异养微生物固定CO2的合成生物学研究进展

人类活动造成大气二氧化碳（CO₂）浓度不断升高,使当今世界面临着气候变化的重大危机。微生物CO₂固定为实现地球“碳中和”提供了一条有前景的绿色发展路线。与自养微生物相比,异养微生物具有更快的生长速度和更先进的遗传工具,但是其固定CO₂的能力还很有限。近年来,基于合成生物学技术强化异养微生物CO₂固定受到诸多关注,主要包括优化能量供给、改造羧化途径以及基于异养微生物间接固定CO₂。本综述将围绕上述3个方面重点讨论异养微生物CO₂固定的研究进展,为将来更好地利用微生物CO₂固定技术实现“碳达峰、碳中和”提供参考。     

皖南休宁新元古界-下寒武统沉积岩的有机碳同位素记录

皖南休宁县蓝田地区震旦系皮园村组和下寒武统荷塘组主要由硅质岩和黑色页岩组成。皮园村组硅质岩的分析结果表明:δ13Corg分析值落在-36.39‰—-31.45‰范围之内,而且从该剖面的底部到顶部呈现出逐步下降的趋势,可能归之于大气和海洋中O2/CO2比值上升,生物氧化作用增强所致;有机碳(TOC)含量<1%,有机氮(TON)含量<1‰,两者均处于蓝田地区埃迪卡拉系—下寒武统地层的最低值,证明晚震旦世时期该地区海洋生物产量比前期(蓝田期)海洋产量显著下降,可能归之于海水加深,不利于海洋生物的繁殖。荷塘组黑色页岩的δ13Corg分析值落在-33‰—-31‰范围之内,TOC和TON含量与皮园村组比较有大幅度提高,尤其黑色页岩下段TOC含量达到13.85%,证明早寒武世海洋生物得到了大发展。由于新元古代冰期后海洋藻类的大量涌现和早寒武世海洋生物得到大发展,生物光合作用产生大量的O2,导致大气和海水中O2/CO2比值进一步升高,可能是引发“寒武纪生物大爆发”的重要因素。     

The CbbQO-type rubisco activases encoded in carboxysome gene clusters can activate carboxysomal form IA rubiscos

The CO₂-fixing enzyme rubisco is responsible for almost all carbon fixation. This process frequently requires rubisco activase (Rca) machinery, which couples ATP hydrolysis to the removal of inhibitory sugar phosphates, including the rubisco substrate ribulose 1,5-bisphosphate (RuBP). Rubisco is sometimes compartmentalized in carboxysomes, bacterial microcompartments that enable a carbon dioxide concentrating mechanism (CCM). Characterized carboxysomal rubiscos, however, are not prone to inhibition, and often no activase machinery is associated with these enzymes. Here, we characterize two carboxysomal rubiscos of the form IA^C clade that are associated with CbbQO-type Rcas. These enzymes release RuBP at a much lower rate than the canonical carboxysomal rubisco from Synechococcus PCC6301. We found that CbbQO-type Rcas encoded in carboxysome gene clusters can remove RuBP and the tight-binding transition state analog carboxy-arabinitol 1,5-bisphosphate from cognate rubiscos. The Acidithiobacillus ferrooxidans genome encodes two form IA rubiscos associated with two sets of cbbQ and cbbO genes. We show that the two CbbQO activase systems display specificity for the rubisco enzyme encoded in the same gene cluster, and this property can be switched by substituting the C-terminal three residues of the large subunit. Our findings indicate that the kinetic and inhibitory properties of proteobacterial form IA rubiscos are diverse and predict that Rcas may be necessary for some α-carboxysomal CCMs. These findings will have implications for efforts aiming to introduce biophysical CCMs into plants and other hosts for improvement of carbon fixation of crops.     

A Comparative Study of Primary Production and Related Factors in Four Saline Lakes in Victoria,Australia

The purpose of the study was to compare the primary plankton productivities of lakes of different salinities and to determine the causative factors involved in their production rates. Four lakes (specific conductivity —mS cm⁻¹ at 18°C) were initially chosen: Coragulac (9), Red Rock (25), Corangamite (38), Pink (250). Sampling and production measurements were made every two to three weeks. Three lakes were dominated by specific phytoplankton blooms: Red Rock (Anabaena spiroides), Corangamite (Nodularia spumigena). Pink (Dunaliella salina). Coragulac Lake had more diverse populations. Red Rock Tarn had some of the highest production values ever recorded. Extremely high soluble phosphate and inorganic carbon concentrations were the most important causative factors. Pink Lake had very low production rates. High salinity and low nutrient concentrations were limiting factors. The other lakes were intermediate in production and nutrient levels. Zooplankton populations were also determined.     

Signal Analysis of Irradiation,Temperature and Primary Production in a Small Artificial Pond. II. The Residual Spectra

Irradiation, water temperature and dissolved oxygen of a small artificial pond were continuously recorded over a two year period. Following the elimination of previously estimated mean trends and forced annual patterns (LINGEMAN 1980) a spectral analysis procedure is proposed and executed for the residual signals of total diurnal irradiation, diel mean temperature and diurnal gross primary production. The residual power spectrum of diurnal irradiation was shown to be essentially the one of a white noise. Several higher frequencies were significantly present in both the signals of temperature and production. Some consideration is given to the cross correlation between the latter two parameters.     

