条斑紫菜低覆盖度基因组草图分析

对条斑紫菜（Porphyra yezoensis）进行Solexa高通量测序,获得低覆盖度全基因组草图。该基因组草图大小约220Mbp,GC质量分数53．08％;包含26629个预测基因,其中16409个基因具有内含子,平均每个基因含2．22个内含子;基因结构分析表明具有内含子的基因平均长度为2214bp,内含子平均大...     

大洋表层沉积物中甲烷代谢古菌群落的组成及分布特征

海洋沉积物中的甲烷代谢微生物是甲烷循环的关键参与者,其代谢过程对大气甲烷浓度及全球气候变化具有显著影响,研究其在全球大洋沉积物中的组成及分布特征是探究微生物介导甲烷循环的基础。采用焦磷酸454高通量测序测定甲烷代谢保守功能基因mcrA（Methyl coenzyme–M reductase A）分析全球大洋沉积物中甲烷代谢微生物群落的组成和多样性;结合荧光实时定量PCR技术检测了古菌和甲烷代谢古菌的丰度分布特征。与其他海洋生境对比,大洋沉积物中甲烷代谢古菌群落结构单一,大西洋和印度洋的α多样性指数显著高于太平洋（p<0.05）。在大洋沉积物样品中鉴定到3个目的甲烷代谢古菌,即甲烷杆菌目（Methanobacteriales）、甲烷八叠球菌目（Methanosarcinales）和甲烷微菌目（Methanomicrobiales）,其中甲烷微菌目占绝对优势,并主要由一簇未知类群（暂名Oceanic Sediments Dominant group,OSD group）组成。大洋沉积物的古菌16S rRNA基因丰度（湿重,下同）平均为8.81×10⁶ copies/g,大西洋的低于印度洋和太平洋;马里亚纳海沟基因丰度低于南海北部,且随着采样深度增加而呈降低趋势。大洋沉积物的mcrA基因丰度为1.38×10³～8.25×10⁴ copies/g。基因丰度大西洋最高,太平洋次之,印度洋最低;马里亚纳海沟略高于南海。本研究发现,相较于冷泉、热液、近海河口等海洋生境,大洋沉积物中甲烷代谢古菌丰度低且群落结构单一,不同海区样品间具有极高的相似性;同时发现OSD group是全球大洋沉积物样品的绝对优势类群,其与已知类群序列亲缘关系均较远,分类进化地位尚不明晰,值得进一步研究。     

Microbial diversity in Huguangyan Maar Lake of China revealed by high-throughput sequencing

Huguangyan Maar Lake is a typical maar lake in the southeast of China. It is well preserved and not disturbed by anthropogenic activities. In this study, microbial community structures in sediment and water samples from Huguangyan Maar Lake were investigated using a high-throughput sequencing method. We found significant differences between the microbial community compositions of the water and the sediment. The sediment samples contained more diverse Bacteria and Archaea than did the water samples. Actinobacteria, Betaproteobacteria, Cyanobacteria, and Deltaproteobacteria predominated in the water samples while Deltaproteobacteria, Anaerolineae, Nitrospira, and Dehalococcoidia were the major bacterial groups in the sediment. As for Archaea, Woesearchaeota (DHVEG-6), unclassified Archaea, and Deep Sea Euryarchaeotic Group were detected at higher abundances in the water, whereas the Miscellaneous Crenarchaeotic Group, Thermoplasmata, and Methanomicrobia were significantly more abundant in the sediment. Interactions between Bacteria and Archaea were common in both the water column and the sediment. The concentrations of major nutrients (NO^3-, PO4^3-, SiO3^2- and NH4^+) shaped the microbial population structures in the water. At the higher phylogenetic levels including phylum and class, many of the dominant groups were those that were also abundant in other lakes;however, novel microbial populations (unclassified) were often seen at the lower phylogenetic levels. Our study lays a foundation for examining microbial biogeochemical cycling in sequestered lakes or reservoirs.     

