西藏羊八井废弃热井沉积物中的真核微生物多样性

【目的】研究西藏羊八井废弃热井沉积物中的真核微生物多样性。【方法】采用ITS-rRNA基因分析法构建了沉积物中真核微生物的ITS-rRNA基因文库, 随机抽取文库中的克隆子进行扩增rDNA限制性酶切片段分析(ARDRA), 并对ITS-rRNA基因进行了系统发育分析。【结果】沉积物中主要的真核微生物有子囊菌、壶菌、担子菌、丝足虫、后生动物和非培养真菌。其中壶菌Chytridiales sp.、Physoderma maydis和Powellomyces sp., 子囊菌的假丝酵母(Candida parapsilosis)、鲁氏接合酵母(Zygosaccharomyces rouxii)和短梗霉(Aureobasidium pullulans)以及后生动物的轮虫(Lecane bulla)均未有报导存在于热泉或热井中。【结论】羊八井热井沉积物中具有丰富的真核微生物多样性。     

Escape of volcanic gas into shallow groundwater systems at Unzen Volcano (Japan): evidence from chemical and stable carbon isotope compositions of dissolved inorganic carbon

 Chemical and stable carbon isotopic analyses of dissolved inorganic carbon (DIC) were carried out for groundwater samples collected from cold springs and shallow wells in the Unzen volcanic region in 1999 and 2000. All of the data sets plotted on the carbon isotope ratio (δ¹³C) vs 1/DIC diagram can be explained by mixing of volcanic CO₂ with DIC equilibrated with soil CO₂. Groundwater DIC showing a high mixing ratio of volcanic CO₂ appears to have a tendency to distribute along two major faults near the activity center of the 1990–1995 eruption. This suggests that these faults are escape routes of volcanic CO₂ diffused into the volcanic edifice. The total flux of the volcanic DIC discharged from the cold springs is shown to be one to two orders of magnitude lower than the roughly estimated flux of volcanic CO₂ discharged from the summit during the eruptive period. Received: November 10, 2001 / Accepted: June 6, 2002 Acknowledgments The Unzen Scientific Drilling Project, Ministry of Education, Culture, Sports, Science and Technology (Japan), provided funding. We acknowledge G. Lyon and W. Gooley for stable carbon isotope measurement, K. Amita for DIC analysis, and students of Kyoto University and Okayama University of Science for assistance in field work. Correspondence to:S. Ohsawa     

Metagenomics of microbial and viral life in terrestrial geothermal environments

Geothermally heated regions of Earth, such as terrestrial volcanic areas (fumaroles, hot springs, and geysers) and deep-sea hydrothermal vents, represent a variety of different environments populated by extremophilic archaeal and bacterial microorganisms. Since most of these microbes thriving in such harsh biotopes, they are often recalcitrant to cultivation; therefore, ecological, physiological and phylogenetic studies of these microbial populations have been hampered for a long time. More recently, culture-independent methodologies coupled with the fast development of next generation sequencing technologies as well as with the continuous advances in computational biology, have allowed the production of large amounts of metagenomic data. Specifically, these approaches have assessed the phylogenetic composition and functional potential of microbial consortia thriving within these habitats, shedding light on how extreme physico-chemical conditions and biological interactions have shaped such microbial communities. Metagenomics allowed to better understand that the exposure to an extreme range of selective pressures in such severe environments, accounts for genomic flexibility and metabolic versatility of microbial and viral communities, and makes extreme- and hyper-thermophiles suitable for bioprospecting purposes, representing an interesting source for novel thermostable proteins that can be potentially used in several industrial processes.     

