Pelagibacterium nitratireducens sp.nov., A Marine Alphaproteobacterium Isolated from the East China Sea

A Gram-negative, rod-shaped, non-spore-forming aerobic bacterium, motile with a single polar flagellum, strain JLT2005^T, was isolated from surface seawater collected from the East China Sea and formed ivory white colonies on a rich organic medium. The strain was positive for catalase, oxidase, and urease. It grew in the presence of 0–12 % (w/v) NaCl (optimum 5 %), at 20–35 °C (optimum 25 °C), or at pH 6–10 (optimum pH 9). The major fatty acids (>10 %) were C_18:1ω7c, C_19:0ω8c cyclo, C_16:0, and C_18:0. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, and five unidentified glycolipids. Ubiquinone-10 and Ubiquinone-11 were present as the major quinones. The DNA G+C content was 74.3 mol%. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain JLT2005^T belongs to the genus Pelagibacterium in the family Hyphomicrobiaceae, class Alphaproteobacteria. The closest neighbors were Pelagibacterium halotolerans B2^T (98.7 % similarity) and Pelagibacterium luteolum 1_C16_27^T (97.1 % similarity). DNA–DNA relatedness values of strain JLT2005^T with P. halotolerans B2^T and with P. luteolum 1_C16_27^T were 31.6 and 25 %. Evidence from genotypic, chemotaxonomic, and phenotypic data shows that strain JLT2005^T represents a novel species of the genus Pelagibacterium, for which the name Pelagibacterium nitratireducens sp. nov is proposed. The type strain is JLT2005^T (=CGMCC 1.10829^T =JCM 17767^T).     

Seasonal Dynamics of Marine Microbial Community in the South Sea of Korea

High-resolution 16S rRNA tag pyrosequencing was used to obtain seasonal snapshots of the bacterial diversity and community structure at two locations in Gosung Bay (South Sea, Korea) over a one year period. Seasonal sampling from the water column at each site revealed highly diverse bacterial communities containing up to 900 estimated Operational Taxonomic Units (OTUs). The Alphaproteobacteria and Gammaproteobacteria were the most abundant groups, and the most frequently recorded OTUs were members of Pelagibacter and Glaciecola. In particular, it was observed that Arcobacter, a genus of the Epsilonproteobacteria, dominated during summer. In addition, Psedoalteromonadaceae, Vibrionaceae and SAR11-1 were predominant members of the OTUs found in all sampling seasons. Environmental factors significantly influenced the bacterial community structure among season, with the phosphate and nitrate concentrations contributing strongly to the spatial distribution of the Alphaproteobacteria; the Gammaproteobacteria, Flavobacteria, and Actinobacteria all showed marked negative correlations with all measured nutrients, particularly silicon dioxide and chlorophyll-a. The results suggest that seasonal changes in environmental variables contribute to the dynamic structure of the bacterial community in the study area.     

Phylogenetic diversity of Synechococcus strains isolated from the East China Sea and the East Sea

Phylogenetic relationships among 33 Synechococcus strains isolated from the East China Sea (ECS) and the East Sea (ES) were studied based on 16S rRNA gene sequences and 16S–23S rRNA gene internal transcribed spacer (ITS) sequences. Pigment patterns of the culture strains were also examined. Based on 16S rRNA gene and ITS sequence phylogenies, the Synechococcus isolates were clustered into 10 clades, among which eight were previously identified and two were novel. Half of the culture strains belonged to clade V or VI. All strains that clustered into novel clades exhibited both phycoerythrobilin and phycourobilin. Interestingly, the pigment compositions of isolates belonging to clades V and VI differed from those reported for other oceanic regions. None of the isolates in clade V showed phycourobilin, whereas strains in clade VI exhibited both phycourobilin and phycoerythrobilin, which is in contrast to previous studies. The presence of novel lineages and the different pigment patterns in the ECS and the ES suggests the possibility that some Synechococcus lineages are distributed only in geographically restricted areas and have evolved in these regions. Therefore, further elucidation of the physiological, ecological, and genetic characteristics of the diverse Synechococcus strains is required to understand their spatial and geographical distribution.     

