Archaeal diversity from hydrothermal systems of Deception Island, Antarctica

Antarctica is an extreme continent composed of cold environments but also of several geothermal sites, among them is Deception Island, an active stratovolcano located in the South Shetland archipelago. From this island, few microbiological studies have been performed, and the presence of archaea has not been reported. In order to investigate the archaeal diversity in hydrothermalism from Deception Island, different submarine samples were taken from the flooded caldera. Samples were analyzed by denaturing gradient gel electrophoresis (DGGE) of the 16S rRNA gene in conjunction with culture-dependent methods at hyperthermophilic temperatures. Analysis from DGGE band sequencing showed the presence of archaea belonging to the hyperthermophilic genus Thermococcus and different uncultured archaea closely related to environmental clones from hydrothermal vents. Archaea from the psychrotolerant genus Methanococcoides were also detected. Additionally, we have successfully isolated an anaerobic hyperthermophilic archaeon closely related to Thermococcus celericrescens. Cells were irregular cocci with a diameter between 0.6 and 2 μm and grew at 50–90 °C and at a NaCl concentration of 1–5 %. Here, we present, based on culture-dependent and culture-independent approaches, the first report on archaea from marine hydrothermal sites of Antarctica.     

Archaeal and bacterial diversity in two hot spring microbial mats from a geothermal region in Romania

The diversity of archaea and bacteria was investigated in two slightly alkaline, mesophilic hot springs from the Western Plain of Romania. Phylogenetic analysis showed a low diversity of Archaea, only three Euryarchaeota taxa being detected: Methanomethylovorans thermophila, Methanomassiliicoccus luminyensis and Methanococcus aeolicus. Twelve major bacterial groups were identified, both springs being dominated by Cyanobacteria, Chloroflexi and Proteobacteria. While at the phylum/class-level the microbial mats share a similar biodiversity; at the species level the geothermal springs investigated seem to be colonized by specific consortia. The dominant taxa were filamentous heterocyst-containing Fischerella, at 45 °C and non-heterocyst Leptolyngbya and Geitlerinema, at 55 °C. Other bacterial taxa (Thauera sp., Methyloversatilis universalis, Pannonibacter phragmitetus, Polymorphum gilvum, Metallibacterium sp. and Spartobacteria) were observed for the first time in association with a geothermal habitat. Based on their bacterial diversity the two mats were clustered together with other similar habitats from Europe and part of Asia, most likely the water temperature playing a major role in the formation of specific microbial communities that colonize the investigated thermal springs.     

Extensive Genome Rearrangements and Multiple Horizontal Gene Transfers in a Population of Pyrococcus Isolates from Vulcano Island, Italy

The extent of chromosome rearrangements in Pyrococcus isolates from marine hydrothermal vents in Vulcano Island, Italy, was evaluated by high-throughput genomic methods. The results illustrate the dynamic nature of the genomes of the genus Pyrococcus and raise the possibility of a connection between rapidly changing environmental conditions and adaptive genomic properties.     

Temporal Variations in Heterotrophic Mesophilic Bacteria from a Marine Shallow Hydrothermal Vent off the Island of Vulcano (Eolian Islands, Italy)

Abstract The fluctuations of the total microbial abundance, the culturable heterotrophic bacterial population, and the composition of heterotrophic bacteria were investigated in relation to environmental parameters in a shallow, marine hydrothermal vent off the Island of Vulcano (Eolian Islands, Italy). Standing stock dynamics were studied by measuring the total population of picoplankton by direct count and the population of viable heterotrophic bacteria in water and sediment samples collected monthly. The environmental factors most strongly linked to the total microbial abundance and heterotrophic bacterial populations were pH and H₂S content in water and C/N ratio in sediment samples. The pattern of variation of microbial populations associated with water was different from those associated with sediment. Assessment of the qualitative composition of aerobic heterotrophic bacterial communities was based on 30 morphological and biochemical characteristics for each strain. Numerical analysis was used for an initial survey of the similarity among the isolates. The data were successively used to determine the structure and the metabolic potential of water and sediment bacteria. Metabolic properties varied between water- and sediment-isolated bacteria. Bacteria from water were structurally more diverse, and active in the use of carbohydrates, than those from sediment. Moreover, most of the sediment bacteria were able to grow at a high temperature (60 and 70°C). The fluctuations of bacterial characteristics in relation to environmental parameters present an evident temporal variation in water, but not in the sediment habitat. Received: 13 January 1997; Accepted: 7 August 1997     

