Archaeal habitats--from the extreme to the ordinary

The domain Archaea represents a third line of evolutionary descent, separate from Bacteria and Eucarya. Initial studies seemed to limit archaea to various extreme environments. These included habitats at the extreme limits that allow life on earth, in terms of temperature, pH, salinity, and anaerobiosis, which were the homes to hyper thermo philes, extreme (thermo)acidophiles, extreme halophiles, and methanogens. Typical environments from which pure cultures of archaeal species have been isolated include hot springs, hydrothermal vents, solfataras, salt lakes, soda lakes, sewage digesters, and the rumen. Within the past two decades, the use of molecular techniques, including PCR-based amplification of 16S rRNA genes, has allowed a culture-independent assessment of microbial diversity. Remarkably, such techniques have indicated a wide distribution of mostly uncultured archaea in normal habitats, such as ocean waters, lake waters, and soil. This review discusses organisms from the domain Archaea in the context of the environments where they have been isolated or detected. For organizational purposes, the domain has been separated into the traditional groups of methanogens, extreme halophiles, thermoacidophiles, and hyperthermophiles, as well as the uncultured archaea detected by molecular means. Where possible, we have correlated known energy-yielding reactions and carbon sources of the archaeal types with available data on potential carbon sources and electron donors and acceptors present in the environments. From the broad distribution, metabolic diversity, and sheer numbers of archaea in environments from the extreme to the ordinary, the roles that the Archaea play in the ecosystems have been grossly underestimated and are worthy of much greater scrutiny.     

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.     

古菌在红树林沉积物中的多样性及其碳代谢机制

红树林湿地生态系统具有维持生物多样性、净化环境及维持海岸带生态平衡等多种功能。古菌普遍存在于红树林沉积物中,在元素的生物地球化学循环中发挥着重要作用。古菌具有丰富的碳代谢多样性,能固定CO_2,参与甲烷循环,产乙酸,降解蛋白质、多聚碳水化合物等有机质,但目前对于红树林沉积物中古菌碳代谢的研究才刚刚起步。高通量测序技术的快速发展促进了大量新的古菌门类的发现,这些新的古菌门类具备多样的碳代谢潜力。本文简要概述古菌的主要类群与分布,综述国内外有关古菌碳代谢多样性的最新研究进展,并阐明这些古菌在红树林生态系统中的生态分布和功能特征,为进一步探究古菌代谢机制提供知识基础。     

Archaea--timeline of the third domain

The Archaea evolved as one of the three primary lineages several billion years ago, but the first archaea to be discovered were described in the scientific literature about 130 years ago. Moreover, the Archaea were formally proposed as the third domain of life only 20 years ago. Over this very short period of investigative history, the scientific community has learned many remarkable things about the Archaea--their unique cellular components and pathways, their abundance and critical function in diverse natural environments, and their quintessential role in shaping the evolutionary path of life on Earth. This Review charts the 'archaea movement', from its genesis through to key findings that, when viewed together, illustrate just how strongly the field has built on new knowledge to advance our understanding not only of the Archaea, but of biology as a whole.     

The influence of vegetation type,soil properties and precipitation on the composition of soil mite and microbial communities at the landscape scale

