Prokaryotic cells of the deep sub-seafloor biosphere identified as living bacteria

Chemical analyses of the pore waters from hundreds of deep ocean sediment cores have over decades provided evidence for ongoing processes that require biological catalysis by prokaryotes. This sub-seafloor activity of microorganisms may influence the surface Earth by changing the chemistry of the ocean and by triggering the emission of methane, with consequences for the marine carbon cycle and even the global climate. Despite the fact that only about 1% of the total marine primary production of organic carbon is available for deep-sea microorganisms, sub-seafloor sediments harbour over half of all prokaryotic cells on Earth. This estimation has been calculated from numerous microscopic cell counts in sediment cores of the Ocean Drilling Program. Because these counts cannot differentiate between dead and alive cells, the population size of living microorganisms is unknown. Here, using ribosomal RNA as a target for the technique known as catalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH), we provide direct quantification of live cells as defined by the presence of ribosomes. We show that a large fraction of the sub-seafloor prokaryotes is alive, even in very old (16 million yr) and deep (> 400 m) sediments. All detectable living cells belong to the Bacteria and have turnover times of 0.25-22 yr, comparable to surface sediments.     

Major viral impact on the functioning of benthic deep-sea ecosystems

Viruses are the most abundant biological organisms of the world's oceans. Viral infections are a substantial source of mortality in a range of organisms-including autotrophic and heterotrophic plankton-but their impact on the deep ocean and benthic biosphere is completely unknown. Here we report that viral production in deep-sea benthic ecosystems worldwide is extremely high, and that viral infections are responsible for the abatement of 80% of prokaryotic heterotrophic production. Virus-induced prokaryotic mortality increases with increasing water depth, and beneath a depth of 1,000 m nearly all of the prokaryotic heterotrophic production is transformed into organic detritus. The viral shunt, releasing on a global scale approximately 0.37-0.63 gigatonnes of carbon per year, is an essential source of labile organic detritus in the deep-sea ecosystems. This process sustains a high prokaryotic biomass and provides an important contribution to prokaryotic metabolism, allowing the system to cope with the severe organic resource limitation of deep-sea ecosystems. Our results indicate that viruses have an important role in global biogeochemical cycles, in deep-sea metabolism and the overall functioning of the largest ecosystem of our biosphere.     

四川盆地中二叠统栖霞组沉积相展布及勘探意义

通过对四川盆地中二叠统栖霞组盆缘野外剖面、岩芯详细观察,结合地震、测井等资料研究分析,建立标准岩性、古生物地层剖面,识别相标志,将沉积相划分为开阔台地相、台地边缘相、斜坡相及盆地相,在平武-茂汶-小金一带识别斜坡相和盆地相,川西地区发育台地边缘滩相带,川西-川中隆起带为开阔台地相台内滩亚相发育带;川北-蜀南低隆带为开阔台地相开阔海和台内滩亚相;川东地区为开阔台地相台内浅洼亚相。区域地层对比及沉积相展布表明,二叠系沉积前古地貌控制栖霞组沉积格局,加里东古隆起地貌及川西裂陷盆地发育共同控制川西地区栖霞组台地边缘相展布。栖霞组台缘相带发育规模相控白云岩储层,与下寒武统优质烃源层形成良好源储匹配关系,栖霞组台缘相带是深层海相碳酸盐岩重点勘探领域,泥盆系-二叠系具有相同源储匹配关系,具备发育大型构造岩性圈闭气藏的地质条件,推覆体下盘发育大型隐伏构造高带,是整体勘探、立体勘探重要有利区带。     

