青海两盐湖细菌多样性研究

用DGGE法和纯培养法,对青海柯柯盐湖、茶卡盐湖底泥及周边土壤样品的细菌多样性进行了研究。结果显示,两个盐湖存在大量的未知细菌, 分离到的纯培养仅占实有细菌的小部分。采用多相分类方法,鉴定了12株纯培养细菌,属5个可能的新种,另有一株菌可能成立一个新属。认为提出新思路、设计新程序,从自然极端环境取样,分离未知菌,是微生物资源开发利用的关键之一。     

Search for life in deep biospheres]

The life in deep biospheres bridges conventional biology and future exobiology. This review focuses the microbiological studies from the selected deep biospheres, i.e., deep-sea hydrothermal vents, sub-hydrothermal vents, terrestrial subsurface and a sub-glacier lake. The dark biospheres facilitate the emergence of organisms and communities dependent on chemolithoautotrophy, which are overwhelmed by photoautotrophy (photosynthesis) in the surface biospheres. The life at deep-sea hydrothermal vents owes much to chemolithoautotrophy based on the oxidation of sulfide emitted from the vents. It is likely that similarly active bodies such as the Jovian satellite Europa may have hydrothermal vents and associated biological communities. Anoxic or anaerobic condition is characteristic of deep subsurface biospheres. Subsurface microorganisms exploit available oxidants, or terminal electron acceptors (TEA), for anaerobic respiration. Sulfate, nitrate, iron (III) and CO2 are the representative TEAs in the deep subsurface. Below the 3000-4000 m-thick glacier on Antarctica, there have been >70 lakes with liquid water located. One of such sub-glacial lakes, Lake Vostok, is about to be drill-penetrated for microbiological studies. These deep biosphere "platforms" provide new knowledge about the diversity and potential of the Earth's life. The expertise obtained from the deep biosphere expeditions will facilitate the capability of exobiologial exploration.     

Microbiology of Lonar Lake and other soda lakes

Soda lakes are saline and alkaline ecosystems that are believed to have existed throughout the geological record of Earth. They are widely distributed across the globe, but are highly abundant in terrestrial biomes such as deserts and steppes and in geologically interesting regions such as the East African Rift valley. The unusual geochemistry of these lakes supports the growth of an impressive array of microorganisms that are of ecological and economic importance. Haloalkaliphilic Bacteria and Archaea belonging to all major trophic groups have been described from many soda lakes, including lakes with exceptionally high levels of heavy metals. Lonar Lake is a soda lake that is centered at an unusual meteorite impact structure in the Deccan basalts in India and its key physicochemical and microbiological characteristics are highlighted in this article. The occurrence of diverse functional groups of microbes, such as methanogens, methanotrophs, phototrophs, denitrifiers, sulfur oxidizers, sulfate reducers and syntrophs in soda lakes, suggests that these habitats harbor complex microbial food webs that (a) interconnect various biological cycles via redox coupling and (b) impact on the production and consumption of greenhouse gases. Soda lake microorganisms harbor several biotechnologically relevant enzymes and biomolecules (for example, cellulases, amylases, ectoine) and there is the need to augment bioprospecting efforts in soda lake environments with new integrated approaches. Importantly, some saline and alkaline lake ecosystems around the world need to be protected from anthropogenic pressures that threaten their long-term existence.     

Physical and chemical limnology of 204 lakes from the Canadian Arctic Archipelago

