氢营养型产甲烷代谢途径研究进展

产甲烷古菌是一类极端厌氧的古菌域微生物,可以利用CO_2、甲醇、乙酸等简单化合物产甲烷并获得能量。目前能够培养的氢营养型(CO_2/H_2)产甲烷古菌的种类较多,而且在三类产甲烷代谢类型中,氢营养型产甲烷途径的产能效率最高,并具有多种模式的特殊能量利用系统。近年来,随着质谱、光谱和晶体技术的发展与运用,人们对产甲烷代谢途径的研究进一步深入,尤其是对氢营养型产甲烷途径的生化机制有了新的认识,揭示了产甲烷古菌在能量极限条件下独特、高效的能量利用模式。本文从能量储存、代谢途径、蛋白功能与催化机制等方面概述产甲烷古菌利用CO_2/H_2产甲烷的详细过程,并对产甲烷古菌代谢途径的研究方向与技术发展进行展望。     

新型产甲烷古菌研究进展

产甲烷古菌是一类能利用简单化合物产生甲烷气体的厌氧菌。近年来,随着测序技术的不断发展,科学家结合宏基因组学和其他技术先后发现了众多之前未被报道的新型产甲烷古菌。基因组分析等研究发现这几类新型产甲烷古菌具有独特的甲烷代谢通路以及广泛的生态分布,科学家推测它们在全球生态调节以及碳循环中可能起到了不可忽视的作用。然而,这些新型产甲烷古菌大部分尚未通过传统培养方法获得纯培养菌株,其确切的生理代谢机制和生态功能还有待深入研究。为了更加系统地了解这些新型产甲烷古菌,本文从它们的分类、系统发育地位、代谢机制、生态分布以及分离培养等方面进行了综述,并对新型产甲烷古菌未来的研究方向进行了展望。     

佛斯特拉古菌门（Verstraetearchaeota）研究进展

产甲烷古菌广泛分布在缺氧环境中,是有机质厌氧降解产甲烷过程中的关键功能微生物。它们在全球碳元素循环、气候变化等方面发挥着十分重要的作用。传统观念认为产甲烷古菌仅分布在广古菌门（Euryarchaeota）中,最新研究发现一系列新的非广古菌门（non-Euryarchaeota）产甲烷古菌,推测其不仅具有产甲烷能力,可能还具有发酵复杂有机物的代谢潜力。本文围绕佛斯特拉古菌门（Verstraetearchaeota）产甲烷古菌,系统阐述了它的系统分类、碳代谢机制和生态学分布等方面的研究进展,并展望了未来发展趋势。     

产甲烷古菌中CRISPR簇的研究

【目的】通过对51个产甲烷古菌基因组中成簇的规律间隔短回文重复序列(Clustered regularly interspaced short palindromic repeats,CRISPR)的组成和来源进行研究,推测产甲烷古菌与环境中其他微生物的物质交换和相互作用,在基因组水平上阐述产甲烷古菌之间的遗传差异。【方法】利用CRISPRdb和CRISPRFinder,找出产甲烷古菌基因组中所有潜在的CRISPR簇。对CRISPR簇的基本组成部分进行分析:利用BLASTCLUST对重复序列(Repeat)进行分类;分别将间隔序列(Spacer)与Refseq病毒基因组、Refseq质粒基因组和Refseq产甲烷古菌基因组进行比对,从而获得间隔序列的物种来源和功能信息的注释。【结果】在51个产甲烷古菌中共找到了196个CRISPR簇,这些CRISPR簇中包含了总共4 355条间隔序列。在这些产甲烷古菌中,CRISPR簇的分布是不均匀的,且每个物种的间隔序列数量与其CRISPR簇数量是不成正比的。在对重复序列进行分类之后,发现Mclu1是分布最广且最具代表性的一类重复序列。在4 355条间隔序列中有388条具有物种注释信息,266条具有功能注释信息。从CRISPR簇间隔序列的来源来看,产甲烷古菌曾受到来自Poxiviridae、Siphoviridae以及Myoviridae属病毒的攻击,并且产甲烷古菌之间存在比较广泛的遗传物质交换。【结论】产甲烷古菌基因组中的CRISPR簇在组成和来源上存在较大的差异,这些差异与它们的生存环境有较大的关系。从CRISPR簇的角度阐述了产甲烷古菌之间基因组序列的差异。     