Dissimilatory Oxidation and Reduction of Elemental Sulfur in Thermophilic Archaea

The oxidation and reduction of elemental sulfur and reduced inorganic sulfur species are some of the most important energy-yielding reactions for microorganisms living in volcanic hot springs, solfataras, and submarine hydrothermal vents, including both heterotrophic, mixotrophic, and chemolithoautotrophic, carbon dioxide-fixing species. Elemental sulfur is the electron donor in aerobic archaea like Acidianus and Sulfolobus. It is oxidized via sulfite and thiosulfate in a pathway involving both soluble and membrane-bound enzymes. This pathway was recently found to be coupled to the aerobic respiratory chain, eliciting a link between sulfur oxidation and oxygen reduction at the level of the respiratory heme copper oxidase. In contrast, elemental sulfur is the electron acceptor in a short electron transport chain consisting of a membrane-bound hydrogenase and a sulfur reductase in (facultatively) anaerobic chemolithotrophic archaea Acidianus and Pyrodictium species. It is also the electron acceptor in organoheterotrophic anaerobic species like Pyrococcus and Thermococcus, however, an electron transport chain has not been described as yet. The current knowledge on the composition and properties of the aerobic and anaerobic pathways of dissimilatory elemental sulfur metabolism in thermophilic archaea is summarized in this contribution.     

Methane oxidation activity and diversity of aerobic methanotrophs in pH-neutral and semi-neutral thermal springs of the Kunashir Island,Russian Far East

Aerobic methane oxidation has been mostly studied in environments with moderate to low temperatures. However, the process also occurs in terrestrial thermal springs, where little research on the subject has been done to date. The potential activity of methane oxidation and diversity of aerobic methanotrophic bacteria were studied in sediments of thermal springs with various chemical and physical properties, sampled across the Kunashir Island, the Kuriles archipelago. Activity was measured by means of the radioisotope tracer technique utilizing ¹⁴C-labeled methane. Biodiversity assessments were based on the particulate methane monooxygenase (pmoA) gene, which is found in all known thermophilic and thermotolerant methanotrophs. We demonstrated the possibility of methane oxidation in springs with temperature exceeding 74 °C, and the most intensive methane uptake was shown in springs with temperatures about 46 °C. PmoA was detected in 19 out of 30 springs investigated and the number of pmoA gene copies varied between 10⁴ and 10⁶ copies per ml of sediment. Phylogenetic analysis of PmoA sequences revealed the presence of methanotrophs from both the Alpha- and Gammaproteobacteria. Our results suggest that methanotrophs inhabiting thermal springs with temperature exceeding 50 °C may represent novel thermophilic and thermotolerant species of the genera Methylocystis and Methylothermus, as well as previously undescribed Gammaproteobacteria.     

Classification of Springs in the Lake Baikal Region by Macroinvertebrate Communities

The macrozoobenthos communities in 15 cold fresh, 12 mineral (sodium chloride), and 19 thermal springs of the Baikal Rift Zone and adjacent areas have been investigated. The classification of springs on the basis of quantitative indicators of abundance was proposed. According to the dominant group of fauna, three types of communities were identified for the cold springs; six types, for mineral springs; and four types, for thermal springs. It was established that communities with the dominance of Chironomidae, Turbellaria, and Oligochaeta are formed in cold springs and communities with the predominance of Gastropoda (one or two species) prevail in thermal springs. It was noted that mineral springs of medium mineralization are characterized by communities with a prevalence of Amphipoda (Gammarus lacustris); those with high salinity are dominated by Brachyceran flies (Diptera, Brachycera).     

Natural CO2 springs in Italy: a resource for examining long-term response of vegetation to rising atmospheric CO2 concentrations

It is estimated that more than 100 geothermal CO₂ springs exist in central-western Italy. Eight springs were selected in which the atmospheric CO₂ concentrations were consistently observed to be above the current atmospheric average of 354μmol mol^-1. CO₂ concentration measurements at some of the springs are reported. The springs are described, and their major topographic and vegetational features are reported. Preliminary observations made on natural vegetation growing around the gas vents are then illustrated. An azonal pattern of vegetation distribution occurs around every CO₂ spring regardless of soil type and phytoclimatic areas. This is composed of pioneer populations of a Northern Eurasiatic species (Agrostis canina L.) which is often associated with Scirpus lacustris L. The potential of these sites for studying the long-term response of vegetation to rising atmospheric CO₂ concentrations is discussed.     

