Identification of archaeon-producing hyperthermophilic alpha-amylase and characterization of the alpha-amylase

The extremely thermophilic anaerobic archaeon strain, HJ21, was isolated from a deep-sea hydrothermal vent, could produce hyperthermophilic alpha-amylase, and later was identified as Thermococcus from morphological, biochemical, and physiological characteristics and the 16S ribosomal RNA gene sequence. The extracellular thermostable alpha-amylase produced by strain HJ21 exhibited maximal activity at pH 5.0. The enzyme was stable in a broad pH range from pH 5.0 to 9.0. The optimal temperature of alpha-amylase was observed at 95 degrees C. The half-life of the enzyme was 5 h at 90 degrees C. Over 40% and 30% of the enzyme activity remained after incubation at 100 degrees C for 2 and 3 h, respectively. The enzyme did not require Ca2+ for thermostability. This alpha-amylase gene was cloned, and its nucleotide sequence displayed an open reading frame of 1,374 bp, which encodes a protein of 457 amino acids. Analysis of the deduced amino acid sequence revealed that four homologous regions common in amylases were conserved in the HJ21 alpha-amylase. The molecular weight of the mature enzyme was calculated to be 51.4 kDa, which correlated well with the size of the purified enzyme as shown by the sodium dodecyl sulfate-polyacrylamide gel electrophoresis.

Fermentative hydrogen production by the new marine Pantoea agglomerans isolated from the mangrove sludge

A new fermentative hydrogen-producing bacterium was isolated from mangrove sludge and identified as Pantoea agglomerans using light microscopic examination, Biolog test and 16S rRNA gene sequence analysis. The isolated bacterium, designated as P. agglomerans BH-18, is a new strain that has never been optimized as a potential hydrogen-producing bacterium. In this study, the culture conditions and the hydrogen-producing ability of P. agglomerans BH-18 were examined. The strain was a salt-tolerant facultative anaerobe with the initial optimum pH value at 8.0-9.0 and temperature at 30 degrees C on cell growth. During fermentation, hydrogen started to evolve when cell growth entered late-exponential phase and was mainly produced in the stationary phase. The strain was able to produce hydrogen over a wide range of initial pH from 5 to 10, with an optimum initial pH of 6. The level of hydrogen production was affected by the initial glucose concentration, and the optimum value was found to be 10 g glucose/l. The maximum hydrogen-producing yield (2246 ml/l) and overall hydrogen production rate (160 ml/l/h) were obtained at an initial glucose concentration of 10 g/l and an initial pH value of 7.2 in marine culture conditions. In particular, the level of hydrogen production was also affected by the salt concentration. Hydrogen production reached a higher level in fresh culture conditions than in marine ones. In marine conditions, hydrogen productivity was 108 ml/l/h at an initial glucose concentration of 20 g/l and pH value of 7.2, whereas, it increased by 27% in fresh conditions. In addition, this strain could produce hydrogen using glucose and many other carbon sources such as fructose, sucrose, sorbitol and so on. As a result, it is possible that P. agglomerans BH-18 is used for biohydrogen production and biological treatment of mariculture wastewater and marine organic waste. (C) 2008 International Association for Hydrogen Energy. Published by Elsevier Ltd. All rights reserved.

Cultivation of the brown alga Hizikia fusiformis (Harvey) Okamura: controlled fertilization and early development of seedlings in raceway tanks in ambient light and temperature

Commercial cultivation of the dioecious brown macroalga Hizikia fusiformis (Harvey) Okamura in East Asia depends on the supply of young seedlings from regenerated holdfasts or from wild population. Recent development of synchronized release of male and female gametes in tumble culture provides a possibility of mass production of young seedlings via sexual reproduction. In this paper, we demonstrate that controlled fertilization can be efficiently realized in ambient light and temperature in a specially designed raceway tank in which the sperm-containing water has been recirculated. The effective fertilization time of eggs by sperm was found to be within six hours. Fast growth and development of the young seedlings relied on the presence of water currents. Velocity tests demonstrated that young seedlings of 2-3 mm in length could withstand a water current of 190 cm s(-1) stop without detachment. Culture experiments at 24 h postfertilization showed that elongation of both the seedlings and their rhizoids were not hampered by high irradiance up to 600 mu mol photons m(-2) stop s(-1) stop. However, growth was slightly retarded if cultured at a temperature of 16 degrees C compared to other culture temperatures of 22, 25 and 29 degrees C. No seedling detachment was observed after transfer of the young seedlings to raft cultivation in the sea after one and 1.5 months post-fertilization, indicating the feasibility of obtaining large quantity of seedlings in such a system.