The physical and chemical limnology of 204 lakes from across the Canadian Arctic Archipelago was examined. Mean summer air temperature did not correlate well with lake chlorophyll levels due to the predominance of ultra-oligotrophic hard-water lakes located in a polar climate. Local geology influences ion budgets and is an important factor in determining pelagic phosphorus availability, carbon cycling and metal concentrations. Ratios of particulate carbon, particulate nitrogen and chlorophyll a indicate that planktonic microorganisms are not always the major producers of organic carbon in arctic lakes. Allochthonous particulate matter contributes significantly to the carbon and phosphorus budgets of small and mid-sized lakes across the Arctic, although the availability of these elements is controlled by many interacting geochemical and biological factors. Phosphorus is generally limiting, however, increases in available phosphorus, nitrogen and carbon are all required to make significant long-term differences in lake productivity. Particulate phosphorus levels can be high in lakes where phosphorus-rich shales or carbonatite bedrock are present. These phosphorus-enriched lakes are found in several areas across the mid-arctic islands, however, only small amounts of this nutrient are available as soluble reactive phosphorus. Although lakes throughout the Arctic are typically ultra-oligotrophic, they still represent an important sink for allochthonous nutrient deposition.     

昆虫体外共生菌研究进展

昆虫体外共生菌是指能在体外与宿主发生互利共生关系的微生物。体外共生菌虽然不如肠道微生物那样普遍存在于昆虫中,但也在宿主生长发育过程中扮演着重要的角色。昆虫体外共生菌一般寄生于昆虫体表或体内特异器官(如储菌器),在特定时期转移到植物组织中。体外共生菌产生的挥发物能作为宿主定位寄主植物的信号物质,能为宿主提供生长发育所需的营养物质,还参与了宿主体外免疫。对昆虫体外共生菌的研究,不仅能进一步揭示昆虫与微生物之间的互作关系,丰富昆虫共生菌的研究,还能从共生菌的角度探索害虫引诱剂和昆虫免疫豁免机制。本文对昆虫体外共生菌寄生方式、传播途径、对宿主的影响等研究成果进行了综述,旨在为害虫综合防控提供新思路。     

Cold-adaptation of Antarctic microorganisms – possible involvement of viable but nonculturable state

Occurrence of the viable but nonculturable (VBNC) form of microorganisms in nature is well known. Evidence available in the literature indicates that low temperature may induce microorganisms to form VBNC cells. The VBNC state of some bacteria, collected from Antarctic lakes, has been recently reported. Hence it is postulated that formation of VBNC cells may be one of the strategies adopted by Antarctic microorganisms to survive in the extreme cold climate. Accepted: 16 October 1999     

Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage

Members of the acI lineage of Actinobacteria are the most abundant microorganisms in most freshwater lakes; however, our understanding of the keys to their success and their role in carbon and nutrient cycling in freshwater systems has been hampered by the lack of pure cultures and genomes. We obtained draft genome assemblies from 11 single cells representing three acI tribes (acI-A1, acI-A7, acI-B1) from four temperate lakes in the United States and Europe. Comparative analysis of acI SAGs and other available freshwater bacterial genomes showed that acI has more gene content directed toward carbohydrate acquisition as compared to Polynucleobacter and LD12 Alphaproteobacteria, which seem to specialize more on carboxylic acids. The acI genomes contain actinorhodopsin as well as some genes involved in anaplerotic carbon fixation indicating the capacity to supplement their known heterotrophic lifestyle. Genome-level differences between the acI-A and acI-B clades suggest specialization at the clade level for carbon substrate acquisition. Overall, the acI genomes appear to be highly streamlined versions of Actinobacteria that include some genes allowing it to take advantage of sunlight and N-rich organic compounds such as polyamines, di- and oligopeptides, branched-chain amino acids and cyanophycin. This work significantly expands the known metabolic potential of the cosmopolitan freshwater acI lineage and its ecological and genetic traits.     

土壤中温泉古菌研究进展

古菌一直被冠以嗜极端环境的特征,直到最近十几年,由于分子生物学技术的发展,越来越多的证据表明,在许多非极端环境,包括海洋、湖泊和土壤中,分布着一类特殊的古菌-非嗜热泉古菌(non-thermophilic Crenarchaeota).该类古菌不仅分布广泛,而且数量巨大.通过16S rRNA基因序列分析发现,中温泉古菌可能参与到全球碳、氮等生物地球化学循环,预示着其在整个生态系统中起着重要的作用.从古菌分类着手,阐述了中温泉古菌在土壤中的分布和数量特征、影响因素,进而对其在氮和碳循环过程中的潜在作用进行了简要介绍,并提出了今后的研究重点.     