Thiosulfate Reduction, an Important Physiological Feature Shared by Members of the Order Thermotogales

Several members of the order Thermotogales in the domain Bacteria, viz., Thermotoga neapolitana, Thermotoga maritima, Thermosipho africanus, Fervidobacterium islandicum, and Thermotoga strain SEBR 2665, an isolate from an oil well, reduced thiosulfate to sulfide. This reductive process enhanced cellular yields and growth rates of all the members but was more significant with the two hyperthermophiles T. neapolitana and T. maritima. This is the first report of such an occurrence in this group of thermophilic and hyperthermophilic anaerobic bacteria. The results suggest that thiosulfate reduction is important in the geochemical cycling of sulfur in anaerobic thermal environments such as the slightly acidic and neutral-pH volcanic hot springs and oil reservoirs.     

Temperature patterns and factors governing thermal response in high elevation springs of the Swiss Central Alps

Temperature monitoring in 41 springs in different parts of the Swiss Central Alps revealed individual patterns, which seem to be determined by different factors. Geology plays an important role since karst springs in limestone rock often show temperatures below 3°C during winter. They are paralleled to the formation of ice and/or a strong decrease in discharge. In karst springs with permanent flow, temperature did not differ from springs of other geological formations. The water temperature of springs depends on thermal exchanges with the rock during the recharge process. Therefore, elevation, exposure, and permafrost location in the catchment area are expected to be the key factors governing water temperatures in alpine springs. The temperature showed a significant decrease of 0.37°C per 100 m of elevation. The water in springs facing north and west was significantly colder than in south-exposed springs. The temperature significantly increased with the distance to regions of permafrost in the catchment. Understanding the factors governing the thermal patterns will help predict the implication of climate change on springs.     

ALGAL COMMUNITIES OF SPRINGS AND STREAMS IN THE MT. ST. HELENS REGION,WASHINGTON, U.S.A. FOLLOWING THE MAY 1980 ERUPTION1

Mt. St. Helens, a volcanic peak in the Cascade Range in southern Washington erupted violently on May 18, 1980, causing enormous damage to both terrestrial and aquatic ecosystems. The initial explosion evaporated, scoured or buried all springs and streams in the blast impact area. Ash fall and erosion from defoliated hillsides subsequently filled most of the lotic habitats with organic debris and volcanic ash. Recolonization of springs and streams by algae occurred quickly in areas where erosion through the ash progressed down to bedrock. Within 15 months or less of the eruption, algal communities were established throughout the blast impact area. However, as a result of the initial and continued disturbance these communities remained in an early successional stage. Floral assemblages were highly variable except that they were composed mostly of diatoms, with Achnanthes minutissima dominating most lotic sites. Springs showed the most rapid development toward stable floras.     

Genetic diversity and connectivity of deep‐sea hydrothermal vent metapopulations

Deep‐sea hydrothermal vents provide ephemeral habitats for animal communities that depend on chemosynthetic primary production. Sporadic volcanic and tectonic events destroy local vent fields and create new ones. Ongoing dispersal and cycles of extirpation and colonization affect the levels and distribution of genetic diversity in vent metapopulations. Several species exhibit evidence for stepping‐stone dispersal along relatively linear, oceanic, ridge axes. Other species exhibit very high rates of gene flow, although natural barriers associated with variation in depth, deep‐ocean currents, and lateral offsets of ridge axes often subdivide populations. Various degrees of impedance to dispersal across such boundaries are products of species‐specific life histories and behaviours. Though unrelated to the size of a species range, levels of genetic diversity appear to correspond with the number of active vent localities that a species occupies within its range. Pioneer species that rapidly colonize nascent vents tend to be less subdivided and more diverse genetically than species that are slow to establish colonies at vents. Understanding the diversity and connectivity of vent metapopulations provides essential information for designing deep‐sea preserves in regions that are under consideration for submarine mining of precious metals.     

Colombian Andean thermal springs: reservoir of thermophilic anaerobic bacteria producing hydrolytic enzymes

Extremophiles - Anaerobic cultivable microbial communities in thermal springs producing hydrolytic enzymes were studied. Thermal water samples from seven thermal springs located in the Andean...     

