Cultivation of the ubiquitous SAR11 marine bacterioplankton clade

The alpha-proteobacterial lineage that contains SAR11 and related ribosomal RNA gene clones was among the first groups of organisms to be identified when cultivation-independent approaches based on rRNA gene cloning and sequencing were applied to survey microbial diversity in natural ecosystems. This group accounts for 26% of all ribosomal RNA genes that have been identified in sea water and has been found in nearly every pelagic marine bacterioplankton community studied by these methods. The SAR11 clade represents a pervasive problem in microbiology: despite its ubiquity, it has defied cultivation efforts. Genetic evidence suggests that diverse uncultivated microbial taxa dominate most natural ecosystems, which has prompted widespread efforts to elucidate the geochemical activities of these organisms without the benefit of cultures for study. Here we report the isolation of representatives of the SAR11 clade. Eighteen cultures were initially obtained by means of high-throughput procedures for isolating cell cultures through the dilution of natural microbial communities into very low nutrient media. Eleven of these cultures have been successfully passaged and cryopreserved for future study. The volume of these cells, about 0.01 micro m(3), places them among the smallest free-living cells in culture.     

The condensing vacuole of exocrine cells is more acidic than the mature secretory vesicle

A number of intracellular, membrane-bound compartments in both the endocytic and exocytic pathways of eukaryotic cells have an acidic internal pH. In endocrine cells, the mature secretory vesicle has an acidic pH; secretory vesicles isolated from exocrine cells, however, appear to have a neutral pH. Recently we have used a newly developed immunocytochemical technique to map low-pH compartments in insulin-secreting islet cells with the electron microscope and find that during the maturation of the secretory vesicle there is a progressive acidification of these vesicles that begins as soon as the trans Golgi condensing vacuoles form. Now we have used this technique to examine two exocrine cells: the pancreatic acinar cell and the parotid serous cell. In both cell types, the trans Golgi condensing vacuoles are acidic and accumulate the low-pH probe to the same extent as condensing vacuoles of insulin-secreting islet cells. Unlike insulin-secreting cells, however, maturation of the granules is accompanied by a return of luminal pH to near neutrality. Therefore, although the pH of storage granules in exocrine and endocrine cells is different, the pH of the condensing vacuoles in both cells is acidic.     

A ubiquitous thermoacidophilic archaeon from deep-sea hydrothermal vents

Deep-sea hydrothermal vents are important in global biogeochemical cycles, providing biological oases at the sea floor that are supported by the thermal and chemical flux from the Earth's interior. As hot, acidic and reduced hydrothermal fluids mix with cold, alkaline and oxygenated sea water, minerals precipitate to form porous sulphide-sulphate deposits. These structures provide microhabitats for a diversity of prokaryotes that exploit the geochemical and physical gradients in this dynamic ecosystem. It has been proposed that fluid pH in the actively venting sulphide structures is generally low (pH < 4.5), yet no extreme thermoacidophile has been isolated from vent deposits. Culture-independent surveys based on ribosomal RNA genes from deep-sea hydrothermal deposits have identified a widespread euryarchaeotal lineage, DHVE2 (deep-sea hydrothermal vent euryarchaeotic 2). Despite the ubiquity and apparent deep-sea endemism of DHVE2, cultivation of this group has been unsuccessful and thus its metabolism remains a mystery. Here we report the isolation and cultivation of a member of the DHVE2 group, which is an obligate thermoacidophilic sulphur- or iron-reducing heterotroph capable of growing from pH 3.3 to 5.8 and between 55 and 75 degrees C. In addition, we demonstrate that this isolate constitutes up to 15% of the archaeal population, providing evidence that thermoacidophiles may be key players in the sulphur and iron cycling at deep-sea vents.     

