Thermoanaerobium lactoethylicum spec. nov. a new anaerobic bacterium from a hot spring of Kamchatka

A new anaerobic thermophilic Gram-positive, nonsporeforming bacterium strain ZE-1 was isolated from a hot spring of Kamchatka (USSR). The cells are rod-shaped, (0.5–0.8 · 2.0–20 m), non-motile. The bacterium can grow between 42 and 75°C; the optimal temperature is 65°C. The growth is possible between pH values 5.0 and 8.5; optimal pH is 7.0. The cultures grow on the media containing peptone, yeast extract, or casein hydrolysate as nitrogen sources in the presence of glucose or some other sugars, mannitol or starch. The main fermentation products of glucose are ethanol, acetate, lactate, H₂, CO₂; byproducts are propionic, butyric and isovaleric acids. Glucose is metabolized via Embden-Meyerhoff-Parnas pathway. Molecular hydrogen does not inhibit growth. The bacterium does not reduce aceton to isopropanol, but is able to form H₂S from elemental sulfur. The bacterium contains a soluble hydrogenase. This enzyme catalyzes both evolution and uptake of H₂ and is active in the presence of methyl viologen. The DNA-base composition is 34.6 mol%; the genome size 2.08x10⁹ D. The name proposed for the isolated bacterium strain ZE-1 is Thermoanaerobium lactoethylicum spec. nov.     

Effect of formaldehyde on growth of obligate methylotroph Methylobacillus flagellatum in a substrate non-limited continuous culture

The ribulose monophosphate cycle methylotroph Methylobacillus flagellatum was grown under oxyturbidostat conditions on mixtures of methanol and formaldehyde. Formaldehyde when added at low concentration (50 mg/l) increased the methanol consumption and the yield of biomass. The presence of 150–300 mg/l of formaldehyde resulted in an increase of the growth rate from 0.74 to about 0.79–0.82 h^-1. The presence of 500 mg/l of formaldehyde in the inflow decreased culture growth characteristics. Activities of methanol dehydrogenase and enzymes participating in formaldehyde oxidation and assimilation were measured. The enzymological profiles obtained are discussed.Abbreviations MDH methanol dehydrogenase - NAD-linked FDDH NAD-linked formaldehyde dehydrogenase - DLFDDH dye-linked formaldehyde dehydrogenase - DLFDH dye-linked formate dehydrogenase - GPDH glucose-6-phosphate dehydrogenase - PGDH 6-phosphogluconate dehydrogenase - RuMP cycle ribulose monophosphate cycle     

Purification of ribulose 1,5-bisphosphate carboxylase/oxygenase and of carboxysomes from Thiobacillus thyasiris the putative symbiont of Thyasira flexuosa (Montagu)

The bacterial symbionts of many marine invertebrates contain ribulose 1,5-bisphosphate (RuBP) carboxylase but apparently no carboxysomes, polyhedral bodies containing RuBP carboxylase. In the few cases where polyhedral bodies have been observed they have not been characterised enzymatically. Polyhedral bodies, 50–90 nm in diameter, were observed in thin cell sections of Thiobacillus thyasiris the putative symbiont of Thyasira flexuosa and RuBP carboxylase activity was detected in both soluble and particulate fractions after centrifugation of cell-free extracts. RuBP carboxylase purified 90-fold from the soluble fraction was of high molecular weight and consisted of large and small subunits, with molecular weights of 53,110 and 11,100 respectively. Particulate RuBP carboxylase activity was associated with polyhedral bodies 50–100 nm in diameter, as revealed by density gradient centrifugation and electron microscopy. Therefore, the polyhedral bodies were inferred to be carboxysomes. Native electrophoresis of isolated carboxysomes demonstrated a major band which comigrated with the purified RuBP carboxylase and three minor bands of lower molecular weight. Sodium dodecyl-sulphate (SDS) gel electrophoresis of SDS-dissociated carboxysomes demonstrated nine major polypeptides two of which were the large and small subunits of RuBP carboxylase. The RuBP carboxylase subunits represented 21% of the total carboxysomal protein. The most abundant polypeptide had a molecular weight of 40,500. Knowledge of carboxysome composition is necessary to provide an understanding of carboxysome function.Abbreviations FPLC fast performance liquid chromatography - IB isolation buffer - PAGE polyacrylamide gel electrophoresis - RuBP carboxylase - ribulose 1,5-bisphosphate carboxylase/oxygenase - SDS sodium dodecyl-sulphate     