Methane-derived authigenic carbonates from the Ulleung basin sediments, East Sea of Korea

Authigenic carbonates were sampled in methane-enriched piston core sediments collected from gas venting sites on the western continental slope of the Ulleung Basin, East Sea of Korea. Multidisciplinary investigations on these carbonates, including the scanning electronic microscope (SEM) observations and mineralogical-geochemical compositions, were carried out to identify the carbon and oxygen sources and the forming mechanism of these carbonates. The authigenic carbonates from the study area correspond to semi-consolidated, compact concretions or nodules ranging from 2 to 9 cm in size. X-ray diffraction and electron microprobe analyses showed that most of the sampled carbonate concretions were composed of almost purely authigenic high-Mg calcite (10.7-14.3 mol% MgCO3). Characteristically, microbial structures such as filaments and rods, which were probably associated with the authigenic minerals, were abundantly observed within the carbonate matrix. The carbonates were strongly depleted in delta C-13 (-33.85 parts per thousand to -39.53 parts per thousand Peedee Belemnite (PDB)) and were enriched in delta O-18 (5.16-5.60 parts per thousand PDB), indicating that the primary source of carbon is mainly derived from the anaerobic oxidation of methane. Such methane probably originated from the destabilization of the underlying gas hydrates as strongly supporting from the enriched O-18 levels. Furthermore, the strongly depleted delta C-13 values (-60.7 parts per thousand to -61.6 parts per thousand PDB) of the sediment void gases demonstrate that the majority of the gas venting at the Ulleung Basin is microbial methane by CO2 reduction. This study provides another example for the formation mechanism of methane-derived authigenic carbonates associated with gas-hydrate decomposition in gas-seeping pockmark environments. (c) 2009 Elsevier Ltd. All rights reserved.

Applications of improved 2-D numerical wave tanks in wave breaking

Song and Banner (2002, henceforth referred to as SB02) used a numerical wave tank (developed by Drimer and Agnon, and further refined by Segre, henceforth referred to as DAS) to study the wave breaking in the deep water, and proposed a dimensionless breaking threshold that based on the behaviour of the wave energy modulation and focusing during the evolution of the wave group. In this paper, two modified DAS models are used to further test the SB02's results, the first one (referred to MDAS1) corrected many integral calculation errors appeared in the DAS code, and the second one (referred to MDAS2) replaced the linear boundary element approximation of DAS into the cubic element on the free surface. Researches show that the results of MDAS1 are the same with those of DAS for the simulations of deep water wave breaking, but, the different values of the wavemaker amplitude, the breaking time and the maximum local average energy growth rate delta(max) for the marginal breaking cases are founded by MDAS2 and MDAS1. However, MDAS2 still satisfies the SB02' s breaking threshold. Furthermore, MDAS1 is utilized to study the marginal breaking case in the intermediate water depth when wave passes over a submerged slope, where the slope is given by 1 : 500, 1 : 300, 1 : 150 or 1 : 100. It is found that the maximum local energy density U increases significantly if the slope becomes steeper, and the delta(max) decreases weakly and increases intensively for the marginal recurrence case and marginal breaking case respectively. SB02's breaking threshold is still valid for the wave passing over a submerged slope gentler than 1 : 100 in the intermediate water depth.