Perspectives in winter limnology: closing the annual cycle of freezing lakes

Winter has traditionally been considered as an ecologically insignificant season and, together with technical difficulties, this has led winter limnology to lag behind summer limnology. Recently, rapidly expanding interest in climate warming has increased water research in winter. It has also become clear that neither winter conditions of lakes nor under-ice communities are as static as often supposed. Although interannual differences in water temperature are small, close to the maximum density temperature, they may have profound effect on under-ice hydrodynamics. Thus, stochastic variations in weather, particularly those preceding the time of freezing and ice melting, may have important consequences for hydrodynamics which then affect the distributions and conditions of microorganisms and probably further to higher trophic levels. Even fish distributions can be dictated by under-ice conditions and their activities as well as behavior can sometimes approach those in summer. Life in freshwater ice is one of the least studied aspects of winter limnology and recent studies suggest that a thorough evaluation is needed. Altogether there are strengthening signs that winter should be considered as an integral part in the functioning and dynamics of lakes affecting quantitative and qualitative characteristics of aquatic communities in summer. There are great prospects that more thorough understanding of the prevailing limnological conditions in winter will improve our understanding of lake ecosystems in their entirety, and there is no doubt that such an approach requires multidisciplinary and long- term studies at different spatial scales.     

Assessing the diversity and specificity of two freshwater viral communities through metagenomics

Transitions between saline and fresh waters have been shown to be infrequent for microorganisms. Based on host-specific interactions, the presence of specific clades among hosts suggests the existence of freshwater-specific viral clades. Yet, little is known about the composition and diversity of the temperate freshwater viral communities, and even if freshwater lakes and marine waters harbor distinct clades for particular viral sub-families, this distinction remains to be demonstrated on a community scale.To help identify the characteristics and potential specificities of freshwater viral communities, such communities from two lakes differing by their ecological parameters were studied through metagenomics. Both the cluster richness and the species richness of the Lake Bourget virome were significantly higher that those of the Lake Pavin, highlighting a trend similar to the one observed for microorganisms (i.e. the specie richness observed in mesotrophic lakes is greater than the one observed in oligotrophic lakes). Using 29 previously published viromes, the cluster richness was shown to vary between different environment types and appeared significantly higher in marine ecosystems than in other biomes. Furthermore, significant genetic similarity between viral communities of related environments was highlighted as freshwater, marine and hypersaline environments were separated from each other despite the vast geographical distances between sample locations within each of these biomes. An automated phylogeny procedure was then applied to marker genes of the major families of single-stranded (Microviridae, Circoviridae, Nanoviridae) and double-stranded (Caudovirales) DNA viruses. These phylogenetic analyses all spotlighted a very broad diversity and previously unknown clades undetectable by PCR analysis, clades that gathered sequences from the two lakes. Thus, the two freshwater viromes appear closely related, despite the significant ecological differences between the two lakes. Furthermore, freshwater viral communities appear genetically distinct from other aquatic ecosystems, demonstrating the specificity of freshwater viruses at a community scale for the first time.     

持久性有毒物污染底泥修复技术进展

评述了底泥中持久性有毒污染物的危害。在分析持久性有毒污染物污染底泥修复技术现状及面临问题的基础上 ,指出浅水湖泊持久性有毒污染物污染底泥修复的发展方向是植物 -微生物联合修复 ,水库、深水湖泊等持久性有毒物污染底泥修复的发展趋势为物理化学 -生物协同修复 ,修复目标是在环保疏浚、生态清淤的基础上 ,实现持久性有毒污染物污染底泥的无害化和资源化处置     

Coexistence of photosynthetic microorganisms with growth rates depending on the spectral quality of light

A new equation for the growth rate of photosynthetic microorganisms is derived. It is based on a series formulation of the mechanism of photosynthesis and it has the form of a functional of the spectral qualities of light. Using this functional to model their growth it is shown that populations of photosynthetic microorganisms can coexist in the same homogeneous environment even though they compete for the available light.     

