Unexpected diversity of small eukaryotes in deep-sea Antarctic plankton

Phylogenetic information from ribosomal RNA genes directly amplified from the environment changed our view of the biosphere, revealing an extraordinary diversity of previously undetected prokaryotic lineages. Using ribosomal RNA genes from marine picoplankton, several new groups of bacteria and archaea have been identified, some of which are abundant. Little is known, however, about the diversity of the smallest planktonic eukaryotes, and available information in general concerns the phytoplankton of the euphotic region. Here we recover eukaryotes in the size fraction 0.2-5 microm from the aphotic zone (250-3,000 m deep) in the Antarctic polar front. The most diverse and relatively abundant were two new groups of alveolate sequences, related to dinoflagellates that are found at all studied depths. These may be important components of the microbial community in the deep ocean. Their phylogenetic position suggests a radiation early in the evolution of alveolates.     

FISH检测中国主要油页岩矿区微生物相对丰度

用荧光原位杂交(FISH)技术调查了我国主要油页岩矿区(辽宁抚顺、吉林桦甸和广东茂名)中砂土、新鲜油页岩和风化油页岩或砂砾岩样品的细菌和古细菌相对丰度.油页岩微生物的杂交优化反应条件:杂交温度为46℃,杂交时间为2.5 h,杂交液中去离子甲酰胺的体积分数为20%时,TRIzol和溶菌酶共处理方式有利于提高杂交率.各类型样品中,细菌相对丰度均在50%以上,古细菌相对丰度均在5%以下,在新鲜油页岩中细菌和古细菌的相对丰度最高.抚顺矿细菌相对丰度最低,其次茂名矿和桦甸矿,而抚顺矿古细菌相对丰度最高,其次茂名矿和桦甸矿.     

Proteorhodopsin lateral gene transfer between marine planktonic Bacteria and Archaea

Planktonic Bacteria, Archaea and Eukarya reside and compete in the ocean's photic zone under the pervasive influence of light. Bacteria in this environment were recently shown to contain photoproteins called proteorhodopsins, thought to contribute to cellular energy metabolism by catalysing light-driven proton translocation across the cell membrane. So far, proteorhodopsin genes have been well documented only in proteobacteria and a few other bacterial groups. Here we report the presence and distribution of proteorhodopsin genes in Archaea affiliated with the order Thermoplasmatales, in the ocean's upper water column. The genomic context and phylogenetic relationships of the archaeal and proteobacterial proteorhodopsins indicate its probable lateral transfer between planktonic Bacteria and Archaea. About 10% of the euryarchaeotes in the photic zone contained the proteorhodopsin gene adjacent to their small-subunit ribosomal RNA. The archaeal proteorhodopsins were also found in other genomic regions, in the same or in different microbial lineages. Although euryarchaeotes were distributed throughout the water column, their proteorhodopsins were found only in the photic zone. The cosmopolitan phylogenetic distribution of proteorhodopsins reflects their significant light-dependent fitness contributions, which drive the photoprotein's lateral acquisition and retention, but constrain its dispersal to the photic zone.     

鄱阳湖南矶湿地苔草植被根际土壤微生物群落结构分析

为探究鄱阳湖南矶湿地苔草植被根际土壤微生物群落结构,该文以鄱阳湖南矶湿地苔草植被根际土壤为研究对象,采取0～15 cm、15～30 cm及30～45 cm深度的土壤,采用Illumina HiSeq高通量测序技术,研究不同深度土壤群落结构及其影响因素.研究结果表明：不同深度土壤样品理化性质和酶活性存在显著差异,随土壤深度的增加呈降低趋势.Pearson相关分析表明鄱阳湖南矶湿地苔草植被根际土壤理化性质与土壤酶活性之间存在不同程度的相关性.高通量测序结果表明不同深度土壤细菌和真菌群落微生物丰富度及多样性未达到在统计学意义上的差异显著水平(P>0.05),土壤古菌群落微生物多样性随土壤深度的增加而增加.在苔草植被根际土壤中共检测到41个细菌门类,其中变形菌门、酸杆菌门、绿弯菌门和硝化螺旋菌门为优势菌门;检测到8个真菌门类,其中子囊菌门、担子菌门和罗兹菌门为优势菌门;检测到10个古菌门类,其中广古菌门、泉古菌门、奇古菌门为优势菌门.冗余分析表明：土壤有机质、全氮、全磷和碱解氮含量是影响细菌群落的主要环境因子;土壤有机质、全氮、有效磷和碱解氮含量是影响真菌群落的主要环境因子;土壤有机质、...     

