Phylogenetic analysis of bacterial community in deep-sea sediment from the western Pacific “warm pool”

A depth profile of bacterial community structure in one deep-sea sediment core of the western Pacific ＂warm pool＂ （WP） was investigated and compared with that in a sediment sample from the eastern Pacific （EP） by phylogenetic analysis of 16S rDNA fragments. Five bacterial 16S rDNA clone libraries were constructed, and 133 clones with different restriction fragment length polymorphism （RFLP） patterns were sequenced. A phylogenetic analysis of these sequences revealed that the bacterial diversity in a sample from the WP was more abundant than that in the EP sample. The bacterial population in the sediment core of WP was composed of eight major lineages of the domain bacteria. Among them the γ-Proteobacteria was the predominant and most diverse group in each section of WP sediment core, followed by the α-Proteobacteria. The genus Colwellia belonging to γ-Proteobacteria was predominant in this sample. The shift of bacterial communities among different sections of the WP sediment core was δ-, ε-Proteobacteria, and Cytopahga-Flexibacteria-Bacteroides （CFB） group. The ratios between them in the bacterial communities all showed inversely proportional to the depth of sediment. The sequences related to sulphate reducing bacteria （SRB） were detected in every section. The bacterial community structure in this sediment core might be related to the environmental characteristics of the surface seawater of the western Pacific WP.     

Molecular genetic diversity of bacteria in the bottom section of arctic sea ice from the Canada Basin

PCR-DGGE approach was used to analyze bacterial diversity in the bottom section of seven arctic sea ice samples colleted from the Canada Basin. Thirty-two 16S rDNA sequences were obtained from prominent DGGE bands. The closest relatives of these sequences are found to be those of cultivated or uncultured bacteria from antarctic or arctic sea ice. Phylogenetic analysis clustered these sequences or phylotypes within α- proteobacteria, γ-proteobacteria and CFB (cytophaga-flexibacter-bacteroides) group. Sequences belonging to γ-proteobacteria were dominant and members of the CFB group were highly abundant. It was suggested that the CFB group was the representative of the bottom section of sea ice samples.     

Isolation and diversity analysis of heterotrophic bacteria associated with sea anemones

A study was undertaken to investigate the heterotrophic bacterial flora associated with the sea anemones. Samples of the sea anemones Anthopleura midori were collected from the coast of Weihai and bacteria were isolated from these samples. Additionally, high numbers of viable bacteria were obtained from the celom wall and surface of anemone, the community of cultivable bacteria was very diverse. As a result of this isolation, 60 strains were obtained, 56 of them were selected for identification and characterization by 16S rRNA gene sequence analysis and limited phenotypic testing. Among these isolates, 16 strains were phylogenetically related to members of the genus Pseudoalteromonas and neighboring taxa. Other isolates included members of the genera Colwellia, Vibrio, Acinetobacter, Pseudomonas, Endozoicomonas, Roseovarius, Paracoccus, Loktanella, Leisingera, Sulfitobacter, Bacillus, Staphylococcus, Plantibacter, Microbacterium, Micrococcus, Joostella, Psychroserpens, Cellulophaga, Krokinobacter, Polaribacter and Psychrobacter. Seven potential novel species were found. Among 60 strains, 17 of them can produce proteolytic exoenzyme, 20 can produce lipolytic exoenzyme. Strain NQ8 has strong antagonistic effects on some Vibrio strains. This study demonstrates that the culturable fraction of bacteria from the sea anemones Anthopleura midori is diverse and appears to possess much potential as a source for the discovery of novel bioactive materials.     