我国产甲烷古菌研究进展与展望

产甲烷古菌广泛分布在湿地、水稻田、动物瘤胃、油藏、海洋和热液等缺氧环境,在全球碳素循环、气候变化和清洁能源生产等领域发挥着重要作用,一直是国内外的研究热点。本文简要回顾了我国产甲烷古菌的研究进展,重点阐述了产甲烷古菌的资源与分类、生理生化、分子生物学、生态学功能和应用等方面的研究进展,并展望了产甲烷古菌的未来研究趋势。     

绰墩山遗址古水稻土细菌与古菌群落的PCR-DGGE分析

在江苏苏州绰墩山遗址考古发掘中,发现了在剖面不同深度埋藏的距今约6280 a的新石器时期灌溉古水稻田土层和距今约3320 a的商周时期的古水稻田土层.为了解古代水稻种植活动对土壤中细菌、古菌及产甲烷古菌群落多样性的影响,以土壤剖面P-01(包含100～116 cm新石器时期水稻土,42～57 cm商周时期水稻土,0～15 cm现代水稻土和174～200 cm土壤母质)为对象, 利用细菌、古菌及产甲烷古菌群落16S rDNA的高可变区V3区的PCR-DGGE分析技术,研究了不同土层细菌、古菌及产甲烷古菌群落多样性.结果表明:利用PCR-DGGE技术成功获得了古水稻土细菌、古菌及产甲烷古菌群落的分子指纹图谱.现代水稻土、商周时期古水稻土和新石器时期古水稻土中细菌、古菌及产甲烷古菌群落的DGGE条带类型各不相同, 并且DGGE条带类型都较母质层丰富多样.UPGAMA聚类分析可以将不同时期水稻土及母质层的细菌、古菌及产甲烷古菌群落区分开来.埋藏古水稻土中仍有较多的细菌、古菌与产甲烷古菌存活.与母质层相比,不同时期水稻种植活动均增加了细菌、古菌与产甲烷古菌群落多样性.不同时期水稻种植活动可以引起特异性的细菌、古菌与产甲烷古菌群落发育,而且不同的栽培措施可能导致不同的优势种群.     

嗜盐古菌分类学研究进展

嗜盐古菌是一类需要高盐维持生长的古菌。到目前为止,已发现的嗜盐古菌都属于古菌域的广古菌门,主要包括:嗜盐甲烷古菌类群、嗜盐古菌纲的全部成员以及尚不能培养的纳米嗜盐古菌类群。嗜盐古菌是盐环境的土著类群,驱动着盐环境生态系统的生物地球化学循环。作为极端微生物,嗜盐古菌在理论研究和应用领域具有重要的研究价值。本文从嗜盐古菌分类学地位的变迁、分类学方法、分类学研究现状及我国的嗜盐古菌分类学研究等方面综述了嗜盐古菌分类学的最新研究进展。     

典型煤层水微生物产甲烷潜力及其群落结构研究

内蒙古自治区二连盆地、海拉尔盆地是我国重要的煤层气产区,其中生物成因煤层气是煤层气的重要来源,但复杂物质转化产甲烷相关微生物群落结构及功能尚不清楚。【目的】研究煤层水中的微生物代谢挥发性脂肪酸产甲烷的生理特征及群落特征。【方法】以内蒙古自治区二连盆地和海拉尔盆地的四口煤层气井水作为接种物,分别添加乙酸钠、丙酸钠和丁酸钠厌氧培养;定期监测挥发性脂肪酸降解过程中甲烷和底物的变化趋势,应用高通量测序技术,分析原始煤层气井水及稳定期产甲烷菌液的微生物群落结构。【结果】除海拉尔盆地H303煤层气井微生物不能代谢丙酸外,其他样品均具备代谢乙酸、丙酸和丁酸产生甲烷的能力,其生理生态参数存在显著差异,产甲烷延滞期依次是乙酸<丁酸<丙酸;最大比产甲烷速率和底物转化效率依次是丙酸<乙酸<丁酸。富集培养后,古菌群落结构与煤层气井水的来源显著相关,二连盆地优势古菌为氢营养型产甲烷古菌Methanocalculus (相对丰度13.5%–63.4%)和复合营养型产甲烷古菌Methanosarcina (7.9%–51.3%),海拉尔盆地的优势古菌为氢营养型产甲烷古菌Methanobact...     