Aim We used a landscape‐scale study of birch invasion onto heather moorland to determine the consistency of changes in vegetation type and soil properties and in the community composition of five soil organism groups. Our aim was to determine whether the degree to which soil organisms respond to natural changes and/or induced changes (e.g. changes in land‐use type and climate) in habitat is consistent across trophic and taxonomic groups in the context of conservation policies for birch woodland and heather moorland. Location Mainland Scotland. Methods We sampled mesostigmatid mites, oribatid mites, fungi, bacteria and archaea in adjacent patches of birch woodland (dominated by Betula pubescens) and heather moorland (dominated by Calluna vulgaris) at 12 sites for which annual rainfall ranged between 713 and 2251 mm. Differences in community composition were visualized using non‐metric multidimensional scaling based on Bray–Curtis dissimilarities. The factors contributing to differences between habitats within sites were explored using general linear models and those among sites using redundancy analysis. Results The communities of all groups differed between habitats within sites, but only the oribatid mites and fungi differed consistently between habitats across sites. Within sites, dissimilarity in fungal communities was positively related to the difference in C. vulgaris cover between habitats, whereas dissimilarities in bacteria and archaea were positively related to differences in soil pH and C:N ratio between habitats, respectively. Main conclusions The influence of vegetation type and soil properties differed between groups of soil organisms, albeit in a predictable manner, across the 12 sites. Organisms directly associated with plants (fungi), and organisms with microhabitat and resource preferences (Oribatida) were strongly responsive to changes in habitat type. The response of organisms not directly associated with plants (bacteria, archaea) depended on differences in soil properties, while organisms with less clear microhabitat and resource preferences (Mesostigmata) were not strongly responsive to either vegetation type or soil properties. These results show that it is possible to predict the impact of habitat change on specific soil organisms depending on their ecology. Moreover, the community composition of all groups was related to variation in precipitation within the study area, which shows that external factors, such as those caused by climate change, can have a direct effect on belowground communities.     

Selenoproteins in Archaea and Gram-positive bacteria

Selenium is an essential trace element for many organisms by serving important catalytic roles in the form of the 21st co-translationally inserted amino acid selenocysteine. It is mostly found in redox-active proteins in members of all three domains of life and analysis of the ever-increasing number of genome sequences has facilitated identification of the encoded selenoproteins. Available data from biochemical, sequence, and structure analyses indicate that Gram-positive bacteria synthesize and incorporate selenocysteine via the same pathway as enterobacteria. However, recent in vivo studies indicate that selenocysteine-decoding is much less stringent in Gram-positive bacteria than in Escherichia coli. For years, knowledge about the pathway of selenocysteine synthesis in Archaea and Eukarya was only fragmentary, but genetic and biochemical studies guided by analysis of genome sequences of Sec-encoding archaea has not only led to the characterization of the pathways but has also shown that they are principally identical. This review summarizes current knowledge about the metabolic pathways of Archaea and Gram-positive bacteria where selenium is involved, about the known selenoproteins, and about the respective pathways employed in selenoprotein synthesis.     

深海氨氧化古菌的环境适应基础及生态功能

氨氧化古菌是地球上丰度最高的微生物类群之一,驱动氮循环。尤其在深海,其相对丰度可达原核生物的20%-40%。然而,纯培养的缺乏严重阻碍了我们全面认知深海氨氧化古菌的生理特性和生态贡献。本文系统性地分析了深海环境特征与微生物适应性之间的关系,聚焦深海氨氧化古菌的潜在生存策略和代谢偏好。这些信息将有助于我们设计适用于深海氨氧化古菌的培养技术。此外,从系统发育和生理特性来看,深海氨氧化古菌与土壤或表层海洋来源的氨氧化古菌有显著区别,提示我们需要根据其特性重新估算全球海洋氮通量。     

Buried treasure: soil biodiversity and conservation

Soils are incredibly biodiverse habitats, yet soil-dwelling organisms have received little attention within the field of conservation biology. Due to difficulties involved in studying soil biota, and to taxonomic biases in conservation research, the full extent of soil biodiversity is not well understood, and soil-dwelling organisms are rarely candidates for conservation. The biogeography of soil biota differs significantly from that of plants or animals aboveground, and the taxonomic and functional diversity of soil-dwellers allows them to have a multitude of ecological effects on aboveground organisms. Soil organisms exhibit levels of biodiversity several orders of magnitude greater than those found in their aboveground counterparts on a per-area basis. The biodiversity of soils underpins many crucial ecosystem services which support the plants and animals typically targeted by conservation efforts. Strategies detailed in this paper provide practitioners with the ability to address many of the challenges related to incorporating soils and soil organisms into conservation planning.     

