荒漠孑遗植物四合木对土壤古菌群落的影响

土壤是植物定居的场所,也是植物-微生物互作的重要界面。古菌是土壤微生物重要组份,在碳、氮、硫、铁等元素的生物地球化学循环和植物的生长发育、适应生境中发挥重要作用。植物定居对土壤古菌群落的影响研究鲜有开展,孑遗植物在研究植物-微生物-环境互作中具有独特的优势。采用扩增子高通量测序技术,研究以荒漠孑遗植物四合木为建群种或优势种的四合木-红砂-珍珠-针茅群落、四合木-针茅群落和四合木群落等三种荒漠植物群落类型中,四合木根区土壤和光板地土体土壤古菌群落特征,揭示四合木定居对土壤古菌物种数量、多样性、群落组成及功能的影响。结果表明,荒漠孑遗植物四合木定居不仅增加了根区土壤古菌的物种数量,提高了根区土壤古菌群落多样性,而且改变了土壤古菌群落组成,减少了奇古菌门Nitrososphaeraceae科未分类的属氨氧化古菌（unclassified_f_Nitrososphaeraceae）和暂定Nitrososphaera属氨氧化古菌（Candidatus Nitrososphaera）相对丰度,增加了Nitrososphaeraceae科暂定Nitrocosmicus属氨氧化古菌（Candidatus Nitrocosmicus）和广古菌门海洋古菌类群Ⅱ中未分类的属（norank_o_Marine_Group_II）相对丰度,广古菌门热原体纲未分类的属（unclassified_c__Thermoplasmata）相对丰度变化显著。植物群落演替对四合木根区土壤和光板地土体土壤古菌群落均无显著影响。Nitrososphaeraceae科氨氧化古菌是三种不同荒漠植物群落类型中土壤古菌的核心微生物组。四合木定居也显著改变土壤古菌群落的功能,减弱了高丰度功能,增强了低丰度功能,对有氧呼吸、核苷酸合成、氨基酸合成等途径影响显著。荒漠孑遗植物四合木定居改变了土壤古菌群落物种数量、多样性、组成、功能等特征。     

不同风化时间碳酸岩表面古菌群落结构与功能特征

【背景】古菌群落是碳酸岩表面微生物群落的重要成员,也是碳酸岩表面生物演替的先锋生物,能够促进碳酸岩风化和加快土壤形成,在生物地球化学循环中起重要作用。【目的】揭示在不同风化时间碳酸岩表面风化残积物中的古菌群落结构及生态功能。方法】采集19-213年风化时间段废弃碳酸岩墓碑表面风化残积物样品(n=18),基于宏基因组测序技术分析其古菌群落结构与功能特征。【结果】门水平上,优势门有广古菌门(Euryarchaeota),随后为奇古菌门(Thaumarchaeota)、未鉴定古菌门(unclassified Archaea)、深古菌门(Bathyarchaeota)和泉古菌门(Crenarchaeota);属水平上,优势属主要由甲烷八叠球菌属(Methanosarcina)、甲烷丝状菌属(Methanothrix)、Methanoperedens、氨氧化古菌属(Nitrosocosmicus)、亚硝化球菌属(Nitrososphaera)及其他未鉴定属组成;C/N、C/P、N/P是显著影响碳酸岩表面古菌群落的主要环境因子。进一步分析发现,碳酸岩表面古菌群落功能丰富,其中新陈代谢(metabo...     

象山港网箱养殖区沉积物的古菌空间分布

对象山港网箱养殖区及其周边沉积物中古菌群落的空间分布进行研究,应用基于16S rRNA基因的T-RFLP(末端限制性片段多态性分析)技术分析象山港网箱养殖区及其周边不同深度沉积物中古菌的群落结构和多样性,并构建克隆文库进行系统发育学分析。测定沉积物各项理化因子,通过PCA和RDA分析了古菌群落分布及其与环境因子之间的关系。结果表明,泉古菌是港口沉积物中的优势古菌群,占古菌群落的50%以上。网箱养殖区沉积物的古菌群落结构较非养殖区简单,多样性降低。非养殖区古菌群落随深度呈现有规律的变化。营养盐类和pH是造成养殖区域古菌群落结构区别于非养殖区域的主要环境因素。     