古丸菌Archaeoglobi的代谢特征

古丸菌纲(Archaeoglobi)是广古菌门下的纲级分类单元,包含古丸菌(Archaeoglobus)、地丸菌(Geoglobus)和铁丸菌(Ferroglobus)三个属,所属菌株均是严格嗜热厌氧菌,主要分布于海洋、陆地热液系统和油田环境中。Archaeoglobus属下的微生物是一类以硫酸盐、亚硫酸盐或硫代硫酸盐为电子受体代谢生成硫化氢(H2S)的化能自养或氢营养型微生物;而Geoglobus和Ferroglobus的成员则主要还原硝酸盐和铁离子。Archaeoglobi地理分布广泛,在元素生物地球化学循环过程中发挥着重要作用,是目前微生物生态学研究的一个热点。在进化方面,Archaeoglobi菌和产甲烷古菌具有较高的亲缘关系;同时,Archaeoglobi基因组中保留着部分产甲烷途径上的功能基因,最新研究表明部分未培养的Archaeoglobi基因组中含有完整的产甲烷通路。这些证据都表明Archaeoglobi菌的基因组特征可能是产甲烷古菌向硫酸盐还原菌进化的活化石。本文梳理了目前发现的11株Archaeoglobi菌株的生理生化特征和基因组分析结果,从化能自养、化能异养、硫化物呼吸、产乙酸、产甲烷等方面综述了已分离的Archaeoglobi菌的代谢特征,并基于宏基因组信息分析了未培养的Archaeoglobi菌基因组中的潜在代谢功能,为进一步分离培养此类未培养厌氧微生物提供理论指导。     

乙酸型甲烷八叠球菌细胞工厂的设计与构建研究进展

在整个地球演化历史过程中,产甲烷古菌在生物地球碳循环中一直扮演着重要角色。据报道,约三分之二的地球生物甲烷通量来自乙酸型产甲烷途径,乙酸型甲烷八叠球菌(Methanosarcina acetivorans)是目前发现为数不多的可以进行乙酸型产甲烷途径的模式产甲烷古菌,对M.acetivorans代谢途径的解析、改造和应用可为温室气体甲烷的减排与其作为能源的合理利用提供新思路。本文综述了M.acetivorans的产甲烷代谢途径、遗传改造策略、细胞工厂构建3个方面的研究进展,分析了M.acetivorans与其他进行乙酸型产甲烷代谢的产甲烷古菌在以上三方面的异同,并对进一步设计和构建其作为微生物细胞工厂所面临的问题与挑战进行了展望。     

Adaptations to energy stress dictate the ecology and evolution of the Archaea

The three domains of life on Earth include the two prokaryotic groups, Archaea and Bacteria. The Archaea are distinguished from Bacteriabased on phylogenetic and biochemical differences, but currently there is no unifying ecological principle to differentiate these groups. The ecology of the Archaea is reviewed here in terms of cellular bioenergetics. Adaptation to chronic energy stress is hypothesized to be the crucial factor that distinguishes the Archaea from Bacteria. The biochemical mechanisms that enable archaea to cope with chronic energy stress include low-permeability membranes and specific catabolic pathways. Based on the ecological unity and biochemical adaptations among archaea, I propose the hypothesis that chronic energy stress is the primary selective pressure governing the evolution of the Archaea.     

Sulfur metabolism in archaea reveals novel processes

Studies on sulfur metabolism in archaea have revealed many novel enzymes and pathways and have advanced our understanding on metabolic processes, not only of the archaea, but of biology in general. A variety of dissimilatory sulfur metabolisms, i.e. reactions used for energy conservation, are found in archaea from both the Crenarchaeota and Euryarchaeota phyla. Although not yet fully characterized, major processes include aerobic elemental sulfur (S(0) ) oxidation, anaerobic S(0) reduction, anaerobic sulfate/sulfite reduction and anaerobic respiration of organic sulfur. Assimilatory sulfur metabolism, i.e. reactions used for biosynthesis of sulfur-containing compounds, also possesses some novel features. Cysteine biosynthesis in some archaea uses a unique tRNA-dependent pathway. Fe-S cluster biogenesis in many archaea differs from that in bacteria and eukaryotes and requires unidentified components. The eukaryotic ubiquitin system is conserved in archaea and involved in both protein degradation and biosynthesis of sulfur-containing cofactors. Lastly, specific pathways are utilized for the biosynthesis of coenzyme M and coenzyme B, the sulfur-containing cofactors required for methanogenesis.     

