岩溶区土壤微生物驱动的自养固碳过程与机制研究进展

自养微生物能够利用无机碳作为碳源合成自身营养物质,具有很强的环境适应能力,在富钙偏碱的岩溶区土壤的碳固定过程中扮演重要角色.本文综述了土壤微生物驱动的自养固碳过程、岩溶区土壤固碳功能微生物、自养固碳的分子机制及其产生的生态环境效应,并提出了亟待解决的关键科学问题.为深入研究和认识岩溶区土壤生态系统自养微生物驱动的固碳过...     

Acetate synthesis from 2 CO2 in acetogenic bacteria: is carbon monoxide an intermediate?

Cultures of Acetobacterium woodii and Clostridium thermoaceticum growing on fructose or glucose, respectively, were found to produce small, but significant amounts of carbon monoxide. In the gas phase of the cultures up to 53 ppm CO were determined. The carbon monoxide production was completely inhibited by 1 mM cyanide. Cultures and cell suspensions of both acetogens incorporated ¹⁴CO specifically into the carboxyl group of acetate. This CO fixation into C₁ of acetate was unaffected by cyanide (1 mM). The findings are taken to indicate that CO (in a bound form) is the physiological precursor of the C₁ of acetate in acetate synthesis from CO₂. The cyanide inhibition experiments support the hypothesis that the cyanide-sensitive carbon monoxide dehydrogenase may serve to reduce CO₂ to CO rather than to incorporate the carbonyl into C₁ of acetate.     

Metabolism of a subtropical Brazilian lagoon

Total community, planktonic and benthic metabolisms were measured by using the carbon dioxide production and consumption, the diurnal curve' method and the in situ bottle incubation technique over an annual cycle in two sublagoons of the Saquarema Lagoon, Brazil. Metabolic rates of the phytoplankton-based lagoon were characterized by considerable daytime and daily variability in production and respiration, by a seasonal shift between net autotrophy and heterotrophy and by an annual balance of production (P = 105 ± 65 mmoles/m²/dayn = 25) and respiration (R = 102 ± 50 mmoles/m²/dayn = 25). Total community metabolism was similar throughout the lagoon, but phytoplankton assimilation rates and benthic respiration showed spatial differences. Bottle incubations compared to total community free water respiration suggested that the pelagic community was 2–5 times more active than the benthos     

Energetics of CO formation and CO oxidation in cell suspensions of Acetobacterium woodii

Cell suspensions of Acetobacterium woodii produced CO from H₂ and CO₂. Depending on the conditions, more than 1,000 ppm CO were measured in the gas phase. This concentration was more than 10-fold higher than the thermodynamic equilibrium concentration that can be calculated to be 83.5 ppm for the experimental conditions used. This finding is taken as evidence that, besides the activation of formate, also CO production from CO₂ is an energy-dependent step in the reduction of CO₂ to acetate. Studies on the influence of ionophores and dicyclohexylcarbodiimide (DCCD) as well as that of CO and formaldehyde on acetate synthesis were undertaken in order to determine whether ATP or is the driving for CO₂ reduction to CO.Cells of A. woodii also catalyzed the conversion of CO (5% in the gas phase) to CO₂ and H₂. This process was coupled to the generation of metabolic energy, which could be used by the cells to drive the uptake of histidine into the cells; histidine uptake was almost completely inhibited by the ionophores valinomycin plus nigericin. The data were taken to indicate that in this acetogen the energy derived from CO oxidation can be converted to metabolic energy.Abbreviations DCCD dicyclohexylcarbodiimide - THF tetrahydrofolate - TCS tetrachlorosalicylanilide - TPP⁺ tetraphenylphosphonium ion - Val valinomycin; Nig, nigericin - DTT dithiothreitol - DTE dithioerythritol - DTE dithioerythritol - membrane potential - electrochemical proton potential - ppm parts per million     

Carbon monoxide production by Methanobacterium thermoautotrophicum

Abstract Methanobacterium thermoautotrophicum was grown in a fermenter gassed with an 80% H₂/20% CO₂ mixture. The effluent gas was found to contain between 30 ppm and 90 ppm carbon monoxide. Approx. 5 nmol CO were produced per min and mg cells (dry weight) by the culture. This is to our knowledge the first report on biological carbon monoxide formation under strictly anaerobic conditions.     