Chemolithotrophic metabolism of the newly-isolated moderately thermophilic,obligately autotrophic Thiobacillus tepidarius

Thiobacillus tepidarius, isolated from the hot springs at Bath, Avon, UK, grew optimally at 43–45°C and pH 6.0–7.5 on thiosulphate or tetrathionate. In batch culture, thiosulphate was oxidized stoichiometrically to tetrathionate, with a rise in pH. The tetrathionate was then oxidized to sulphate, supporting growth and producing a fall in pH to a minimum of ph 4.8. The organism contained high levels of thiosulphate-oxidizing enzyme, rhodanese and ribulose bisphosphate carboxylase. It was obligately chemolithotrophic and autotrophic. In chemostat culture, T. tepidarius grew autotrophically with the following sole energy-substrates: sulphide, thiosulphate, trithionate, tetrathionate, hexathionate or heptathionate. Thiocyanate, dithionate and sulphite were not used as sole substrates, although sulphite enhanced growth yields in the presence of thiosulphate. Maximum specific growth rate on tetrathionate was 0.44 h^-1. True growth yields (Y _max) and maintenance coefficients (m) were calculated for sulphide, thiosulphate, trithionate and tetrathionate and observed yields at a single fixed dilution rate compared with those on hexathionate and heptathionate. Mean values for Y _max, determined from measurements of absorbance, dry wt, total organic carbon and cell protein, were similar for sulphide, thiosulphate and trithionate (10.9 g dry wt/mol substrate) as expected from their equivalent oxygen consumption for oxidation. Y _max for tetrathionate (20.5) and the relative Y _o values (as g dry wt/g atom oxygen consumed) for thiosulphate and all four polythionates indicated that substrate level phosphorylation did not contribute significantly to energy conservation. These Y _max values were 40–70% higher than any of those previously reported for obligately aerobic thiobacilli. Mean values for m were 6.7 mmol substrate oxidized/g dry wt·h for sulphide, thiosulphate and trithionate, and 2.6 for tetrathionate.Abbreviation PIPES Piperazine-N,N-bis(ethane sulphonic acid)     

Chloroherpeton thalassium gen. nov. et spec. nov., a non-filamentous,flexing and gliding green sulfur bacterium

A flexing and gliding green sulfur bacterium has been isolated from marine sources off the North East coast of the USA. Chloroherpeton thalassium is an obligate phototroph, and requires CO₂ and S^2- for growth; some organic acids can contribute to cell carbon, and N₂ may be fixed. The cells contain typical chlorosomes, and gas vesicles may be present. Bacteriochlorophyll c is the main light harvesting pigment, and a small quantity of bacteriochlorophyll a is also present. Over 80% of the carotenoid is -carotene. DNA base composition of the isolates ranges from 45.0–48.2 mol% G+C.In memory of R. Y. Stanier     

Effects of feeding and starvation on growth and swimming activity in an obligatory air-breathing fish

Reared in (tubular) aquaria containing different depths of water, Ophiocephalus striatus (0.7 g, 4.5 cm body length), an obligatory air-breathing tropical fish, swam long or short distances to enable themselves to exchange atmospheric air. In each tested depth (2.5, 5.0, 15.5, 31.0 and 40.0 cm) series, one group was starved, while the other was fed ad libitum twice a day on fish muscle. In the shallowest water (2.5 cm depth), the feeding group surfaced 1,294 times, travelling 64.7 m at an energy cost of 20.4 mg dry fish substance/g live fish/day, against those exposed to the deepest water (40 cm depth), which expended 35.8 mg/g/day, swimming 1,503.4 m on 1,879 visits to the surface. The starving group surfaced only 482 times, travelling 24.1 m at an expense of 5.8 mg/g/day in the shallowest water, while those at 40 cm depth surfaced 504 times, swimming 403.2 m at an energy cost of 7.4 mg/g/day. Owing to the sustained swimming activity and the consequent fatigue, the test individuals belonging to both groups in all the tested series hang to the surface for a definite interval, repaying the O₂ debt. Observations were also made to assess the duration of hanging to precisely estimate the distance travelled. Irrespective of changes in depths of water, the duration of hanging to surface was only 3.0 hr/day for the feeding groups, while it was as much as 15.5 hr/day for the starving groups. The maximum sustained metabolic level of O.striatus reared in 40 cm depth was equivalent to 1.23 ml O₂/g/hr, which is about 2 times higher than the value reported for the active metabolism of swimming Oncorhynchus nerka at 15°C in Brett's (1964) respirometer. O.striatus reared in 2.5 cm depth fed 32.0 mg and converted 6.7 mg dry food/g live fish/day, while those exposed to the deepest water fed 49.1 mg, but converted only 5.5 mg/g/day. Culturing obligatory air-breathing fishes in shallow waters will be advantageous.     