Chloroquine and ammonium chloride prevent terminal glycosylation of immunoglobulins in plasma cells without affecting secretion

The generation of an acidic pH in intracellular organelles is required for several membrane and protein recycling processes. For instance, the internalization of ligands by receptor-mediated endocytosis is followed by the development of an acidic pH inside endosomes; this allows dissociation of the ligand, which is then transported to the lysosomes, from the receptor, which is recycled to the cell surface. There is evidence that part of this recycling process involves the distal region of the Golgi complex, where terminal glycosylation occurs: when the plasma membrane transferrin receptor is desialylated by neuraminidase treatment, it acquires new sialic acid molecules after endocytosis and before cell-surface re-expression. Golgi membranes have been shown to contain a proton pump and the distal Golgi cisternae appear to have an acidic content. Here, we have studied the effects of chloroquine and ammonium chloride, which raise the pH of acidic intracellular compartments, on the processing and secretion of immunoglobulins by plasma cells. Sialic acid transfer to terminal galactose residues, a reaction known to occur in the distal Golgi shortly before secretion, is completely and rapidly inhibited in the presence of these drugs, without significant modification of the secretion rate. This effect is accompanied by a dilatation of the Golgi cisternae and is not rapidly reversible.     

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.     

里氏木霉和黑曲霉产酸性木聚糖酶及酶学特性比较

【目的】对黑曲霉和里氏木霉产酸性木聚糖酶的性能及所产粗酶的酶学特性进行分析比较,尤其是考察pH值为4时木聚糖酶酶活力及稳定性,从而确定潜在的较为理想的酸性木聚糖酶。【方法】将里氏木霉和黑曲霉接种至培养基进行产酶培养,比较分析两者的酸性木聚糖酶、酸性木糖苷酶的酶活力及酶学特性。【结果】黑曲霉酸性木聚糖酶和酸性木糖苷酶的酶活力最高分别达(52.36±2.61)U/mL和(0.57±0.01)U/mL,酸性木聚糖酶最适温度和pH值分别为55℃、5.0,酸性木糖苷酶最适温度和pH值分别为75℃、5.0;里氏木霉酸性木聚糖酶和酸性木糖苷酶的酶活力最高分别达(10.12±0.95)U/mL和(0.32±0.05)U/mL,酸性木聚糖酶最适温度和pH值分别为65℃、6.5,酸性木糖苷酶最适温度和pH值分别为65℃、4.5。黑曲霉和里氏木霉的酸性木聚糖酶兼有酸性CMCase酶活力,分别为(5.26±0.21)U/mL、(1.72±0.21)U/mL。【结论】黑曲霉所产酸性木聚糖酶明显比里氏木霉的更优良,是潜在的较为理想的酸性木聚糖酶。     

A 'molten-globule' membrane-insertion intermediate of the pore-forming domain of colicin A

The 'molten' globular conformation of a protein is compact with a native secondary structure but a poorly defined tertiary structure. Molten globular states are intermediates in protein folding and unfolding and they may be involved in the translocation or insertion of proteins into membranes. Here we investigate the membrane insertion of the pore-forming domain of colicin A, a bacteriocin that depolarizes the cytoplasmic membrane of sensitive cells. We find that this pore-forming domain, the insertion of which depends on pH, undergoes a native to molten globule transition at acidic pH. The variation of the kinetic constant of membrane insertion of the protein into negatively charged lipid vesicles as a function of the interfacial pH correlates with the appearance of the acidic molten globular state, indicating that this state could be an intermediate formed during the insertion of colicin A into membranes.     

从文蛤分离丝状真菌

分离海洋微生物是开发海洋药物的重要内容.对共附生在双壳贝文蛤的真菌,采用平板直接分离和液体富集后涂布分离两种方法,以及6种不同的分离培养基,分离到23株丝状真菌,其中9株丝状真菌在淡水及海水培养基中均能生长、繁殖.对分离菌(W16)的生长特性研究结果表明,盐浓度、pH值,以及海水和淡水的不同环境,对其生长和代谢有明显的影响.     