The influence of moisture regimes on the population and activity of soil microorganisms

This paper deals with the influence of soil moisture on the fungal population, bacterial population, CO₂-evolution and dehydrogenase activity. Correlation coefficients of various parameters of the soil with different moisture regimes are given. It is demonstrated that soil moisture significantly alters the microbial population, its activity and the relationships between various parameters.     

Photosynthetic electron transport and anaerobic metabolism in purple non-sulfur phototrophic bacteria

Purple non-sulfur phototrophic bacteria, exemplifed byRhodobacter capsulatus andRhodobacter sphaeroides, exhibit a remarkable versatility in their anaerobic metabolism. In these bacteria the photosynthetic apparatus, enzymes involved in CO₂ fixation and pathways of anaerobic respiration are all induced upon a reduction in oxygen tension. Recently, there have been significant advances in the understanding of molecular properties of the photosynthetic apparatus and the control of the expression of genes involved in photosynthesis and CO₂ fixation. In addition, anaerobic respiratory pathways have been characterised and their interaction with photosynthetic electron transport has been described. This review will survey these advances and will discuss the ways in which photosynthetic electron transport and oxidation-reduction processes are integrated during photoautotrophic and photoheterotrophic growth.     

Catalysis of an isotopic exchange between CO2 and the carboxyl group of acetate by Methanosarcina barkeri grown on acetate

Cell suspensions of Methanosarcina barkeri (strain Fusaro) grown on acetate were found to catalyze the formation of methane and CO₂ from acetate (30–40 nmol/min·mg protein) and an isotopic exchange between the carboxyl group of acetate and ¹⁴CO₂ (30–40 nmol/min·mg protein). An isotopic exchange between [¹⁴C]-formate and acetate was not observed. Cells grown on methanol mediated neither methane formation from acetate nor the exchange reactions. The data indicate that the isotopic exchange between CO₂ and the carboxyl group of acetate is a partial reaction of methanogenesis from acetate. Both reactions were completely inhibited by low concentrations of cyanide (20 M) or of hydrogen (0.5% in the gas phase). Methane formation from acetate was also completely inhibited by low concentrations of carbon monoxide (0.2% in the gas phase) whereas only significantly higher concentrations of CO had an effect on the exchange reaction. In the concentration range tested KCN, H₂ and CO had no effect on methane formation from methanol or from H₂ and CO₂; however, cyanide (20 M) also affected methane formation from CO. The results are discussed with respect to proposed mechanisms of methane and CO₂ formation from acetate.     

Treponema succinifaciens sp. nov., an anaerobic spirochete from the swine intestine

The morphology, the general physiological characteristics, and the energy-yielding metabolism of an obligately anaerobic spirochete isolated from the colon of a swine were studied. Electron microscopy showed that the helical spirochetal cells possessed an outer sheath, a protoplasmic cylinder, and 4 periplasmic fibrils in a 2-4-2 arrangement. The spirochete grew in an atmosphere of N₂ in prereduced media containing a carbohydrate, NaHCO₃, rumen fluid, yeast extract, peptone, l-cysteine, and inorganic salts. The spirochete fermented carbohydrates and required substrate amounts of CO₂ (HCO ₃ ^- ) for growth. Amino acids were not fermented. Major fermentation products of cells growing with glucose as the substrate and in the presence of CO₂ were acetate, formate, succinate, and lactate. Small amounts of 2,3-butanediol, pyruvate, and acetoin were also formed. Determinations of enzymatic activities in cell extracts, and of radioactivity in products formed by growing cells from [1-¹⁴C]glucose, indicated that this sugar was dissimilated to pyruvate via the Embden-Meyerhof pathway. The spirochetes used a coliform-type clastic reaction to metabolize pyruvate. Determinations of radioactivity in products formed from [¹⁴C]NaHCO₃ indicated that CO₂ was assimilated and used in succinate production. The guanine+cytosine content of the DNA was 36 mol%. This study indicates that this intestinal spirochete represents a new species of Treponema. It is proposed that the new species be named Treponema succinifaciens.Abbreviations cpm counts per minute - DTT dithiothreitol - EM Embden-Meyerhof - GC guanine plus cytosine - IgG immunoglobulin G - PC protoplasmic cylinder - PF periplasmic fibrils (axial fibrils) - OS outer sheath     

Effect of CO2 concentration on the PIC/POC ratio in the coccolithophore Emiliania huxleyi grown under light-limiting conditions and different daylengths