Comparison of Archaeal Populations in Soil and Their Encapsulated Iron-Manganese Nodules in Four Locations Spanning from North to South China

To characterize the archaeal community composition in soil originating iron-manganese nodules, four types of soils—brown soil, yellow-cinnamon soil, yellow brown soil and red soil—and their associated iron-manganese nodules were collected from Queyu (QY), Zaoyang (ZY), Wuhan (WH) and Guiyang (GY), China, respectively, and subjected to quantitative polymerase chain reaction, cloning and sequencing analyses. The results showed that the archaeal 16S rRNA gene copy numbers in nodules, ranging between 3.59 × 10² and 4.17 × 10³ copies g^?1 dry nodule, were about 50–1000 times lower than those in their corresponding soils (1.87 × 10⁵ to 1.08 × 10⁶ copies g^?1 dry soil), correlating with the low organic matter in the nodules, while archaea accounted for a relatively higher proportion of total prokaryote in nodules than in soils. Community composition analysis suggested that the archaeal diversity in both soils and nodules were much lower than bacterial, but archaeal community structures were similar to each other among the soils and nodules from the same location but varied among four locations, converse to the previous observation that bacterial community shifted markedly between nodules and soils as the result of habitat filtering. The archaeal communities in both soils and nodules were predominated by Thaumarchaeota Group I.1b with the relative abundance ranging between 73.88 and 94.17%, except that Euryarchaeota dominated the archaeal community in one nodule sample (WHn) developed from lake sediment. The finding shed new light on the archaeal diversity and their ecophysiology in different habitats, and further supported the opinion that archaea are more adaptable to stress and unfavorable conditions.     

Archaeal phospholipids: Structural properties and biosynthesis

Phospholipids are major components of the cellular membranes present in all living organisms. They typically form a lipid bilayer that embroiders the cell or cellular organelles, constitute a barrier for ions and small solutes and form a matrix that supports the function of membrane proteins. The chemical composition of the membrane phospholipids present in the two prokaryotic domains Archaea and Bacteria are vastly different. Archaeal lipids are composed of highly-methylated isoprenoid chains that are ether-linked to a glycerol-1-phosphate backbone while bacterial phospholipids consist of straight fatty acids bound by ester bonds to the enantiomeric glycerol-3-phosphate backbone. The chemical structure of the archaeal lipids and their compositional diversity ensures the required stability at extreme environmental conditions as many archaea thrive at such conditions including high or low temperature, high salinity and extreme acidic or alkaline pH values. However, not all archaea are extremophiles, and the presence of ether-linked phospholipids is a phylogenetic marker that distinguishes Archaea from other life forms. During the past decade, our understanding of the biosynthesis of archaeal lipids has progressed resulting in the characterization of the main biosynthetic steps of the pathway including the reconstitution of lipid biosynthesis in vitro. Here we describe the chemical and physical properties of archaeal lipids and membranes derived thereof, summarize the existing knowledge about the enzymology of the archaeal lipid biosynthetic pathway and discuss evolutionary theories associated with the “Lipid Divide” that resulted in the differentiation of bacterial and archaeal organisms. This article is part of a Special Issue entitled: Bacterial Lipids edited by Russell E. Bishop.     

Quantity and taxonomic composition of ultramicrobacteria in soils

The number, physiological state, and taxonomic composition of ultramicrobacteria and archaea in various soils (alluvial meadow, sod-podzolic, leached chernozem, and peat) were studied. In all of the tested soil samples, a large number of ultramicrobacteria (tens and hundreds of millions of cells per 1 g of soil) was revealed by fluorescence microscopy. The portion of cells with intact membranes was larger among ultra-microbacteria than among the ordinary-size cells (95–98 and 50%, respectively). Ultramicrobacteria were characterized by high taxonomic diversity and included representatives of the main phylogenetic groups widespread in soils, such as Archaea, Actinobacteria, Cytophaga, and Proteobacteria. The results indicate that ultramicrobacteria are widespread in soils in a viable state and are involved in soil processes.     