内源激活剂驱油藏内微生物菌群结构变化分析

油藏内源功能微生物的激活能有效提高采油效率。其中激活后功能微生物的群落变化分析及相关代谢基因丰度的变化对内源激活剂的筛选及激活机理研究具有重要的指导意义。本实验利用高通量测序技术准确分析了内源激活剂注入井（WJW199.1）和对照井（WJW202）中内源微生物（包括古菌和细菌）基于门、纲、属水平的种群多样性和群落结构。结果表明采出水中Thaumarchaeota门的古菌占主导,而丰度最高的细菌属于Proteobacteria门和 Firmicutes门。不管对于古菌还是细菌,注入井中的微生物多样性都远高于对照井,说明激活剂的添加有效激活了其中的内源微生物,提高了群落结构多样性。尤其是Pseudomonas,Arcobacter等具有产表活剂能力的功能微生物。同时,硫酸盐还原菌脱硫弧菌属等有害菌被抑制,丰度降低。表明从微生物种群变化的程度来看内源激活剂的注入降低了有害菌的丰度,激活了功能微生物,增强了整体微生物的驱油能力。     

SAR11 clade dominates ocean surface bacterioplankton communities

The most abundant class of bacterial ribosomal RNA genes detected in seawater DNA by gene cloning belongs to SAR11-an alpha-proteobacterial clade. Other than indications of their prevalence in seawater, little is known about these organisms. Here we report quantitative measurements of the cellular abundance of the SAR11 clade in northwestern Sargasso Sea waters to 3,000 m and in Oregon coastal surface waters. On average, the SAR11 clade accounts for a third of the cells present in surface waters and nearly a fifth of the cells present in the mesopelagic zone. In some regions, members of the SAR11 clade represent as much as 50% of the total surface microbial community and 25% of the subeuphotic microbial community. By extrapolation, we estimate that globally there are 2.4 x 10(28) SAR11 cells in the oceans, half of which are located in the euphotic zone. Although the biogeochemical role of the SAR11 clade remains uncertain, these data support the conclusion that this microbial group is among the most successful organisms on Earth.     

A marine microbial consortium apparently mediating anaerobic oxidation of methane

A large fraction of globally produced methane is converted to CO2 by anaerobic oxidation in marine sediments. Strong geochemical evidence for net methane consumption in anoxic sediments is based on methane profiles, radiotracer experiments and stable carbon isotope data. But the elusive microorganisms mediating this reaction have not yet been isolated, and the pathway of anaerobic oxidation of methane is insufficiently understood. Recent data suggest that certain archaea reverse the process of methanogenesis by interaction with sulphate-reducing bacteria. Here we provide microscopic evidence for a structured consortium of archaea and sulphate-reducing bacteria, which we identified by fluorescence in situ hybridization using specific 16S rRNA-targeted oligonucleotide probes. In this example of a structured archaeal-bacterial symbiosis, the archaea grow in dense aggregates of about 100 cells and are surrounded by sulphate-reducing bacteria. These aggregates were abundant in gas-hydrate-rich sediments with extremely high rates of methane-based sulphate reduction, and apparently mediate anaerobic oxidation of methane.     

广西钦州湾浮游植物群落结构特征

在广西钦州湾海域设置15个调查站位,分别于2010年5月（春季）、8月（夏季）、11月（秋季）和2011年2月（冬季）采集表层海水,用Shannon—Wiener多样性指数和Pielou均匀度指数分析该海域浮游植物种类组成、优势种类、丰度的变化以及群落多样性等群落结构特征。共鉴定浮游植物79属193种（包括变型和变种）,隶属于6个门,硅藻种类最多,共48属149种,占总种类的77．2％,其种数和丰度都占绝对优势,平均丰度为10．47×10^4cells／L;其次为甲藻,16属28种,占总种类的14．5％,平均丰度为0．46×10^4cells／L。浮游植物丰度0．49×10^4～67．74×10^4cells／L,平均值为11．94×10^4cells／L,丰度变化为典型双峰型,春秋季高,夏冬季低。调查期间共出现10种优势种,不同季节优势种既有交叉又有演替。浮游植物群落的多样性指数冬季最高,春季最低。     