Photosynthetic microbial mats in the 3,416-Myr-old ocean

Recent re-evaluations of the geological record of the earliest life on Earth have led to the suggestion that some of the oldest putative microfossils and carbonaceous matter were formed through abiotic hydrothermal processes. Similarly, many early Archaean (more than 3,400-Myr-old) cherts have been reinterpreted as hydrothermal deposits rather than products of normal marine sedimentary processes. Here we present the results of a field, petrographic and geochemical study testing these hypotheses for the 3,416-Myr-old Buck Reef Chert, South Africa. From sedimentary structures and distributions of sand and mud, we infer that deposition occurred in normal open shallow to deep marine environments. The siderite enrichment that we observe in deep-water sediments is consistent with a stratified early ocean. We show that most carbonaceous matter was formed by photosynthetic mats within the euphotic zone and distributed as detrital matter by waves and currents to surrounding environments. We find no evidence that hydrothermal processes had any direct role in the deposition of either the carbonaceous matter or the enclosing sediments. Instead, we conclude that photosynthetic organisms had evolved and were living in a stratified ocean supersaturated in dissolved silica 3,416 Myr ago.     

呼和湖凹陷地震相

目的 预测海拉尔盆地呼和湖凹陷下白垩统有利储集相带和复合圈闭。方法 在南屯组生油层系弱振幅反射背景上，识别沉积背斜、前积、退积、振幅异常等多种地震相类型，并将它们与测井、岩心及构造图分析相结合。结果 在凹陷内圈定了与主河口有关的扇三角洲前缘、水下扇等骨架砂体的展布，识别出了构造、岩性及复合等多种可能的有利圈闭。结论 南屯组可生油的半深．深湖相带只发育在深陷带和陡坡带，所圈定的陡坡水下扇体具有较好的生储盖和圈闭条件。     

The ring of life provides evidence for a genome fusion origin of eukaryotes

Genomes hold within them the record of the evolution of life on Earth. But genome fusions and horizontal gene transfer seem to have obscured sufficiently the gene sequence record such that it is difficult to reconstruct the phylogenetic tree of life. Here we determine the general outline of the tree using complete genome data from representative prokaryotes and eukaryotes and a new genome analysis method that makes it possible to reconstruct ancient genome fusions and phylogenetic trees. Our analyses indicate that the eukaryotic genome resulted from a fusion of two diverse prokaryotic genomes, and therefore at the deepest levels linking prokaryotes and eukaryotes, the tree of life is actually a ring of life. One fusion partner branches from deep within an ancient photosynthetic clade, and the other is related to the archaeal prokaryotes. The eubacterial organism is either a proteobacterium, or a member of a larger photosynthetic clade that includes the Cyanobacteria and the Proteobacteria.     

Lithospheric thermal-rheological structures of the continental margin in the northern South China Sea

Thermal structures of three deep seismic profiles in the continental margin in the northern South China Sea are calculated, their "thermal" lithospheric thicknesses are evaluated based on the basalt dry solidus, and their rheological structures are evaluated with linear frictional failure criterion and power-law creep equation. "Thermal" lithosphere is about 90 km in thickness in shelf area, and thins toward the slope, lowers to 60-65 km in the lower slope, ocean crust and Xisha Trough. In the mid-west of the studied area, the lithospheric rheological structure in shelf area and Xisha Islands is of four layers: brittle, ductile, brittle and ductile. Because of uprising of heat mantle and thinning of crust and lithosphere in Xisha Trough, the bottom of the upper brittle layer is only buried at 16 km. In the eastern area, the bottom of the upper brittle layer in the north is buried at 20 km or so, while in lower slope and ocean crust, the rheological structure is of two layers of brittle and ductile, and crust and uppermost mantle form one whole brittle layer whose bottom is buried at 30-32 km. Analyses show that the characteristics of rheological structure accord with the seismic result observed. The character of rheological stratification implies that before the extension of the continent margin, there likely was a ductile layer in mid-lower crust. The influence of the existence of ductile layer to the evolution of the continent margin and the different extensions of ductile layer and brittle layer should not be overlooked. Its thickness, depth and extent in influencing continent margin's extension and evolution should be well evaluated in building a dynamic model for the area.     