The amount of carbon released from peat and forest fires in Indonesia during 1997

Tropical peatlands are one of the largest near-surface reserves of terrestrial organic carbon, and hence their stability has important implications for climate change. In their natural state, lowland tropical peatlands support a luxuriant growth of peat swamp forest overlying peat deposits up to 20 metres thick. Persistent environmental change-in particular, drainage and forest clearing-threatens their stability, and makes them susceptible to fire. This was demonstrated by the occurrence of widespread fires throughout the forested peatlands of Indonesia during the 1997 El Ni?o event. Here, using satellite images of a 2.5 million hectare study area in Central Kalimantan, Borneo, from before and after the 1997 fires, we calculate that 32% (0.79 Mha) of the area had burned, of which peatland accounted for 91.5% (0.73 Mha). Using ground measurements of the burn depth of peat, we estimate that 0.19-0.23 gigatonnes (Gt) of carbon were released to the atmosphere through peat combustion, with a further 0.05 Gt released from burning of the overlying vegetation. Extrapolating these estimates to Indonesia as a whole, we estimate that between 0.81 and 2.57 Gt of carbon were released to the atmosphere in 1997 as a result of burning peat and vegetation in Indonesia. This is equivalent to 13-40% of the mean annual global carbon emissions from fossil fuels, and contributed greatly to the largest annual increase in atmospheric CO(2) concentration detected since records began in 1957 (ref. 1).     

Discovery of novel intermediate forms redefines the fungal tree of life

Fungi are the principal degraders of biomass in terrestrial ecosystems and establish important interactions with plants and animals. However, our current understanding of fungal evolutionary diversity is incomplete and is based upon species amenable to growth in culture. These culturable fungi are typically yeast or filamentous forms, bound by a rigid cell wall rich in chitin. Evolution of this body plan was thought critical for the success of the Fungi, enabling them to adapt to heterogeneous habitats and live by osmotrophy: extracellular digestion followed by nutrient uptake. Here we investigate the ecology and cell biology of a previously undescribed and highly diverse form of eukaryotic life that branches with the Fungi, using environmental DNA analyses combined with fluorescent detection via DNA probes. This clade is present in numerous ecosystems including soil, freshwater and aquatic sediments. Phylogenetic analyses using multiple ribosomal RNA genes place this clade with Rozella, the putative primary branch of the fungal kingdom. Tyramide signal amplification coupled with group-specific fluorescence in situ hybridization reveals that the target cells are small eukaryotes of 3-5?μm in length, capable of forming a microtubule-based flagellum. Co-staining with cell wall markers demonstrates that representatives from the clade do not produce a chitin-rich cell wall during any of the life cycle stages observed and therefore do not conform to the standard fungal body plan. We name this highly diverse clade the cryptomycota in anticipation of formal classification.     

Evidence from fluid inclusions for microbial methanogenesis in the early Archaean era

Methanogenic microbes may be one of the most primitive organisms, although it is uncertain when methanogens first appeared on Earth. During the Archaean era (before 2.5 Gyr ago), methanogens may have been important in regulating climate, because they could have provided sufficient amounts of the greenhouse gas methane to mitigate a severely frozen condition that could have resulted from lower solar luminosity during these times. Nevertheless, no direct geological evidence has hitherto been available in support of the existence of methanogens in the Archaean period, although circumstantial evidence is available in the form of approximately 2.8-Gyr-old carbon-isotope-depleted kerogen. Here we report crushing extraction and carbon isotope analysis of methane-bearing fluid inclusions in approximately 3.5-Gyr-old hydrothermal precipitates from Pilbara craton, Australia. Our results indicate that the extracted fluids contain microbial methane with carbon isotopic compositions of less than -56 per thousand included within original precipitates. This provides the oldest evidence of methanogen (> 3.46 Gyr ago), pre-dating previous geochemical evidence by about 700 million years.     

纤溶酶高产菌株筛选及其液体发酵条件研究

研究实验室自主分离的2株纤溶酶高产菌株发酵条件,采用4因素、3水平的正交试验设计方法对液体发酵培养基的碳源、氮源、无机盐进行了优化,并对培养基初始pH、发酵时间、发酵温度对产酶量的影响进行了测定.结果表明:菌株1液体发酵合适的产酶培养基配方为大豆粉的质量分数为6%,葡萄糖2%,CaCl2 0.06%,MgSO4 0.07%;菌株2液体发酵合适的产酶培养基配方为大豆粉的质量分数为6%,玉米淀粉2%,CaCl2 0.06%,MgSO4 0.07%.培养基初始pH均为6.5时酶活性最高;发酵温度均以38℃最好;而菌株1和菌株2的适宜发酵时间分别为48～84 h和60～84 h.在优化条件下,菌株1、菌株2液体发酵最高酶活分别为306.46 IU/mL和319.76 IU/mL。     

