Phycobilisomes linker family in cyanobacterial genomes: divergence and evolution

Cyanobacteria are the oldest life form making important contributions to global CO2 fixation on the Earth. Phycobilisomes (PBSs) are the major light harvesting systems of most cyanobacteria species. Recent availability of the whole genome database of cyanobacteria provides us a global and further view on the complex structural PBSs. A PBSs linker family is crucial in structure and function of major light-harvesting PBSs complexes. Linker polypeptides are considered to have the same ancestor with other phycobiliproteins (PBPs), and might have been diverged and evolved under particularly selective forces together. In this paper, a total of 192 putative linkers including 167 putative PBSs-associated linker genes and 25 Ferredoxin-NADP oxidoreductase (FNR) genes were detected through whole genome analysis of all 25 cyanobacterial genomes (20 finished and 5 in draft state). We compared the PBSs linker family of cyanobacteria in terms of gene structure, chromosome location, conservation domain, and polymorphic variants, and discussed the features and functions of the PBSs linker family. Most of PBSs-associated linkers in PBSs linker family are assembled into gene clusters with PBPs. A phylogenetic analysis based on protein data demonstrates a possibility of six classes of the linker family in cyanobacteria. Emergence, divergence, and disappearance of PBSs linkers among cyanobacterial species were due to speciation, gene duplication, gene transfer, or gene loss, and acclimation to various environmental selective pressures especially light.

Wangia profunda gen. nov., sp nov., a novel marine bacterium of the family Flavobacteriaceae isolated from southern Okinawa Trough deep-sea sediment

An orange-pigmented, Gram-negative, nonmotile, strictly aerobic and oxidase- and catalase-positive bacterium (SM-A87(T)) was isolated from the deep-sea sediment of the southern Okinawa Trough area. The main fatty acids were i15 : 0, i17 : 0 3OH, i15 : 1 G, i17 : 1 omega 9c, 15 : 0, i15 : 0 3OH and summed feature 3 (comprising i-15 : 0 2OH and/or 16 : 1 omega 7c). MK-6 was the predominant respiratory quinone. DNA G+C content was 35.8 mol%. Flexirubin-type pigments were absent. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain SM-A87(T) formed a distinct lineage within the family Flavobacteriaceae, with < 93% sequence similarity to the nearest strain of genus Salegentibacter. Moreover, strain SM-A87(T) could be distinguished from the nearest phylogenetic neighbors by a number of chemotaxonomic and phenotypic properties. On the basis of polyphasic analyses, it is proposed that strain SM-A87(T) be classified in a novel genus and a new species in the family Flavobacteriaceae, designated Wangia profunda gen. nov., sp. nov. The type strain is SM-A87(T) (CCTCC AB 206139(T)=DSM 18752).

中国海蓝子鱼科Family Siganidae分类和动物地理学特点

蓝子鱼科鱼类隶属于鲈形目、刺尾鱼亚目，广泛分布于我国东海、南海及台湾海域。本文根据中国科学院海洋研究所多年来在我国海域采集并收藏的以及部分补充采集的蓝子鱼标本，参考国际最新研究资料，对我国海域蓝子鱼科鱼类进行分类和动物地理学研究，共记录中国海域蓝子鱼科鱼类1属2亚属11种。经研究分析，得到如下结论： 1.中国沿海蓝子鱼科鱼类的多样性问题。国内曾有13种蓝子鱼的分布记录，其中蠕纹蓝子鱼Siganus vermiculatus和暗体蓝子鱼S. punctatissimus仅以前的学者做过名录形式的记载，并无标本收藏，本文中不做介绍。此外尖嘴蓝子鱼Siganus unimaculatus也可能存在于中国海域，有待于进一步研究。目前确定在中国海域有分布的蓝子鱼为11种，约占世界总种数（27）的40％多，种的多样性较高。 2. 形态学比较研究说明，蓝子鱼在体形、体色、牙齿、头骨、椎骨、耳石等特征方面存在种间差异，可作为蓝子鱼科鱼类分类的有效鉴别特征。对于外部形态极其相似的种，可借助内部解剖特征相辅助予以区分。 3．对蓝子鱼动物地理学特点研究分析结论如下：a.中国海域存在的11种蓝子鱼在印度－太平洋海域均有分布，没有地方特有种。b.长鳍蓝子鱼和褐蓝子鱼在我国东海、台湾海域和南海均有分布，褐蓝子鱼在黄海北部亦有分布，种群数量较大；其它9种，除凹吻蓝子鱼仅分布于南海外，均分布于南海及台湾海域，种群数量较小。c.中国海域蓝子鱼种类组成与邻近的菲律宾、马来西亚、印度尼西亚海域比较相似，中国分布的种类在这些海域均有分布，且分布于这一区域而中国没有记录的有5种。与日本相比，种类组成也比较相似，中日共有种达9种，仅分布于中国海域2种，仅分布于日本海域1种。 4. 作者参照国际最新研究结果和较为公认的分类系统Nelson（1994），将蓝子鱼科置于刺尾鱼亚目，而不再使用国内学者长期惯用的蓝子鱼亚目。蓝子鱼科包括一属蓝子鱼属Siganus Forsskål, 1775，两亚属：蓝子鱼亚属Siganus Forsskål, 1775 和罗蓝子鱼亚属 Lo Seale, 1906，同时使全部种名的变动和确定与国际最新研究结果(Woodland, 1990; 2001）取得一致。