Discovery of the non-cosmopolitan lineages in Candidatus Thermoprofundales

The recently proposed order Candidatus Thermoprofundales, currently containing only one family-level lineage Marine Benthic Group-D (MBG-D), is distributed in global subsurface ecosystems and ecologically important, but its diversity, evolution and metabolism remain largely unknown. Here we described two novel family-level specialized lineages in Ca. Thermoprofundales, JdFR-43 and HyVt, which are restricted to specific biotopes (primarily in marine hydrothermal vents and occasionally in oil reservoirs and hot springs) in contrast to the cosmopolitan lineage MBG-D. The comparative genomics revealed that the specialized lineages have streamlined genomes, higher GC contents, enriched genes associated with nucleotide biosynthesis, ribosome biogenesis and DNA repair and additional thermostable aminopeptidases, enabling them to adapt to high-temperature habitats such as marine hydrothermal vents, deep subsurface oil reservoirs and hot springs. On the contrary, the unique metabolic traits of the cosmopolitan MBG-D, motility, glycolysis, butanoate metabolism, secondary metabolites production and additional genes for specific peptides and carbohydrates degradation potentially enhance its response to environmental change. Substrate preference is found for most MAGs across all lineages with the ability to utilize both polysaccharides (chitin and starch) and proteinaceous substances, whereas JdFR-43 members from oil reservoirs can only utilize proteins. These results expand the diversity of Ca. Thermoprofundales significantly and further improve our understandings of the adaptations of Ca. Thermoprofundales to various environments.     

Intertidal rocky shore seaweed communities subject to the influence of shallow water hydrothermal activity in São Miguel (Azores, Portugal)

The volcanic origin of the Azores archipelago (Portugal) gives rise to active deep sea and shallow water hydrothermal activity that affects benthic communities. Intertidal seaweed surveys were conducted at two shores affected by intense shallow water hydrothermal vents. Water temperature, acidity and salinity were monitored. Seaweed communities were found to be species poor and have a disproportionally larger number of filamentous early successional species on shores that are subject to the effect of hot and acidic freshwater of volcanic origin. There is an ecological resemblance between hydrothermally affected seaweed communities in the Azores and those affected by acid mine drainage in the UK, thus indicating that hydrothermalism can be a useful scenario for pollution studies under conditions of ocean warming and acidification.     

Volcanic calderas delineate biogeographic provinces among Yellowstone thermophiles

It has been suggested that the distribution of microorganisms should be cosmopolitan because of their enormous capacity for dispersal. However, recent studies have revealed that geographically isolated microbial populations do exist. Geographic distance as a barrier to dispersal is most often invoked to explain these distributions. Here we show that unique and diverse sequences of the bacterial genus Sulfurihydrogenibium exist in Yellowstone thermal springs, indicating that these sites are geographically isolated. Although there was no correlation with geographic distance or the associated geochemistry of the springs, there was a strong historical signal. We found that the Yellowstone calderas, remnants of prehistoric volcanic eruptions, delineate biogeographical provinces for the Sulfurihydrogenibium within Yellowstone (χ²: 9.7, P  = 0.002). The pattern of distribution that we have detected suggests that major geological events in the past 2 million years explain more of the variation in sequence diversity in this system than do contemporary factors such as habitat or geographic distance. These findings highlight the importance of historical legacies in determining contemporary microbial distributions and suggest that the same factors that determine the biogeography of macroorganisms are also evident among bacteria.     

Importance of main-chain hydrophobic free energy to the stability of thermophilic proteins

Living organisms are found in the most unexpected places, including deep-sea vents at 100 degrees C and several hundred bars pressure, in hot springs. Needless to say, the proteins found in thermophilic species are much more stable than their mesophilic counterparts. There are no obvious reasons to say that one would be more stable than others. Even examination of the amino acids and comparison of structural features of thermophiles with mesophilies cannot bring satisfactory explanation for the thermal stability of such proteins. In order to bring out the hidden information behind the thermal stabilization of such proteins in terms of energy factors and their combinations, analysis were made on good resolution structures of thermophilic and their mesophilic homologous from 23 different families. From the structural coordinates, free energy contributions due to hydrophobic, electrostatic, hydrogen bonding, disulfide bonding and van der Waals interactions are computed. In this analysis, a vast majority of thermophilic proteins adopt slightly lower free energy contribution in each energy terms than its mesophilic counterparts. The major observation noted from this study is the lower hydrophobic free energy contribution due to carbon atoms and main-chain nitrogen atoms in all the thermophilic proteins. The possible combination of different free energy terms shows majority of the thermophilic proteins have lower free energy strategy than their mesophilic homologous. The derived results show that the hydrophobic free energy due to carbon and nitrogen atoms and such combinations of free energy components play a vital role in the thermostablisation of such proteins.     