我国8个典型水稻土中产甲烷古菌群落组成的空间分异特征

【目的】产甲烷古菌主导稻田甲烷生成,是稻田生态系统的模式微生物类群之一,具有重要的生态学意义。然而,水稻土产甲烷古菌群落组成的空间分异却鲜有报告。【方法】本研究沿20.55°N至47.43°N梯度,采集了我国不同纬度上8个典型水稻土,利用PCR-DGGE指纹图谱和系统发育树分析揭示不同地点水稻土中产甲烷古菌群落的组成;结合多个环境因子,利用生物信息学,典范对应分析(Canonical Correspondence Analysis,CCA)和维恩图(Venn diagram)明确产甲烷古菌的空间分异规律。【结果】研究发现p H值是驱动水稻土中产甲烷古菌群落组成分异的主要因子;此外,沿纬度梯度,8个地区的产甲烷古菌群落组成也呈现出规律性变化。【结论】本研究首次阐明了稻田中产甲烷古菌群落分布情况,并揭示其主要驱动因子。该认知不仅有助于我们更好地了解产甲烷古菌的生物地理学分布,还有助于从微生物学机制上阐明我国温度梯度带上有机质转化空间的差异。     

外源砷胁迫对两种土壤中细菌和古菌群落的影响

采矿和冶炼等活动会导致土壤中砷的累积,给农产品质量安全和土壤微生物带来不利影响。本文研究了外源砷进入黄壤(YS)和紫色砂页岩发育土壤(RS)后有效砷含量随时间的变化,并采用MiSeq高通量测序研究土壤中细菌和古菌在未加砷和外源砷胁迫1、30、360 d后的群落变化,探讨砷胁迫下土壤细菌和古菌的适应机制。结果表明: 外源砷进入土壤后,土壤有效砷含量随时间推移逐渐降低,并显著影响土壤细菌和古菌的群落组成。土壤细菌的优势菌群丰度变化显著;而古菌中仅丰度较低的菌群发生显著改变,优势菌群丰度变化较小,推测古菌群落具有高耐砷性和稳定性。与砷胁迫时间相比,土壤砷的有效性对细菌和古菌群落结构的影响更大。研究结果可为砷污染农田的安全利用及微生物修复等提供参考。     

环梅山岛海域春季浮游古菌群落空间分布特征研究

【目的】海洋浮游古菌是生物地球化学循环的关键驱动者,但其在近岸海域的水平空间分布特征还未被充分了解。本研究以与陆地紧密相连的环梅山岛海域为例研究浮游古菌在海陆过渡带的水平分布模式。【方法】利用16S rRNA基因扩增子测序,以期从优势类群分布、群落组成变化和物种共现模式3个层面揭示梅山湾潟湖区和临近海域春季浮游古菌的空间分布特征。【结果】该海域浮游古菌在原核生物群落中的相对丰度为0.6%–26.5%,向海侧古菌丰度显著高于潟湖区。浮游古菌群落由奇古菌门Marine Group(MG)I和广古菌门MGII主导,MGI的物种组成较为单一,而MGII的系统发育多样性较高。古菌群落的空间分布受同质扩散、环境选择和非主导过程(包括生态漂变)的共同塑造,其中环境选择主要由悬浮颗粒物、硝酸盐、溶解氧、水温和铵盐驱动。通过网络分析发现MGI与红杆菌科细菌呈广泛的负相关,MGII则普遍与SAR11、SAR116和SAR86等异养细菌类群呈正相关。【结论】本研究初步揭示了环梅山岛海域春季浮游古菌群落的空间分布特征及其调控因子,拓展了对古菌在海陆过渡带分布规律的认识。     

长期集约种植对雷竹林土壤氨氧化古菌群落的影响

应用荧光定量PCR以及PCR-DGGE技术研究了雷竹林长期集约种植过程中土壤氨氧化古菌种群数量及群落结构的演变趋势,并利用典范对应分析(CCA)方法研究影响土壤氨氧化古菌群落的主要环境因子。研究结果表明,水稻田改种雷竹后,土壤氨氧化古菌种群数量显著增加,在4 a时达到最高,但在集约种植后快速下降,9 a雷竹林土壤氨氧化古菌数量最低,随后逐渐稳定。雷竹林土壤氨氧化古菌种群主要为不可培养泉古菌,聚类分析结果表明集约种植前后氨氧化古菌群落结构存在明显差异,长期集约经营雷竹林土壤以适应较低pH值的物种为主要优势种群。CCA分析表明,集约种植时间较长的11 a和15 a林地群落结构较为类似,与7 a和9 a样地明显区分。土壤NO-3-N与氨氧化古菌群落变化的相关性最强,说明氨氧化古菌在雷竹林土壤硝化过程中发挥着重要作用。土壤pH值及速效养分对土氨氧化古菌群落也具有较大影响,它们与NO-3-N合计解释了59.7%的样本总变异,表明土壤酸化以及过量养分的积累对氨氧化古菌群落具有重要影响。     

