Natural Communities of Novel Archaea and Bacteria with a String-of-Pearls-Like Morphology: Molecular Analysis of the Bacterial Partners

A recently discovered bacterial/archaeal association, growing in a string-of-pearls-like structure, thrives in the cold (~10°C) sulfidic marsh water of the Sippenauer Moor near Regensburg, Bavaria, Germany. It forms characteristic, macroscopically visible globules, the pearls, containing microcolonies of novel euryarchaeota, which are surrounded by mainly filamentous bacteria (C. Rudolph, G. Wanner, and R. Huber, Appl. Environ. Microbiol. 67:2336-2344, 2001). Single pearls in series are connected by white threads. Here we report the first detailed molecular investigations of the taxonomic affiliation of the bacteria contributing to the strings of pearls. Phylogenetic analysis showed the dominance of a single phylotype (clone sipK4) within single pearls most closely related to Thiothrix unzii. The presence of Thiothrix sipK4 as a major constituent of single pearls and of the pearl-connecting white threads was verified by fluorescence in situ hybridization.     

Natural communities of novel archaea and bacteria with a string-of-pearls-like morphology: molecular analysis of the bacterial partners

A recently discovered bacterial/archaeal association, growing in a string-of-pearls-like structure, thrives in the cold (approximately 10 degrees C) sulfidic marsh water of the Sippenauer Moor near Regensburg, Bavaria, Germany. It forms characteristic, macroscopically visible globules, the pearls, containing microcolonies of novel euryarchaeota, which are surrounded by mainly filamentous bacteria (C. Rudolph, G. Wanner, and R. Huber, Appl. Environ. Microbiol. 67:2336-2344, 2001). Single pearls in series are connected by white threads. Here we report the first detailed molecular investigations of the taxonomic affiliation of the bacteria contributing to the strings of pearls. Phylogenetic analysis showed the dominance of a single phylotype (clone sipK4) within single pearls most closely related to Thiothrix unzii. The presence of Thiothrix sipK4 as a major constituent of single pearls and of the pearl-connecting white threads was verified by fluorescence in situ hybridization.     

Loss of viability during freeze–thaw of intact and adherent human embryonic stem cells with conventional slow-cooling protocols is predominantly due to␣apoptosis rather than cellular necrosis

Summary A major challenge in the widespread application of human embryonic stem (hES) cells in clinical therapy and basic scientific research is the development of efficient cryopreservation protocols. Conventional slow-cooling protocols utilizing standard cryoprotectant concentrations i.e. 10% (v/v) DMSO, yield extremely low survival rates of <5% as reported by previous studies. This study characterized cell death within frozen–thawed hES colonies that were cryopreserved under standard conditions. Surprisingly, our results showed that immediately after post-thaw washing, the overwhelming majority of hES cells were viable (≈98%), as assessed by the trypan blue exclusion test. However, when the freshly-thawed hES colonies were incubated within a 37 °C incubator, there was observed to be a gradual reduction in cell viability over time. The kinetics of cell death was drastically slowed-down by keeping the freshly-thawed hES colonies at 4 °C, with >90% of cells remaining viable after 90 min of incubation at 4 °C. This effect was reversible upon re-exposing the cells to physiological temperature. The vast majority of low temperature-exposed hES colonies gradually underwent cell death upon incubation for a further 90 min at 37 °C. Terminal deoxynucleotidyl transferase (TdT)-mediated dUTP nick-end-labeling (TUNEL) assay confirmed apoptosis-induced nuclear DNA fragmentation in frozen–thawed hES cells after incubation at 37 °C for 90 min. Expression of active caspase-3 enzyme, which is another prominent marker of apoptosis, was confirmed by immunocytochemical staining, while transmission electron microscopy showed typical ultrastructural features of apoptosis such as chromatin condensation and margination to the nuclear membrane. Hence, our results demonstrated that apoptosis instead of cellular necrosis, is the major mechanism of the loss of viability of cryopreserved hES cells during freeze–thawing with conventional slow-cooling protocols.     

