The micro-biota of a sub-surface monument the medieval chapel of St. Virgil (Vienna, Austria)

The medieval chapel of St. Virgil is located sub-surface beneath the square of the dome of St. Stephen, in the heart of Vienna. The walls of the chapel are in direct contact with the surrounding soil. The water migrating horizontally into the walls of the chapel carries a huge load of soluble salts which crystallize on the surface of the walls and within the material. This phenomenon is causing material losses and destruction of original medieval fineries and paintings. Moreover, the salt creates special living conditions for microbes growing on and in the walls which is characterized by a high osmotic stress. The diversity of the micro-biota was studied both by cultivation and molecular techniques [a combination of denaturing gradient gel electrophoresis (DGGE) of PCR-amplified DNA encoding 16S rRNA and the construction of clone libraries]. The fungal diversity was found to be relatively low, albeit cell counts show more than 10⁵ colony forming units per gram of wall material. In the contrary, the diversity of bacteria was found to be high (more than 8 different genera). Furthermore, a community of extremely halophilic archaea was detected consisting of different species of two predominant genera, i.e., Halococcus and Halobacterium.     

Metal cation binding by the hyperthermophilic microorganism,Archaea Methanocaldococcus Jannaschii,and its effects on silicification

Abstract: A series of experiments was conducted to determine the capacity of an archaeal strain, Methanocaldococcus jannaschii, to bind metals and to study the effects of metal binding on the subsequent silicification of the microorganisms. The results showed that M. jannaschii can rapidly bind several metal cations (Fe³⁺, Ca²⁺, Pb²⁺, Zn²⁺, Cu²⁺). Considering the lack of silicification of this strain without metal binding, these experiments demonstrate that Fe(III) ion binding to the cell wall components was of fundamental importance for successful silicification and, especially, for the excellent preservation of the cell wall. This study brings new elements to the understanding of fossilization processes, showing that the positive effect of Fe(III) on silicification, already known for Bacteria, can also apply to Archaea and that this preliminary binding can be decisive for the subsequent fossilization of these organisms. Knowledge of these mechanisms can be helpful for the search and the identification of microfossils in both terrestrial and extraterrestrials rocks, and in particular on Mars.     

The Prokaryote-to-Eukaryote Transition Reflected in the Evolution of the V/F/A-ATPase Catalytic and Proteolipid Subunits

Changes in the primary and quarternary structure of vacuolar and archaeal type ATPases that accompany the prokaryote-to-eukaryote transition are analyzed. The gene encoding the vacuolar-type proteolipid of the V-ATPase from Giardia lamblia is reported. Giardia has a typical vacuolar ATPase as observed from the common motifs shared between its proteolipid subunit and other eukaryotic vacuolar ATPases, suggesting that the former enzyme works as a hydrolase in this primitive eukaryote. The phylogenetic analyses of the V-ATPase catalytic subunit and the front and back halves of the proteolipid subunit placed Giardia as the deepest branch within the eukaryotes. Our phylogenetic analysis indicated that at least two independent duplication and fusion events gave rise to the larger proteolipid type found in eukaryotes and in Methanococcus. The spatial distribution of the conserved residues among the vacuolar-type proteolipids suggest a zipper-type interaction among the transmembrane helices and surrounding subunits of the V-ATPase complex. Important residues involved in the function of the F-ATP synthase proteolipid have been replaced during evolution in the V-proteolipid, but in some cases retained in the archaeal A-ATPase. Their possible implication in the evolution of V/F/A-ATPases is discussed. Received: 27 August 1997 / Accepted: 14 January 1998     

The Variation of Microbial Communities in a Depth Profile of Peat in the Gahai Lake Wetland Natural Conservation Area

The Gahai Lake wetland natural conservation area in northwestern China includes peatland that has been accumulating over hundreds of years and is seldom disturbed by industry. Bacteria and archaea in peat soil, which is a reservoir for carbon and water, may influence its ecological function. The objective of this study was to obtain a clearer understanding of peat microbial ecology and its relationship to the environmental conditions of this area. Hence, the microbial community of the peatland ecosystem was investigated by sequencing bacterial and archaeal DNA extracted from samples collected at different peat depths. Results showed that in all samples the dominant bacterial phyla were Proteobacteria (relative abundance 0.39 ± 0.12) and Chloroflexi (0.16 ± 0.09), while the dominant archaeal phyla were Miscellaneous Crenarchaeotic Group (MCG) (0.62 ± 0.21) and Euryarchaeota (0.27 ± 0.16). The diversity and microbial community structure at deeper depths (90 and 120 cm below the peat surface) significantly differ from that at shallower depths (10, 30 and 50 cm deep). In contrast to the shallow layers, the deeper layers became more abundant in the bacterial phyla Chloroflexi, Bacteroidetes, Atribacteria, Aminicenantes, Chlorobi, TA06, Caldiserica and Spirochaetae; and in the archaeal phyla MCG and Miscellaneous Euryarchaeotic Group (MEG). This study revealed a significant shift in microbial community in peat between 50 cm and 90 cm deep, as probably influenced by the oxygen supply at different depths. Furthermore, new insights into the microbial taxa were obtained, thus providing a baseline for future studies of this peat ecosystem.     

Bacteria and archaea as the sources of traits for enhanced plant phenotypes

Rising global demand for food and population increases are driving the need for improved crop productivity over the next 30 years. Plants have inherent metabolic limitations on productivity such as inefficiencies in carbon fixation and sensitivity to environmental conditions. Bacteria and archaea inhabit some of the most inhospitable environments on the planet and possess unique metabolic pathways and genes to cope with these conditions. Microbial genes involved in carbon fixation, abiotic stress tolerance, and nutrient acquisition have been utilized in plants to enhance plant phenotypes by increasing yield, photosynthesis, and abiotic stress tolerance. Transgenic plants expressing bacterial and archaeal genes will be discussed along with emerging strategies and tools to increase plant growth and yield.     

