控制赤潮，首先要对引发赤潮的生物种类进行准确鉴定并对自然水域的赤潮生物进行监控，并建立赤潮藻的快速鉴定与检测方法。本文分别对几株赤潮微藻进行了形态和系统进化分析，并探讨了荧光原位杂交在赤潮检测中的应用。 分别对5株分离自中国沿海不同水域的中肋骨条藻[Skeletonema costatum (Greville) Cleve]类似种 (SK-BH、SK-FQ、 SK-HH、SK-DH和SK-XM) 进行光镜和扫描电镜观察，并PCR扩增了转录内间隔区 (含5.8S rDNA)(ITS) 和核糖体大亚基 (D1-D2)区 (LSU)，获得的序列与其它已报道的骨条藻的同源序列进行了进化分析，以探讨５株骨条藻与已报道的骨条藻之间的进化关系。5株骨条藻在形态上各不相同，其中，只有1株 (SK-XM)被鉴定为中肋骨条藻，而其余4株皆与已报道的骨条藻的形态学特征不符。ITS树和LSU树具有不同的拓扑结构，并表明5株骨条藻至少分属3个不同的种。遗传距离分析提示了在地理距离上靠近的种，在进化上也可能靠近。此外，还可以观察到这5株藻之间的细微的形态学“进化”关系。所有结果表明了中国沿海骨条藻属种的多样性。 对1株分离自赤潮水域的裸甲藻 (Gymnodinium)类似种进行了形态学分析，并探讨了该藻与裸甲藻、凯伦藻(Karena)、旋沟藻(Gyrodinium)、下沟藻(Karlodinium)和共生甲藻(Symbiodinium)的进化关系。光镜观察表明该藻具有裸甲藻的一些典型的形态学特征，而我们没能获得细胞形态保存完好的电镜样品；进化分析初步鉴定该藻为一种共生甲藻。 获得了赤潮异湾藻[Heterosigma akashiwo (Hada) Hada]的LSU和ITS序列，设计了以胞质rRNA和胞核rDNA为靶序列的特异性探针，建立了赤潮异湾藻的全细胞和细胞核荧光原位杂交技术，对探针的特异性进行了验证，并考察了杂交信号和检测率在整个细胞周期的变化情况。探针能分别使整个细胞和细胞核呈现明亮的绿色荧光。探针是特异性的，不与其它受试藻进行交叉反应。杂交信号在整个细胞周期内变化不明显，且检测率为70%–80%。整个检测过程不到1 ｈ，能实现赤潮异湾藻的快速、准确、特异和半定量检测。 获得了海洋原甲藻(Prorocentrum micans Ehrenberg)的LSU和ITS序列，设计了以胞质rRNA为靶序列的特异性探针，建立了海洋原甲藻的全细胞荧光原位杂交技术，并对探针的特异性进行了验证。探针能使整个细胞呈现强烈的绿色荧光。探针不与其它受试藻种进行交叉反应，表明是特异性的。

胶州湾超微型浮游真细菌16s rDNA RFLP分析相关技术的研究

通过生态学与分子生物学相结合的方法，对胶州湾超微型浮游真细菌从16s rDNA的角度分析其多样性，建立了一系列行之有效的方法，对于今后开展特定的超微型生物的研究提供他有益的借鉴。主要结果如下：1.建立了行之有效的从极稀密度的海水中提取浮游细菌总基因组DNA的方法，其得率约为0.3～0.5 μg/L海水，并且提供了DNA浓缩、纯化的一系列步骤，最后所制得的DNA其纯度和含量足以开展后续工作。2.建立了可靠的具有较高转化效率的感受态细胞，并从多个途径来制备，并对各种方法的成败及注意事项进行了探讨。3.对PCR反应的条件进行了深入的探讨，成功在从混合型基因组中扩增出细菌特异性引物(Universal 1406R和Eubacterial 68F)所对应的16s rDNA。并且对PCR的几个控制因子进行了分析，对于今后采用不同引物的高效扩增将提供有益的帮助。4.深入地对TA克隆效率进行了探讨，较好地将PCR混合产物分离开，并成功地导入大肠杆菌DH5α菌株，并对重组质粒进行了初步的RFLP分析，为今后通过序列测定构建系统进化树奠定了基础。5.RFLP分析表明胶州湾海水中至少含有7种亲缘关系较远的真细菌。

Further Indo-West Pacific palaemonoid shrimps (Crustacea : Decapoda : Palaemonoidea), principally from the New Caledonian region

Based on the material deposited in the Museum national d'Histoire naturelle, Paris, collected from the Indo-West Pacific, principally from the New Caledonian region, the present paper reports 117 palaemonoid shrimp species, which belong, respectively, to Anchistioididae ( one genus, one species), Gnathophyllidae ( one genus, one species), Palaemonidae Palaemoninae ( seven genera, nine species), and Palaemonidae Pontoniinae ( 30 genera, 106 species), including eight new species. The new species are all Pontoniinae: Mesopontonia brevicarpalis sp. nov., Palaemonella komaii sp. nov., Periclimenes crosnieri sp. nov., Periclimenes forgesi sp. nov., Periclimenes loyautensis sp. nov., Periclimenes paralcocki sp. nov., Periclimenes paraleator sp. nov., and Periclimenes pseudalcocki sp. nov. The last six new species are members of the deep-water "Periclimenes alcocki species complex'', which has more than two ( usually four) pairs of dorsolateral telson spines anterior to the posterior telson margin, the cornea is usually reduced, the dactyl of the major second chela is generally flanged and the chela is sometimes covered with small tubercles. The complex is usually found at more than 200m depth in the West Pacific. The species can be distinguished from each other by the armature of ambulatory propod and dactyl, diameter of cornea, rostrum shape and the number of pairs of dorsolateral telson spines. Mesopontonia brevicarpalis sp. nov., from the southeast coast of Africa, is the seventh species of the genus. Palaemonella komaii sp. nov. is very similar to Palaemonella dolichodactylus Bruce, 1991 and Palaemonella hachijo Okuno, 1999. These three species share the features of very long and slender ambulatory pereiopods with the dactyl more than eight times longer than its basal depth and with several long setae on the dorsal dactylar margin.