Molecular identification of filterable bacteria and archaea in the water of acidic lakes of northern Russia

Wetland ecosystems are the natural centers of freshwater formation in northern Russia lowland landscapes. The humic acidic waters formed in bogs feed the numerous lakes of the northern regions. One milliliter of the water in these lakes contains up to 10⁴ ultrasmall microbial cells that pass through “bacterial” filters with a pore size of 0.22 μm. The vast majority of these cells do not grow on nutrient media and cannot be identified by routine cultivation-based approaches. Their identification was performed by analysis of clone libraries obtained by PCR amplification of archaeal and bacterial 16S rRNA genes from the fraction of cells collected from water filtrates of acidic lakes. Most of the obtained bacterial 16S rRNA gene sequences represented the class Betaproteobacteria and exhibited the highest homology of (94–99%) with 16S rRNA genes of representatives of the genera Herbaspirillum, Herminiimonas, Curvibacter, and Burkholderia. The archaeal 16S rRNA gene clone library comprised genes of Euryarchaeota representatives. One-third of these genes exhibited 97–99% homology to the 16S rRNA genes of taxonomically described organisms of the orders Methanobacteriales and Methanosarcinales. The rest of the cloned archaeal 16S rRNA genes were only distantly related (71–74% homology) to those in all earlier characterized archaea.     

Bacterial and archaeal populations at two shallow hydrothermal vents off Panarea Island (Eolian Islands, Italy)

The aim of this study was to investigate the microbial community thriving at two shallow hydrothermal vents off Panarea Island (Italy). Physico-chemical characteristics of thermal waters were examined in order to establish the effect of the vents on biodiversity of both Bacteria and Archaea. Water and adjacent sediment samples were collected at different times from two vents, characterised by different depth and temperature, and analysed to evaluate total microbial abundances, sulphur-oxidising and thermophilic aerobic bacteria. Total microbial abundances were on average of the order of 10⁵ cells ml⁻¹, expressed as picoplanktonic size fraction. Picophytoplanktonic cells accounted for 0.77–3.83% of the total picoplanktonic cells. The contribution of bacterial and archaeal taxa to prokaryotic community diversity was investigated by PCR–DGGE fingerprinting method. The number of bands derived from bacterial DNA was highest in the DGGE profiles of water sample from the warmest and deepest site (site 2). In contrast, archaeal richness was highest in the water of the coldest and shallowest site (site 1). Sulphur-oxidising bacteria were detected by both culture-dependent and -independent methods. The primary production at the shallow hydrothermal system of Panarea is supported by a complex microbial community composed by phototrophs and chemolithotrophs.     

Microbial Diversity in Sediments of Saline Qinghai Lake, China: Linking Geochemical Controls to Microbial Ecology

Saline lakes at high altitudes represent an important and extreme microbial ecosystem, yet little is known about microbial diversity in such environments. The objective of this study was to examine the change of microbial diversity from the bottom of the lake to sediments of 40 cm in depth in a core from Qinghai Lake. The lake is saline (12.5 g/L salinity) and alkaline (pH 9.4) and is located on the Qinghai–Tibetan Plateau at an altitude of 3196 m above sea level. Pore water chemistry of the core revealed low concentrations of sulfate and iron (<1 mM), but high concentrations of acetate (40–70 mM) and dissolved organic carbon (1596–5443 mg/L). Total organic carbon and total nitrogen contents in the sediments were ∼2 and <0.5%, respectively. Acridine orange direct count data indicated that cell numbers decreased from 4 × 10⁹ cells/g at the water–sediment interface to 6× 10⁷ cells/g wet sediment at the 40-cm depth. This change in biomass was positively correlated with acetate concentration in pore water. Phospholipid fatty acid (PLFA) community structure analyses determined decrease in the proportion of the Proteobacteria and increase in the Firmicutes with increased depth. Characterization of small subunit (SSU) rRNA genes amplified from the sediments indicated a shift in the bacterial community with depth. Whereas the α-, β-, and γ-Proteobacteria and the Cytophaga/Flavobacterium/Bacteroides (CFB) were dominant at the water–sediment interface, low G + C gram-positive bacteria (a subgroup of Firmicutes) became the predominant group in the anoxic sediments. Both PLFA and the sequence data showed similar trend. The Proteobacteria, CFB, and gram-positive bacteria are present in other saline lakes, but thepresence of Actinobacteria and Acidobacteria/Holophaga in significant proportions in the Qinghai Lake sediments appears to be unique. The archaeal diversity was much lower, and clone sequences could be grouped inthe Euryarchaeota and Crenarchaeota domains. The archaeal clones were not related to any known cultures but to sequences previously found in methane-rich sediments. Acetate-utilizing methanogens were isolated from sediment incubations, and α- and γ-proteobacterial isolates were obtained from a water sample from the lakebottom (23 m). Our data collectively showed that the observed diversity and shift in the community structure with depth was correlated with geochemical parameters (the redox state and availability of electron acceptor and donor). Heterotrophic methanogenesis is possibly adominant metabolic process in the Qinghai Lake sediments. These results reinforce the importance of geochemical controls on microbial ecology in saline and alkaline lake environments.     