The biodiversity and ecology of Antarctic lakes: models for evolution

Antarctic lakes are characterised by simplified, truncated food webs. The lakes range from freshwater to hypersaline with a continuum of physical and chemical conditions that offer a natural laboratory in which to study evolution. Molecular studies on Antarctic lake communities are still in their infancy, but there is clear evidence from some taxonomic groups, for example the Cyanobacteria, that there is endemicity. Moreover, many of the bacteria have considerable potential as sources of novel biochemicals such as low temperature enzymes and anti-freeze proteins. Among the eukaryotic organisms survival strategies have evolved, among which dependence on mixotrophy in phytoflagellates and some ciliates is common. There is also some evidence of evolution of new species of flagellate in the marine derived saline lakes of the Vestfold Hills. Recent work on viruses in polar lakes demonstrates high abundance and high rates of infection, implying that they may play an important role in genetic exchange in these extreme environments.     

Ecology and habitats of extremophiles

This review describes the main natural extreme environments, characterized by high temperature, high and low pH and high salinity, that can be colonized by microorganisms. The environments covered are: freshwater alkaline hot springs; acidic solfatara fields; anaerobic geothermal mud and soils; acidic sulphur and pyrite areas; carbonate springs and alkaline soil; and soda and highly saline lakes. The community structure, in terms of available energy sources and representative autotrophic and heterotrophic microorganisms, is discussed for each type of habitat.The authors are with the Department of Biotechnology. Technological Institute of Iceland, Keldnaholt, 112 Reykjavik, Iceland and with the Institute of Biology, University of Iceland, Reykjavik, Iceland     

Planktonic microbial assemblages and the potential effects of metazooplankton predation on the food web of lakes from the maritime Antarctica and sub-Antarctic islands

Antarctica is the continent with the harshest climate on the Earth. Antarctic lakes, however, usually presents liquid water, at least during part of the year or below the ice cover, especially those from the sub-Antarctic islands and the maritime Antarctic region where climatic conditions are less extreme. Planktonic communities in these lakes are mostly dominated by microorganisms, including bacteria and phototrophic and heterotrophic protists, and by metazooplankton, usually represented by rotifers and calanoid copepods, the latter mainly from the genus Boeckella. Here I report and discuss on studies performed during the last decade that show that there is a potential for top–down control of the structure of the planktonic microbial food web in sub-Antarctic and maritime Antarctic lakes. In some of the studied lakes, the effect of copepod grazing on protozoa, either ciliates or flagellates, depending on size of both the predator and the prey, could promote cascade effects that would be transmitted to the bacterioplankton assemblage.     

The cardiolipin analogues of Archaea

The present article reviews studies of the structure and functional roles of the cardiolipin analogues of extremely halophilic prokaryotes belonging to the Archaea domain. Analogies and differences between the archaeal bisphosphatidylglycerol and the mitochondrial cardiolipin are presented. Furthermore the structure of archaeal glycophospholipid dimers is illustrated together with the available information on their function. The studies on the function of cardiolipin analogues in archaebacteria point out the tight interaction established by these phospholipids with membrane proteins and their role as bioactive lipids in the adaptation of microorganisms to osmotic stress.     

The bioenergetic basis for the decrease in metabolic diversity at increasing salt concentrations: implications for the functioning of salt lake ecosystems

