东太平洋深海沉积物中DNA的提取及细菌多样性初步分析

以东太平洋海隆附近深海柱状沉积物为材料,通过化学裂解和酶消化相结合的方法提取了沉积物微生物的总基因组DNA,并进行了纯化。结果表明所得到的DNA分子片段大小在21kb左右,纯化后的DNA可直接用于PCR等分子生物学操作。细菌16SrDNAV3可变区的PCR—DGGE图谱展示出15条以上条带,表明深海沉积物中细菌多样性较高,群落结构比较复杂。对其中9条主要条带进行回收、测序和系统发育分析,结果表明所获得的序列分属放线菌门（Actinobacteria）,绿弯菌门（Chloroflexi）,γ-变形细菌亚门（Gamma—proteobacteria）,α-变形细菌亚门（Alpha—proteobacteria）和嗜酸菌门（Acidobacteria）5个大类群。     

中国南部沿海尖头斜齿鲨遗传多样性研究

采用随机引物扩增多态性DNA(RAPD)技术,对中国南部沿海闽东霞浦-浙南瑞安海域(MD)、闽南-台湾浅滩渔场(MN)、粤西湛江-阳江海域(YX)、北部湾海域(BBW)4个尖头斜齿鲨地理群体遗传多样性进行分析,29个随机引物在4个群体中共检测出282个位点.4个群体各自检测出的位点数分别为273、274、272、276,其中多态位点数分别为54、57、52、45,多态位点比例分别为19.78%、20.80%、19.12%、16.30%.Shannon多样性指数分别为0.104、0.107、0.103、0.090,表明尖头斜齿鲨群体的遗传多样性水平较低.遗传距离和UPGMA聚类分析结果显示尖头斜齿鲨的基因交流模式属于距离隔离模式,遗传差异大小与地理距离远近相关.进行分子方差分析(AMOVA)得到遗传变异固定指数(Fst＝0.019,p＜0.05),显示大部分变异(98.06%)发生在群体内部,群体间变异较小(1.94%).     

Complementary DNA sequencing (cDNA): an eff ective approach for assessing the diversity and distribution of marine benthic ciliates along hydrographic gradients

The Yellow Sea Cold Water Mass(YSCWM)is a distinct hydrographic phenomenon of the Yellow Sea,and the distribution pattern of meio-and macrobenthos diff ers inside and outside of the YSCWM.However,such a pattern has never been observed in the microbenthic ciliate communities.Therefore,we hypothesized that benthic ciliates followed a similar distribution pattern as meio-and macrobenthos,but this pattern has not been uncovered by morphological methods.We evaluated the diversity and distribution of benthic ciliates at fi ve stations along hydrographic gradients across the YSCWM and adjacent shallow water by using morphology and DNA and complementary DNA(cDNA)high-throughput sequencing of the V4 region of 18S rRNA gene.Results showed that the diversity of benthic ciliates detected by DNA(303 OTUs),and the cDNA(611 OTUs)sequencing was much higher than that detected by the morphological method(79 species).Morphological method detected roughly diff erent ciliate communities inside and outside of the YSCWM,but without statistical signifi cance.No clear pattern was obtained by DNA sequencing.In contrast,cDNA sequencing revealed a distinct distribution pattern of benthic ciliate communities like meioand macrobenthos,which coincided well with the results of the environmental parameter analysis.More than half of the total sequences detected by DNA sequencing belonged to planktonic ciliates,most(if not all)of which were recovered from historic DNA originating through the sedimentation of pelagic forms because none of them were observed morphologically.The irrelevant historic DNA greatly infl uenced the recovery of rare species and thus limited the understanding of the benthic ciliate diversity and distribution.Our research indicates that the methods used have signifi cant eff ects on the investigation of benthic ciliate communities and highlights that cDNA sequencing has great advantages in estimating the diversity and distribution of benthic ciliates,as well as the potential for benthic environmental assessments.     