Archaeal Communities in Boreal Forest Tree Rhizospheres Respond to Changing Soil Temperatures

Temperature has generally great effects on both the activity and composition of microbial communities in different soils. We tested the impact of soil temperature and three different boreal forest tree species on the archaeal populations in the bulk soil, rhizosphere, and mycorrhizosphere. Scots pine, silver birch, and Norway spruce seedlings were grown in forest humus microcosms at three different temperatures, 7–11.5°C (night–day temperature), 12–16°C, and 16–22°C, of which 12–16°C represents the typical mid-summer soil temperature in Finnish forests. RNA and DNA were extracted from indigenous ectomycorrhiza, non-mycorrhizal long roots, and boreal forest humus and tested for the presence of archaea by nested PCR of the archaeal 16S rRNA gene followed by denaturing gradient gel electrophoresis (DGGE) profiling and sequencing. Methanogenic Euryarchaeota belonging to Methanolobus sp. and Methanosaeta sp. were detected on the roots and mycorrhiza. The most commonly detected archaeal 16S rRNA gene sequences belonged to group I.1c Crenarchaeota, which are typically found in boreal and alpine forest soils. Interestingly, also one sequence belonging to group I.1b Crenarchaeota was detected from Scots pine mycorrhiza although sequences of this group are usually found in agricultural and forest soils in temperate areas. Tree- and temperature-related shifts in the archaeal population structure were observed. A clear decrease in crenarchaeotal DGGE band number was seen with increasing temperature, and correspondingly, the number of euryarchaeotal DGGE bands, mostly methanogens, increased. The greatest diversity of archaeal DGGE bands was detected in Scots pine roots and mycorrhizas. No archaea were detected from humus samples from microcosms without tree seedling, indicating that the archaea found in the mycorrhizosphere and root systems were dependent on the plant host. The detection of archaeal 16S rRNA gene sequences from both RNA and DNA extractions show that the archaeal populations were living and that they may have significant contribution to the methane cycle in boreal forest soil, especially when soil temperatures rise.     

Phenotypic changes in the regenerating rabbit bladder muscle. Role of interstitial cells and innervation on smooth muscle cell differentiation

 We have studied the phenotypic changes in regenerating smooth muscle (SM) tissue of detrusor muscle after local application of a necrotizing, freeze–thaw injury to the serosal surface of rabbit bladder. Bromo-deoxyuridine (BrdU) incorporation and immunofluorescence studies were performed on bladder cryosections from day 2 up to day 15 after surgery with monoclonal antibodies specific for some cytoskeletal markers [desmin, vimentin, non-muscle (NM) myosin] and for SM-specific proteins (α-actin, myosin, and SM22). Four days after lesion, some clls incorporated in regenerating SM bundles are BrdU positive, but all display a phenotypic pattern identical to that of the interstitial, highly proliferating cells, i.e., expression of vimentin. By days 7–15 the differentiation profile of regenerating SM returns to that of uninjured SM tissue (appearance of desmin, SM-type α-actin, and SM myosin). A chemical denervation achieved by 6-hydroxydopamine treatment for 2 weeks induces the formation of vimentin/SM α-actin/NM myosin/SM22-containing myofibroblasts in the interstitial, fibroblast-like cells of uninjured bladder. In the bladder wall, alteration of reinnervation during the regenerating SM process produces: (1) in the outer region, the activation of vimentin/SM α-actin/desmin myofibroblasts in the de novo SM cell bundles; and (2) in the inner region of bladder, including the muscularis mucosae, the formation of proliferating, fully differentiated SM cells peripherally to newly formed SM cell bundles. These findings suggest that: (1) the de novo SM tissue formation in the bladder can occur via incorporation of interstitial cells into growing SM bundles; and (2) the alteration of reinnervation during the regenerating process induces a spatial-specific differentiation of interstitial myofibroblasts in SM cells before SM cell bundling. Accepted: 14 May 1997     