We compared the effect of CO₂ concentration ([CO₂], ranging from ∼5 to ∼34 μmol l⁻¹) at four different photon flux densities (PFD=15, 30, 80 and 150 μmol m⁻² s⁻¹) and two light/dark (L/D) cycles (16/8 and 24/0 h) on the coccolithophore Emiliania huxleyi. With increasing [CO₂], a decrease in the particulate inorganic carbon to particulate organic carbon (PIC/POC) ratio was observed at all light intensities and L/D cycles tested. The individual response in cellular PIC and POC to [CO₂] depended strongly on the PFD. POC production increased with rising [CO₂], irrespective of the light intensity, and PIC production decreased with increasing [CO₂] at a PFD of 150 μmol m⁻² s⁻¹, whereas below this light level it was unaffected by [CO₂]. Cell growth rate decreased with decreasing PFD, but was largely independent of ambient [CO₂]. The diurnal variation in PIC and POC content, monitored over a 38-h period (16/8 h L/D, PFD=150 μmol m⁻² s⁻¹), exceeded the difference in carbon content between cells grown at high (∼29 μmol l⁻¹) and low (∼4 μmol l⁻¹) [CO₂]. However, consistent with the results described above, cellular POC content was higher and PIC content lower at high [CO₂], compared to the values at low [CO₂], and the offset was observed throughout the day. It is suggested that the observed sensitivity of POC production for ambient [CO₂] may be of importance in regulating species-specific primary production and species composition.     

Metabolism of 2-carboxyarabinitol 1-phosphate and regulation of ribulose-1,5-bisphosphate carboxylase activity

Metabolism of 2-carboxy-D-arabinitol 1-phosphate (CA1P) is an important component in the light-dependent regulation of ribulose-1,5-bisphosphate carboxylase (Rubisco) activity and whole leaf photosynthetic CO₂ assimilation in many species, and functions as one mechanism for regulating Rubisco activity when photosynthesis is light-limited. Species differ in their capacity to accumulate CA1P, ranging from those which can synthesize levels of this compound approaching or in excess of the Rubisco catalytic site concentration, to those which apparently lack the capacity for CA1P synthesis. CA1P is structurally related to the six carbon transition state intermediate of the carboxylation reaction and binds tightly to the carbamylated catalytic site of Rubisco, making that site unavailable for catalysis. Under steady-state, the concentration of CA1P in the leaf is highest at low photon flux density (PFD) or in the dark. Degradation of CA1P and recovery of Rubisco activity requires light and is stimulated by increasing PFD. The initial degradation reaction is catalyzed by an enzyme located in the chloroplast stroma, CA1P phosphatase, which yields carboxyarabinitol (CA) and inorganic phosphate as its products. The pathway of CA metabolism in the plant remains to be determined. Synthesis of CA1P occurs in the dark, and in Phaseolus vulgaris this process has been shown to be stimulated by low PFD. The pathway of CA1P synthesis and its relationship to the degradative pathway remains unknown at the present time. The discovery of the existence of this previously unknown carbon pathway in photosynthesis indicates that we still have much to learn concerning the regulation of Rubisco activity and photosynthesis.Abbreviations CA 2-carboxy-D-arabinitol - CA1P 2-carboxy-D-arabinitol 1-phosphate - CABP 2-carboxy-D-arabinitol-1,5-bisphosphate (transition state analog) - PFD photon flux density - P₁ inorganic phosphate - Rubisco ribulose-1,5-bisphosphate carboxylase/oxygenase (EC 4.1.1.39) - RuBP ribulose-1,5-bisphosphate     

Bio-CO2 fixation with formate dehydrogenase from Saccharomyces cerevisiae and water-soluble zinc porphyrin by visible light

The CO₂ fixation system, that is formic acid production from CO₂ with FDH from Saccharomyces cerevisiae and reduced Methyl viologen produced by the visible light photosensitization of zinc tetrakis(4-methylpyridyl) porphyrin, was investigated. When the sample solution containing triethanolamine, zinc tetrakis(4-methylpyridyl) porphyrin, Methyl viologen, NaHCO₃ and FDH in phosphate buffer was irradiated, formic acid was produced. The amount of formic acid production and the yield of CO₂ to formic acid were estimated to be 0.104 ± 0.008 mM and 10.4%, respectively.     