The virophage as a unique parasite of the giant mimivirus

Viruses are obligate parasites of Eukarya, Archaea and Bacteria. Acanthamoeba polyphaga mimivirus (APMV) is the largest known virus; it grows only in amoeba and is visible under the optical microscope. Mimivirus possesses a 1,185-kilobase double-stranded linear chromosome whose coding capacity is greater than that of numerous bacteria and archaea1, 2, 3. Here we describe an icosahedral small virus, Sputnik, 50 nm in size, found associated with a new strain of APMV. Sputnik cannot multiply in Acanthamoeba castellanii but grows rapidly, after an eclipse phase, in the giant virus factory found in amoebae co-infected with APMV4. Sputnik growth is deleterious to APMV and results in the production of abortive forms and abnormal capsid assembly of the host virus. The Sputnik genome is an 18.343-kilobase circular double-stranded DNA and contains genes that are linked to viruses infecting each of the three domains of life Eukarya, Archaea and Bacteria. Of the 21 predicted protein-coding genes, eight encode proteins with detectable homologues, including three proteins apparently derived from APMV, a homologue of an archaeal virus integrase, a predicted primase-helicase, a packaging ATPase with homologues in bacteriophages and eukaryotic viruses, a distant homologue of bacterial insertion sequence transposase DNA-binding subunit, and a Zn-ribbon protein. The closest homologues of the last four of these proteins were detected in the Global Ocean Survey environmental data set5, suggesting that Sputnik represents a currently unknown family of viruses. Considering its functional analogy with bacteriophages, we classify this virus as a virophage. The virophage could be a vehicle mediating lateral gene transfer between giant viruses.     

Significant contribution of Archaea to extant biomass in marine subsurface sediments

Deep drilling into the marine sea floor has uncovered a vast sedimentary ecosystem of microbial cells. Extrapolation of direct counts of stained microbial cells to the total volume of habitable marine subsurface sediments suggests that between 56 Pg (ref. 1) and 303 Pg (ref. 3) of cellular carbon could be stored in this largely unexplored habitat. From recent studies using various culture-independent techniques, no clear picture has yet emerged as to whether Archaea or Bacteria are more abundant in this extensive ecosystem. Here we show that in subsurface sediments buried deeper than 1 m in a wide range of oceanographic settings at least 87% of intact polar membrane lipids, biomarkers for the presence of live cells, are attributable to archaeal membranes, suggesting that Archaea constitute a major fraction of the biomass. Results obtained from modified quantitative polymerase chain reaction and slot-blot hybridization protocols support the lipid-based evidence and indicate that these techniques have previously underestimated archaeal biomass. The lipid concentrations are proportional to those of total organic carbon. On the basis of this relationship, we derived an independent estimate of amounts of cellular carbon in the global marine subsurface biosphere. Our estimate of 90 Pg of cellular carbon is consistent, within an order of magnitude, with previous estimates, and underscores the importance of marine subsurface habitats for global biomass budgets.     

大蕉胚性培养物及其原生质体再生植株的染色体分析

 采用看护培养法对大蕉胚性细胞悬浮系（Embryogenic cell suspensions, ECS）来源的原生质体进行培养,并研究了不同品种的看护细胞对原生质体培养的影响,以及大蕉ECS及其原生质体再生植株的染色体数目。结果发现,采用贡蕉ECS作为看护细胞时,大蕉原生质体培养15 d后细胞分裂频率达到8.5%,培养30 d后细胞团形成率为0.35%;而以大蕉ECS作为看护细胞时,全部原生质体褐化,不能正常发育。染色体检测结果表明,大蕉ECS的染色体数目不稳定,除含有正常的三倍体染色体数目的细胞（2n=3x=33）外,还出现大量染色体数目异常的细胞。其中绝大部分细胞含有多倍和非整倍的染色体数目,仅14.5%的细胞含正常三倍体染色体数目;但通过ECS原生质体培养获得的再生植株具有正常的三倍体染色体数目（2n=3x=33）。     

Redistribution of energy available for ocean mixing by long-range propagation of internal waves

Ocean mixing, which affects pollutant dispersal, marine productivity and global climate, largely results from the breaking of internal gravity waves--disturbances propagating along the ocean's internal stratification. A global map of internal-wave dissipation would be useful in improving climate models, but would require knowledge of the sources of internal gravity waves and their propagation. Towards this goal, I present here computations of horizontal internal-wave propagation from 60 historical moorings and relate them to the source terms of internal waves as computed previously. Analysis of the two most energetic frequency ranges--near-inertial frequencies and semidiurnal tidal frequencies--reveals that the fluxes in both frequency bands are of the order of 1 kW x m(-1) (that is, 15-50% of the energy input) and are directed away from their respective source regions. However, the energy flux due to near-inertial waves is stronger in winter, whereas the tidal fluxes are uniform throughout the year. Both varieties of internal waves can thus significantly affect the space-time distribution of energy available for global mixing.     