Primate eta-globin DNA sequences and man's place among the great apes

Molecular studies indicate that chimpanzee and gorilla are the closest relatives of man (refs 1-7 and refs therein). The small molecular distances found point to late ancestral separations, with the most recent being between chimpanzee and man, as judged by DNA hybridization. Kluge and Schwartz contest these conclusions: morphological characters group a chimpanzee-gorilla clade with the Asian ape orang-utan in Kluge's cladistic study and with an orang-utan-human clade in Schwartz's study. Clearly, extensive sequencing of nuclear DNA is needed to resolve by cladistic analysis the branching order within Hominoidea. Towards this goal, we are sequencing orthologues of the primate psi eta-globin locus. Here, we compare the newly completed sequences of orang-utan and rhesus monkey with human, chimpanzee, gorilla, owl monkey, lemur and goat orthologues. Our findings substantially increase the evidence indicative of a human-chimpanzee-gorilla clade with ancestral separations around 8 to 6 Myr ago. We also verify that neutral hominoid DNA evolved at markedly retarded rates.     

A new mechanism for the neutralization of enveloped viruses by antiviral antibody

Despite the considerable research that has been carried out into viral neutralization by antiviral antibody, its mechanisms remain poorly understood. Cases have been reported in which antiviral antibody can inhibit viral replication without inhibiting the binding and uptake of virus by susceptible cells. It has been shown that many enveloped viruses enter their target cells by endocytosis and are subsequently located in cellular compartments of increasing acidity. With several enveloped viruses this acidic pH can catalyse a fusion reaction between the membrane of the virus particle and that of a prelysosomal endosome, thus enabling the viral core to enter the cytosol and replication to commence. We have recently demonstrated that such an endosomal fusion event at mild acidic pH is involved in the entry pathway of the enveloped flavivirus, West Nile virus (WNV), into macrophages. We now show that antiviral antibody can neutralize WNV by inhibiting this intraendosomal acid-catalysed fusion step and we speculate on possible implications for the future design of antiviral vaccines.     

纳豆激酶产生菌的固体发酵参数优化

对影响纳豆激酶产生菌固体发酵时产酶影响因子如碳源/氮源、含水量、温度、pH和培养时间等进行了优化.实验结果表明,菌株1适宜的固体发酵产酶培养基豆粕:麸皮比为3∶1;菌株2适宜的固体发酵产酶培养基豆粕:麸皮比为1∶1时产酶活性最高;菌株1适宜的培养基含水以50%最好,菌株2以70%最好;培养基初始pH均在7.0时酶活最高;发酵温度均以25℃最好,不易超过30℃;两个菌株的适宜发酵时间分别为36 h(菌株1)和72 h(菌株2).在优化发酵条件下,两个菌株单位发酵物中纤溶酶平均酶活力可分别达到1 407.25 U/g(菌株1)和953 U/g(菌株2).     

襄阳孔明菜卤水中耐盐污染菌的分离与鉴定

襄阳孔明菜是在高盐下腌制的一种腌菜,在大规模露天腌制过程中,由于雨水污染等原因会在卤水表面长白色菌膜,导致孔明菜的软化,影响口感．从襄阳孔明菜卤水污染物中分离污染菌并进行鉴定,旨在对防控该污染菌奠定基础．将污染菌膜接种于不同浓度梯度氯化钠的YPD固体培养基上,分别在28℃与37℃培养3d后,从28℃分离到一种耐盐酵母,单菌落呈圆形、乳白色,3d培养直径为0．1～0．2cm,表面湿润、粘稠、易挑起．对该菌的进一步研究显示,该菌可以在含有0％～15％NaCl的YPD培养基中生长,最适生长盐浓度为5％;最适生长温度为28℃,可以在pH值5．5～6．5之间生长,最适生长pH值为6．0．抽提该菌的总DNA,扩增部分18SrDNA片段,测序后进行同源比对,结果显示,该耐盐酵母的18SrDNA序列和Zygosaccharomyces rouxii DoNor8、IFO0510、M2的18SrDNA序列一致性达到100％,根据clustal X和MEGA 4．1建构的系统进化树进行分析,该酵母与Z．rouxii在同一分支上,再结合形态和生理特征,认定分离的嗜盐酵母是Zygosaccharomyces rouxii．该菌的分离和鉴定为研究腌制食品中污染菌的防控有一定意义．     