Lack of mitochondrial genetic structure in the endangered giant clam populations of Tridacna maxima (Bivalvia: Cardiidae: Tridacninae) across the Saudi Arabian coast

The present investigation focuses on population genetic structure analysis of the endangered giant clam species Tridacna maxima across part of the Red Sea,with the main aim of assessing the influence of postulated potential barriers to gene flow(i.e.,particular oceanographic features and marked environmental heterogeneity)on genetic connectivity among populations of this poorly dispersive bivalve species.For this purpose,a total of 44 specimens of T.maxima were collected from five sampling locations along the Saudi Arabian coast and examined for genetic variability at the considerably variable mitochondrial gene cytochrome c oxidase I(COI).Our results revealed lack of population subdivision and phylogeographic structure across the surveyed geographic spectrum,suggesting that neither the short pelagic larval dispersal nor the various postulated barriers to gene flow in the Red Sea can trigger the onset of marked genetic differentiation in T.maxima.Furthermore,the discerned shallow COI haplotype genealogy(exhibiting high haplotype diversity and low nucleotide diversity),associated with recent demographic and spatial expansion events,can be considered as residual effect of a recent evolutionary history of the species in the Red Sea.     

基于DNA条形码研究中国枪乌贼和鸢乌贼的食物种类组成*

中国枪乌贼(Uroteuthis chinensis)和鸢乌贼(Sthenoteuthis oualaniensis)作为中国南海头足类的关键种, 对海洋生态系统的物质流动与能量循环具有重要影响, 其摄食生态的研究将对海洋食物网的构建具有重要意义。由于传统胃含物分析法难以准确鉴定糜状饵料生物的组成, 本研究利用DNA条码技术, 针对中国枪乌贼和鸢乌贼不可辨认的食物糜提取组织DNA, 选用线粒体基因细胞色素C氧化酶亚基I(Mitochondrial cytochrome oxidase subunit I, COI)作为分子标记, 获得的序列在Genbank中进行比对分析, 并使用GMYC(Generalized Mixed Yule Coalescent)模型进行物种界定和构建系统进化关系。结果成功鉴定出中国枪乌贼饵料物种有13种, 鸢乌贼饵料物种有8种, 共20种(其中1种为共有饵料)。比较发现, 汕头-台湾浅滩渔场的中国枪乌贼主要摄食鱼类、甲壳类和头足类, 而南海中部海域鸢乌贼则主要摄食鱼类和头足类。两物种均存在同类相食现象, 但鸢乌贼表现更明显。     

Evaluation of DNA Damage in the Marine Mussel Crenomytilus grayanus as a Genotoxic Biomarker of Pollution

Marine pollution affects all life processes in aquatic organisms. The genotoxic effect of pollution on the mussel Crenomytilus grayanus was assessed. Bivalves were collected from the ‘clean'(Vostochnaya Cove) and polluted(Nakhodka Bay) areas in the Peter the Great Bay. The degree of DNA damage in C. grayanus was determined by alkaline comet assay as mean percentage of DNA in tail, and the genetic damage index was calculated. Our results indicate that almost one-third of DNA in cells of gills and digestive gland of C. grayanus inhabiting the Nakhodka Bay had destructive changes compared to the individuals of this species from the Vostochnaya Cove. This study has shown that chronic pollution of the aquatic environment causes destructive changes to DNA in gill and digestive gland cells of C. grayanus.     

丹江口库区表层沉积物细菌多样性及功能预测分析

湖泊沉积物微生物是水生态系统的重要组成部分,目前关于丹江口库区沉积物细菌群落和功能研究鲜见报道.于2017年5月对丹江口库区内5个典型生态点位表层沉积物进行采集,采用高通量测序技术对表层沉积物细菌群落组成进行研究,结果表明细菌群落主要由变形菌门(Proteobacteria)、绿弯菌门(Chloroflexi)、拟杆菌门(Bacteroidetes)、疣微菌门(Verrucomicrobia)和硝化螺旋菌门(Nitrospirae)等33个门和318个属组成,具有丰富的群落组成.沉积物细菌群落和理化指标冗余分析(RDA)结果表明,pH值、总磷、有机质和铵态氮含量均能显著影响沉积物细菌群落组成.细菌属分类单元与环境因子Spearman相关分析表明,变形菌门中11个属的细菌与环境因子显著相关,为与环境因子显著相关细菌的主要组成(占47.62%).采用细菌群落功能预测软件PICRUSt(Phylogenetic Investigation of Communities by Reconstruction of Unobserved States)对表层沉积物细菌群落进行分析,结果表明沉积物细菌功能主要涉及能量产生和转换、信号转导机制、氨基酸运输和代谢、细胞壁/细胞膜/膜结构的生物合成等24个基因功能家族,表现出功能上的丰富性.基因功能家族预测基因拷贝数表现为台子山宋岗库心渠首黑鸡嘴.     