Phylogenetic diversity and phenotypic characterization of cultivable bacterioplankton isolated from polar oceans

A set of 27 marine planktonic bacteria isolated from the polar regions was characterized by 16S rDNA sequencing and physiological and biochemical testing. More than half of these bacteria were positive for caseinase, gelatinase and 13-glucosidase, and could utilize glucose, maltose or malic acid as carbon source for cell growth. Twelve isolates expressed nitrate reduction activities. Except for one antarctic isolate BSwlO175 belonging to Actinobacteria phylum, these isolates were classified as γ-Proteobacteria, suggesting that γ-Proteobacteria dominated in cultivable marine bacterioplankton at both poles. Genus Pseudoalteromonas was the predominant group in the Chukchi Sea and the Bering Sea, and genus ShewaneUa dominated in cultivable bacterioplankton in the Prydz Bay. With sequence similarities above 97%, genus Psychrobacter was found at both poles. These 27 isolates were psychrotolerant, and significant 16S rDNA sequence similarities were found not only between arctic and antarctic marine bacteria （ 〉 99% ）, but also between polar marine bacteria and bacteria from other aquatic environments （ ≥ 98.8% ）, including temperate ocean, deep sea, pond and lake, suggesting that in the polar oceans less temperature-sensitive bacteria may be cosmopolitan and have a bipolar, even global, distribution at the species level.     

Phylogenetic diversity of planktonic bacteria in the Chukchi Borderland region in summer

Planktonic bacteria are abundant in the Chukchi Borderland region. However, little is known about their diversity and the roles of various bacteria in the ocean. Seawater samples were collected from two stations K2S and K4S where sea ice was melting obviously. The analysis of water samples with fluorescence in situ hybridization (FISH) showed that DMSP-degrading bacteria accounted for 13% of the total bacteria at the station K2S. No aerobic anoxygenic phototrophic (AAP) bacteria were detected in both samples. The bacterial communities were characterized by two 16S rRNA gene clone libraries. Sequences fell into four major lineages of the domain Bacteria, including Proteobacteria (Alpha, Beta and Gamma subclasses), Bacteroidetes, Actinobacteria and Firmicutes. No significant difference was found between the two clone libraries. SAR11 and Rhodobacteraceae clades of Alphaproteobacteria and Pseudoalteromonas of Gammapro-teobacteria constituted three dominant fractions in the clone libraries. A total of 191 heterotrophic bacterial strains were isolated and 76% showed extracellular proteolytic activity. Phylogenetic analysis reveals that the isolates fell into Gammaproteobacteria, Bacteroidetes, Actinobacteria and Firmicutes. The most common genus in both the bacterial isolates and protease-producing bacteria was Pseudoalteromonas. UniFrac data showed suggestive differences in bacterial communities between the Chukchi Borderland and the northern Bering Sea.     

北极海洋沉积物细菌和古菌群落结构分析

This study was to investigate bacterial and archaeal community structure of pan-Arctic Ocean sediments by pyrosequencing.In total,investigation of three marine sediments revealed 15 002 bacterial and 4 362 archaeal operational taxonomic units(OTUs) at the 97% similarity level.Analysis of community structure indicated that these three samples had high bacterial and archaeal diversity.The most relatively abundant bacterial group in Samples CC1 and R05 was Proteobacteria,while Firmicutes was dominant in Sample BL03.Thaumarchaeota was the most relatively abundant archaeal phylum in Samples CC1 and R05,and the relative abundance of Thaumarchaeota was almost as high as that of Euryarchaeota in Sample BL03.These two phyla accounted for nearly 100% of the archaeal OTUs.δ-Proteobacteria and γ-Proteobacteria were the two most relatively abundant classes at Proteobacterial class level,and their relative abundance was more than 60% in Samples CC1 and R05.There were also differences in the top 10 relatively abundant bacterial and archaeal OTUs among the three samples at the 97% similarity,and only 12 core bacterial OTUs were detected.Overall,this study indicated that there were distinct microbial communities and many unique OTUs in these three samples.     