审美价值的人类学研究

在审美人类学的研究中 ,人类的审美行为与艺术创造不是孤立存在的 ,它与它所处的文化环境、社会环境及自然环境有着千丝万缕的联系 ,而人类的审美行为与艺术创造 ,就是纠缠于这些联系之中 ,它们在一起结成一个混沌的文化整体 ,我们只有将其放在这样的整体中我们才会真正清楚地认识它们。在对人类的审美和艺术的研究中 ,我们最要关心的不仅仅是审美和艺术本身 ,而是它们和人类社会与文化及大自然之间所发生的种种联系     

Adsorption of Cd(II) from acidic aqueous solutions by tourmaline as a novel material

Batch experiments were conducted to investigate the behavior and mechanisms for the adsorption of Cd(Ⅱ) from aqueous solutions by tourmaline under acidic conditions. The results indicated that the adsorption of Cd(Ⅱ) significantly depend on the adsorption time, temperature, and the initial concentration of the metal ion. Furthermore, tourmaline had a very good adsorption capacity for Cd(Ⅱ) in acidic, neutral and alkaline aqueous solutions. This good adsorption capacity is attributed to the observation that tourmaline can automatically adjust the pH values of acidic (except pH 2.0 and 3.0), neutral or alkaline aqueous solutions to 6.4. Specifically, the removal capacity for Cd(Ⅱ) was higher at strongly acidic pH values (in contrast to industrial wastewater pH values) compared to that obtained for other types of adsorbents. Furthermore, the results obtained in this study showed good fits to the Langmuir and Freundlich adsorption isotherms. However, the Langmuir model fit better than the Freundlich model. The maximum uptake of Cd(Ⅱ) by tourmaline was 31.77, 33.11 and 40.16 mg/g at pH 4.0 at 15, 25 and 35°C, respectively. Therefore, tourmaline is an effective adsorbent for the removal of Cd(Ⅱ) from acidic aqueous solutions. In addition, the kinetics for the Cd(Ⅱ) adsorption by tourmaline closely followed the pseudo-second-order model. The thermodynamic parameters indicated that adsorption was feasible, spontaneous, and endothermic. Furthermore, the pH variation after adsorption, ζ-potential, metal ions desorbed and released, and FT-IR analysis indicated that the physisorption and chemisorption mechanisms of tourmaline for heavy metals. These mechanisms included water that was automatically polarized by tourmaline, the ion exchange process, and electropolar adsorption. Among the mechanisms, the automatic polarization of water caused by tourmaline is a unique adsorption mechanism for tourmaline.     

Iron corrosion by novel anaerobic microorganisms

Corrosion of iron presents a serious economic problem. Whereas aerobic corrosion is a chemical process, anaerobic corrosion is frequently linked to the activity of sulphate-reducing bacteria (SRB). SRB are supposed to act upon iron primarily by produced hydrogen sulphide as a corrosive agent and by consumption of 'cathodic hydrogen' formed on iron in contact with water. Among SRB, Desulfovibrio species--with their capacity to consume hydrogen effectively--are conventionally regarded as the main culprits of anaerobic corrosion; however, the underlying mechanisms are complex and insufficiently understood. Here we describe novel marine, corrosive types of SRB obtained via an isolation approach with metallic iron as the only electron donor. In particular, a Desulfobacterium-like isolate reduced sulphate with metallic iron much faster than conventional hydrogen-scavenging Desulfovibrio species, suggesting that the novel surface-attached cell type obtained electrons from metallic iron in a more direct manner than via free hydrogen. Similarly, a newly isolated Methanobacterium-like archaeon produced methane with iron faster than do known hydrogen-using methanogens, again suggesting a more direct access to electrons from iron than via hydrogen consumption.