Archaeal and bacterial diversity in hot springs on the Tibetan Plateau, China

The diversity of archaea and bacteria was investigated in ten hot springs (elevation >4600 m above sea level) in Central and Central-Eastern Tibet using 16S rRNA gene phylogenetic analysis. The temperature and pH of these hot springs were 26-81°C and close to neutral, respectively. A total of 959 (415 and 544 for bacteria and archaea, respectively) clone sequences were obtained. Phylogenetic analysis showed that bacteria were more diverse than archaea and that these clone sequences were classified into 82 bacterial and 41 archaeal operational taxonomic units (OTUs), respectively. The retrieved bacterial clones were mainly affiliated with four known groups (i.e., Firmicutes, Proteobacteria, Cyanobacteria, Chloroflexi), which were similar to those in other neutral-pH hot springs at low elevations. In contrast, most of the archaeal clones from the Tibetan hot springs were affiliated with Thaumarchaeota, a newly proposed archaeal phylum. The dominance of Thaumarchaeota in the archaeal community of the Tibetan hot springs appears to be unique, although the exact reasons are not yet known. Statistical analysis showed that diversity indices of both archaea and bacteria were not statistically correlated with temperature, which is consistent with previous studies.     

Archaeal diversity and community development in deep-sea hydrothermal vents

Over the past 35 years, researchers have explored deep-sea hydrothermal vent environments around the globe and studied a number of archaea, their unique metabolic and physiological properties, and their vast phylogenetic diversity. Although the pace of discovery of new archaeal taxa, phylotypes and phenotypes in deep-sea hydrothermal vents has slowed recently, bioinformatics and interdisciplinary geochemistry-microbiology approaches are providing new information on the diversity and community composition of archaea living in deep-sea vents. Recent investigations have revealed that archaea could have originated and dispersed from ancestral communities endemic to hydrothermal vents into other biomes on Earth, and the community structure and productivity of chemolithotrophic archaea are controlled primarily by variations in the geochemical composition of hydrothermal fluids.     

Archaeal diversity in naturally occurring and impacted environments from a tropical region

AIMS: To evaluate archaeal diversity in natural and impacted habitats from Rio de Janeiro state, Brazil, a tropical region of South America. METHODS AND RESULTS: 16S rRNA gene was amplified directly by polymerase chain reaction (PCR) from genomic DNA, extracted from Guanabara Bay (GB) water, halomarine sediment (HS), municipal landfill leachate, agricultural soil and wastewater treatment (WT) system. Five archaeal 16S rDNA clone libraries were constructed. A total of 123 clones, within the five libraries analysed, were clustered into 29 operational taxonomic units, related to cultivated (24%) and uncultivated (76%) organisms. Rarefaction analysis showed that the libraries contained different levels of diversity. PCR-denaturing gradient gel electrophoresis (DGGE) of 16S-23S intergenic spacer regions confirmed the presence of a dominant phylotype, revealed by the WT system clone library. CONCLUSIONS: Archaeal communities of impacted environments seem to be confined to specific ecosystems with similar physicochemical properties, while communities from natural environments appear to be widely distributed. The presence of a high number of phylotypes related to uncultivated organisms suggests new archaeal lineages. SIGNIFICANCE AND IMPACT OF THE STUDY: This study reports, for the first time, the analysis of archaeal diversity in tropical environments from Brazil, and adds sequences from this region to the developing database of 16S rRNA clone libraries from environmental samples.     