鄂霍次克海天然气水合物区与东海内陆架泥质区沉积物古菌多样性研究

为研究鄂霍次克海天然气水合物区沉积物古菌、甲烷厌氧氧化古菌和硫酸盐还原细菌的多样性分布，我们以PCR技术为基础构建mcrA、dsrAB和古菌16S rRNA 基因文库。对所获得的序列进行系统进化和统计学分析发现：鄂霍次克海古菌类群主要为Marine Benthic Group D (MBG-D)、Marine Benthic Group B (MBG-B)、Marine Crenarchaeotic Group I(MG- I)，另外少量古菌16S rRNA基因序列为Anaerobic Methanotrophs 2c（ANME-2c），主要分布在LV39-25H岩心的表层沉积物中。LV39-40H岩心表层的古菌群落结构与其他六个层位古菌群落结构相比有着显著的差异。mcrA基因序列主要为催化甲烷厌氧氧化的古菌ANME-2（c和d簇），在所研究的各个层位的沉积物中均广泛分布。少量的ANME-1（a簇）发现于LV39-40H岩心表层以下的沉积物中。产甲烷古菌数目不多，集中分布在LV39-25H岩心200cm和LV39-40H岩心180cm的沉积物中。dsrAB基因文库分析表明硫酸盐还原细菌种类丰富，表层沉积物中硫酸盐还原细菌多样性最高。在两个岩心所有层位的沉积物中都有一定数量的克隆属于DSS簇，它们可能与ANME共生催化甲烷的厌氧氧化作用。总之，所有数据表明在鄂霍次克海天然气水合物区存在着较活跃的甲烷厌氧氧化作用，揭示了参与甲烷厌氧氧化作用的微生物群落结构和多样性。 为研究东海内陆架闽浙沿岸泥质区不同深度沉积物中古菌群落垂向分布特征，通过古菌16S rRNA 基因文库共得到473个有效克隆50个OTUs (Operational Taxonomic Units)。16S rRNA基因序列系统进化和统计分析发现古菌分别归属于泉古生菌（Crenarchaeota）和广古生菌（Euryarchaeota），其中以Miscellaneous Crenarchaeotic Group（MCG）为主，仅含少量的MBG-B、South African Gold Mine Euryarchaeotic Group(SAGMEG)、 ANME-3、MG- I和MBG-D。该泥质区沉积物可能存在由ANME-3催化的甲烷厌氧氧化作用，同源序列分析表明其古菌群落分布与周边环境有较大联系。UniFrac与沉积物环境因子分析表明该泥质区古菌群落垂向分布与沉积物有机质含量和粒度变化密切相关。 通过对比发现，鄂霍次克海天然气水合物区甲烷厌氧氧化古菌主要为ANME-2和少量的ANME-1，而东海内陆架泥质区甲烷厌氧氧化古菌仅为极少量的ANME-3；鄂霍次克海天然气水合物区广古生菌和泉古生菌数量各占一半，主要为MBG-D、MBG-B、MG-I。东海内陆架泥质区沉积物古菌序列主要为泉古生菌（MCG）。海域类型的不同以及有机碳含量等环境因子的差异可能是这两个海域古菌群落结构差异的主要原因.

Matrix-bound phosphine: A new form of phosphorus found in sediment of Jiaozhou Bay

Matrix-bound phosphine (PH3), a new form of phosphorus, was found in sediment of Jiaozhou Bay in December 2001. Concentration and distribution of PH3 in different layers of sediment with different stations were analyzed. The results show that PH3 concentrations are various with different layers and different stations. PH3 concentrations in the bottom layer of sediment (20-30 cm) are usually higher than those in the surface layer (0-4 cm). The highest PH3 concentration in our investigation reaches 685 ng/kg (dry), which is much higher than those in terrestrial paddy soil, marsh and landfill that have been reported up to now. The correlation analysis indicates that there is no apparent correlation between the concentrations of PH3 and inorganic phosphorus in sediment. However, the correlation between the concentrations of phosphine and organic phosphorus in the bottom layer of sediment is remarkable (R-2=0.83). It is mainly considered that PH3 in sediment of Jiaozhou Bay is produced from the decomposition of organic phosphorus in the anaerobic condition, and so PH3 concentrations are related to organic phosphorus concentration and anaerobic environment in sediment. The discovery of PH3 in sediment will give people some new ideas on the mechanisms of phosphorus supplement and biogeochemical cycle in Jiaozhou Bay.

Morphology and infraciliature of three species of Metaurostylopsis (Ciliophora, Stichotrichia): M. songi n. sp., M. salina n. sp., and M. marina (Kahl 1932) from sediments, saline ponds, and coastal waters.