Fructans of the saline world

Saline and hypersaline environments make up the largest ecosystem on earth and the organisms living in such water-restricted environments have developed unique ways to cope with high salinity. As such these organisms not only carry significant industrial potential in a world where freshwater supplies are rapidly diminishing, but they also shed light upon the origins and extremes of life. One largely overlooked and potentially important feature of many salt-loving organisms is their ability to produce fructans, fructose polymers widely found in various mesophilic Eubacteria and plants, with potential functions as storage carbohydrates, aiding stress tolerance, and acting as virulence factors or signaling molecules. Intriguingly, within the whole archaeal domain of life, Archaea possessing putative fructan biosynthetic enzymes were found to belong to the extremely halophilic class of Halobacteria only, indicating a strong, yet unexplored link between the fructan syndrome and salinity. In fact, this link may indeed lead to novel strategies in fighting the global salinization problem. Hence this review explores the unknown world of fructanogenic salt-loving organisms, where water scarcity is the main stress factor for life. Within this scope, prokaryotes and plants of the saline world are discussed in detail, with special emphasis on their salt adaptation mechanisms, the potential roles of fructans and fructosyltransferase enzymes in adaptation and survival as well as future aspects for all fructanogenic salt-loving domains of life.     

Thermococcus chitonophagus sp. nov., a novel,chitin-degrading,hyperthermophilic archaeum from a deep-sea hydrothermal vent environment

From a hydrothermal vent site off the Mexican west coast (20°50′N, 109°06′W) at a depth of 2,600 m, a novel, hyperthermophilic, anaerobic archaeum was isolated. Cells were round to slightly irregular cocci, 1.2–2.5 μm in diameter and were motile by means of a tuft of flagella. The new isolate grew between 60 and 93°C (optimum: 85°C), from pH 3.5 to 9 (optimum: pH 6.7), and from 0.8 to 8% NaCl (optimum: 2%). The isolate was an obligate organotroph, using chitin, yeast extract, meat extract, and peptone for growth. Chitin was fermented to H₂, CO₂, NH₃, acetate, and formate. H₂S was formed in the presence of sulfur. The chitinoclastic enzyme system was oxygen-stable, cell-associated, and inducible by chitin. The cell wall was composed of a surface layer of hex- americ protein complexes arranged on a p6 lattice. The core lipids consisted of glycerol diphytanyl diethers and acyclic and cyclic glycerol diphytanyl tetraethers. The G+C content was 46.5 mol%. DNA/DNA hybridization and 16S rRNA sequencing indicated that the new isolate belongs to the genus Thermococcus, representing a new species, Thermococcus chitonophagus. The type strain is isolate GC74, DSM 10152. Received: 8 May 1995 / Accepted: 26 June 1995     

Thermococcus alcaliphilus sp. nov., a new hyperthermophilic archaeum growing on polysulfide at alkaline pH

A novel coccoid-shaped, hyperthermophilic, heterotrophic member of the archaea was isolated from a shallow marine hydrothermal system at Vulcano Island, Italy. The isolate grew between 56 and 90° C with an optimum around 85° C. The pH range for growth was 6.5 to 10.5, with an optimum around 9.0. Polysulfide and elemental sulfur were reduced to H₂S. Sulfur stimulated the growth rate. The isolate fermented yeast extract, peptone, meat extract, tryptone, and casein. Isovalerate, isobutyrate, propionate, acetate, CO₂, NH₃, and H₂S (in the presence of S°) were detected as end products. Growth was not inhibited by H₂. Based on DNA-DNA hybridization and 16S rRNA partial sequences, the new isolate represents a new species of Thermococcus, which we named Thermococcus alcaliphilus. The type strain is isolate AEDII12 (DSM 10322) Received: 7 July 1995 / Accepted: 25 August 1995     

Uptake and turnover of acetate in hypersaline environments

Abstract: Acetate uptake and turnover rates were determined for the heterotrophic community in hypersaline environments (saltern crystallizer ponds, the Dead Sea) dominated by halpphilic Archaea. Acetate was formed from glycerol, which is potentially the major available carbon source for natural communities of halophilic Archaea. Values of [ K _t+ S _n] (the sum of the substrate affinity and the substrate concentration present in situ) for acetate measured in saltern crystallizer ponds were around 4.5–11.5 μM, while in the Dead Sea during a Dunaliella bloom values up to 12.8 μM were found. Maximal theoretical rates ( V _max) of acetate uptake in saltern crystallizer ponds were 12–56 nmol l⁻¹ h⁻¹, with estimated turnover times for acetate ( T _t) between 127–730 h at 35°C. V _max values measured in the Dead Sea were between 0.8 and 12.8 nmol l⁻¹ h⁻¹, with turnover times in the range of 320–2190 h. V _max values for acetate were much lower than those for glycerol. Comparisons with pure cultures of halophilic Archaea grown under different conditions showed that the natural communities were not adapted for preferential use of acetate. Both in natural brines and in pure cultures of halophilic Archaea, acetate incorporation rates rapidly decreased above the optimum pH value, probably since acetate enters the cell only in its unionized form. The low affinity for acetate, together with low potential utilization rates result in the long acetate turnover times, which explains the accumulation of acetate observed when low concentrations of glycerol are supplied as a nutrient to natural communities of halophilic Archaea.