Bacterial diversity and community structure in the East China Sea by 454 sequencing of the 16S rRNA gene

The 454 sequencing method was used to detect bacterial diversity and community structure in the East China Sea. Overall, 149 067 optimized reads with an average length of 454 nucleotides were obtained from 17 seawater samples and five sediment samples sourced in May 2011. A total of 22 phyla, 34 classes, 74 orders, 146 families, and 333 genera were identified in this study. Some of them were detected for the first time from the East China Sea. The estimated richness and diversity indices were both higher in the sediment samples compared with in the seawater samples. All the samples were divided by their diversity indices into four regions. Similarity analysis showed that the seawater samples could be classified into six groups. The groups differed from each other and had unique community structure characteristics. It was found that different water masses in the sampling areas may have had some influence on the bacterial community structure. A canonical correspondence analysis revealed that seawater samples in different areas and at different depths were affected by different environmental parameters. This study will lay the foundation for future research on microbiology in the East China Sea.     

一种有向权图的拓扑排序算法及其应用

提出一种有向权图的拓扑排序算法，并给出一实例说明其应用。     

宁波沿海陆源排污口假单胞菌属(Pseudomonas)分布特点

采用高通量454焦磷酸测序方法对宁波沿海2个重点排污口、8个一般排污口的20个站位水样进行分析, 得到2011年3月、5月、8月、10月份各排污口假单胞菌属的分布情况。结果表明, 宁波沿海陆源排污口中存在较多的假单胞菌属。在检出的假单胞菌属中, 维罗纳假单胞菌(Pseudomonas veronii)和莓实假单胞菌(Pseudomonas fragi)的含量相对较多, 分别占56.72%、13.904%; 排污口中假单胞菌属的数量存在季节性差异, 3月份、5月份假单胞菌的数量相对较多, 8月份和10月份较少, 推测与季节性温度变化有关; 假单胞菌属的含量与排污口的主要污染物有关, 氨氮含量较高的排污口假单胞菌属的含量更高。     

岩溶区与非岩溶区3种土地利用方式下土壤细菌群落结构比较

为研究岩溶区土壤微生物的特性,揭示其在岩溶土壤碳循环的作用,选取桂林毛村岩溶试验场为研究点,采集岩溶区、混合区与非岩溶区中的稻田、玉米和柑橘园表层土壤,采用高通量测序方法,对比细菌群落丰度、组成及多样性特征的异同。结果显示,在得到的48 159条序列中,共有2 602个OTUs。土壤细菌优势门（相对丰度>10%）为变形菌门（Proteobacteria）、酸杆菌门（Acidobacteria）和放线菌门（Actinobacteria）;优势纲（相对丰度>10%）为酸杆菌纲（Acidobacteria）和β-变形菌纲（β-proteobateria）。岩溶区土壤细菌门水平上的变形菌门和Latescibacteria的细菌和目水平上的酸杆菌亚群GP6的丰度均高于混合区和非岩溶区,而科水平上酸杆菌亚群GP1和目水平上的酸杆菌亚群GP2的相对丰度低于混合区和非岩溶区。冗余分析结果表明,土壤有机碳、pH和总氮等是引起细菌群落结构变化的关键因子。      

近海水体环境DNA沉降对沉积物中纤毛虫分子多样性评估的影响

在陆架海区沉积物中, DNA高通量测序技术可检获大量浮游寡毛类和舞毛类等非底栖纤毛虫,这些源于水体的环境DNA(eDNA)如何影响对沉积物中纤毛虫分子多样性的评估,以及影响程度如何尚不明确。本研究选取了黄海冷水团中的两个站位,通过提取水体和沉积物中DNA和RNA,并采用直接提取法和洗脱法提取沉积物DNA,结合DNA和cDNA测序技术,探讨了水体和沉积物中纤毛虫分子多样性的关系。研究表明,基于洗脱DNA法、直接提取DNA法和cDNA法获得的沉积物中纤毛虫OTUs数分别为451、312和324个,其中211个OTUs同时由三种方法检获;而164个OTUs仅通过洗脱DNA法检获,其中89%为相对丰度低于0.1%的稀有类群。直接提取DNA法所获的寡毛类和舞毛类序列数占比达46%,而在洗脱DNA法和cDNA法中占比仅为12%和10%。沉积物中检获的43%—71%的舞毛类和寡毛类OTUs与浅层水(<40m)共有,仅19%—29%与深层水(>40m)共有,且这些共有的OTUs可同时在浅层水中检获。本研究发现,对沉积物中纤毛虫分子多样性评价造成影响的浮游类群主要来自浅层水,洗脱DNA与cD...