Fungicidal and Cytotoxic Activity of a Capsicum chinense Defensin Expressed by Endothelial Cells

Plant defensins are antimicrobial peptides that exhibit mainly antifungal activity against a broad range of plant fungal pathogens. However, their actions against Candida albicans have not been extensively studied. The mRNA for γ-thionin, a defensin from Capsicum chinense, has been expressed in bovine endothelial cells. The conditioned medium of these cells showed antifungal activity on germ tube formation (60–70% of inhibition) and on the viability of C. albicans (70–80% of inhibition). Additionally, C. albicans was not able to penetrate transfected cells. Conditioned medium from these cells also inhibited the viability (80%) of the human tumor cell line, HeLa.     

Microbial Diversity in Sediments Collected from the Deepest Cold-Seep Area, the Japan Trench

The Japan Trench land slope at a depth of 6,400 m is the deepest cold-seep environment with Calyptogena communities. Sediment samples from inside and beside the Calyptogena communities were collected, and the microbial diversity in the sediment samples was studied by molecular phylogenetic techniques. From DNA extracted directly from the sediment samples, 16S rDNAs were amplified by the polymerase chain reaction method. The sequences of the amplified 16S rDNAs selected by restriction fragment length polymorphism analysis were determined and compared with sequences in DNA databases. The results showed that 33 different bacterial 16S rDNA sequences from the two samples analyzed fell into similar phylogenetic categories, the α-, γ-, δ-, and ɛ-subdivisions of Proteobacteria, Cytophaga, and gram-positive bacteria; some of the 16S rDNA sequences were common to both samples. δ- and ɛ-Proteobacteria-related sequences were abundant in both sediments. These sequences are mostly related to sulfate-reducing or sulfur-reducing bacteria and epibionts, respectively. Eight different archaeal 16S rDNA sequences were cloned from the sediments. The majority of the archaeal 16S rDNA sequences clustered in Crenarchaeota and showed high similarities to marine group I archaeal rDNA. A Methanococcoides burtonii–related sequence obtained from the sediment clustered in the Euryarchaeota indicating that M. burtonii–related strains in the area of Calyptogena communities may contribute to production of methane in this environment. From these results, we propose a possible model of sulfur circulation within the microbial community and that of Calyptogena clams in the cold-seep environment. Received June 15, 1998; accepted November 10, 1998.     

Effects of temperature shift on cell cycle, apoptosis and nucleotide pools in CHO cell batch cultues

Temperature reduction in CHO cell batch culture may be beneficial in the production of recombinant protein and in maintenance of viability. The effects on cell cycle, apoptosis and nucleotide pools were studied in cultures initiated at 37°C and temperature shifted to 30 °C after 48 hours. In control cultures maintained at 37 °C, viable cells continued to proliferate until the termination of the culture, however, temperature reduction caused a rapid decrease in the percent of cells in S phase and accumulation of cells in G-1. This was accompanied by a concurrent reduction in U ratio (UTO/UDP-GNAc), previously shown to be a sensitive indicator of growth rate. Culture viability was extended following temperature shift, as a result of delayed onset of apoptosis, however, once initiated, the rate and manner of cell death was similar to that observed at 37 °C. All nucleotide pools were similarly degraded at the time of apoptotic cell death. Temperature reduction to 30 °C did not decrease the energy charge of the cells, however, the overall rate of metabolism was reduced. The latter may be sufficient to extend culture viability via a reduction in toxic metabolites and/or limitation of nutrient deprivation. However, the possibility remains that the benefits of temperature reduction in terms of both viability and productivity are more directly associated with cultures spending extended time in G-1.     