Planktonic primary production in the German Wadden Sea

By combining weekly data of irradiance, attenuation and chlorophylla concentrations with photosynthesis (P) versus light intensity(E) curve characteristics, the annual cycle of planktonic primaryproduction in the estuarine part of the Northfrisian WaddenSea was computed for a 2 year period. Daily water column particulategross production ranged from 5 to 2200 mg C m^–2 day^–1and showed a seasonal pattern similar to chlorophyll a. Budgetcalculation yielded annual gross particulate primary productionsof 124 and 176 g C m^–2 year^–1 in 1995 and 1996,respectively. Annual amounts of phytoplankton respiration, calculatedaccording to a two-compartment model of Langdon [in Li,W.K.W.and Maestrini,S.Y. (eds), Measurement of Primary Productionfrom the Molecular to the Global Scale. International Councilfor the Exploration of the Sea, Copenhagen, 1993, pp. 20–36],and dissolved production in 1996, were both in the range of24–39 g C m^–2 year^–1. Annual total net productionwas thus very similar to particulate gross production (127 and177 g C m^–2 year^–1 in 1995 and 1996, respectively).Phytoplankton growth was low or even negative in winter. Inspring and summer, production/biomass (Pr/B) ratios varied from0.2 up to 1.7. Phytoplankton growth during the growth seasonalways surpassed average flushing time in the area, thus underliningthe potential of local phytoplankton bloom development in thispart of the Wadden Sea. The chlorophyll-specific maximum photosyntheticrate (P^B_max) ranged from 0.8 to 9.9 mg C mg^–1 Chl h^–1and was strongly correlated with water temperature (r² = 0.67).By contrast, there was no clear seasonal cycle in ^B, which rangedfrom 0.007 to 0.039 mg C mg^–1 Chl h^–1 (µmolphotons m^–2 s^–1)^–1. Its variability was muchless than P^B_max and independent of temperature. The magnitudeand part of the variability of P^B_max and ^B are presumably causedby changes in species composition, as evidenced from the rangeof these parameters found among 10 predominant diatom speciesisolated from the Wadden Sea. The ratio of average light conditionsin the water column (E_av) to the light saturation parameterE_k indicates that primary production in the Wadden Sea regionunder study is predominantly controlled by light limitationand that nutrient limitation was likely to occur for a few hoursper day only during 5 (dissolved inorganic nitrogen) to 10 (PO₄,Si) weeks in the 2 year period investigated.     

Ether Lipids of Planktonic Archaea in the Marine Water Column

Acyclic and cyclic biphytanes derived from the membrane ether lipids of archaea were found in water column particulate and sedimentary organic matter from several oxic and anoxic marine environments. Compound-specific isotope analyses of the carbon skeletons suggest that planktonic archaea utilize an isotopically heavy carbon source such as algal carbohydrates and proteins or dissolved bicarbonate. Due to their high preservation potential, these lipids provide a fossil record of planktonic archaea and suggest that they have thrived in marine environments for more than 50 million years.     

Simulation of drifting seaweeds in East China Sea

Drifting seaweeds plays a major role in areas where they are present. We describe a computer model, JeoSim that clarifies the roles of those seaweeds in relation to their transport using particle-tracking algorithm. The Euler rule with trapezoidal approximation, used to calculate drifting paths, is implemented in JeoSim in discrete events fashion in order to simulate the path and movement of seaweeds. Pre-processing of the ocean currents is done with the Princeton Ocean circulation Model (POM). Simulated current constitutes the data that provides force and directions for the calculations of drifting paths. Along with the implementation of the particle-tracking algorithm in discrete event fashion, the originality of the JeoSim software lies in its Object Oriented architecture which makes it especially suited to perform simulation of living, cross scale systems with complex behavior. Behavior of drifting seaweeds of the Sargasso family has been implemented in JeoSim, and experimented in East China Sea following a drifting seaweed collection campaign in May 2002. Despite a relatively low resolution ocean currents data, simulated results compare well with the observed distribution.     