Conversion of energy in halobacteria: ATP synthesis and phototaxis

Halobacteria are aerobic chemo-organotroph archaea that grow optimally between pH 8 and 9 using a wide range of carbon sources. These archaea have developed alternative processes of energy provision for conditions of high cell densities and the reduced solubility of molecular oxygen in concentrated brines. The halobacteria can switch to anaerobic metabolism by using an alternative final acceptor in the respiratory chain or by fermentation, or alternatively, they can employ photophosphorylation. Light energy is converted by several retinal-containing membrane proteins that, in addition to generating a proton gradient across the cell membrane, also make phototaxis possible in order to approach optimal light conditions. The structural and functional features of ATP synthesis in archaea are discussed, and similarities to F-ATPases (functional aspects) or vacuolar ATPases (structural aspects) are presented. Received: 18 December 1995 / Accepted: 3 April 1996     

Artificial construction of the biocoenosis of deep-sea ecosystem via seeping methane

Deep-sea ecosystems, such as cold seeps and hydrothermal vents, have high biomass, even though they are located in the benthic zone, where no sunlight is present to provide energy for organism proliferation. Based on the coexistence of the reduced gases and chemoautotrophic microbes, it is inferred that the energy from the reduced gases supports the biocoenosis of deep-sea ecosystems. However, there is no direct evidence to support this deduction. Here, we developed and placed a biocoenosis generator, a device that continuously seeped methane, on the 1000-m deep-sea floor of the South China Sea to artificially construct a deep-sea ecosystem biocoenosis. The results showed that microorganisms, including bacteria and archaea, appeared in the biocoenosis generator first, followed by jellyfish and Gammaridea arthropods, indicating that a biocoenosis had been successfully constructed in the deep sea. Anaerobic methane-oxidizing archaea, which shared characteristics with the archaea of natural deep-sea cold seeps, acted as the first electron acceptors of the emitted methane; then, the energy in the electrons was transferred to downstream symbiotic archaea and bacteria and finally to animals. Nitrate-reducing bacteria served as partners to complete anaerobic oxidation of methane process. Further analysis revealed that viruses coexisted with these organisms during the origin of the deep-sea biocoenosis. Therefore, our study mimics a natural deep-sea ecosystem and provides the direct evidence to show that the chemical energy of reduced organic molecules, such as methane, supports the biocoenosis of deep-sea ecosystems.     

微生物纳米导线的导电机制及功能

微生物种间直接电子传递是指在厌氧条件下,一种微生物将电子直接传递给另外一种微生物,将两种不同微生物的代谢途径耦合在一起,以达到互养共生的目的。细菌-古菌之间的直接电子传递是其物质转换与能量代谢的新途径和新调控机制,直接参与甲烷的合成以及与硫酸盐还原耦合的厌氧甲烷氧化,在驱动碳和硫的地球化学转化与循环中起着十分重要的作用。目前研究结果认为细菌-古菌之间的直接电子传递主要是由含多个血红素的C型细胞色素介导的,这些细胞色素能形成不间断的胞外电子传递途径,以电子多步跃迁机制在细菌和古菌的细胞质膜之间传递电子。     

鄱阳湖周边稻田对白鹤的承载力

鄱阳湖是世界重要的候鸟越冬地,承载了全球约98%的白鹤(Leucogeranus leucogeranus)。然而,近年来鄱阳湖沉水植被退化严重,白鹤的传统食物苦草(Vallisneria spp.)冬芽丰富度急剧减少。食物短缺导致白鹤的觅食生境由自然湿地的浅水生境转移至稻田、藕塘等人工生境,稻田在白鹤保护中发挥的作用日益突出。了解鄱阳湖周边稻田对白鹤的承载力可为白鹤的保护和管理提供科学依据。为此,调查了鄱阳湖周边稻田散落稻谷的生物量,测量了稻谷的营养成分,并利用遥感影像对鄱阳湖周边10 km范围内稻田的总面积进行估算,从而得出鄱阳湖周边稻田散落稻谷能提供的总能量。然后,计算稻田中以稻谷为主要食物的6种鸟类的日能量消耗,用以表示日能量摄入。最后,依据稻田能提供的总能量、鸟类的日能量摄入、鸟类的越冬时长、以及各种鸟类的数量占比,计算得出鄱阳湖周边稻田能承载的白鹤数量。结果表明,鄱阳湖周边稻田散落稻谷的生物量为6.494 g/m²,环鄱阳湖周边10 km范围内稻田的总面积为1984.46 km²,这些稻田能承载的鸟类总数量为140860只,其中能承载的白鹤数量为10775只,超过了全球白鹤的总数量(3500-4000只)。因此,鄱阳湖周边稻田能为白鹤等鸟类提供丰富的食物资源。     