Two new urostylid ciliates, Metaurostylopsis songi n. sp. and Metaurostylopsis salina n. sp. and Metaurostylopsis marina (Kahl 1932) are investigated using live observation and protargol impregnation. These species were isolated in Korea from intertidal sediments, saline ponds, and coastal waters. Metaurostylopsis songi is in vivo about 120 pm x 25 mu m, has a slenderly ellipsoidal body, colorless cortical granules in rows on ventral and dorsal body sides, about 54 macronuclear nodules, 28-47 adoral membranelles, five frontal, two or three frontoterminal and six or seven transverse cirri, and 9-12 midventral cirral pairs followed posteriorly by 1-3 single cirri. In vivo M. salina is about 60 pin x 25 mu m, has a pyriform body, colorless cortical granules irregularly arranged, about 45 macronuclear nodules, 18-23 adoral membranelles, three frontal, three to five frontoterminal and two to five transverse cirri, and four or five midventral cirral pairs followed posteriorly by five to seven single cirri. Both species have three marginal cirral rows on each body side and 3 long dorsal kineties. The Korean specimens of M. marina match the Chinese population in all main features. Metaurostylopsis songi differs from M. marina by the more slender body, the number of frontal cirri (invariably five vs. four), and the arrangement of cortical granules (in rows on dorsal and ventral cortex vs. only along dorsal kinetics and anterior body margin). Metaurostylopsis salina differs from its congeners by the distinctly smaller size, the pyriform body shape, the scattered cortical granules (vs. in rows), and number of frontal cirri. It differs from M. marina also by the number of midventral cirral pairs (four or five vs. seven to 11).

Effects of anaerobe in sea bottom sediment on the corrosion of carbon steel

The in-situ study of steel corrosion in sea bottom sediment (SBS) was carried out by Transplanting Burying Plate method (TBP method). It was found that the corrosion rate of steel in the sea bottom sediment with sulfate reducing bacteria (SRB) could be as high as ten times of that in sea bottom sediment without SRB. The experiments in simulated sea bottom sediments with different SRB contents by artificial culturing showed that the electrochemical behavior of steel in the sea bottom sediment with SRB was different from that without SRB. SRB altered the polarization behavior of steel significantly. The environment was acidified due to the activity of SRB and the corrosion of steel was accelerated. The corrosion of carbon steel in sea bottom sediment is anaerobic corrosion, and the main factor is anaerobe. There are SRB commonly in SBS, and the amount of SRB decreases along with the depth of sediment. Because of the asymmetry and variation of sea bottom sediment, the most dangerous corrosion breakage of steel in SBS is local corrosion caused by SRB. So the main countermeasure of corrosion protection of sea bottom steel facilities should be controlling of the corrosion caused by anaerobe.

Diversities in hepatic HIF-1, IGF-I/IGFBP-1, LDH/ICD, and their mRNA expressions induced by CoCl2 in Qinghai-Tibetan plateau mammals and sea level mice

Ochotona curzoniae and Microtus oeconomus are the native mammals living on the Qinghai-TibetanPlateau of China. The molecular mechanisms of their acclimatization to the Plateau-hypoxia remain unclear. Expressions of hepatic hypoxia-inducible factor (HIF)-1 alpha, insulin-like growth factor-I (IGF-I)/IGF binding protein (BP)-1(IGFBP-1; including genes), and key metabolic enzymatic genes [lactate dehydrogenase (LDH)-A/isocitrate dehydrogenase (ICD)] are compared in Qinghai-Tibetan- Plateau mammals andsea- level mice after injection of CoCl2 (20, 40, or 60 mg/ kg) and normobaric hypoxia (16.0% O-2, 10.8% O-2, and 8.0% O-2) for 6 h, tested by histochemistry, Western blot analysis, ELISA, and RT-PCR. Major results are CoCl2 markedly increased 1) HIF-1 alpha only in mice, 2) hepatic and circulatory IGF-I in M. oeconomus, 3) hepatic IGFBP-1 in mice and O. curzoniae, and 4) LDH-A but reduced ICD mRNA in mice (CoCl2 20 mg/kg) but were unchanged in the Tibetan mammals. Normobaric hypoxia markedly 1) increased HIF-1 alpha and LDH-A mRNA in mice and M. oeconomus (8.0% O-2) not in O. curzoniae, and 2) reduced ICD mRNA in mice and M. oeconomus (8.0% O-2) not in O. curzoniae. Results suggest that 1) HIF-1 alpha responsiveness to hypoxia is distinct in lowland mice and plateau mammals, reflecting a diverse tolerance of the three species to hypoxia; 2) CoCl2 induces diversities in HIF-1, IGF-I/IGFBP-1 protein or genes in mice, M. oeconomus, and O. curzoniae. In contrast, HIF-1 mediates IGFBP-1 transcription only in mice and in M. oeconomus (subjected to severe hypoxia); 3) differences in IGF-I/IGFBP-1 expressions induced by CoCl2 reflect significant diversities in hormone regulation and cell protection from damage; and 4) activation of anaerobic glycolysis and reduction of Krebs cycle represents strategies of lowland-animals vs. the stable metabolic homeostasis of plateau- acclimatized mammals.