青海湖与中国内陆盐湖古菌群落组成的比较

【目的】本研究旨在全面揭示中国最大的内陆咸水湖——青海湖的古菌群落结构,并对青海湖与盐湖的古菌多样性及群落结构进行比较。【方法】随机选取了青海省的茶卡盐湖、陕西省的花马池盐湖和苟池盐湖以及山西省的运城盐湖作为盐湖组。青海湖与盐湖组每个湖泊各采取5个样品,采用针对16S rRNA基因的高通量测序技术分析5个湖泊中的古菌群落组成。【结果】研究发现,青海湖的优势菌群为DHVEG-6_norank、Methanomicrobia_unclassified、Methanobacterium(甲烷细菌属)、Methanolobus(甲烷叶菌属)、Candidatus_Methanomethylophilus、Miscellaneous_Euryarchaeotic_Group(MEG)_norank、AMOS1A-4113-D04_norank、Methanosarcina(甲烷八叠球菌属)、Miscellaneous_Crenarchaeotic_Group_norank。其中,DHVEG-6_norank(70.46%)占绝对优势,但该类群在盐湖中含量极少。4个盐湖的共有优势属为Halonotius、Halorubrum(盐红菌属)、Natronomonas(嗜盐碱单孢菌属)、Halobellus和Haloarcula(盐盒菌属)。对于青海湖与盐湖之间的古菌群落多样性,影响最大的因素为湖水的矿化度,矿化度与5个湖泊的古菌多样性呈负相关,矿化度较低的青海湖群落组成与其他4个盐湖差异显著,无共同优势菌;其次为pH,pH与湖泊中古菌群落多样性呈微弱正相关,小幅度影响到某些菌属的丰度;而本文研究范围内的海拔与其群落结构及多样性没有明显相关性。【结论】青海湖与其他4个盐湖之间的群落结构及多样性有显著差异,矿化度对古菌群落多样性具有显著影响。另,本次测序发现5个湖泊中均有大量未分类的古菌,应为潜在的新种。     

杨树人工林根际古菌群落随细根生长的演变

研究细根不同生长时期根际土壤古菌群落组成结构差异,对深入了解林木细根与土壤微生物互作关系具有重要理论意义.依据细根表面颜色,采集杨树一级细根不同生长时期(白色新生根、黄色成熟根、褐色衰老根)根际土壤并提取微生物总DNA,采用特异性引物对古菌16S rDNA V4-V5区进行扩增,利用Illumina MiSeq平台进行古菌高通量测序分析.结果表明: 新生根和衰老根根际土壤古菌群落操作分类单元(OTU)丰富度相似,而成熟根根际土壤古菌群落OTU数量较少.新生根和成熟根根际土壤共同含有134个OTU;成熟根和衰老根根际土壤共同含有87个OTU,新生根和衰老根根际土壤共同拥有90个OTU.α多样性分析表明,成熟根根际土壤古菌群落Chao1指数和ACE指数显著低于新生根和衰老根根际土壤,而衰老根根际土壤古菌群落Simpson指数和Shannon指数显著低于新生根和成熟根根际土壤.PERMANOVA分析表明,新生根和衰老根根际土壤古菌群落组成有显著差异.物种注释显示,杨树根际土壤共包含12个古菌属,其中新生根5个、成熟根10个、衰老根6个.β多样性指数表明,杨树根际土壤古菌群落相似度随着细根的生长逐渐下降,不同生长阶段细根根际土壤的古菌群落结构有较大差异.其中,占绝对优势的古菌为氨氧化古菌Candidatus_Nitrososphaera,其相对丰度超过70%.且随细根生长发育,该类古菌在根际土壤中的丰度呈现上升趋势,表明其可能与细根的生长发育关系密切.     

深部生物圈古菌的研究进展与展望

古菌作为深部生物圈中常见的原核生物,广泛分布于各类海洋沉积生境中,在沉积物生物地球化学循环中发挥着重要作用。由于不同的古菌类群对环境条件存在生理适应性差异,它们分别在近岸沿海和开阔大洋沉积物中构成了厌氧微生物生态系统和好氧微生物生态系统。本文通过对近岸与远洋、沉积物与上覆水体两个不同维度的古菌群落结构进行比较,以及对出现在深部生物圈中的常见古菌(奇古菌门(Thaumarchaeota)、深古菌门(Bathyarchaeota)、底栖古菌目(Thermoprofundales)、Asgard古菌超级门、乌斯古菌门(Woesearchaeota))的分布、代谢和环境适应机制进行论述,总结了深部生物圈中古菌的研究进展,并在此基础上展望了几个未来研究的方向与重点。     

The archaeal cell envelope

At first glance, archaea and bacteria look alike; however, the composition of the archaeal cell envelope is fundamentally different from the bacterial cell envelope. With just one exception, all archaea characterized to date have only a single membrane and most are covered by a paracrystalline protein layer. This Review discusses our current knowledge of the composition of the archaeal cell surface. We describe the wide range of cell wall polymers, O- and N-glycosylated extracellular proteins and other cell surface structures that archaea use to interact with their environment.     