Archaeal abundance in relation to root and fungal exudation rates

Archaea are ubiquitous in forest soils, but little is known about the factors regulating their abundance and distribution. Low molecular weight organic compounds represent an important energy source for archaea in marine environments, and it is reasonable to suspect that archaeal abundance is dependent on such compounds in soils as well, represented by, for example, plant and fungal exudates. To test this hypothesis, we designed a microcosm experiment in which we grew ponderosa pine, sitka spruce, and western hemlock in forest soil. Root and mycorrhizal exudation rates were estimated in a 13C pulse-chase experiment, and the number of archaeal and bacterial 16S rRNA genes was determined by qPCR. Archaeal abundance differed among plant species, and the number of archaeal 16S rRNA genes was generally lower in soil receiving high concentration of exudates. The mycorrhizal fungi of ponderosa pine seemed to favor archaea, while no such effect was found for mycorrhized sitka spruce or western hemlock. The low abundance of archaea in the proximity of roots and mycorrhiza may be a result of slow growth rates and poor competitive ability of archaea vs. bacteria and does not necessarily reflect a lack of heterotrophic abilities of the archaeal community.     

Haloadaptation: insights from comparative modeling studies of halophilic archaeal DHFRs

Proteins of halophilic archaea function in high-salt concentrations that inactivate or precipitate homologous proteins from non-halophilic species. Haloadaptation and the mechanism behind the phenomenon are not yet fully understood. In order to obtain useful information, homology modeling studies of dihydrofolate reductases (DHFRs) from halophilic archaea were performed that led to the construction of structural models. These models were subjected to energy minimization, structural evaluation and analysis. Complementary approaches concerning calculations of the amino acid composition and visual inspection of the surfaces and cores of the models, as well as calculations of electrostatic surface potentials, in comparison to non-halophilic DHFRs were also performed. The results provide evidence that sheds some light on the phenomenon of haloadaptation: DHFRs from halophilic archaea may maintain their fold, in high-salt concentrations, by sharing highly negatively charged surfaces and weak hydrophobic cores.     

Unwinding the structure and function of the archaeal MCM helicase

During chromosomal DNA replication, the replicative helicase unwinds the duplex DNA to provide the single-stranded DNA substrate for the polymerase. In archaea, the replicative helicase is the minichromosome maintenance (MCM) complex. The enzyme utilizes the energy of ATP hydrolysis to translocate along one strand of the duplex and unwind the complementary strand. Much progress has been made in elucidating structure and function since the first report on the biochemical properties of an archaeal MCM protein in 1999. We now know the biochemical and structural properties of the enzyme from several archaeal species and some of the mechanisms by which the enzyme is regulated. This review summarizes recent studies on the archaeal MCM protein and discusses the implications for helicase function and DNA replication in archaea.     

The cell membrane plays a crucial role in survival of bacteria and archaea in extreme environments

The cytoplasmic membrane of bacteria and archaea determine to a large extent the composition of the cytoplasm. Since the ion and in particular the proton and/or the sodium ion electrochemical gradients across the membranes are crucial for the bioenergetic conditions of these microorganisms, strategies are needed to restrict the permeation of these ions across their cytoplasmic membrane. The proton and sodium permeabilities of all biological membranes increase with the temperature. Psychrophilic and mesophilic bacteria, and mesophilic, (hyper)thermophilic and halophilic archaea are capable of adjusting the lipid composition of their membranes in such a way that the proton permeability at the respective growth temperature remains low and constant (homeo-proton permeability). Thermophilic bacteria, however, have more difficulties to restrict the proton permeation across their membrane at high temperatures and these organisms have to rely on the less permeable sodium ions for maintaining a high sodium-motive force for driving their energy requiring membrane-bound processes. Transport of solutes across the bacterial and archaeal membrane is mainly catalyzed by primary ATP driven transport systems or by proton or sodium motive force driven secondary transport systems. Unlike most bacteria, hyperthermophilic bacteria and archaea prefer primary ATP-driven uptake systems for their carbon and energy sources. Several high-affinity ABC transporters for sugars from hyperthermophiles have been identified and characterized. The activities of these ABC transporters allow these organisms to thrive in their nutrient-poor environments. This revised version was published online in August 2006 with corrections to the Cover Date.