黄土中主要温室气体组分特征

Scientists have paid much attention to the greenhouse effects and the greenhouse gases for the fact of global warming. There are many uncertainties in the prediction of future climatic change. One of the important reasons causing the uncertainties is insufficient researches of the sources and sinks of greenhouse gases, especially, there is a missing sink in the global carbon cycle. The recent researches proposal that there may be an important carbon sink in the middle-latitude terrestrial ecosystems (vegetation and soil) in the North Hemisphere, despite that there is much disputation about its position and amplitude. Chinese loess is located in the middle latitude area in the North Hemisphere, what kind of role does it play in and how does it influence on the balance of the global greenhouse gases budget? For this reason, many samples were taken and analyzed from wide range and multi-stratum of Chinese loess to understand characteristics of major greenhouse gases in loess and loess possible effect on global greenhouse gas budget. Using self-made spiral corer, we totally took 81 gas samples and 65 soil samples from 7 loess profiles in China such as Zhaitang loess section of Beijing, Pianguan, Xingxian, Lishi, Puxian, Jishan loess section of Shanxi Province, and Luochuan loess section of Shaanxi Province. The gas concentrations for CO_2, CH_4 and N_2O, the contents of N_2, O_2 and carbonate, and the carbon isotopic compositions of CO_2 and carbonate in loess strata sequences are observed and measured. In addition, 19 gas samples data of the Weinan loess section, Shaanxi Province are combination with this research to study characteristics of greenhouse gases in loess. This research indicates that (1) the free gases in loess are neither paleo-atmospheric gases nor modern atmospheric gases; (2) the concentrations of CO_2, CH_4 and N_2O in loess are higher than atmospheric level; (3) the δ~(13)C of loess CO_2 shows that the CO_2 in loess mainly comes from the oxygenolysis of organic matters, but because of isotopic exchange with carbonate in loess, the carbon isotopic exchange with carbonate in loess, the carbon isotopic compositions of loess CO_2 are much more heavier than organic original CO_2; (4) the concentration of CH_4 in Malan loess is lower because it is not favorable for the decomposition of anaerobic bacteria in the Malan Loess; (5) estimation of the total amount of the carbonate in loess reveals that loess is a huge carbon reservoir (about 850PgC). In addition, the impact of the deuterogenic carbonatization during the loess accumulation on the global carbon cycle was discussed, and the preliminary conclusion is that the research work is still not enough to evaluate the effect of loess on the sources and sinks of the anthropogenic CO_2.