东北地区早二叠世岩相古地理研究

利用野外地质剖面、关键钻井剖面和区域地质资料,在地层划分对比和构造格局研究基础上,运用沉积相分析的方法,探讨了东北地区早二叠世岩相古地理特征,将早二叠世分为阿瑟尔期-亚丁斯克期、空谷期两个编图单元进行岩相古地理编图,恢复了东北地区早二叠世的岩相古地理面貌。研究表明,早二叠世东北地区主要发育半深海沉积体系、浅海陆棚沉积体系、碳酸盐台地沉积体系、无障壁海岸沉积体系、障壁海岸沉积体系及河流沉积体系;阿瑟尔期-亚丁斯克期存在漠河古陆、松辽古陆、佳木斯古陆及华北北缘高地四个古陆,物源区碎屑物质供应充分,研究区为浅海、海陆交互及河流沉积区,周边古陆的格局;至空谷期,松辽古陆消失,研究区为浅海-半深海沉积,周边古陆的格局。     

昆嵛山混合杂岩体的地质特征及成因

昆嵛山混合岩体是胶东东部出露面积最大的岩体,是金牛山金矿带的寄主岩体。野外地质特征以及同位素年代学的研究,确定岩体形成于134.3Ma。但是,在元古代,胶东地区还曾受到栖霞运动的影响,广泛地发生了区域变质作用。岩石学、岩石化学、地球化学等方面的研究结果,表明混合岩的原岩是上地壳沉积岩与来源下地壳或上地幔的火山岩的混合物,岩体由交代-重熔作用形成。混合岩对原岩的许多性质具有明显的继承性。岩体的形成是受牟平—即墨深断裂控制。断裂长期活动所引起的变质作用,混合岩化作用以及成矿作用等地质特征已成为我国东部中生代活动大陆边缘的重要特征之一。     

西秦岭南带中志留统的岩石学特征与沉积环境

详细研究了西秦岭南带中志留统岩石学特征,对遭受重结晶作用的碳酸盐岩进行了结构成因分类。分析了该区中志留世的沉积环境及变化特征。在该区发现的层孔虫生物礁及其它“浅水”标志,表明志留纪时,为若尔盖微古陆北侧的边缘浅海环境。西部为局限陆棚环境,可分为:局限内陆棚、海湾、礁滩-泻湖-潮坪(孤立台地)等亚环境;东部为开阔陆棚环境,可分为浅海砂滩、内陆棚、外陆棚等亚环境。     

模糊环境下的海上溢油应急选址模型

针对海上环境的复杂性和不确定性,为了合理选择海上溢油应急服务设施点,从最大覆盖选址问题进行研究,构建了基于三角模糊数的最大覆盖模型,并给出模型的具体算法.结果表明,该模型对解决模糊环境下的海上溢油应急服务设施点布设是有效的.     

Carbon dioxide release from the North Pacific abyss during the last deglaciation

Atmospheric carbon dioxide concentrations were significantly lower during glacial periods than during intervening interglacial periods, but the mechanisms responsible for this difference remain uncertain. Many recent explanations call on greater carbon storage in a poorly ventilated deep ocean during glacial periods, but direct evidence regarding the ventilation and respired carbon content of the glacial deep ocean is sparse and often equivocal. Here we present sedimentary geochemical records from sites spanning the deep subarctic Pacific that--together with previously published results--show that a poorly ventilated water mass containing a high concentration of respired carbon dioxide occupied the North Pacific abyss during the Last Glacial Maximum. Despite an inferred increase in deep Southern Ocean ventilation during the first step of the deglaciation (18,000-15,000 years ago), we find no evidence for improved ventilation in the abyssal subarctic Pacific until a rapid transition approximately 14,600 years ago: this change was accompanied by an acceleration of export production from the surface waters above but only a small increase in atmospheric carbon dioxide concentration. We speculate that these changes were mechanistically linked to a roughly coeval increase in deep water formation in the North Atlantic, which flushed respired carbon dioxide from northern abyssal waters, but also increased the supply of nutrients to the upper ocean, leading to greater carbon dioxide sequestration at mid-depths and stalling the rise of atmospheric carbon dioxide concentrations. Our findings are qualitatively consistent with hypotheses invoking a deglacial flushing of respired carbon dioxide from an isolated, deep ocean reservoir, but suggest that the reservoir may have been released in stages, as vigorous deep water ventilation switched between North Atlantic and Southern Ocean source regions.     