Neutrophilic lithotrophic iron-oxidizing prokaryotes and their role in the biogeochemical processes of the iron cycle

Biology of lithotrophic neutrophilic iron-oxidizing prokaryotes and their role in the processes of the biogeochemical cycle of iron are discussed. This group of microorganisms is phylogenetically, taxonomically, and physiologically heterogeneous, comprising three metabolically different groups: aerobes, nitratedependent anaerobes, and phototrophs; the latter two groups have been revealed relatively recently. Their taxonomy and metabolism are described. Materials on the structure and functioning of the electron transport chain in the course of Fe(II) oxidation by members of various physiological groups are discussed. Occurrence of iron oxidizers in freshwater and marine ecosystems, thermal springs, areas of hydrothermal activity, and underwater volcanic areas are considered. Molecular genetic techniques were used to determine the structure of iron-oxidizing microbial communities in various natural ecosystems. Analysis of stable isotope fractionation of ^56/54Fe in pure cultures and model experiments revealed a predominance of biological oxidation over abiotic ones in shallow aquatic habitats and mineral springs, which was especially pronounced under microaerobic conditions at the redox zone boundary. Discovery of anaerobic bacterial Fe(II) oxidation resulted in development of new hypotheses concerning the possible role of microorganisms and the mechanisms of formation of the major iron ore deposits during Precambrian era until the early Proterozoic epoch. Paleobiological data are presented on the microfossils and specific biomarkers retrieved from ancient ore samples and confirming involvement of anaerobic biogenic processes in their formation.     

Considerations about the composition of benthic algal flora in Lake Kinneret

Blue-green benthic algae are represented in Kinneret by numerous taxa but biomasses produced by them are inconspicuous. Diatoms, although less diversified show overwhelming biological activity. A comparative insight into the flora of the lake and the surrounding springs reveals many species in common, of which the diatoms develop the richest biomasses on the lake littoral, while the blue-greens reach their maximal biological success in the mineral and thermal springs. It is assumed that diatoms migrate from the lake to the surrounding springs, while the Cyanophyceae originating in the springs, move toward the lake. Climatic and hydrological changes, which had place throughout the geological history of the region, enhanced alternately one of the two algal groups competing for the lake's littoral, while limiting the other. Periods of high temperatures and salinities were favorable for the immigrants from the springs decreasing competitive capacity of diatoms; cold, rainy climates had opposite effect, enhancing diatoms but limiting growth of the thermophilic blue-greens on the lake shores. Vicinity of mineral and thermal springs creates constant “blue-green pressure” on the lake, which at present shows merely qualitative character but in suitable conditions may come to quantitative expression as well.     

Molten earth and the origin of prebiological molecules.

Evidence for the molten Earth at its accretion time has been accumulated through the geochemical investigations and the observations of the surfaces of planets by space probes such as Venera 8, Mariner 9, Surveyor, Luna, and Apollo. The primitive terrestrial atmosphere might have been derived from the volcanic gases, as suggested by Rubey, but of a higher temperature than so far assumed. A thermochemical calculation of the composition of the volcanic gas suggests the following possibilities: (1) Large amounts of H2 and CO were present in the primitive atmosphere. This gives a theoretical basis for the HCN-production experiment by Abelson. (2) HCHO and NH3 existed in the primitive oceans, of the amount comparable with the weight of the present biosphere. (3) Plenty of NO3-, SO4, and PO4 were expected in the primitive oceans. The NO3- ions might have been useful for the nitrate respiration advocated by Egami. In an appendix, it is argued, on ;he basis of the observational evidence of the exospheric temperatures of planets by space probes, that a highly reducing atmosphere would (if it existed on the primitive Earth) have disappeared very quickly due to the thermal escape of hydrogen from its exosphere.