东海竹筴鱼的食性

以2008年5月、8月、11月和2009年2月东海灯光围网采集到的453条东海竹筴鱼为研究对象,对其胃含物进行分析,应用K-W非参数检验、卡方检验、聚类分析等方法,对不同季节和发育阶段条件下东海竹筴鱼的食性进行研究.结果表明:东海竹筴鱼的饵料生物有124种(包括未鉴定种),浮游甲壳类和小型鱼类为其主要饵料类群.优势饵料生物依次是麦氏犀鳕(IRI％=39.2％)、长尾类糠虾幼体(IRI％=18.4％)、短尾类大眼幼体(IRI％ =7.6％)和太平洋磷虾(IRI％=6.6％)等.季节和叉长对东海竹筴鱼的摄食强度均有显著影响(P＜0.01),东海竹筴鱼春季摄食强度最高,而冬季最低;叉长140 ～ 159 mm的竹筴鱼摄食强度最高,叉长45～99 mm的幼鱼的摄食强度较高,其余叉长的鱼摄食强度相对较低.聚类分析结果表明,叉长100 mm是东海竹筴鱼摄食取向的拐点.东海竹筴鱼四季的平均营养级为3.51,属于低级肉食性鱼类.     

东海浮游枝角类生态学研究

根据1997~2000年在东海23°30′~33°00′N、118°30′~128°00′E海域4个季节的海洋调查资料,探讨了东海浮游枝角类生态特征、数量变化和相应的动力学。结果表明,枝角类丰度夏季最高(17.16 ind.(100 m3)-1),秋季(14.68 ind.(100 m3)-1)次之,春季(0.63 ind.(100 m3)-1)较低,冬季该类未出现。春、夏、秋季的肥胖三角氵蚤(Evadne tergestina)和夏季的鸟喙尖头氵蚤(Penilia avirostris)是影响枝角类数量分布的主要种;春、夏、秋季枝角类总丰度与盐度呈负线性相关关系,与水温相关关系不显著。枝角类较高丰度区常位于沿岸淡水水团与其他水团交汇处偏沿岸水一侧。其数量变化动力主要来自沿岸冲淡水势力,特别是长江冲淡水势力的消长。枝角类在东海出现率较低,有一定的集群性,较高丰度的分布基本上局限在冲淡水势力影响范围内,其高丰度的水域是沿岸水团的一个重要标志。     

东海和黄海主要鱼类的食物竞争

以2000年和2001年在东、黄海两次大面调查所收集的、占总生物量90%的重要生物种类中的鱼类为研究对象,通过分析胃含物获得各饵料成分的重量百分比,用Pianka(1973)提出的公式计算的饵料重叠系数分析了东、黄海主要鱼类之间的食物竞争状况,以了解食物竞争与种群变动和优势种交替之间的相互关系。结果表明:黄海主要鱼类的食物竞争对象主要为太平洋磷虾、脊腹褐虾和,东海主要鱼类的食物竞争对象主要为太平洋磷虾、细条天竺鱼、发光鲷、、七星底灯鱼和带鱼。东、黄海鱼类通过摄食种类、摄食食物大小、摄食时间和栖息地的分化来减少食物竞争,从而维持群落结构的动态平衡。渔业资源群落结构的变化将导致食物竞争状况发生改变;鱼类食物竞争状况也会影响种群动态,但要确定食物竞争程度还需进一步深入研究     