Microbial diversity in nonsulfur, sulfur and iron geothermal steam vents

Fumaroles, commonly called steam vents, are ubiquitous features of geothermal habitats. Recent studies have discovered microorganisms in condensed fumarole steam, but fumarole deposits have proven refractory to DNA isolation. In this study, we report the development of novel DNA isolation approaches for fumarole deposit microbial community analysis. Deposit samples were collected from steam vents and caves in Hawaii Volcanoes National Park, Yellowstone National Park and Lassen Volcanic National Park. Samples were analyzed by X-ray microanalysis and classified as nonsulfur, sulfur or iron-dominated steam deposits. We experienced considerable difficulty in obtaining high-yield, high-quality DNA for cloning: only half of all the samples ultimately yielded sequences. Analysis of archaeal 16S rRNA gene sequences showed that sulfur steam deposits were dominated by Sulfolobus and Acidianus, while nonsulfur deposits contained mainly unknown Crenarchaeota. Several of these novel Crenarchaeota lineages were related to chemoautotrophic ammonia oxidizers, indicating that fumaroles represent a putative habitat for ammonia-oxidizing Archaea. We also generated archaeal and bacterial enrichment cultures from the majority of the deposits and isolated members of the Sulfolobales. Our results provide the first evidence of Archaea in geothermal steam deposits and show that fumaroles harbor diverse and novel microbial lineages.     

Archaeal rRNA diversity and methane production in deep boreal peat

Northern peatlands play a major role in the global carbon cycle as sinks for CO₂ and as sources of CH₄. These diverse ecosystems develop through accumulation of partially decomposed plant material as peat. With increasing depth, peat becomes more and more recalcitrant due to its longer exposure to decomposing processes. Compared with surface peat, deeper peat sediments remain microbiologically poorly described. We detected active archaeal communities even in the deep bottom layers (−220/−280 cm) of two Finnish fen-type peatlands by 16S rRNA-based terminal restriction fragment length polymorphism analysis. In the sediments of the northern study site, all detected archaea were methanogens with Rice Cluster II (RC-II) and Methanosaetaceae as major groups. In southern peatland, Crenarchaeota of a rare unidentified cluster were present together with mainly RC-II methanogens. RNA profiles showed a larger archaeal diversity than DNA-based community profiles, suggesting that small but active populations were better visualized with rRNA. In addition, potential methane production measurements indicated methanogenic activity throughout the vertical peat profiles.     

Climate, energy and diversity

In recent years, a number of species-energy hypotheses have been developed to explain global patterns in plant and animal diversity. These hypotheses frequently fail to distinguish between fundamentally different forms of energy which influence diversity in dissimilar ways. Photosynthetically active radiation (PAR) can be utilized only by plants, though their abundance and growth rate is also greatly influenced by water. The Gibbs free energy (chemical energy) retained in the reduced organic compounds of tissue can be utilized by all heterotrophic organisms. Neither PAR nor chemical energy influences diversity directly. Both, however, influence biomass and/or abundance; diversity may then increase as a result of secondary population dynamic or evolutionary processes. Temperature is not a form of energy, though it is often used loosely by ecologists as a proxy for energy; it does, however, influence the rate of utilization of chemical energy by organisms. It may also influence diversity by allowing a greater range of energetic lifestyles at warmer temperatures (the metabolic niche hypothesis). We conclude that there is no single species/energy mechanism; fundamentally different processes link energy to abundance in plants and animals, and diversity is affected secondarily. If we are to make progress in elucidating these mechanisms, it is important to distinguish climatic effects on species' distribution and abundance from processes linking energy supply to plant and animal diversity.     

Archaeal diversity and a gene for ammonia oxidation are coupled to oceanic circulation

Evidence of microbial zonation in the open ocean is rapidly accumulating, but while the distribution of communities is often described according to depth, the other physical factors structuring microbial diversity and function remain poorly understood. Here we identify three different water masses in the North Water (eastern Canadian Arctic), defined by distinct temperature and salinity characteristics, and show that they contained distinct archaeal communities. Moreover, we found that one of the water masses contained an increased abundance of the archaeal alpha-subunit of the ammonia monooxygenase gene ( amoA ) and accounted for 70% of the amoA gene detected overall. This indicates likely differences in putative biogeochemical capacities among different water masses. The ensemble of our results strongly suggest that the widely accepted view of depth stratification did not explain microbial diversity, but rather that parent water masses provide the framework for predicting communities and potential microbial function in an Arctic marine system. Our results emphasize that microbial distributions are strongly influenced by oceanic circulation, implying that shifting currents and water mass boundaries resulting from climate change may well impact patterns of microbial diversity by displacing whole biomes from their historic distributions. This relocation could have the potential to establish a substantially different geography of microbial-driven biogeochemical processes and associated oceanic production.     