丹江口水库上下游古菌优势菌群落结构特征分析

采用16S rRNA Illumina Miseq高通量测序技术, 分析丹江口水库库区及汉江下游古菌物种组成, 并对大坝上、下游水体与沉积物中占优势的氨氧化古菌(Ammonia-oxidizing archaea, AOA)和产甲烷古菌(Methanogenic archaea)群落结构进行分析。结果表明, 优势种群落结构组成受到水体与沉积物样本差异的影响, 可由氨氧化古菌的好氧特性与产甲烷古菌的厌氧特性合理地解释。网络图分析表明, 丹江口水库上游氨氧化古菌与产甲烷古菌具有显著的相关关系。受丹江口水库运行的影响, 大坝下游水体及沉积物中氨氧化古菌丰度皆比大坝上游少, 而沉积物中产甲烷古菌丰度较高, 二者间相关性不明显。     

青藏高原东缘风毛菊属中两种植物的核型报道

利用压片法研究青藏高原东缘两种风毛菊属(Saussurea DC.)植物的染色体数目和核型,结果表明,紫苞雪莲(S.iodostegia)和抱茎风毛菊(S.chingiana)的染色体数目和核型分别为2n=2x=32=18m+14sm,2n=2x=28=24m+2sm+2st.根据Stebbins提出的核型分类原则,这2个种的核型都为2A型.2个种的染色体中均未发现随体.     

川产五味子五个种、变种核型研究

本文首次报导了我国川产五味子五个种、变种的核型研究结果,即翅枝五味子Schisandra henryi、红花五味子S.rubriflora、华中五味子S.sphenanthera、柔毛五味子S.pubescens、毛脉五味子S.pbueecens var.pubineryis。它们的染色体都是28条,核型比较对称。翅枝五味子、柔毛五味子和毛脉五味子的核型公式为:2n=28=24m+4sm,红花五味子的核型公式为:2n=28=22m+6sm,华中五味子的核型公式为:2n=28=26m+2sm。     

一种纳米计算结构上的(m,n)选择网络

通过分析一种新的结构模型--Cell MatrixTM,以及在其上实现的(m,n)选择网络,在晶格结构上实现比较器单元,然后构建互连网络连接各级比较器,从而实现了平衡分组选择网络.实验用晶格开销数目和晶格延迟时间数来衡量算法实现的复杂度,给出了该网络的开销(均是多项式级),具有良好的使用性.该模型上算法的实现过程以及开销分析,体现了Cell MatrixTM结构上计算的便捷性与独特性.     

Novel microbial communities of the Haakon Mosby mud volcano and their role as a methane sink

Mud volcanism is an important natural source of the greenhouse gas methane to the hydrosphere and atmosphere. Recent investigations show that the number of active submarine mud volcanoes might be much higher than anticipated (for example, see refs 3-5), and that gas emitted from deep-sea seeps might reach the upper mixed ocean. Unfortunately, global methane emission from active submarine mud volcanoes cannot be quantified because their number and gas release are unknown. It is also unclear how efficiently methane-oxidizing microorganisms remove methane. Here we investigate the methane-emitting Haakon Mosby Mud Volcano (HMMV, Barents Sea, 72 degrees N, 14 degrees 44' E; 1,250 m water depth) to provide quantitative estimates of the in situ composition, distribution and activity of methanotrophs in relation to gas emission. The HMMV hosts three key communities: aerobic methanotrophic bacteria (Methylococcales), anaerobic methanotrophic archaea (ANME-2) thriving below siboglinid tubeworms, and a previously undescribed clade of archaea (ANME-3) associated with bacterial mats. We found that the upward flow of sulphate- and oxygen-free mud volcano fluids restricts the availability of these electron acceptors for methane oxidation, and hence the habitat range of methanotrophs. This mechanism limits the capacity of the microbial methane filter at active marine mud volcanoes to <40% of the total flux.     

皖西天堂寨三种黄精属植物的核型研究

首次报道了皖西天堂寨三种黄精属(Polygonatum)植物的染色体数目和核型,结果如下:湖北黄精(P. zanlanscianense) 核型为20n=2x=28=10m 8sm 10st,染色体长度比值3.49,属于3B核型;多花黄精(P. cyrtonema)核型为 2n=2x=22=2m 18sm 4st, 染色体长度比值2.38,属于3B核型;玉竹(P. odoratum)核型为2n=2x=18=8m 10sm(3sc), 染色体长度比值2.84, 属于2B核型.分别与产自其它地区的同种植物的染色体数目和核型差异明显.