南大西洋沉积物中多环芳香化合物的组成特征研究

10 samples of sediments obtained from the South Mid-Atlantic Ridge were measured for the abundances and distributions of polycyclic aromatic compounds(PAHs). The total concentrations of PAHs(∑PAHs) ranged from 2.768 to 9.826 μg/g dry sediment. The ∑PAHs was higher in sample 22V-TVG10 and sample 26V-TVG05 which were close to hydrothermal fields, with the lowest value in sample 22V-TVG14 which was farthest from hydrothermal fields, suggesting a probable hydrothermal origin of ∑PAHs of samples. Approximately nine kinds of PAHs were identified, and low molecular mass tricyclic and tetracyclic aromatic compounds were predominant in the samples. The concentrations of fluoranthene which were typical as hydrothermal alteration compounds were the highest among PAHs with dry weight between 0.913–3.157 μg/g. The phenanthrene homologue was most abundant in the samples, and the ratios between parent phenanthrene and methylphenanthrene which probably reflected the degree of hydrothermal alteration ranged from 0.097 to 1.602. The sample 22V-TVG10 possessing a maximum ratio value showed the intense influence of the hydrothermal alteration on this sample, which might further imply that PAHs in sediments were mainly derived from the hydrothermal alteration.     

Preliminary study on the distribution of nutrients, organic matter, trace metals in sea surface microlayer in Xiamen Bay and Jiulong Estuary

-The enrichment of nutrients (NOa-, NOa-, PO43-), suspended particles, organic matter (POC, PON,DOC) , and trace metals (Cu, Ni, Cd) was determined in the sea surface microlayer of Xiamen Bay and Jiulong Estuary. The mean enrichment factors ([Xi]microlayer/[Xi ]15cm in depth) mostly ranged between 1 . 0 and 2. 0. The dissolved forms were the major forms of the components measured, the enrichment of dissolved organic matter and suspended particles could lead to the changes in the total amount and speciation of nutrients and trace metals. No correlation was observed between sample concentrations, speciation, enrichment factors and sample locations. However, some evidence shows that these parameters are correlated with sea state, indicating the complexity and dynamic nature of the sea surface microlayer.     

Distribution of ammonia-oxidizing Betaproteobacteria community in surface sediment off the Changjiang River Estuary in summer

The spatial distribution of ammonia-oxidizing Betaproteobacteria ( β AOB) was investigated by FISH (fluorescence in situ hybridization) and DGGE (denaturing gradient gel electrophoresis) techniques in the sediment off the Changjiang River Estuary.Sediment samples were collected from eight stations in June before the formation of hypoxia zone in 2006.The abundance of β AOB ranged from 1.87 × 10 5 to 3.53 × 10 5 cells/g of sediment.β AOB abundance did not present a negative correlation with salinity,whereas salinity was implicated as the primary factor affecting nitrification rates.The DGGE profiles of PCR-amplified amo A gene fragments revealed that the β AOB community structure of sample S2 separated from other samples at the level of 40% similarity.The variations in composition of β AOB were significantly correlated with the salinity,temperature,absorption ability of sediments and TOC. The statistical analysis indicates that the β AOB abundance was a main factor to influence nitrification rates with an influence ratio of 87.7% at the level of 40% biodiversity similarity.Considering the good correlation between β AOB abundance and nitrification estimates,the abundance and diversity of β AOB community could be expected as an indirect index of nitrification activity at the study sea area in summer.     

The bacterial diversity in surface sediment from the South China Sea

16S rDNA sequencing results from this study and literatures demonstrate that sediment bacteria in the South China Sea (SCS) were very diverse,which contained 22 of the 24 phyla of bacteria investigated from marine sediment,however,it was very imbalance among stations.So bacterial diversity from 15 samples which covered a wide range of sediment types from 20 to 3 888 m in depth was studied in DGGE (denature gradient gel electrophoresis) in this paper.The DGGE results indicate that both sediment bacterial diversity and diversity difference among stations were significant.Thirty representative and differential fingerprints among samples were recovered and sequenced,phylogenetic analysis indicates that they may belong to Proteobacteria (α-,β-,γ-,δ-,ε-),Planctomycetes,Firmicutes,Chloroflexi,Acidobacteria,Actinobacteria,Nitrospirae,Gemmatimonadetes,candidate division WS3 and so on,of which,Gemmatimonadetes and candidate division WS3 bacteria were first detected in SCS sediment.This study also shows that bacterial diversity analysis based on DGGE was more potential than traditional 16S rDNA clone library in multiple sample analysis.     