Causal analysis of the diversity of medusae in East China Sea

Based on the maritime data collected from 23°30′–33°00′ N and 118°30′–128°00′ E of the East China Sea (ECS) in four seasons during 1997–2000, the dynamics of medusae diversity and their causes were analyzed. A total of 103 medusae species were identified, and these species mainly distributed in the southern and northern offshore areas of the ECS. Species diversity index (H′) of medusae was higher in the south than those in the north, higher in summer and winter than in spring and autumn, and higher in offshore than in the nearshore areas. The species number was closely correlated with H′ value, whereas the abundance of species had no significant relationship with the diversity index. The lower H′ value of the nearshore in spring and autumn resulted from the aggregation of Muggiaea atlantica in the south nearshore and Diphyes chamissonis in the north nearshore. In addition, water temperature, followed by salinity, is the main environmental factor influencing the distribution of species diversity. The H′ value was related to the water temperature at the 10 m layer in winter and spring, and it was associated with the surface water temperature in summer and with the 10 m-salinity-layer in autumn. In spring and summer, the isoline distribution of H′ value reflected the direction of the Taiwan Warm Current and the variation of the water masses in the ECS. In winter, the isoline of the H′ value indicated the incursion of Kuroshio current. In conclusion, the H′ isoline is an good indicator for water masses in ECS. __________ Translated from Biodiversity Science, 2006, 14(6): 508–516 [译自:生物多样性]     

Community Structure and Function of Planktonic Crenarchaeota: Changes with Depth in the South China Sea

Marine Crenarchaeota represent a widespread and abundant microbial group in marine ecosystems. Here, we investigated the abundance, diversity, and distribution of planktonic Crenarchaeota in the epi-, meso-, and bathypelagic zones at three stations in the South China Sea (SCS) by analysis of crenarchaeal 16S rRNA gene, ammonia monooxygenase gene amoA involved in ammonia oxidation, and biotin carboxylase gene accA putatively involved in archaeal CO₂ fixation. Quantitative PCR analyses indicated that crenarchaeal amoA and accA gene abundances varied similarly with archaeal and crenarchaeal 16S rRNA gene abundances at all stations, except that crenarchaeal accA genes were almost absent in the epipelagic zone. Ratios of the crenarchaeal amoA gene to 16S rRNA gene abundances decreased ~2.6 times from the epi- to bathypelagic zones, whereas the ratios of crenarchaeal accA gene to marine group I crenarchaeal 16S rRNA gene or to crenarchaeal amoA gene abundances increased with depth, suggesting that the metabolism of Crenarchaeota may change from the epi- to meso- or bathypelagic zones. Denaturing gradient gel electrophoresis profiling of the 16S rRNA genes revealed depth partitioning in archaeal community structures. Clone libraries of crenarchaeal amoA and accA genes showed two clusters: the “shallow” cluster was exclusively derived from epipelagic water and the “deep” cluster was from meso- and/or bathypelagic waters, suggesting that niche partitioning may take place between the shallow and deep marine Crenarchaeota. Overall, our results show strong depth partitioning of crenarchaeal populations in the SCS and suggest a shift in their community structure and ecological function with increasing depth.     

Abundance of drifting seaweeds in eastern East China Sea

Drifting seaweeds play important ecological roles in offshore waters. Recently, large amounts of drifting seaweed rafts were found in the eastern East China Sea between the continental shelf and the oceanic front of the Kuroshio Current. However, so far there have been no quantitative reports about this particular area. Two research cruises were organized to survey abundance and standing crop of drifting seaweeds in eastern East China Sea in May 2002 and March 2004, using visual census and net sampling of drifting seaweeds. Visual census data were composed of drifting seaweed raft diameter, perpendicular distance from the transect (navigation course of the research vessel) to the raft, and positions. Using these data, we calculated the “effective stripe width” using the DISTANCE software. Drifting seaweed abundance (composed exclusively of Sargassum horneri) in waters located between the continental shelf peripheral area and the Kuroshio oceanic front was estimated to be higher than in any other area within eastern East China Sea in March and May. Abundance means in May 2002 and March 2004 were 6.14 and 29.05 rafts km⁻², respectively, while standing crop reached 126.81 and 20.35 kg km⁻² (wet weight). Mean diameter and drifting seaweed rafts in May 2002 were significantly greater than in March 2004, reflecting seasonal growth of Sargassum horneri.     