Genetic diversity in a feral horse population from Sable Island, Canada

The present-day Sable Island horse population, inhabiting an island off the eastern coast of Canada, is believed to have originated mainly from horses confiscated from the early French settlers in Nova Scotia in the latter half of the 18th century. In 1960, the Sable Island horses were given legal protected status and no human interference has since been allowed. The objective of this study was to characterize the current genetic diversity in Sable Island horses in comparison to 15 other horse breeds commonly found in Canada and 5 Spanish breeds. A total of 145 alleles from 12 microsatellite loci were detected in 1093 horses and 40 donkeys. The average number of alleles per locus ranged from 4.67 in the Sable Island horse population to 8.25 in Appaloosas, whereas the mean observed heterozygosity ranged from 0.626 in the Sable Island population to 0.787 in Asturcons. Various genetic distance estimates and clustering methods did not permit to support that the Sable Island horses originated from shipwrecked Spanish horses, according to a popular anecdote, but closely resemble light draft and multipurpose breeds commonly found in eastern Canada. Based on the Weitzman approach, the loss of the Sable Island horse population to the overall diversity in Canada is comparable or higher than any other horse breed. The Sable Island horse population has diverged enough from other breeds to deserve special attention by conservation interest groups.     

Cooperation in a deep helical energy well

In contrast to random coil polymers, polyisocyanates maintain a highly extended helical conformation in solution. This structural characteristic causes unusually large chiral optical properties to arise from copolymerization of tiny proportions of optically active monomer isocyanates with achiral isocyanates or even from stereospecific placement of deuterium in the side chain of poly(n-hexyl isocyanate). These effects can be understood as phenomenologically related to the optical activity amplification properties of vinyl polymers studied by Pino and his co-workers and ascribed to breaking the energetic degeneracy of the otherwise equally populated left- and right-handed helical states of the backbone. Statistical thermodynamic calculations, based on this model, and analogous to those carried out earlier on the vinyl polymers, allow matching the temperature and molecular weight dependence of the optical activity in poly((R)-1-deuterio-1-hexyl isocyanate) to the approximate responsible energy terms.     

Phylotype diversity in a benthic cyanobacterial mat community on King George Island, maritime Antarctica

Cyanobacterial 16S ribosomal RNA gene diversity was examined in a benthic mat on Fildes Peninsula of King George Island (62o09′54.4′′S, 58o57′20.9′′W), maritime Antarctica. Environmental DNA was isolated from the mat, a clone library of PCR-amplified 16S rRNA gene fragments was prepared, and amplified ribosomal DNA restriction analysis (ARDRA) was done to assign clones to seven groups. Low cyanobacterial diversity in the mat was suggested in that 83% of the clones were represented by one ARDRA group. DNA sequences from this group had high similarity with 16S rRNA genes of Tychonema bourrellyi and T. bornetii isolates, whose geographic origins were southern Norway and Northern Ireland. Cyanobacterial morphotypes corresponding to Tychonema have not been reported in Antarctica, however, this morphotype was previously found at Ward Hunt Lake (83oN), and in western Europe (52oN). DNA sequences of three of the ARDRA groups had highest similarity with 16S rDNA sequences of the Tychonema group accounting for 9.4% of the clones. Sequences of the remaining three groups (7.6%) had highest similarity with 16S rRNA genes of uncultured cyanobacteria clones from benthic mats of Lake Fryxell and fresh meltwater on the McMurdo Ice Shelf.     

A new chromosomal race of the house mouse, Mus musculus domesticus, in the Vulcano Island-Aeolian Archipelago, Italy

In this paper we describe a new Robertsonian (Rb) race of the house mouse from Vulcano (Aeolian archipelago) through the identification of the metacentric chromosomes. We analysed fifteen mice. All the specimens were found to have the same karyotype 2n=26. This karyotype is characterized by Rb(1.2), Rb(3.9), Rb(4.13), Rb(5.14), Rb(8.12), Rb(10.16) and Rb(15.17). The differences between the race of Vulcano and the races in a neighbour island (Lipari) consist in the presence of Rb(10.16) and Rb(15.17) in the former and Rb(6.16) and Rb(10.15) in the latter. We discuss the possible hypotheses regarding the origin between these two races including the possible occurrence of a whole arm reciprocal translocation (WART) on the Vulcano island.     