热带西太平洋的小粟虫属的四种有孔虫(原生动物)的形态学研究以及Miliolinella obesa nov. spec. 新种描述

Foraminiferal oozes were sampled from the tropical West Pacific seamount and seabed of deep sea,by a remotely operated vehicle(ROV)in December 2014 and March 2016.Using standard morphological method,four Miliolinella species,including Miliolinella obesa,M.circularis,M.suborbicularis and M.subrotunda were described.Among the four species,M.obesa is a new species.It is a large member(about 500μm in length)of the genus.This species is characterized by having a very stout and transverse broadly circular outline,and its body width is greater than the body length.In addition,its chamber demarcations are obscure from the exterior appearance.Three chambers are unclearly visible on one side and two chambers are visible on the opposite.Finally,we provided very detailed taxonomic microphotographs and the ecological distribution information for each species.     

Integration of the nuclease protection assay with sandwich hybridization (NPA-SH) for sensitive detection of Heterocapsa triquetra

Microalgae are photosynthetic microorganisms that function as primary producers in aquatic ecosystems. Some species of microalgae undergo rapid growth and cause harmful blooms in marine ecosystems. Heterocapsa triquetra is one of the most common bloom-forming species in estuarine and coastal waters worldwide. Although this species does not produce toxins, unlike some other Heterocapsa species, the high density of its blooms can cause significant ecological damage. We developed a H. triquetra species-specific nuclease protection assay sandwich hybridization (NPA-SH) probe that targets the large subunit of ribosomal RNA (LSU rRNA). We tested probe specificity and sensitivity with five other dinoflagellates that also cause red tides. Our assay detected H. triquetra at a concentration of 1.5×10⁴ cells/mL, more sensitive than required for a red-tide guidance warning by the Korea Ministry of Oceans and Fisheries in 2015 (3.0×10⁴ cells/mL). We also used the NPA-SH assay to monitor H. triquetra in the Tongyeong region of the southern sea area of Korea during 2014. This method could detect H. triquetra cells within 3 h. Our assay is useful for monitoring H. triquetra under field conditions.     

基于复合模型的西南大西洋阿根廷滑柔鱼（Illex argentinus）时空分布研究

本文利用2003-2011年西南大西洋阿根廷滑柔鱼渔业数据和海洋环境数据，包括海表温度（sea surface temperature， SST），海面高度（sea surface height， SSH）和叶绿素浓度（chlorophyll a， Chl a），开发基于广义加性模型（GAM）和神经网络模型（NNM）的复合模型研究滑柔鱼资源时空分布。GAM用于选择关键影响因子，并分析与单位捕捞努力量渔获量（catch per unit effort， CPUE）的关系，NNM用于建立关键影响因子与CPUE之间的预报模型。结果表明：GAM选择的影响因子的偏差解释率为53.8%，空间变量（经度和纬度），环境变量（SST、SSH、Chl a）均匀CPUE之间存在显著相关性。CPUE与SST和SSH之间为非线性关系，与Chl a之间为线性关系。NNM模型的MSE和ARV较低，其精度高且稳定。此复合模型也能够解释解释西南大西洋阿根廷滑柔鱼时空变化趋势和迁徙模式。     

四种贝类和鱼类外寄生车轮虫的国内新纪录

车轮虫是一类主要寄生于贝类和鱼类体表的缘毛类纤毛虫原生动物。本文对分别寄生于海洋贝类－－虾夷扇贝Mizuhopecten yessoensis，半咸水鱼类－－鲻鱼Mugil cephalus和双色鳗鲡Anguilla bicolor bicolor，以及淡水鱼类－－光唇鱼Acrossocheilus fasciatus鳃表和体表的虾夷扇贝车轮虫Trichodina pectenis，亚卓车轮虫T.jadranica，急尖车轮虫T.acuta和喙状车轮虫T.rostrata，进行了详细的分类学研究。本文第一次报道了虾夷扇贝车轮虫的活体和蛋白银染色后特征，该虫体也是国内新记录种。其它三个车轮虫物种感染的鱼类，均属新纪录宿主。同时，也报道了这四种车轮虫对宿主的感染率和感染强度。     