Community analysis of methanogenic archaea within a riparian flooding gradient

Anoxic soils in river floodplains (or riparian soils) are a source of methane emission. However, little is known about the ecology and community structure of archaeal methanogenic microbes, which are a crucial component of methane flux in those habitats. We studied the archaeal community in the vertical profile of four different sites along the River Waal in the Netherlands. These sites differ in their annual flooding regime ranging from never or seldom to permanently flooded. The archaeal community structure has been characterized by terminal restriction fragment length polymorphism (T-RFLP) and comparative sequence analysis of the archaeal SSU rRNA gene and the mcrA gene. The latter gene codes for the alpha-subunit of methyl-coenzyme M reductase. Additionally, the potential methanogenic activity was determined by incubation of soil slurries under anoxic conditions. The community composition differed only slightly with the depth of the soil (0-20 cm). However, the diversity of archaeal SSU rRNA genes increased with the frequency of flooding. Terminal restriction fragment length polymorphism analysis of mcrA gene amplicons confirmed the results concerning methanogenic archaea. In the never and rarely flooded soils, crenarchaeotal sequences were the dominant group. In the frequently and permanently flooded soils, Methanomicrobiaceae, Methanobacteriaceae, Methanosarcinaceae and the uncultured Rice Clusters IV and VI (Crenarchaeota) were detectable independently from duration of anoxic conditions. Methanosaetaceae, on the other hand, were only found in the permanently and frequently flooded soils under conditions where concentrations of acetate were < 30 microM. The results indicate that methanogens as well as other archaea occupy characteristic niches according to the flooding conditions in the field. Methanosaetaceae, in particular, seem to be adapted (or proliferate at) to low acetate concentrations.     

In vitro proof of direct regulation of glutamine synthetase by GlnK proteins in the extreme halophilic archaeon Haloferax mediterranei

Haloferax mediterranei is an extreme halophilic micro-organism belonging to the Archaea domain that was isolated from the Santa Pola solar salterns (Alicante, Spain) in 1983. The biochemistry of the proteins involved in nitrogen metabolism is being studied, but the knowledge of their regulation is very scarce at present. The PII superfamily is constituted by major regulators of nitrogen metabolism, which are widespread in prokaryotic and eukaryotic organisms. These trimeric proteins (12?kDa per subunit) have in Escherichia coli long been known to regulate GS (glutamine synthetase) activity via its adenylyltransferase/adenylyl-removing enzyme and, more recently, to be able to interact directly with this enzyme in methanogenic archaea. We have tested the possible role of PII proteins in the regulation of ammonium assimilation in our model organism and the results clearly indicate that the direct influence of GS by PII proteins can also take place in halophilic archaea, starting with the comprehension of nitrogen regulation in those organisms.     

RNA polyadenylation in Archaea: not observed in Haloferax while the exosome polynucleotidylates RNA in Sulfolobus

The addition of poly(A) tails to RNA is a phenomenon common to all organisms examined so far. No homologues of the known polyadenylating enzymes are found in Archaea and little is known concerning the mechanisms of messenger RNA degradation in these organisms. Hyperthermophiles of the genus Sulfolobus contain a protein complex with high similarity to the exosome, which is known to degrade RNA in eukaryotes. Halophilic Archaea, however, do not encode homologues of these eukaryotic exosome components. In this work, we analysed RNA polyadenylation and degradation in the archaea Sulfolobus solfataricus and Haloferax volcanii. No RNA polyadenylation was detected in the halophilic archaeon H. volcanii. However, RNA polynucleotidylation occurred in hyperthermophiles of the genus Sulfolobus and was mediated by the archaea exosome complex. Together, our results identify the first organism without RNA polyadenylation and show a polyadenylation activity of the archaea exosome.     

Survival of Methanogenic Archaea from Siberian Permafrost under Simulated Martian Thermal Conditions

Methanogenic archaea from Siberian permafrost complementary to the already well-studied methanogens from non-permafrost habitats were exposed to simulated Martian conditions. After 22 days of exposure to thermo-physical conditions at Martian low- and mid-latitudes up to 90% of methanogenic archaea from Siberian permafrost survived in pure cultures as well as in environmental samples. In contrast, only 0.3%–5.8% of reference organisms from non-permafrost habitats survived at these conditions. This suggests that methanogens from terrestrial permafrost seem to be remarkably resistant to Martian conditions. Our data also suggest that in scenario of subsurface lithoautotrophic life on Mars, methanogenic archaea from Siberian permafrost could be used as appropriate candidates for the microbial life on Mars.     