Feeding behaviour of yaks on spring, transitional, summer and winter pasture in the alpine region of the Qinghai-Tibetan plateau

Of the present estimated world population of 14.2 million yaks, approximately 13.3 million occur within Chinese territories (Food and Agriculture Organization of the United Nations, 2003). Although there is an extensive bibliography covering the species, few studies have been conducted in the area of foraging behaviour. The present study was conducted at pasture during the spring, transitional, summer and winter seasons to determine the daily temporal patterns of grazing and ruminating behaviour by yaks. During each study period, two 24 h recordings were undertaken with each of six mature dairy yaks. One study period was conducted on each of the transitional, summer and winter pastures, whereas, due to the considerable changes occurring in the morphology of the spring pasture, three separate studies were completed during March, April and May. During the second of these studies (April), the effect of level of concentrate supplementation on grazing and ruminating behaviour was also examined. Behaviour recordings were made using solid-state behaviour recorders. Short-term intake rates (IR, g min(-1)) were calculated by weighing yaks before and after approximately 1 h of grazing, retaining the faeces and urine excreted and applying a correction for insensible weight loss. Yaks spent less time grazing during the dry season (the early period on the spring pasture) compared with the later green swards (the later period on the spring pasture, the transitional pasture and the summer pasture) (P < 0.05). When the forage quality improved, but there was still insufficient mass (the later period on the spring pasture), the yaks extended their grazing time at the expense of other activities. During the early periods on the spring pasture, the short-term IR by yaks was up to 53 g DM min(-1), significantly higher than at other times (P < 0.05). The level of concentrate offered had little or no effect on grazing or ruminating time. The total eating time of the yaks offered 0.5 or 1.0 kg concentrate was 2.9 and 4.5 h day(-1) respectively, significantly lower than unsupplemented yaks (6.8 h) (P < 0.05). In general, yaks can regulate their foraging behaviour according to the changes of sward conditions in order to achieve optimal grazing strategies. (C) 2007 Published by Elsevier B.V.

Phylogenetic origins of the Himalayan endemic Dolomiaea, Diplazoptilon and Xanthopappus (Asteraceae : Cardueae) based on three DNA regions

Background and Aims It is an enduring question as to the mechanisms leading to the high diversity and the processes producing endemics with unusual morphologies in the Himalayan alpine region. In the present study, the phylogenetic relationships and origins of three such endemic genera were analysed, Dolomiaea, Diplazoptilon and Xanthopappus, all in the tribe Cardueae of Asteraceae.Methods The nuclear rDNA internal transcribed spacer (ITS) and plastid trnL-F and psbA-trnH regions of these three genera were sequenced. The same regions for other related genera in Cardueae were also sequenced or downloaded from GenBank. Phylogenetic trees were constructed from individual and combined data sets of the three types of sequences using maximum parsimony, maximum likelihood and Bayesian analyses.Key Results The phylogenetic tree obtained allowed earlier hypotheses concerning the relationships of these three endemic genera based on gross morphology to be rejected. Frolovia and Saussurea costus were deeply nested within Dolomiaea, and the strong statistical support for the Dolomiaea-Frolovia clade suggested that circumscription of Dolomiaea should be more broadly redefined. Diplazoptilon was resolved as sister to Himalaiella, and these two together are sister to Lipschitziella. The clade comprising these three genera is sister to Jurinea, and together these four genera are sister to the Dolomiaea-Frolovia clade. Xanthopappus, previously hypothesized to be closely related to Carduus, was found to be nested within a well-supported but not fully resolved Onopordum group with Alfredia, Ancathia, Lamyropappus, Olgaea, Synurus and Syreitschikovia, rather than the Cardinis group. The crude dating based on ITS sequence divergence revealed that the divergence time of Dolomiaea-Frolovia from its sister group probably occurred 13.6-12.2 million years ago (Ma), and the divergence times of the other two genera, Xanthopappus and Diplazoptilon, from their close relatives around 5.7-4.7 Ma and 2.0-1.6 Ma, respectively.Conclusions The findings provide an improved understanding of the intergeneric relationships in Cardueae. The crude calibration of lineages indicates that the uplifts of the Qiinghai -Tibetan Plateau since the Miocene might have served as a continuous stimulus for the production of these morphologically aberrant endemic elements of the Himalayan flora.

Molecular authentication of the traditional Tibetan medicinal plant Swertia mussotii

Swertia mussotii is an important species in Tibetan folk medicine. However, it is quite expensive and frequently adulterated, so reliable methods for authentication of putative specimens and preparations of the species are needed to protect consumers and to support conservation measures. We show here that the chloroplast (cp) DNA rpl16 intron has limited utility for differentiating S. mussotii from closely related species, since the cpDNA rpl16 sequences are identical in S. mussotii and two other species of Swertia. However, the rDNA internal transcribed spacer (ITS) sequences differ significantly between S. mussotii and all of 13 tested potential adulterants. Thus, the ITS region provides a robust molecular marker for differentiating the medicinal S. mussotii from related adulterants. Therefore, a pair of allele-specific diagnostic primers based on the divergent ITS region was designed to distinguish S. mussotii from the other species. Authentication by allele-specific diagnostic PCR using these primers is convenient, effective and both simpler and less time-consuming than sequencing the ITS region.