暖池区1.53 Ma以来上层海水变化的颗石藻证据

对位于西太平洋暖池区核心的大洋钻探计划(ODP)807站1.53Ma以来深海沉积样品进行了颗石藻化石分析,通过Florisphaeraprofunda数量百分比讨论了营养跃层深度变化的趋势,并计算了初级生产力.结果表明1.53Ma以来暖池核心区海水营养跃层经历了明显变化:从1.53~0.9Ma,营养跃层深度逐渐变浅;自0.9Ma起营养跃层开始变深并保持到0.48Ma;0.48~0.28Ma之间是营养跃层深度明显变浅的一个时期,在这以后营养跃层逐渐变深.根据颗石藻得出的海水营养跃层变化与初级生产力变化基本一致,也与根据浮游有孔虫转换函数得出的温跃层深度变化趋势基本一致.对比ODP807站和南海ODP1143站F.profunda数量百分比和初级生产力变化曲线,两站在0.9Ma以前变化的趋势相反,而0.9Ma以后基本一致.说明0.9Ma以前暖池核心地区与边缘区上层海水的变化有差异,而0.9Ma以后两者则趋同.     

Eocene global warming events driven by ventilation of oceanic dissolved organic carbon

'Hyperthermals' are intervals of rapid, pronounced global warming known from six episodes within the Palaeocene and Eocene epochs (～65-34 million years (Myr) ago). The most extreme hyperthermal was the ～170 thousand year (kyr) interval of 5-7 °C global warming during the Palaeocene-Eocene Thermal Maximum (PETM, 56?Myr ago). The PETM is widely attributed to massive release of greenhouse gases from buried sedimentary carbon reservoirs, and other, comparatively modest, hyperthermals have also been linked to the release of sedimentary carbon. Here we show, using new 2.4-Myr-long Eocene deep ocean records, that the comparatively modest hyperthermals are much more numerous than previously documented, paced by the eccentricity of Earth's orbit and have shorter durations (～40?kyr) and more rapid recovery phases than the PETM. These findings point to the operation of fundamentally different forcing and feedback mechanisms than for the PETM, involving redistribution of carbon among Earth's readily exchangeable surface reservoirs rather than carbon exhumation from, and subsequent burial back into, the sedimentary reservoir. Specifically, we interpret our records to indicate repeated, large-scale releases of dissolved organic carbon (at least 1,600 gigatonnes) from the ocean by ventilation (strengthened oxidation) of the ocean interior. The rapid recovery of the carbon cycle following each Eocene hyperthermal strongly suggests that carbon was re-sequestered by the ocean, rather than the much slower process of silicate rock weathering proposed for the PETM. Our findings suggest that these pronounced climate warming events were driven not by repeated releases of carbon from buried sedimentary sources, but, rather, by patterns of surficial carbon redistribution familiar from younger intervals of Earth history.     

海洋中硒的双箱模式及地球化学特性

海洋浮游植物对海水硒的富集系数为228,表明硒是一种生物亲合力很强的元素。在真光层中,75％的硒为海洋生物所利用,显示硒在海洋环境是中等生物制约元素。28％的含硒生物颗粒沉溶解在深层水体,导致硒在表层水中消和浑水中富集,类似于营养盐。利用Broeeker双箱模式计算,粗略地显示了硒在大洋中的循环图象,初步确立各界面硒的通量。     