中国海豆蟹科Family Pinnotheridae分类学研究

本文根据中国科学院海洋研究所收藏的豆蟹科标本和国内外相关文献，进行了中国海域豆蟹科的分类学研究。作者克服了豆蟹科分类难度大，研究积累较少，种的界限不清等困难，在短期内初步查清了中国海域豆蟹科种类及分布情况，共记述5亚科12属 40种。发现4新记录属，9新记录种，和豆蟹属1未定种Pinnotheres sp.，丰富了中国海豆蟹科区系内容，列出了共栖种中国海域全部记录过的宿主。 作者对鉴定过程中出现的疑难问题：“中型三强蟹Tritodynamia intermedia Shen, 1935是否为霍氏三强蟹 Tritodynamia horvathi Nobili, 1905的同物异名” 进行了细致比较、研究，否定了通行多年的Sakai（1976）的“T. intermedia Shen为T. horvathi Nobili的次异名”的结论，肯定了二者均为有效种。 对中国海域豆蟹科种类地理分布初步研究表明其分布与日本海域和东南亚海域都有相似之处，但有显著不同：仅发现于中国海域而未见于日本海域的豆蟹属Pinnotheres多达8种：涨腹豆蟹Pinnotheres excussus Dai et al., 1980，球豆蟹Pinnotheres pilulus Dai et al., 1980，锯颚豆蟹Pinnotheres serrignathus Shen, 1932，宽豆蟹Pinnotheres dilatatus Shen, 1932，青岛豆蟹Pinnotheres tsingtaoensis Shen, 1932，海阳豆蟹Pinnotheres haiyangensis Shen, 1932，钝颚豆蟹Pinnotheres obtusidentata（Dai et al., 1980），光豆蟹Pinnotheres luminatus Dai et al., 1980）；仅发现于中国海域的三强蟹属Tritodynamia有4种：福建三强蟹Tritodynamia fujianensis Chen, 1979，长腿三强蟹Tritodynamia longipropodum Dai et al., 1980，宽身三强蟹 Tritodynamia dilatatum Yang et Sun,1996和海南三强蟹 Tritodynamia hainanensis Dai et al.g, 1980；而未发现于中国海域的日本特有种多达13种。结果表明这一类群由于共栖和地域分化程度较高乃至地区性特有种数显著较多。 论文通过对豆蟹科系统分类和初步的动物地理学研究，搞清了中国海豆蟹科的种和分布、多样性及其宿主等基本情况。为今后研究豆蟹科种类生物学、生态学特性提供了基础资料。

Two new species of Family Prasiolaceae (Prasiolales, Chlorophyta) from China Sea

Amomg the 30 known species of the algal family Prasiolaceae (Prasiolales, Chlorophyta), nine marine species have been found in marine environments but none in China seas. We reported here two new species Prasiola fangchengensis Luan et Ding sp. nov. and Prasiola volcanica Luan et Ding sp. nov. from subtropical coastal water of southern China.

