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.     

Blooms of Prorocentrum donghaiense reduced the species diversity of dinoflagellate community

Most of reported harmful algal blooms(HABs)of microalgae(75%)have been caused by dinoflagellates.Studies on the negative effects of HABs have generally focused on animals,valuable organisms in particular,and environmental factors such as dissolved oxygen and nutrients,but relatively fewer on community level,particularly that using metagenomic approach.In this study,we reported an investigation on the effects of a HAB caused by the dinoflagellate Prorocentrum donghaiense on the species diversity and community structure of the dinoflagellate sub-community via a pyrosequencing approach for the samples taken before,during,and after the bloom season of P.donghaiense in the East China Sea.We sequenced partial 28S rRNA gene of dinoflagellates for the field samples and evaluated the species richness and diversity indices of the dinoflagellate community,as a sub-community of the total phytoplankton.We obtained 800185 valid sequences(categorized into 560 operational taxonomic units,OTUs)of dinoflagellates from 50 samples and found that the biodiversity of dinoflagellate community was significantly reduced during the blooming period in comparison to that in pre-and after-blooming periods,as reflected in the four diversity indices:the species richness expressed as the number of OTUs,Chao1 index,Shannon index(evenness),and Gini-Simpson index.These four indices were all found to be negatively correlated to the cell density of the bloom species P.donghaiense.Correlation analyses also revealed that the P.donghaiense cell abundance was correlated negatively with NO3--N,and NO2--N,but positively with total nitrogen(TN)and total phosphorus(TP).Principal coordinates analysis(PCoA)showed that the community structure of dinoflagellates was markedly different among the different sampling periods,while the redundancy analysis(RDA)revealed P.donghaiense abundance,salinity,NO3--N,and SiO32-were the most four significant factors shaping the dinoflagellate community structure.Our results together demonstrated that HABs caused by the dinoflagellate P.donghaiense could strongly impact the aquatic ecosystem on the sub-community level which the blooming species belongs to.     

北极深海沉积物中细菌和古菌群落结构研究

在北极深海沉积物生态系统中,微生物的群落结构由有机质输入、能量的可用性及其他环境因素决定.然而,全球气候变暖及其导致的冰盖提前融化正在影响微生物的多样性.为描述北极深海沉积物中的微生物群落结构及其与环境因素的相关性,我们利用罗氏454对北极深海沉积物样品的16S rDNA扩增子进行了测序,对细菌和古菌群落的丰富度、成分、结构及其系统发育分类地位进行了描述.硫还原和化能有机营养类是细菌群落中的主要类群;而古细菌群落主要是由微生物的关系最为密切的氨氧化奇古菌门(96.66%)和产甲烷古生菌界(3.21%).这项研究描述了北极极点附近深海沉积物(> 3500米)中的微生物多样性,将为以后研究类似环境中微生物代谢过程和途径等功能分析奠定基础.     

Diversity and distribution of bacterial community in the coastal sediments of Bohai Bay, China

In order to understand the diversity and distribution of the bacterial community in the coastal sediment of the Bohai Bay,China,high-throughput barcoded pyrosequencing of the 16 S r RNA gene was used.Metagenomic DNA was extracted from the sediment samples,and was sequenced using a 454 GS FLX Titanium system.At 97%similarity,the sequences were assigned to 22 884 operational taxonomic units(OTUs) which belonged to 41 phyla,84 classes,268 genera and 789 species.At the different taxonomic levels,both the dominants and their distribution varied significantly among the six coastal sediments.Proteobacteria was the first dominant phylum across all the six coastal sediments,representing 57.52%,60.66%,45.10%,60.92%,56.63% and 56.59%,respectively.Bacteroidetes was the second dominant phylum at Stas S1,S2 and S4,while Chloroflexi was the second dominant phylum at Stas S3,S5 and S6.At class level,γ-Proteobacteria was the first dominant class at Stas S1,S2,S4 and S6,while δ-Proteobacteria became the first dominant class at Stas S3 and S5.In addition,a large proportion of unclassified representatives have distributed at the different taxonomic levels.Canonical correspondence analysis(CCA) results indicated that the sediment texture,water depth(D),dissolved oxygen(DO),total nitrogen(TN) and nine EPA priority control polycyclic aromatic hydrocarbons(PAHs) including naphthalene,acenaphthylene,acenaphthene,fluorine,phenanthrene,fluoranthene,pyrene,benzo[a]anthracene and indeno[1,2,3-cd]pyrene were the important factors in regulating the bacterial community composition.Those results are very important to further understand the roles of bacterial community in the coastal biogeochemical cycles.     