Relationships of morphological and phototextural attributes of presumptive ovine zygotes and early embryos to their developmental competence in vitro: a preliminary assessment using time-lapse imaging

The assessment of morphology and digital image opacity may provide valuable information on the present embryo quality. Time-lapse imaging has been employed in research to establish a means of monitoring the dynamic nature of preimplantation embryo development. The aim of present study was to use time-lapse imaging for assessing various prospective morphometric and phototextural markers of the developmental potential of in vitro-derived ovine embryos. Oocytes were obtained by scarification of ovaries from nine Polish Longwool ewes. After in vitro maturation (IVM) and fertilization (IVF) of oocytes with fresh ram semen, the development of embryos to the blastocyst stage was monitored and evaluated using Primo Vision time-lapse imaging technology. Commercially available Image-Pro^® Plus software was used to measure zona pellucida thickness, embryo diameter, total area of the perivitelline space, cellular grey-scale pixel intensity and cellular pixel heterogeneity. Statistical assessment of all attributes was done at various time points during embryo development (i.e., presumptive zygote stage: t(0); first cleavage detected at t(2) or t(3); and second cleavage detected at t(4) or t(6)). Out of thirty-seven zygotes analyzed in this study, five did not divide, 26 arrested before and six developed to the blastocyst stage. Our present results indicate that most parameters analyzed did not differ among embryos varying in their developmental fate except for the perivitelline space area that was greater (P<0.05) for non-dividing zygotes than future blastocysts at the presumptive zygote stage (4040±1850 vs. 857±262 µm², respectively; means±SEM). Consequently, the measurement of perivitelline space at t(0) can potentially be used to prognosticate developmental potential of in vitro-produced ovine embryos albeit further confirmational studies are needed.     

Signal Analysis of Irradiation,Temperature and Primary Production in a Small Artificial Pond: I. The Annual Signals

This paper provides an example of some initial steps in signal analysis applied to a simple aquatic ecosystem in the form of a small artificial pond. Irradation, water temperature and dissolved oxygen concentration were continuously recorded over a two year period. Following the definition and discussion of several related parameters, an analysis procedure for trends and forced annual patterns was proposed and carried out. The annual pattern of photosynthetic fixation of solar energy is characterized by the annual level transfer efficiency, and for the periodic part of the process, by the transfer gain and phase shift. The possible role of temperature is briefly discussed.     

Methane production in littoral sediment of Lake Constance

Maximum rates of CH₄ production in the littoral sediment were observed in 2–5 cm depth. The CH₄ production rates increased during the year from about 5 mmol m⁻²d⁻¹ in December to a maximum of about 95 mmol m⁻²d⁻¹ in September. CH₄ production rates showed a temperature optimum at 30°C and an apparent activation energy of 76 kJ mol⁻¹. A large part of the seasonality of CH₄ production could be ascribed to the change of the sediment temperature. Most of the produced CH₄ was lost by ebullition. Gas bubbles contained about 60–70% CH₄ with an average δ¹³C of −56.2% and δD of −354%, and 2% CO₂ with an average δ¹³C of −14.1% indicating that CH₄ was produced from methyl carbon, i.e. mainly using acetate as methanogenic substrate. This result was confirmed by inhibition of methanogenesis with chloroform which resulted in an accumulation rate of acetate equivalent to 81% of the rate of CH₄ production. Most probable numbers of methanogenic bacteria were in the order of 10⁴ bacteria g⁻¹d.w. sediment for acetate-, methanol- or formate-utilizing, and of 10⁵ for H₂-utilizing methanogens. The turnover times of acetate were in the order of 2.3–4.8 h which, with in situ acetate concentrations of about 25–50 μM, resulted in rates of acetate turnover which were comparable to the rates of CH₄ production. The respiratory index (RI) showed that [2−¹⁴C]acetate was mainly used by methanogenesis rather than by respiratory processes, although the zone of CH₄ production in the sediment overlapped with the zone of sulfate reduction.     

Dimethylsulfoxide reduction by marine sulfate-reducing bacteria

Abstract Dimethylsulfoxide (DMSO) reduction occurred in five out of nine strains of sulfate-reducing bacteria from marine or saline environments, but not in three freshwater isolates. DMSO reduction supported growth in all positive strains. In Desulfovibrio desulfuricans strain PA2805, DMSO reduction occurred simultaneously with sulfate reduction and was not effectively inhibited by molybdate, a specific inhibitor of sulfate reduction. The growth yield per mol lactate was 26% higher with DMSO than with sulfate as electron acceptor. In extracts of cells of strain PA2805 grown on sulfate, a low level of DMSO-reducing activity was present (0.013 μmol (mg protein)⁻ min⁻); higher levels were found in cells grown on DMSO (0.56 μmol (mg protein)⁻ min⁻). In anoxic marine environments DMSO reduction by sulfate-reducing bacteria may lead to enhanced dimethylsulfide emission rates.