富硫流体的成因与硫酸盐还原作用研究

Origins of H_2S, thiols, thiophenes in natural gases and sulphur-enriched oils are complicated and thus some debates exist on them. The post-doctoral research is based upon oil- and gas-field data. Cases for study include Triassic Jianglingjiang Formation natural gases, Wolonghe Field, Sichuan Basin, Paleozoic oils and bitumen, Central Tarim, gases reserviored nearby Carboniferious - Ordovician unconformity, Hetianhe Field, Tarim Basin and sulphur-enriched oils in Tertiary reserviors in Jinxian Sag, Bohai Bay Basin. We have carried out analyses on the oils and gases for chemistry, δ~(13)C, δ~(34)S, and molecular composition of biomarkers, analyzed authigenetic pyrite forδ~(34)S, formation water for chemistry and δD and δ~(18)O along with petroleum system and burial history analyses, The aims are to assess the origins of the H2S and authigenetic pyrite, to discuss the possibility of reduced sulphur incorporation into hydrocarbons and to determine the mechanisms of hydrocarbon secondary alteration in the above four cases by comparison. The research shows that the reduced sulphur in the four cases is the result of thermochemical and biological sulphate reduction., TSR and BSR, respectively. No evidence indicates an origin of decomposition of organic matter or mantle - derived H2S in the cases. Elevated H_2S contents (up to 32%) in the Triassic Jialingjiang Formation are considered to result from TSR while relatively low H_2S (up to 2000ppm) in the Hetianhe Field resulted from BSR. However, it is not the case for the Central Tarim where relatively low H2S but abundant authigenetic pyrite occurr. Part of the H_2S in the Central Tarim reservoirs has reacted with iron released from clay minerals to precipitate pyrite. Thus, reduced sulphur δ~(34)S and reservoir temperatures rather than the H2S amount are reliable parameters to distinguish between TSR and BSR. TSR in Sichuan Basin Triassic Jialingjiang Formation and Central Tarim Paleozoic reservoirs are showed to take place at more than 125℃. the H2S and authigenetic pyrite have δ~(34)S close to parent anhydrite. In contrast, BSR in the reservoirs near the Carboniferous - Ordovician unconformity in the Hetianhe Field and in the Tertiary in the Jinxian Sag took place at temperatures less than 80℃with sulphide δ~(34)S as light as -24.9‰ and -12.5‰, anhydrite δ~(34)S as heavy as +26‰and +3 5-+40‰, respectively. Chemistry and isotopic composition of the natural gases change as the result of sulphate reduction. It has been observed that relative composition of light hydrocarbon gases is changed along with a rise in H_2S and CO_2. TSR in the Triassic Jialingjiang Formation and BSR in the Hetianhe Field result in a greater degree of preferential depletion of methane than larger molecular hydrocarbon gases. As TSR or BSR proceeds, hydrocarbon gases evolved to heavier carbon isotope as the result of kinetic isotopic fractionation, i.e., selective anaerobic oxidation of ~(12)C. Using the model of residual methane (Whiticar, 1999) to describe the relationship among the proportion of methane oxidation, isotopic shift and fraction factor, about 30% methane is calculated to have been oxidized during BSR in the western part of the Hetianhe Field. From the above, it can be concluded that in the area where H_2S is abundant, empiricalδ~(13)C -Ro relationships do not work. Sulphate reduction results in a rise in sulphur content, gravity and viscosity of an oil as well as changes in δ~(13)C and δ~(34)S. On special conditions, the reduced sulphur from sulphates might be incorporated into oils, i.e., the increasing sulphur is derived from secondarily reduced sulphur. A positive correlative relationship exists between sulphur content and δ~(34)S in the oils in Paleozoic reservoirs in Central Tarim, indicating that enhanced sulphur is ~(34)S-enriched, originated from TSR. The Jinxian oil with the highest sulphur content has the lightest δ~(34)S, suggesting part of the sulphur in the oil is ~(34)S-depleted, originated from BSR. In the Jinxian oil with increasing sulphur content, asphaltenes shows higher content and more negative δ~(13)C, and saturates shows evidence of biodegradetion and a decreasing content and a positive δ~(13)C shift. Thus, asphaltenes have δ~(13)C values closer to saturates. All the above indicate that the reduced sulphur has been incorporated into biodegradated saturates to generate new asphaltenes with relatively light δ~(13)C of saturates. Thiols and thiophenes in natural gases in the Triassic Jialingjiang Formation may result from reaction of H_2S with hydrocarbon. In the Jialingjiang Formation hydrocarbon gases are dominated by methane thus have a high dryness coefficient and thiols are showed to be positively related to H_2S content, suggesting that the thiols may result from H_2S reaction with short chain hydrocarbons. In contrast, high thiophenes occur in wet gases in Jurassic reservoirs with their source rock from sulphur - depleted type I kerogen, indicating that thiophenes may be a product of reaction of H2S with longer chain hydrocarbons.