Archaeal dominance in the mesopelagic zone of the Pacific Ocean

The ocean's interior is Earth's largest biome. Recently, cultivation-independent ribosomal RNA gene surveys have indicated a potential importance for archaea in the subsurface ocean. But quantitative data on the abundance of specific microbial groups in the deep sea are lacking. Here we report a year-long study of the abundance of two specific archaeal groups (pelagic euryarchaeota and pelagic crenarchaeota) in one of the ocean's largest habitats. Monthly sampling was conducted throughout the water column (surface to 4,750 m) at the Hawai'i Ocean Time-series station. Below the euphotic zone (> 150 m), pelagic crenarchaeota comprised a large fraction of total marine picoplankton, equivalent in cell numbers to bacteria at depths greater than 1,000 m. The fraction of crenarchaeota increased with depth, reaching 39% of total DNA-containing picoplankton detected. The average sum of archaea plus bacteria detected by rRNA-targeted fluorescent probes ranged from 63 to 90% of total cell numbers at all depths throughout our survey. The high proportion of cells containing significant amounts of rRNA suggests that most pelagic deep-sea microorganisms are metabolically active. Furthermore, our results suggest that the global oceans harbour approximately 1.3 x 10(28) archaeal cells, and 3.1 x 10(28) bacterial cells. Our data suggest that pelagic crenarchaeota represent one of the ocean's single most abundant cell types.     

任意形状港湾的水波振动

利用线性势流理论对定常水深且置于广阔海域中的任意形状港湾在入射波作用下的港内振动进行了研究，利用源汇分布法，在港湾边界上布置源汇，并在入口处利用内外场的匹配条件，来求解置于港湾边界上的源强，进而求得港湾内的整个流场，作为算例，就一矩形港湾在不同方向，不同波数入射波情况下的港内水波振动问题进行了计算分析，结果表明，在一定入射波条件下矩形港湾会产生明显的水波振动，双开口港湾的共振程度在某些情况下要小于单开口情况。     

Genomic and functional adaptation in surface ocean planktonic prokaryotes

The understanding of marine microbial ecology and metabolism has been hampered by the paucity of sequenced reference genomes. To this end, we report the sequencing of 137 diverse marine isolates collected from around the world. We analysed these sequences, along with previously published marine prokaryotic genomes, in the context of marine metagenomic data, to gain insights into the ecology of the surface ocean prokaryotic picoplankton (0.1-3.0?μm size range). The results suggest that the sequenced genomes define two microbial groups: one composed of only a few taxa that are nearly always abundant in picoplanktonic communities, and the other consisting of many microbial taxa that are rarely abundant. The genomic content of the second group suggests that these microbes are capable of slow growth and survival in energy-limited environments, and rapid growth in energy-rich environments. By contrast, the abundant and cosmopolitan picoplanktonic prokaryotes for which there is genomic representation have smaller genomes, are probably capable of only slow growth and seem to be relatively unable to sense or rapidly acclimate to energy-rich conditions. Their genomic features also lead us to propose that one method used to avoid predation by viruses and/or bacterivores is by means of slow growth and the maintenance of low biomass.     

Eocene/Oligocene ocean de-acidification linked to Antarctic glaciation by sea-level fall

One of the most dramatic perturbations to the Earth system during the past 100 million years was the rapid onset of Antarctic glaciation near the Eocene/Oligocene epoch boundary (approximately 34 million years ago). This climate transition was accompanied by a deepening of the calcite compensation depth--the ocean depth at which the rate of calcium carbonate input from surface waters equals the rate of dissolution. Changes in the global carbon cycle, rather than changes in continental configuration, have recently been proposed as the most likely root cause of Antarctic glaciation, but the mechanism linking glaciation to the deepening of calcite compensation depth remains unclear. Here we use a global biogeochemical box model to test competing hypotheses put forward to explain the Eocene/Oligocene transition. We find that, of the candidate hypotheses, only shelf to deep sea carbonate partitioning is capable of explaining the observed changes in both carbon isotope composition and calcium carbonate accumulation at the sea floor. In our simulations, glacioeustatic sea-level fall associated with the growth of Antarctic ice sheets permanently reduces global calcium carbonate accumulation on the continental shelves, leading to an increase in pelagic burial via permanent deepening of the calcite compensation depth. At the same time, fresh limestones are exposed to erosion, thus temporarily increasing global river inputs of dissolved carbonate and increasing seawater delta13C. Our work sheds new light on the mechanisms linking glaciation and ocean acidity change across arguably the most important climate transition of the Cenozoic era.