Expression of smooth muscle myosin light chain 17 and unloaded shortening in single smooth muscle cells

These experiments were performed totest the hypotheses that myosin light chain 17 (MLC₁₇) aand b isoform expression varies between individual vascular smoothmuscle (SM) cells and that their expression correlates with cellunloaded shortening velocity. Single SM cells isolated from rabbitaorta and carotid arteries were used to measure unloaded shorteningvelocity and subsequently were analyzed via RT-PCR forMLC₁₇ a and b mRNA ratio. The MLC_17b/a mRNA andprotein ratios from adjacent tissue sections correlate very well(R² = 0.68), allowing use of the mRNA ratio topredict the protein ratio. The rabbit MLC₁₇ isoform proteinsequence was found to be similar to, but unique from, the swine, mouse,and chicken sequences. Isolated single SM cells from the aorta andcarotid have resting lengths of 70-280 µm and shorten to33-88 µm after contraction. Isolated cell maximum unloadedshortening velocity is highly variable (0.5-7.5 µm/s) butbecomes more uniform when normalized to initial cell length(0.01-0.05 cell lengths/s). Carotid cells activated in thepresence of okadaic acid (1 µm) have mean maximal unloaded shorteningvelocities not significantly different from carotid cells activatedwithout okadaic acid (0.016 vs. 0.019 cell lengths/s). Resting celllength before activation is significantly correlated with final celllength after unloaded shortening. Neither initial cell length, finalcell length, total cell length change, nor maximum unloaded shorteningvelocity (absolute or normalized) was significantly correlated withsingle-cell MLC_17b/a mRNA ratio. These studies wereperformed in isolated single SM cells where unloaded shorteningvelocity and MLC_17b/a mRNA ratios were measured in the samecell. In this preparation, the three-dimensional organization andmilieu of the cell is kept intact, but without the intercellularheterogeneity concerns of multicellular preparations. These resultssuggest the MLC_17b/a ratio is variable between individual SM cells from the same tissue, but it is not a determinant of unloadedshortening velocity in single SM cells.

     

Evidence for substantial maintenance of membrane integrity and cell viability in normally developing grape (Vitis vinifera L.) berries throughout development

Fluorescein diacetate (FDA) was used as a vital stain to assaymembrane integrity (cell viability) in mesocarp tissue of thedeveloping grape (Vitis vinifera L.) berry in order to testthe hypothesis that there is a substantial loss of compartmentationin these cells during ripening. This technique was also usedto determine whether loss of viability was associated with symptomsof a ripening disorder known as berry shrivel. FDA fluorescenceof berry cells was rapid, bright, and stable for over 1 h atroom temperature. Confocal microscopy detected FDA stainingthrough two to three intact surface cell layers (300–400µm) of bisected berries, and showed that the fluorescencewas confined to the cytoplasm, indicating the maintenance ofintegrity in both cytoplasmic as well as vacuolar membranes,and the presence of active cytoplasmic esterases. FDA clearlydiscriminated between living cells and freeze-killed cells,and exhibited little, if any, non-specific staining. Propidiumiodide and DAPI, both widely used to assess cell viability,were unable to discriminate between living and freeze-killedcells, and did not specifically stain the nuclei of dead cells.For normally developing berries under field conditions therewas no evidence of viability loss until about 40 d after veraison,and the majority (80%) of mesocarp cells remained viable pastcommercial harvest (26 °Brix). These results are inconsistentwith current models of grape berry development which hypothesizethat veraison is associated with a general loss of compartmentationin mesocarp cells. The observed viability loss was primarilyin the locule area around the seeds, suggesting that a localizedloss of viability and compartmentation may occur as part ofnormal fruit development. The cell viability of berry shrivel-affectedberries was similar to that of normally developing berries untilthe onset of visible symptoms (i.e. shrivelling), at which timeviability declined in visibly shrivelled berries. Berries withextensive shrivelling exhibited very low cell viability (15%). Key words: Apoplast, berry shrivel, compartmentation, DAPI, FDA, fluorescence, fruit ripening, locule, propidium iodide Received 19 September 2007; Revised 16 December 2007 Accepted 26 December 2007     

Spatiotemporal variations in the abundances of the prokaryotic rRNA genes, <Emphasis Type="Italic">pmoA</Emphasis>, and <Emphasis Type="Italic">mcrA</Emphasis> in the deep layers of a peat bog in Sarobetsu-genya wetland,Japan