Causal analysis of the diversity of medusae in East China Sea

Based on the maritime data collected from 23°30'-33°00' N and 118°30'-128°00' E of the East China Sea (ECS) in four seasons during 1997-2000,the dynamics of medusae diversity and their causes were ana-lyzed.A total of 103 medusae species were identified,and these species mainly distributed in the southern and north-ern offshore areas of the ECS.Species diversity index (H') of medusae was higher in the south than those in the north,higher in summer and winter than in spring and autumn,and higher in offshore than in the nearshore areas.The species number was closely correlated with H' value,whereas the abundance of species had no significant rela-tionship with the diversity index.The lower H' value of the nearshore in spring and autumn resulted from the aggrega-tion of Muggiaea atlantica in the south nearshore and Diphyes chamissonis in the north nearshore.In addition,water temperature,followed by salinity,is the main envir-onmental factor influencing the distribution of species diversity.The H' value was related to the water temperature at the 10 m layer in winter and spring,and it was associated with the surface water temperature in summer and with the 10 m-salinity-layer in autumn.In spring and summer,the isoline distribution of H' value reflected the direction of the Taiwan Warm Current and the variation of the water masses in the ECS.In winter,the isoline of the H' value indicated the incursion of Kuroshio current.In conclusion,the H' isoline is an good indicator for water masses in ECS.     

High Nitrate Concentrations in Vacuolate, Autotrophic Marine Beggiatoa spp

Massive accumulations of very large Beggiatoa spp. are found at a Monterey Canyon cold seep and at Guaymas Basin hydrothermal vents. Both environments are characterized by high sediment concentrations of soluble sulfide and low levels of dissolved oxygen in surrounding waters. These filamentous, sulfur-oxidizing bacteria accumulate nitrate intracellularly at concentrations of 130 to 160 mM, 3,000- to 4,000-fold higher than ambient levels. Average filament widths range from 24 to 122 (mu)m, and individual cells of all widths possess a central vacuole. These findings plus recent parallel discoveries for Thioploca spp. (H. Fossing, V. A. Gallardo, B. B. Jorgensen, M. Huttel, L. P. Nielsen, H. Schulz, D. E. Canfield, S. Forster, R. N. Glud, J. K. Gundersen, J. Kuver, N. B. Ramsing, A. Teske, B. Thamdrup, and O. Ulloa, Nature (London) 374:713-715, 1995) suggest that nitrate accumulation may be a universal property of vacuolate, filamentous sulfur bacteria. Ribulose bisphosphate carboxylase-oxygenase and 2-oxoglutarate dehydrogenase activities in the Beggiatoa sp. from Monterey Canyon suggest in situ autotrophic growth of these bacteria. Nitrate reductase activity is much higher in the Monterey Beggiatoa sp. than in narrow, laboratory-grown strains of Beggiatoa spp., and the activity is found primarily in the membrane fraction, suggesting that the vacuolate Beggiatoa sp. can reduce nitrate coupled to electron flow through an electron transport system. Nitrate-concentrating and respiration potentials of these chemolithoautotrophs suggest that the Beggiatoa spp. described here are an important link between the sulfur, nitrogen, and carbon cycles at the Monterey Canyon seeps and the Guaymas Basin hydrothermal vents where they are found.     