Indicators from archaeal secretomes

Just as in the Eukarya and the Bacteria, members of the Archaea need to export proteins beyond the cell membrane. This would be required to fulfill a variety of essential functions such as nutrient acquisition and biotransformations, maintenance of extracellular structures and more. Apart from the Eukarya and the Bacteria however, members of the Archaea share a number of unique characteristics. Does this uniqueness extend to the protein secretion system? It was the objective of this study to answer this question. To overcome the limited experimental information on secreted proteins in Archaea, this study was carried out by subjecting the available archaeal genomes, which represent halophiles, thermophiles, and extreme thermophiles, to bioinformatics analysis. Specifically, to examine the properties of the secretomes of the Archaea using the ExProt program. A total of 24 genomes were analyzed. Secretomes were found to fall in the range of 6% of total ORFs (Methanopyrus kandleri) to 19% (Halobacterium sp. NRC-1). Methanosarcina acetivorans has the highest fraction of lipoproteins (at 89) and the lowest (at 1) were members of the Thermoplasma, Pyrobaculum aerophilum, and Nanoarchaeum equitans. Based on the Tat consensus sequence, contribution of these secreted proteins to the secretomes were negligible, making up 8 proteins out of a total of 7105 predicted exported proteins. Amino acid composition, an attribute of signal peptides not used as a selection criteria by ExProt, of predicted archaeal signal peptides show that in the haloarchaea secretomes, the frequency of the amino acid Lys is much lower than that seen in bacterial signal peptides, but is compensated for by a higher frequency of Arg. It also showed that higher frequencies for Thr, Val, and Gly contribute to the hydrophobic character in haloarchaeal signal peptides, unlike bacterial signal peptides in which the hydrophobic character is dominated by Leu and Ile.     

The archaeal PCNA proteins

PCNA (proliferating-cell nuclear antigen) is a ring-shaped protein that encircles duplex DNA and plays an essential role in many DNA metabolic processes. The PCNA protein interacts with a large number of cellular factors and modulates their enzymatic activities. In the present paper, we summarize the structures, functions and interactions of the archaeal PCNA proteins.     

DNA replication: archaeal oriGINS

GINS is an essential eukaryotic DNA replication factor that is found in a simplified form in Archaea. A new study in this issue of BMC Biology reveals the first structure of the archaeal GINS complex. The structure reveals the anticipated similarity to the previously determined eukaryotic complex but also has some intriguing differences in the relative disposition of subunit domains.     

Mobile elements in archaeal genomes

The recent availability of several archaeal genome sequences has provided a basis for detailed analyses of the frequency, location and phylogeny of archaeal mobile elements. All the known elements fall into two main types, autonomous insertion sequence (IS) elements and the non-autonomous miniature inverted repeat element (MITE)-like elements. Both classes are considered to be mobilized via transposases that are encoded by the IS elements, although mobility has only been demonstrated experimentally for a few elements. The number, and diversity, of the elements differs greatly between the genomes. At one extreme Sulfolobus solfataricus P2 and Halobacterium NRC-1 are very rich in elements while Methanobacterium thermoautotrophicum contains none. The former also show examples of complex clusters of interwoven elements. An analysis of the genomic distribution in S. solfataricus suggests that the putative oriC and terC regions act as barriers for the mobility of both IS and MITE-like elements. Moreover, the very high level of truncated IS elements in the genomes of S. solfataricus, Sulfolobus tokodaii and Thermoplasma volcanium suggests that there may be a cellular mechanism for selectively inactivating IS elements at a point when they become too numerous and disadvantageous for the cell. Phylogenetically, archaeal IS elements are confined to 11 of the 17 known families of bacterial and eukaryal IS elements where some generate distinct subgroups. Finally, DNA viruses, plasmids and DNA fragments can also be inserted into, and excised from, archaeal genomes by means of an integrase-mediated mechanism that has special archaeal characteristics.     

Multi-scale architecture of archaeal chromosomes

1. Download : Download high-res image (109KB)
2. Download : Download full-size image

     

Biotechnological uses of archaeal extremozymes

Archaea have developed a variety of molecular strategies to survive the often harsh environments in which they exist. Although the rules that allow archaeal enzymes to fulfill their catalytic functions under extremes of salinity, temperature or pressure are not completely understood, the stability of these extremophilic enzymes, or extremozymes, in the face of adverse conditions has led to their use in a variety of biotechnological applications in which such tolerances are advantageous. In the following, examples of commercially important archaeal extremozymes are presented, potentially useful archaeal extremozyme sources are identified and solutions to obstacles currently hindering wider use of archaeal extremozymes are discussed.