太平洋褶柔鱼冬生群资源丰度变动对ENSO事件的响应研究

太平洋褶柔鱼为大洋性经济鱼种，具有一年生命周期，其资源变动受气候和海洋环境条件的显著影响。本研究根据日本提供的2003-2012年太平洋褶柔鱼冬生群体的渔业统计数据，结合产卵场环境数据以及尼诺指数ONI（定义为Niño 3.4区海表温度距平值），分析不同气候条件下（厄尔尼诺和拉尼娜）太平洋褶柔鱼冬生群体产卵场海表温度（SST）、叶绿素a（Chl-a）浓度以及适宜产卵面积（SSA）的变动情况及对其资源丰度（CPUE）的影响。结果表明，太平洋褶柔鱼冬生群体产卵场SST、Chl-a浓度和SSA具有明显的季节性变化。相关分析表明，各年CPUE与Chl-a浓度以及SSA具有显著的正相关关系（p<0.05），但与SST相关性不显著（p>0.05）。此外，厄尔尼诺和拉尼娜事件通过驱动太平洋褶柔鱼冬生群体产卵场SSA和关键海域（25°-29°N，122.5°-130.5°E）内的Chl-a空间分布和大小变化，从而改变其资源丰度，但影响作用随各异常事件的强度不同而变化，具体表现为：发生弱强度厄尔尼诺事件时，产卵场SSA较高，Chl-a浓度处于较低水平，导致资源补充量处于较低水平，CPUE降低；发生中等强度厄尔尼诺事件时，产卵场SSA较低，但Chl-a浓度处于较高水平，导致资源补充量增加，CPUE处于上升水平；发生中等强度拉尼娜事件时，产卵场SSA和Chl-a浓度均处于较高水平，资源补充量显著增加，CPUE显著升高。研究表明，厄尔尼诺和拉尼娜事件对太平洋褶柔鱼冬生群体产卵场摄食孵化环境和资源丰度变动具有显著影响。     

一套具有更高时空分辨率的全球海洋叶绿素浓度遥感融合产品数据集

认识海洋在全球碳循环中的作用及其对环境变化的响应，需要高时空分辨率的观测数据。由于轨道宽度、云雨天气、太阳耀斑等的影响，单一的水色传感器的观测能力十分有限，将多源海洋水色卫星进行融合是提高水色数据时空覆盖的一种有效途径。SeaWiFS和MERIS分别于2010年12月11日和2012年5月9日停止运行，在很大程度上降低了水色融合产品时空覆盖的提升。我们在融合过程中加入了FY-3 MERSI数据，生成了全球海洋叶绿素浓度遥感融合产品数据集。数据源包括SeaWiFS、MERIS、MODIS-Aqua、VIIRS和MERSI。结果表明：加入MERSI后，融合产品的日平均有效空间覆盖提高了9%；采样频率（同一区域一年中获取有效数据的次数）由57天/年提高到109天/年。利用实测数据和国外同类融合产品（ESA GlobColour和NASA MEaSUREs）对新的数据集进行了质量评价。与实测数据相比，加入MERSI的融合产品精度与未加入MERSI的融合产品基本一致；与国外同类融合产品的偏差小于10%。新数据集的时间序列特性与未加入MERSI的融合产品以及单传感器的一致。     

强光照和黑暗条件下刺参体壁的基因表达差异

参对光照变化非常敏感，研究刺参对光照的分子响应非常重要。本研究应用RNA测序获取了刺参暴露于强光（“强光”）、正常光照（“对照”）和完全黑暗（“黑暗”）环境下体壁的基因表达谱情况，通过“对照”与“黑暗”，“对照”与“强光”和“黑暗”与“强光”的比较，在|log₂ ratio|≥1和FDR≤0.001的标准下分别发现了1161、113和1705个差异表达基因（DEGs）。基因本体分析表明，“cellular process”和“binding”在“生物过程”和“分子功能”类别中的DEGs富集最多，而“cell”和“cell part”在“细胞组分”类别中的DEGs富集最多。将DEGs与Kyoto Encyclopedia基因和基因组数据库上的于214、41和229条通路进行比对，发现了51、2和57条通路分别显著富集。本研究发现的光特异性DEGs可作为深入研究刺参对光照变化的生化适应机制的重要目标基因。     