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。     

Non-phototrophic CO 2 fixation by soil microorganisms

Although soils are generally known to be a net source of CO₂ due to microbial respiration, CO₂ fixation may also be an important process. The non-phototrophic fixation of CO₂ was investigated in a tracer experiment with ¹⁴CO₂ in order to obtain information about the extent and the mechanisms of this process. Soils were incubated for up to 91 days in the dark. In three independent incubation experiments, a significant transfer of radioactivity from ¹⁴CO₂ to soil organic matter was observed. The process was related to microbial activity and could be enhanced by the addition of readily available substrates such as acetate. CO₂ fixation exhibited biphasic kinetics and was linearly related to respiration during the first phase of incubation (about 20–40 days). The fixation amounted to 3–5% of the net respiration. After this phase, the CO₂ fixation decreased to 1–2% of the respiration. The amount of carbon fixed by an agricultural soil corresponded to 0.05% of the organic carbon present in the soil at the beginning of the experiment, and virtually all of the fixed CO₂ was converted to organic compounds. Many autotrophic and heterotrophic biochemical processes result in the fixation of CO₂. However, the enhancement of the fixation by addition of readily available substrates and the linear correlation with respiration suggested that the process is mainly driven by aerobic heterotrophic microorganisms. We conclude that heterotrophic CO₂ fixation represents a significant factor of microbial activity in soils.     

Enzymology of the Acetyl-CoA Pathway of CO2 Fixation

Abstract

We know of three routes that organisms have evolved to synthesize complex organic molecules from CO₂: the Calvin cycle. the reverse tricarboxylic acid cycle, and the reductive acetyl-CoA pathway. This review describes the enzymatic steps involved in the acetyl-CoA pathway, also called the Wood pathway, which is the major mechanism of CO₂ fixation under anaerobic conditions. The acetyl-CoA pathway is also able to form acetyl-CoA from carbon monoxide.

There are two parts to the acetyl-CoA pathway: (1) reduction of CO₂ to methyltetrahydrofolate (methyl-H₄folate) and (2) synthesis of acetyl-CoA from methyl-H, folate, a carboxyl donor such as CO or CO₂, and CoA. This pathway is unique in that the major intermediates are enzyme-bound and are often organometallic complexes. Our current understanding of the pathway is based on radioactive and stable isotope tracer studies, purification of the component enzymes (some extremely oxygen sensitive), and identification of the enzyme-bound intcrmediates by chromatographic, spectroscopic. and electrochemical techniques. This review describes the remarkable series of enzymatic steps involved in acetyl-CoA formation by this pathway that is a key component of the global carbon cycle.     

地质封存二氧化碳与深地微生物相互作用研究进展

地质封存将工业和能源相关领域生产活动产生的二氧化碳（CO₂）进行捕集并注入到深部地下岩石构造中,以实现长期储存的目标,是降低温室气体排放、实现CO₂长期封存的重要可行性手段之一。向深部地下地质构造中注入大量CO₂会导致深地环境发生显著变化,进而引起原生微生物活性及群落结构发生明显改变。因此,地质封存CO₂能够直接或间接影响深地微生物驱动的生物地球化学过程。同时,微生物在短期和长期的超临界CO₂（scCO₂）胁迫作用下,也会通过不同的适应性进化方式影响CO₂在地下环境中的迁移、转化和赋存形态。本文介绍了国内外二氧化碳捕获与封存发展现状以及地质封存CO₂影响条件下的scCO₂-水-微生物-矿物的相互作用领域的最新科研进展,并展望了利用深地微生物强化CO₂固定以及将其转化为高附加值产物的潜力。     

Total synthesis of acetyl coenzyme a involved in autotrophic CO2 fixation inAcetobacterium woodii

The Gram positive anaerobeAcetobacterium woodii is able to grow autotrophically with a mixture of H₂ and CO₂ as the energy and carbon source. The question, by which pathway CO₂ is assimilated, was studied using long term isotope labeling.Autotrophically growing cultures produced acetate parallel to cell proliferation, and, when U-[¹⁴C]acetate was present as tracer, incorporated radioactivity into all cell fractions. The specific radioactivity and the label positions were determined for those representative cell compounds which biosynthetically originated directly from acetyl CoA (N-acetyl groups), pyruvate (alanine), oxaloacetate (aspartate), -ketoglutarate (glutamate), and hexosephosphates (glucosamine). Per mol compound the same amount of labeled acetate was incorporated into N-acetyl groups, alanine (C-2, C-3), aspartate (C-2, C-3), and twice the amount into glutamate (C-2, C-3, C-4, C-5) and into glucosamine. Consequently, the unlabeled carbon atoms of the C₃–C₆ compounds must have been derived from CO₂ by carboxylation subsequent to acetyl CoA synthesis. When 0.2 mM 2-[¹⁴C]pyruvate was added to autotrophically growing cultures, also a substantial amount of radioactivity was incorporated. Two important differences in comparison to the acetate experiment were observed: The N-acetyl groups were almost unlabeled and glutamate contained the same specific radioactivity as alanine or aspartate.These data showed that acetyl CoA is the central intermediate for biosynthesis and excluded the operation of the Calvin cycle inA. woodii. The results were consistent with the operation of a different autotrophic CO₂ fixation pathway in which CO₂ is converted into acetyl CoA by total synthesis via methyltetrahydrofolate; acetyl CoA is then further reductively carboxylated to pyruvate.     