西藏米拉山土壤古菌16S rRNA及amoA基因多样性?分析

摘要：【目的】硝化作用在全球土壤氮循环中具有重要的作用,虽然细菌一度被认为单独负责催化这个过程的限速步骤,但是最近一些研究结果表明泉古菌具有氨氧化的能力。本文通过构建古菌16S rRNA 基因克隆文库和氨氧化古菌amoA基因文库,分析西藏米拉山高寒草甸土壤中古菌及氨氧化古菌群落结构组成情况,为揭示青藏高原高寒草甸土壤古菌的多样性提供理论基础。【方法】采用未培养技术直接从土壤中提取微生物总DNA,分别利用通用引物构建古菌16S rRNA 基因和氨氧化古菌amoA基因克隆文库。【结果】通过构建系统发育树,表明古菌16S rRNA 基因克隆文库包括泉古菌门和未分类的古菌两大类,并且所有泉古菌均属于热变形菌纲。氨氧化古菌amoA基因克隆文库中序列均为泉古菌。通过DOTUR软件分析,古菌16S rRNA基因和古菌amoA基因克隆文库分别包括64个OTUs和 75个OTUs。【结论】西藏米拉山高寒草甸土壤中古菌多样性比较丰富,表明古菌在高寒草甸土壤的氮循环中可能具有重要的作用。所获得的一些序列与已知环境中土壤、淡水及海洋沉积物中获得的一些序列具有很高的相似性,其古菌及氨氧化古菌来自不同环境的可能性比较大,可能与青藏高原的地质历史变迁过程有关。米拉山古菌及氨氧化古菌与陆地设施土壤中相似性最高,说明与西藏米拉山高寒草甸土壤的退化有关。     

Do extreme environments provide a refuge from pathogens? A phylogenetic test using serpentine flax

Abiotically extreme environments are often associated with physiologically stressful conditions, small, low-density populations, and depauperate flora and fauna relative to more benign settings. A possible consequence of this may be that organisms that occupy these stressful habitats receive fitness benefits associated with reductions in the frequency and/or intensity of antagonistic species interactions. I investigated a particular form of this effect, formalized as the "pathogen refuge hypothesis," through a study of 13 species of wild flax that grow on stressful serpentine soils and are often infected by a pathogenic fungal rust. The host species vary in the degree of their serpentine association: some specialize on extreme serpentine soils, while others are generalists that occur on soils with a wide range of serpentine influence. Phylogenetically explicit analyses of soil chemistry and field-measured disease levels indicated that rust disease was significantly less frequent and severe in flax populations growing in more stressful, low-calcium serpentine soils. These findings may help to explain the persistence of extremophile species in habitats where stressful physical conditions often impose strong autecological fitness costs on associated organisms. Ancestral state reconstruction of serpentine soil tolerance (approximated using soil calcium concentrations) suggested that the ability to tolerate extreme serpentine soils may have evolved multiple times within the focal genus.     

病毒生态学研究进展

病毒是目前所知的最简单的生命单元,通常由外壳蛋白和包裹在外壳蛋白内的核酸两部分组成。病毒本身缺乏完整的酶系统及能量转化系统,当游离于环境中时,它只是一个有机大分子,只有侵染宿主后才具有生命特征,进行复制。病毒也是地球上最丰富的生物实体,是微生物群落和功能的重要影响因素。尽管病毒在生态系统中发挥着重要的作用,但因病毒间缺少通用的标记基因,病毒生态学的研究远远滞后于细菌和真核生物。近年来高通量测序技术的发展应用帮助人们发现和认识了许多未知的新病毒及其基因,极大地丰富了病毒基因数据库,直接推动了病毒生态学的发展。从生态学角度对病毒的结构与分类、病毒生态学研究方法、病毒的生态功能及土壤病毒生态学研究进展作一简要综述,并提出今后土壤病毒生态学研究的重点。