Examination of the microbial diversity in hypersaline lakes of increasing salt concentrations shows that certain types of dissimilatory metabolism do not occur at the highest salinities. Examples are methanogenesis from hydrogen and carbon dioxide or from acetate, dissimilatory sulfate reduction with oxidation of acetate, and autotrophic nitrification. The observations can be explained on the basis of the energetic cost of haloadaptation used by the different metabolic groups and the free-energy change associated with the dissimilatory reactions. All halophilic microorganisms spend large amounts of energy to maintain steep gradients of Na⁺ and K⁺concentrations across their cytoplasmic membrane. Most Bacteria and also the methanogenic Archaea produce high intracellular concentrations of organic osmotic solutes at a high energetic cost. The halophilic aerobic Archaea (order Halobacteriales) and the halophilic fermentative Bacteria (order Halanaerobiales) use KCl as the main intracellular solute. This strategy, while requiring far-reaching adaptations of the intracellular machinery, is energetically more favorable than production of organic compatible solutes. By combining information on the amount of energy available to each physiological group and the strategy used to cope with salt stress, a coherent model emerges that provides explanations for the upper salinity limit at which the different microbial conversions occur in hypersaline lakes.     

Ancient lakes revisited: from the ecology to the genetics of speciation

Explosive speciation in ancient lakes has fascinated biologists for centuries and has inspired classical work on the tempo and modes of speciation. Considerable attention has been directed towards the extrinsic forces of speciation—the geological, geographical and ecological peculiarities of ancient lakes. Recently, there has been a resurgence of interest in the intrinsic nature of these radiations, the biological characteristics conducive to speciation. While new species are thought to arise mainly by the gradual enhancement of reproductive isolation among geographically isolated populations, ancient lakes provide little evidence for a predominant role of geography in speciation. Recent phylogenetic work provides strong evidence that multiple colonization waves were followed by parallel intralacustrine radiations that proceeded at relatively rapid rates despite long‐term gene flow through hybridization and introgression. Several studies suggest that hybridization itself might act as a key evolutionary mechanism by triggering major genomic reorganization/revolution and enabling the colonization of new ecological niches in ancient lakes. These studies propose that hybridization is not only of little impediment to diversification but could act as an important force in facilitating habitat transitions, promoting postcolonization adaptations and accelerating diversification. Emerging ecological genomic approaches are beginning to shed light on the long‐standing evolutionary dilemma of speciation in the face of gene flow. We propose an integrative programme for future studies on speciation in ancient lakes.     

Microbes on the edge of global biosphere]

The search for life on the edge of global biosphere is a frontier to bridge conventional bio/ecology and exo/astrobiology. This communication reviews the foci of microbiological studies on the inhabitants of the selected "edges", i.e., deep-sea, deep subsurface and Antarctic habitats. The deep-sea is characterized as the no-light (non-photosynthetic) habitat, and the primary production is mostly due to the chemosynthetic autotrophy at the hydrothermal vents and methane-rich seeps. Formation of the chemosynthesis-dependent animal communities in the deep leads to the idea that such communities may be found in "ocean" of the Jovian satellite, Europa. The oxygen minimal layer (OML) in mid-water provides another field of deep-sea research. Modern OML is a relatively thin layer, found between the water depth of 200 and 1000 m, but was much thicker during the periods of oceanic anoxia events (OAEs) in the past. The history of oceanic biosphere is regarded as the cycle of OAE and non-OAE periods, and the remnants of the past OAEs may be seen in the modem OML. Anoxic (no-O2) condition is also characteristic of deep subsurface biosphere. Microorganisms in deep subsurface biosphere exploit every available oxidant, or terminal electron acceptor (TEA), for anaerobic respiration. Sulfate, nitrate, iron (III) and CO2 are the representative TEAs in the deep subsurface. Subsurface of hydrothermal vents, or sub-vent biosphere, may house brine (high salt) habitats and halophilic microorganisms. Some sub-vent halophiles were phylogenetically closely similar to the ones found in the Antarctic habitats which are extremely dry by the liophilizing climate. Below the 3000-4000 m-thick glacier on Antarctica, there have been >70 lakes with liquid water located. One of such sub-glacial lakes, Lake Vostok, has been a target of "life in extreme environments" and is about to be drill-penetrated for microbiological studies. These 'microbiological platforms' will provide new knowledge about the diversity and potential of the Earth's life and facilitate the capability of astrobiologial exploration.