Anaerobic acetate oxidation to CO2 by Desulfotomaculum acetoxidans

Desulfotomaculum acetoxidans oxidizes acetate to CO₂ with sulfate. This organism metabolizes acetate via a pathway in which C₁ units rather than tri- and dicarboxylic acids are intermediates. We report here that cell extracts of D. acetoxidans catalyzed an exchange between CO₂ and the carboxyl group of acetate at a rate of 90 nmol · min^-1 · mg^-1 protein which is sufficient to account for the in vivo acetate oxidation rate of 250 nmol · min^-1 · mg^-1 protein. The reaction was strictly dependent on both ATP and coenzyme A. The extracts contain high activities of acetate kinase (6.3 U · mg^-1 protein) and phosphotransacetylase (60 U · mg^-1 protein). These findings indicate that acetyl-CoA rather than acetyl-phosphate or acetate is the substrate of the carbon-carbon cleavage activity. Exchange was only observed in the presence of strong reducing agents such as Ti³⁺. Interestingly, the cell extracts also catalyzed the reduction of CO₂ to CO with Ti³⁺ as electron donor (120 nmol · min^-1 · mg^-1 protein). Carbon monoxide dehydrogenase and other oxidoreductases involved in acetate oxidation were found to be partially associated with the membrane fraction suggesting a membrane localization of these enzymes.Abbreviations MOPS Morpholinopropane sulfonic acid - Tricine N-tris(hydroxymethyl)-methylglycine - DTT d,l-1,4-Dithiothreitol - DMN 2,3-Dimethyl-1,4-naphthoquinone - MV_OX Methyl viologen, oxidized - APS Adenosinephosphosulfate - SRB Sulfate reducing bacteria - U mol product formed per min     

Acetyl CoA,a central intermediate of autotrophic CO2 fixation in Methanobacterium thermoautotrophicum

The pathway of autotrophic CO₂ fixation in Methanobacterium thermoautotrophicum has been investigated by long term labelling of the organism with isotopic acetate and pyruvate while exponentially growing on H₂ plus CO₂. Maximally 2% of the cell carbon were derived from exogeneous tracer, 98% were synthesized from CO₂. Since growth was obviously autotrophic the labelled compounds functioned as tracers of the cellular acetyl CoA and pyruvate pool during cell carbon synthesis from CO₂. M. thermoautotrophicum growing in presence of U-¹⁴C acetate incorporated ¹⁴C into cell compounds derived from acetyl CoA (N-acetyl groups) as well as into compounds derived from pyruvate (alanine), oxaloacetate (aspartate), -ketoglutarate (glutamate), hexosephosphates (galactosamine), and pentosephosphates (ribose). The specific radioactities of N-acetylgroups and of the three amino acids were identical. The hexosamine exhibited a two times higher specific radioactivity, and the pentose a 1.6 times higher specific radioactivity than e.g. alanine. M. thermoautotrophicum growing in presence of 3-¹⁴C pyruvate, however, did not incorporate ¹⁴C into cell compounds directly derived from acetyl CoA. Those compounds derived from pyruvate, dicarboxylic acids and hexosephosphates became labelled. The specific radioactivities of alanine, aspartate and glutamate were identical; the hexosamine had a specific radioactivity twice as high as e.g. alanine.The finding that pyruvate was not incorporated into compounds derived from acetyl CoA, whereas acetate was incorporated into derivatives of acetyl CoA and pyruvate in a 1:1 ratio demonstrates that pyruvate is synthesized by reductive carboxylation of acetyl CoA. The data further provide evidence that in this autotrophic CO₂ fixation pathway hexosephosphates and pentosephosphates are synthesized from CO₂ via acetyl CoA and pyruvate.