基于线粒体DNA控制区序列的黑鲷亲鱼、放流及海捕群体遗传多样性比较分析

为了解黑鲷(Acanthopayrus schlegelii)种质资源现状以及放流群体可能对野生群体产生的遗传学影响,本研究采用线粒体DNA控制区序列对采自舟山、莱州和南通的黑鲷亲鱼、放流群体和海捕群体进行了遗传学比较研究。研究显示：764尾黑鲷个体共检测到69个单倍型,其中亲鱼群体与放流群体的共享单倍型为5个、亲鱼群体与海捕群体的共享单倍型为6个,放流群体与海捕群体的共享单倍型为27个。亲鱼群体、放流群体和海捕群体的单倍型多样度分别为0.849,0.786～0.935和0.850～0.951,核苷酸多样度分别为0.011,0.005～0.009和0.008～0.009。群体间遗传分化指数F_ST显示,黑鲷亲鱼群体与放流群体、放流群体间以及放流群体与海捕群体均产生中等程度的遗传分化。研究结果表明,黑鲷亲鱼群体、放流群体以及海捕群体的遗传多样性均较高,说明放流群体的种质资源良好,但黑鲷苗种与海捕群体间存在较大的遗传分化,仍需开展其遗传多样性监测工作,以保护黑鲷的优质种质资源。     

河南安阳殷墟孝民屯遗址出土家养黄牛的DNA研究

作为晚商的都城和当时最大都市的殷墟(1300~1046 BCE),家养黄牛是最重要的大型家养动物之一.殷墟的家养黄牛可以肉食、可以役用,骨料可做骨器,是最主要的祭牲,其肩胛骨还可以用于占卜、可以记载甲骨文.本文对安阳殷墟孝民屯遗址普通灰坑和祭祀坑出土的15例牛骨线粒体DNA控制区285 bp的片段进行分析研究,其中有13例获取了所需的DNA序列.DNA分析表明12例属于家养普通牛(Bos taurus),1例属于野生原始牛(Bos primigenius).殷墟孝民屯家养普通牛的单倍型类群分布频率为以T3为主约占58.3%,T4次之约占33.3%,T2最少约占8.3%,该遗传多样性在当时已经达到或保持在可能的最高水平了.推测作为都城和大都市的殷墟聚集了中国早期各个地区的黄牛.孝民屯祭祀坑和普通灰坑出土牛骨线粒体DNA单倍型类群没有明显的差异,表明孝民屯用于祭祀的黄牛没有经过特殊的"母系"筛选,但不排除有对核DNA控制的特殊体质、生理或行为等性状进行有意识地筛选,以示祭祀的神圣性和特殊性.本文有限的DNA数据显示普通灰坑出土牛骨的DNA保存相对较差,暗示着普通灰坑的牛骨作为食余废弃物可能经历了更多炊煮活动中的高温处理,坑内埋藏环境不同也可能使普通灰坑的牛骨保存状况不如祭祀坑内的牛骨,普通灰坑牛骨样本DNA降解和破坏得更厉害.     

无机砷As(Ⅲ、Ⅴ)对牟氏角毛藻生长、叶绿素荧光特性及基因组DNA甲基化水平的影响

以AsO2-和HAsO42-分别暴露处理牟氏角毛藻(Chaetocerosmulleri)研究As(Ⅲ、V)毒性作用,As(Ⅲ)浓度梯度为0、10、50、100、300和500 μmol/L,As(V)浓度梯度为0、30、60、120、300和600 μmol/L,分别在第1、3、7d取样,研究不同浓度的As(Ⅲ、V)...