First record of the family Spengeliidae (Hemichordata : Enteropneusta) from Chinese waters, with description of a new species

Six species belonging to two families of Hemichordata have previously been recorded in Chinese waters. This paper records the discovery and description of a new species of the genus Glandiceps found in Jiaozhou Bay, Qingdao, Shandong Province, named Glandiceps qingdaoensis. The new species has a long proboscis with dorsal and ventral grooves, a stomochord with a long vermiform process, a proboscis cavity with a dorsal median, right and left glomeruli, right and left glomeruli very large and encircling the stomochord, a proboscis skeleton in the cavity extends into the median posterior of the collar, a well-developed dorsal ventral muscular septum in the proboscis cavity dividing the cavity completely into two separate parts. The collar cord is without giant nerve roots. The trunk with four distinct regions that can be recognized externally: branchial-genital region, genital region, hepatic region, and intestinal region. The dorsal pharynx is large and the gill pores are small. The tongue bars are encircled by vesicles, and the first gonad commences at the level of the second or third gill slit.

The Apertospathulidae, a new family of haptorid ciliates (Protozoa, Ciliophora)

We studied the morphology of three rare haptorid ciliates, using live observation and silver impregnation: Apertospathula verruculifera n. sp., Longispatha elegans n. gen., n. sp., and Rhinothrix porculus (Penard, 1922) n. gen., n. comb. Simple ethanol fixation (50-70%, v/v) is recommended to reveal the ciliary pattern of "difficult" ciliates, such as R. porculus, by protargol impregnation. The three genera investigated have a distinct feature in common, viz., a lasso-shaped oral bulge and circumoral kinety, where the right half is slightly to distinctly longer than the left and the circumoral kinety is open ventrally. Thus, they are united in a new spathidiid family, the Apertospathulidae n. fam., which probably evolved from a Bryophyllum-like ancestor by partial reduction of the oral bulge and circumoral kinety. Apertospathula verruculifera has a wart-like process, the palpus dorsalis, at the anterior end of the dorsal brush. The right branch of the circumoral kinety is only slightly longer than the left one. Longispatha elegans has a straight oral bulge and circumoral kinety, the right branch of which extends to the posterior end of the body while the left branch ends in the anterior third of the body. Rhinothrix porculus, a curious ciliate with a snout-like dorsal elongation of the oral bulge, the palpus oralis, has a highly characteristic ciliary pattern: the oral pattern is as in Longispatha, but the bulge and circumoral kinety extend spirally to the posterior end of the body while the somatic kinetics course meridionally. This is achieved by inserting some shortened kinetics in the curves of the oral bulge.

Taxonomic study on the family Mitridae (Mollusca : Gastropoda : Neogastropoda) from the China's Seas. Subfamilies: Imbricariinae and Cylindromitrinae

Ninteen species of subfamilies Imbricariinae and Cylindromitrinae, family Mitridae, are recorded from the China's seas. Of which, one genus and six species are recorded for the first time from China's seas, i.e., genus Ziba Adams H and Adams A, Cancilla (Cancilla) carnicolor, Ziba duplilirata, Z. insculpta, Neocancilla circula, Scabricola (Scabricola) desetangsii, Scabricola (Swainsonia) ocellata ocellata.

The floristic of the family Gramineae of Karakorum and Kunlun area, China

There are 47 genera and 161 species of Gramineae except the cultivated species in the area of the Karakorum and Kunlun Mountains. The results of research on the distribution of the genera and species of Gramineae in the Karakorum and Kunlun Mountains show that (1) The Gramineae mainly contains elements of North Temperate, rich Old Word Temperate and other Temperate. It is obvious that the floristic nature of Gramineae in the Karakorum and Kunlun Mountains is the North Temperate; (2) All Pantropic genera can stretch to the Temperate Zone in this region, which all parts of the Pantropic type are the Temperate nature to a certain degree. For example, Erianthus ravennae from mediterranean to the Karakorum and Kunlun Mountains through the Central Asia; (3) As most genera of Grasses are the type of Temperate and the Frigid Zone, they have distinct floristic characteristics of mountainous and plateau flora such as Orinus, Alopecurus, Elymus, Trisetum, Littledalea, Elytrigia, Stephanachne and Paracolpodium etc. All of these indicate adaptive phenomenon of alpine specialization and cold-xerophilization on Grasses in this area; (4) Endemic genus of Gramineae is absent due to its nature and history and the endemic species are also rare in the Karakorum and Kunlun Mountains. Most of the genera with one or fewer species have originated from its relative and widespread genera, such as Ptilagrostis from Stipa, Timouria from Achnatherum, and so on; (5) Flora of the Karakorum and Kunlun Mountains is most closely related to the flora of Tibet, and is also extensively to its adjacent areas.