Spatiotemporal variations in microbial gene abundances were investigated to identify potential zones of methanotroph and methanogen biomass in a peat bog in Sarobetsu-genya wetland. The abundances of the bacterial and archaeal 16S rRNA genes, pmoA, and mcrA were 10⁷–10⁹, 10⁷–10⁸, 10⁴–10⁶, and 10⁴–10⁷ copies g⁻¹ dry peat, respectively. Correlation analysis based on microbial gene abundances and environmental factors showed that the spatiotemporal distributions of the abundances of the four microbial genes in peat layers were similar. The mcrA abundance showed a significant negative correlation with the dissolved organic carbon content and a significant positive correlation with the peat temperature. The pmoA abundance was not detectable during the spring thaw when the lowest peat temperature at a depth of 50 cm was recorded. At a depth of 200 cm, the peat temperature exceeded 6°C throughout the year, and the mcrA abundance exceeded 10⁴ copies g⁻¹ dry peat. These results indicate that the seasonal microbial activity related to methane should be evaluated in not only the shallow but also the deep peat layers in order to elucidate the methane dynamics in boreal wetlands.     

Molecular characterization of mesophilic and thermophilic sulfate reducing microbial communities in expanded granular sludge bed (EGSB) reactors

The microbial communities established in mesophilic and thermophilic expanded granular sludge bed reactors operated with sulfate as the electron acceptor were analyzed using 16S rRNA targeted molecular methods, including denaturing gradient gel electrophoresis, cloning, and phylogenetic analysis. Bacterial and archaeal communities were examined over 450 days of operation treating ethanol (thermophilic reactor) or ethanol and later a simulated semiconductor manufacturing wastewater containing citrate, isopropanol, and polyethylene glycol 300 (mesophilic reactor), with and without the addition of copper(II). Analysis, of PCR-amplified 16S rRNA gene fragments using denaturing gradient gel electrophoresis revealed a defined shift in microbial diversity in both reactors following a change in substrate composition (mesophilic reactor) and in temperature of operation from 30°C to 55°C (thermophilic reactor). The addition of copper(II) to the influent of both reactors did not noticeably affect the composition of the bacterial or archaeal communities, which is in agreement with the very low soluble copper concentrations (3–310 μg l⁻¹) present in the reactor contents as a consequence of extensive precipitation of copper with biogenic sulfides. Furthermore, clone library analysis confirmed the phylogenetic diversity of sulfate-reducing consortia in mesophilic and thermophilic sulfidogenic reactors operated with simple substrates.     

Pressure and temperature effects on growth and viability of the hyperthermophilic archaeon Thermococcus peptonophilus

We studied the effects of high temperatures and elevated hydrostatic pressures on the physiological behavior and viability of the extremely thermophilic deep-sea archaeon Thermococcus peptonophilus. Maximal growth rates were observed at 30 and 45 MPa although no significant increases in cell yields were detected. Growth at 60 MPa was slower. The optimal growth temperature shifted from 85° C at 30 MPa to 90–95° C at 45 MPa. Cell viability during the stationary phase was also enhanced under high pressure. A trend towards barophily at pressures greater than those encountered in situ at the sea floor was demonstrated at increasing growth temperatures. The viability of cells during starvation, at high temperature (90, 95° C), and at low temperature (10° C) was enhanced at 30 and 45 MPa as compared to atmospheric pressure. These results show that the extremely thermophilic archaeon T. peptonophilus is a barophile. Received: 21 October 1996 / Accepted: 5 February 1997     

Two-dimensional fluorescence spectroscopy – a new tool for the determination of plant cell viability

 Two-dimensional fluorescence spectroscopy (2D-FS) has been used as a new method for determining the viability of tobacco cells (Nicotiana tabacum L.). Both horizontal beam geometry and a vertical set-up achieved with bifurcated fibres were tested. The latter arrangement enabled us to avoid the negative effect of cell sedimentation. Incubation of a tobacco BY-2 cell suspension with dimethylsulfoxide (DMSO) (0–10% v/v) resulted in cell samples differing in their viability – from fully viable (0–2% DMSO) to totally non-viable (8–10%DMSO). The validity of determining viability by means of measuring cell esterase activity by 2D-FS using fluorescein diacetate as a fluorogenic substrate was verified by comparison with microscopic evaluation of fluorescein fluorescence as well as with the routinely adopted trypan blue exclusion test. Received: 6 June 2000 / Revision received: 9 October 2000 / Accepted: 9 October 2000     