Genomic and Metabolic Diversity of Marine Group I Thaumarchaeota in the Mesopelagic of Two Subtropical Gyres

Marine Group I (MGI) Thaumarchaeota are one of the most abundant and cosmopolitan chemoautotrophs within the global dark ocean. To date, no representatives of this archaeal group retrieved from the dark ocean have been successfully cultured. We used single cell genomics to investigate the genomic and metabolic diversity of thaumarchaea within the mesopelagic of the subtropical North Pacific and South Atlantic Ocean. Phylogenetic and metagenomic recruitment analysis revealed that MGI single amplified genomes (SAGs) are genetically and biogeographically distinct from existing thaumarchaea cultures obtained from surface waters. Confirming prior studies, we found genes encoding proteins for aerobic ammonia oxidation and the hydrolysis of urea, which may be used for energy production, as well as genes involved in 3-hydroxypropionate/4-hydroxybutyrate and oxidative tricarboxylic acid pathways. A large proportion of protein sequences identified in MGI SAGs were absent in the marine cultures Cenarchaeum symbiosum and Nitrosopumilus maritimus, thus expanding the predicted protein space for this archaeal group. Identifiable genes located on genomic islands with low metagenome recruitment capacity were enriched in cellular defense functions, likely in response to viral infections or grazing. We show that MGI Thaumarchaeota in the dark ocean may have more flexibility in potential energy sources and adaptations to biotic interactions than the existing, surface-ocean cultures.     

Planktonic ciliates of the Baltic Sea (a review)

The data on the ciliates species composition are given for the Baltic Sea, a brackish-water semi-closed water body where a considerable part of the planktonic fauna is presented by freshwater species. During the observation period, 789 species of ciliates were found, 160 of which are typical planktonic forms. The ecological characteristics of ciliates are given, along with an assessment of their role in the productivity of the Baltic Sea pelagic communities.     

东黄海秋季浮游动物优势种聚集强度与鲐鲹渔场的关系

一、前言日本鲐鱼(Pneumatophorus japonicus)和蓝圆鲹(Decaterus maruadsi)是东黄海主要中上层鱼类资源。秋季鲐鲹鱼在黄海南部和东海北部(北纬32°00′—33°30′,东经124°00′—128°30′)以及东海中南部(北纬26°30′—29°00′,东经123°00′—126°00′)形成两个索饵渔场,前者简称为北部渔场,后者简称为南部渔场。为了开发和利用东黄海鲐鲹鱼索饵渔场资源,需要对两渔场鲐鲹鱼资源分布的特点进行研究。根据以往国内外的一些报道,鲐鲹鱼是一类以浮游动物为主食的鱼类,其分布特点往往同浮游动物的分布有密切关系。因此,本     

Amino Acid Cycling in Colonies of the Planktonic Marine Cyanobacterium Trichodesmium thiebautii

We examined diel trends in internal pools and net efflux of free amino acids in colonies of the nonheterocystous, diazotrophic cyanobacterium Trichodesmium thiebautii, freshly collected from waters of the Caribbean and the Bahamas. The kinetics of glutamate uptake by whole colonies were also examined. While intracolonial pools of most free amino acids were relatively constant through the day, pools of glutamate and glutamine varied over the diel cycle, with maxima during the early afternoon. This paralleled the daily cycle of nitrogenase activity. We also observed a large net release of these two amino acids from intact colonies. Glutamate release was typically 100 pmol of N colony^-1 h^-1. This is about one-fourth the concurrent rate of N₂ fixation during the day. However, while nitrogenase activity only occurs during the day, net release of glutamate and glutamine persisted into the night and may therefore account for a greater loss of recently fixed N on a daily basis. This release may be an important route of new N input into tropical, oligotrophic waters. Whole colonies also displayed saturation kinetics with respect to glutamate uptake. The K_s for whole colonies varied from 1.6 to 3.2 μM, or about 100-fold greater than typical ambient concentrations. Thus, uptake systems appear to be adapted to the higher concentrations of glutamate found within the intracellular spaces of the colonies. This suggests that glutamate may be a vehicle for N exchange among trichomes in the colony.