宁波沿海陆源排污口弓形杆菌属(Arobacter sp.)和梭菌属(Clostridium sp.)的分布特点

弓形杆菌属(Arobacter sp.)和梭菌属(Clostridium sp.)广泛存在于水体和寄生在动物体内,极易造成水体污染和人畜共患病。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1年中的3月、5月、8月和10月份各排污口弓形杆菌属和梭菌属生物的分布情况。研究结果表明:弓形杆菌属检测出两个种,分别是嗜低温弓形杆菌(Arcobacter cryaerophilus)、布氏弓形杆菌(Arcobacter butzleri)。梭菌属共检测出12个种,其中产气荚膜梭菌(Clostridium perfringens)检出次数最高,丁酸梭菌(Clostridium butyricum)次之;排污口的类型是影响弓形杆菌属检出量的重要因素。弓形杆菌属主要分布在氮,磷含量较高的工业排污口和市政排污口,而梭菌属只在3月份的S7宁海西店崔家综合排污口呈现出相对较高的比例(7.5%),其它排污口检出量均在2%以下;弓形杆菌属和梭菌属在10个排污口20个站位4个月份的检出次数呈现正相关性;由季节性的变化引起的气温差异也是影响弓形杆菌属生长的重要因素,弓形杆菌属在5月份的时候检出次数最大,梭菌属适宜生长温度范围较广10—65°C,受温度影响较小。     

海洋沉积物氨氧化菌群落结构的测序分析

本文以氨氧化细菌(ammonia-oxidizing bacteria,AOB)特征基因氨单加氧酶(ammonia monooxygenase,AMO)α亚基基因(amoA)为目标基因(～491bp),分别采用克隆文库、454高通量测序和illumina测序技术对其群落结构进行了比较研究。结果表明, 454高通量测序和illumina测序技术得到的菌群多样性及丰富度均高于克隆文库技术。在菌群组成方面,虽然3种测序技术检测到的优势类群均为亚硝化螺菌,但在菌群丰度方面存在差异。3种测序技术中,克隆文库技术在很大程度上可能高估物种丰度,且对部分低丰度类群的检测能力有限;illumina单端测序由于其测序片段较短,可能存在物种注释错误、不能准确区分各物种间序列差异等问题;比较而言, 454高通量测序技术能较为全面和准确地反映海洋沉积物中AOB的菌群结构特征。     

东印度洋细菌类群水平与垂直分布初探

作为海洋食物网的重要组成部分,微生物在海洋的生物化学循环以及能量和元素流动中起着重要的作用。目前对东印度洋中微生物的种群结构和分布知之甚少。本研究运用分子生物学手段,包括多聚酶链式反应-变形梯度凝胶电泳(PCR-DGGE)技术和高通量测序技术,对东印度洋的赤道区域以及邻近的孟加拉湾区域水体中细菌的16S rRNA基因进行了探索。结果表明,Bacteroidetes, Proteobacteria (Alpha和Gamma类群), Actinobacteria, Cyanobacteria和Planctomycetes为研究区域微生物的主要类群。通过PCR-DGGE,发现微生物类群具有显著的水平分布模式;进一步的高通量测序的结果更加清晰的显示出细菌类群的垂直分布模式:相对其他两层,Cyanobacteria和Actinobacteria在25米水层出现更多;Bacteroidetes在25m和150m为主要类群,而在75m水层相对较少;Proteobacteria (主要为Alphaproteobacteria)类群在75m水层为优势类群。随着水层的加深,不同站位的细菌类群组成趋于一致。结果表明高通量测序能够把占据微小部分的微生物类群区分出来。本研究是针对东印度洋水体中细菌的水平和垂直分布以及多样性信息的首次报道,研究结果对于进一步发现潜在微生物功能类群以及探索这些微生物在东印度洋中的能量和物质循环中的作用有所帮助。     

An atlas of predicted exotic gravitational lenses

We present an investigation of the relationships between the radio properties of a giant radio galaxy MRC B0319−454 and the surrounding galaxy distribution with the aim of examining the influence of intergalactic gas and gravity associated with the large-scale structure on the evolution in the radio morphology. Our new radio continuum observations of the radio source, with high surface brightness sensitivity, images the asymmetries in the megaparsec-scale radio structure in total intensity and polarization. We compare these with the three-dimensional galaxy distribution derived from galaxy redshift surveys. Galaxy density gradients are observed along and perpendicular to the radio axis: the large-scale structure is consistent with a model wherein the galaxies trace the ambient intergalactic gas and the evolution of the radio structures are ram-pressure limited by this associated gas. Additionally, we have modelled the off-axis evolution of the south-west radio lobe as deflection of a buoyant jet backflow by a transverse gravitational field: the model is plausible if entrainment is small. The case study presented here is a demonstration that giant radio galaxies may be useful probes of the warm-hot intergalactic medium believed to be associated with moderately over dense galaxy distributions.