Escherichia coli and Lactobacillus plantarum responses to osmotic stress

Escherichia coli and Lactobacillus plantarum were subjected to final water potentials of −5.6 MPa and −11.5 MPa with three solutes: glycerol, sorbitol and NaCl. The water potential decrease was realized either rapidly (osmotic shock) or slowly (20 min) and a difference in cell viability between these conditions was only observed when the solute was NaCl. The cell mortality during osmotic shocks induced by NaCl cannot be explained by a critical volume decrease or by the intensity of the water flow across the cell membrane. When the osmotic stress is realized with NaCl as the solute, in a medium in which osmoregulation cannot take place, the application of a slow decrease in water potential resulted in the significant maintenance of cell viability (about 70–90%) with regard to the corresponding viability observed after a sudden step change to same final water potential (14–40%). This viability difference can be explained by the existence of a critical internal free Na⁺ concentration. Received: 20 May 1998 / Received revision: 31 July 1998 / Accepted: 31 July 1998     

A new obligately chemolithoautotrophic,nitrite-oxidizing bacterium,Nitrospira moscoviensis sp. nov. and its phylogenetic relationship

A gram-negative, non-motile, non-marine, nitrite-oxidizing bacterium was isolated from an enrichment culture initiated with a sample from a partially corroded area of an iron pipe of a heating system in Moscow, Russia. The cells were 0.9–2.2 μm × 0.2–0.4 μm in size. They were helical- to vibroid-shaped and often formed spirals with up to three turns 0.8–1.0 μm in width. The organism possessed an enlarged periplasmic space and lacked intracytoplasmic membranes and carboxysomes. The cells tended to excrete extracellular polymers, forming aggregates. The bacterium grew optimally at 39°C and pH 7.6– 8.0 in a mineral medium with nitrite as sole energy source and carbon dioxide as sole carbon source. The optimal nitrite concentration was 0.35 mM. Nitrite was oxidized to nitrate stoichiometrically. The doubling time was 12 h in a mineral medium with 7.5 mM nitrite. The cell yield was low; only 0.9 mg protein/l was formed during oxidation of 7.5 mM nitrite. Under anoxic conditions, hydrogen was used as electron donor with nitrate as electron acceptor. Organic matter (yeast extract, meat extract, peptone) supported neither mixotrophic nor heterotrophic growth. At concentrations as low as 0.75 g organic matter/l or higher, growth of nitrite-oxidizing cells was inhibited. The cells contained cytochromes of the b- and c-type. The G+C content of DNA was 56.9 ± 0.4 mol%. The chemolithoautotrophic nitrite-oxidizer differed from the terrestrial members of the genus Nitrobacter with regard to morphology and substrate range and equaled Nitrospira marina in both characteristics. The isolated bacterium is designated as a new species of the genus Nitrospira. Comparative analysis of 16S rRNA gene sequences revealed a moderate phylogenetic relationship to Nitrospira marina, leptospirilla, Thermodesulfovibrio yellowstonii, "Magnetobacterium bavaricum," and the isolate OPI-2. Initial evidence is given that these organisms represent a new phylum of the domain bacteria. Received: 17 February 1995 / Accepted: 18 April 1995     

长期不同耕作措施对土壤团聚体特征及微生物多样性的影响

以豫西丘陵地区15年的保护性耕作试验为平台,研究了不同耕作措施对土壤水稳性团聚体分布及稳定性和土壤细菌、古菌及真菌多样性的影响.结果表明: 与传统耕作相比,免耕、深松覆盖和小麦-花生两茬耕作处理增加了>2000 μm粒级团聚体的相对含量,减少了<53 μm粒级团聚体的相对含量;显著提高了土壤团聚体平均质量直径(MWD),提高幅度分别为18.0%、12.2%和50.4%.免耕、深松覆盖和两茬耕作处理均可提高细菌、古菌和真菌的Shannon指数(H),细菌分别提高0.3%、0.3%和0.6%,古菌分别提高20.2%、40.5%和49.1%,真菌分别提高23.7%、19.5%和25.8%.土壤细菌和古菌的H指数与大团聚体含量(R_0.25)和MWD显著相关,而真菌的H指数与R_0.25和MWD相关性不显著.综上,采用免耕、深松结合小麦秸秆覆盖以及小麦-花生轮作等措施均可改善土壤团聚体状况,提高土壤微生物多样性指数.