Seasonal and Spatial Variability of Bacterial and Archaeal Assemblages in the Coastal Waters near Anvers Island, Antarctica

A previous report of high levels of members of the domain Archaea in Antarctic coastal waters prompted us to investigate the ecology of Antarctic planktonic prokaryotes. rRNA hybridization techniques and denaturing gradient gel electrophoresis (DGGE) analysis of the bacterial V3 region were used to study variation in Antarctic picoplankton assemblages. In Anvers Island nearshore waters during late winter to early spring, the amounts of archaeal rRNA ranged from 17.1 to 3.6% of the total picoplankton rRNA in 1996 and from 16.0 to 1.0% of the total rRNA in 1995. Offshore in the Palmer Basin, the levels of archaeal rRNA throughout the water column were higher (average, 24% of the total rRNA) during the same period in 1996. The archaeal rRNA levels in nearshore waters followed a highly seasonal pattern and markedly decreased during the austral summer at two stations. There was a significant negative correlation between archaeal rRNA levels and phytoplankton levels (as inferred from chlorophyll a concentrations) in nearshore surface waters during the early spring of 1995 and during an 8-month period in 1996 and 1997. In situ hybridization experiments revealed that 5 to 14% of DAPI (4′,6-diamidino-2-phenylindole)-stained cells were archaeal, corresponding to 0.9 × 10⁴ to 2.7 × 10⁴ archaeal cells per ml, in late winter 1996 samples. Analysis of bacterial ribosomal DNA fragments by DGGE revealed that the assemblage composition may reflect changes in water column stability, depth, or season. The data indicate that changes in Antarctic seasons are accompanied by significant shifts in the species composition of bacterioplankton assemblages and by large decreases in the relative proportion of archaeal rRNA in the nearshore water column.     

Island biogeography, diversity and dominance of zooplankton in crater lakes on the Azores

In July and August 1988 samples of zooplankton were collected from 17 lakes on four islands. Five species of Cladocera, three species of Copepoda and 30 species of Rotifera were found. The maximum numbers of species in any one lake were four planktonic Cladocera, two Copepoda and seven planktonic Rotifera (with up to six additional non-planktonic species). The smallest, most distant island had fewer species than the largest island nearest to the mainland, but the number of species in each lake was determined more by the size of the lake than by its location. This results in the most distant island having lakes containing the same number of species as lakes of similar size on islands nearer to the mainland. The numbers of zooplankton species in each of these lakes are significantly lower than the world average, and the dominance ratios are significantly higher.     

Archaeal diversity in permafrost deposits of Bunger Hills Oasis and King George Island (Antarctica) according to the 16S rRNA gene sequencing

Archaeal communities of permafrost deposits of King George Island and Bunger Hills Oasis (Antarctica) differing in the content of biogenic methane were analyzed using the clone libraries of two 16S rRNA gene regions. Phylotypes belonging to methanogenic archaea were identified in all horizons.     

Biomass production and energy source of thermophiles in a Japanese alkaline geothermal pool

Microbial biomass production has been measured to investigate the contribution of planktonic bacteria to fluxations in dissolved organic matter in marine and freshwater environments, but little is known about biomass production of thermophiles inhabiting geothermal and hydrothermal regions. The biomass production of thermophiles inhabiting an 85°C geothermal pool was measured by in situ cultivation using diffusion chambers. The thermophiles' growth rates ranged from 0.43 to 0.82 day^?1, similar to those of planktonic bacteria in marine and freshwater habitats. Biomass production was estimated based on cellular carbon content measured directly from the thermophiles inhabiting the geothermal pool, which ranged from 5.0 to 6.1 μg C l^?1 h^?1. This production was 2–75 times higher than that of planktonic bacteria in other habitats, because the cellular carbon content of the thermophiles was much higher. Quantitative PCR and phylogenetic analysis targeting 16S rRNA genes revealed that thermophilic H₂‐oxidizing bacteria closely related to Calderobacterium and Geothermobacterium were dominant in the geothermal pool. Chemical analysis showed the presence of H₂ in gases bubbling from the bottom of the geothermal pool. These results strongly suggested that H₂ plays an important role as a primary energy source of thermophiles in the geothermal pool.