东印度洋5种缘毛类纤毛虫(钟虫属和聚缩虫)水平分布初次报道

腹壁纤毛虫是一种附着在浮游动物上的原生生物，尤其是附着在桡足类和甲壳类上的。而缘毛虫是可以以自由或寄生的形式在世界各沿海地区和港湾处被发现。本研究首次对东印度洋表层至200 m深海域的缘毛类纤毛虫以及其水平分布展开了研究。根据纤毛虫的形态、纤毛结构和茎的形态等的特征，在2014年4月10日至5月13日东印度洋航次的浮游生物拖网样品中鉴定出了五种富腹纤毛虫，海洋钟形虫Vorticella oceanica、交替聚缩虫Zoothamnium alternans、阿拉聚缩虫Zoothamnium alrasheidi、远洋聚缩虫Zoothamnium pelagicum和海洋聚缩虫Zoothamnium marinum。并通过光显微镜和扫描显微镜拍摄的照片，说明了其形态、尺寸和特征。研究结果表明，海洋钟形虫和远洋聚缩虫的分布与硅藻（如，密聚角毛藻Chaetoceros coarctatus）和桡足类（如，短角长腹剑水蚤Oithona brevicornis）等寄主有关，也包括甲藻（如，三角角藻Ceraitum tripose）周围的一些个体。这些附着纤毛虫的分布在东印度洋海域东南区以海洋钟形虫、远洋聚缩虫和海洋聚缩虫为主，而在孟加拉湾北部则有大量的阿拉聚缩虫。这种分布的变化可能是与寄主的分布有关，如桡足类（短角长腹剑水蚤）和硅藻（密聚角毛藻）的分布影响。     

利用基于环境因子的动态产量模型评估西南大西洋阿根廷滑柔鱼

西南大西洋阿根廷滑柔鱼，Illex argentinus，巴塔哥尼亚南部群体是重要的经济种类。海洋环境因子在柔鱼资源分布中起着重要的作用。本研究利用基于环境因子的动态产量模型评估2000-2010年的滑柔鱼的资源量。假设海洋环境因子（滑柔鱼产卵场最适宜海表温度占比）影响动态产量模型的参数K，DIC值表明在正态分布和均匀分布下均是基于环境因子的评估模型优于基本的动态产量模型。阿根廷滑柔鱼的最大可持续产量（MSY）在351600吨到685 100吨之间，资源生物量在1322400吨到1 803 000吨之间，其捕捞死亡系数均小于F_0.1和F_MSY，资源处在良好状态，没有遭受过度捕捞。本研究为应用环境因子在柔鱼类的资源评估与管理提中供了科学的参考方法。     

发现于我国渤海辽东湾的海洋甲藻新种-渤海异冒藻(Heterocapsa bohaiensis sp. nov.)

A small armed dinoflagellate bloomed in the aquaculture ponds off the coast of Liaodong Bay, Bohai Sea of China,resulting in heavy mortalities of the cultured prawns(Penaeus japonicus) and larvae of Chinese mitten handed crabs(Eriocheir sinensis). The bloom-forming species was successfully isolated, and cellular morphology of the specimen was consequently investigated through light, fluorescent and electron microscopy. The small((14.4±1.6) μm in length) ellipsoid cells show typical Heterocapsa thecal plate arrangement(Po, cp, 5′, 3 a, 7′′, 6 c,5 s, 5′′′, 2′′′′). The episome is evidently bigger than the hyposome. One to three spherical pyrenoids are located above or beside the large elongated nucleus. The body scale is characterized by a triangle basal plate with one central upright and nine peripheral spines. Above all, Heterocapsa bohaiensis could be distinguished from other Heterocapsa species by the combination of the cell size, morphology, cellular structure and body scale. Sequence analyses of both ITS and LSU regions reveal the significant genetic divergence between H. bohaiensis and other established species in this genus, further supporting novelty of this species. Noticeably, different sample treatment methods resulted in morphological variation of the apical pore complex(APC) of H. bohaiensis, which needs to be taken into account in future study.