Microbial metabolite fluxes in a model marine anoxic ecosystem

Permanently anoxic regions in the ocean are widespread and exhibit unique microbial metabolic activity exerting substantial influence on global elemental cycles and climate. Reconstructing microbial metabolic activity rates in these regions has been challenging, due to the technical difficulty of direct rate measurements. In Cariaco Basin, which is the largest permanently anoxic marine basin and an important model system for geobiology, long‐term monitoring has yielded time series for the concentrations of biologically important compounds; however, the underlying metabolite fluxes remain poorly quantified. Here, we present a computational approach for reconstructing vertical fluxes and in situ net production/consumption rates from chemical concentration data, based on a 1‐dimensional time‐dependent diffusive transport model that includes adaptive penalization of overfitting. We use this approach to estimate spatiotemporally resolved fluxes of oxygen, nitrate, hydrogen sulfide, ammonium, methane, and phosphate within the sub‐euphotic Cariaco Basin water column (depths 150–900 m, years 2001–2014) and to identify hotspots of microbial chemolithotrophic activity. Predictions of the fitted models are in excellent agreement with the data and substantially expand our knowledge of the geobiology in Cariaco Basin. In particular, we find that the diffusivity, and consequently fluxes of major reductants such as hydrogen sulfide, and methane, is about two orders of magnitude greater than previously estimated, thus resolving a long‐standing apparent conundrum between electron donor fluxes and measured dark carbon assimilation rates.     

Alpha-proteobacteria cultivated from marine sponges display branching rod morphology

PCR amplification of two CHS gene fragments of the obligate biotroph Plasmopara viticola, the causal agent of downy mildew of grapevine, is described. While one fragment shows homology to fungal class IV chitin synthases, the other fragment groups with other oomycete chitin synthases to form a novel class of chitin synthases most closely related to class I-III. RT-PCR experiments indicate that PvCHS1 is constitutively expressed, whereas PvCHS2 is specifically transcribed in sporangiophores and sporangia. Analyses of wheat germ agglutinin labeling patterns by confocal laser scanning microscopy show that chitin is present on the surface of hyphal cell walls during in planta growth, and of sporangiophores and sporangia.     

The Association Between Breeding System and Transposable Element Dynamics in <Emphasis Type="Italic">Daphnia Pulex</Emphasis>

Transposable elements (TEs) are major sources of genetic variation, and mating systems are believed to play a significant role in their dynamics. For example, insertion number is expected to be higher in sexual than in asexual organisms due to the inability of TEs to colonize new genomes in the absence of sex. The goal of this study was to determine the impact of the loss of sexual reproduction on TE load. Daphnia pulex has two reproductive modes, obligate and cyclical parthenogenesis, which differ with respect to the production of diapausing eggs. Cyclical parthenogens produce them meiotically, while obligate parthenogens produce them clonally. Pokey is a TTAA-specific DNA transposon, and is a stable component of Daphnia genomes. We used a PCR-based approach, TE-Display, to estimate the number of Pokey insertions in 22 cyclic and 22 obligate isolates of D. pulex. As expected, the copy number of Pokey insertions is significantly higher in cyclic than in obligate isolates. However, the distribution of elements among isolates within each breeding system is similar, which is congruent with the recent establishment of obligate lineages from a cyclic ancestor. We also assayed 46 isolates from eight cyclic populations and found that very few Pokey insertions were observed in more than one isolate, suggesting that Pokey has been active recently. Sequencing of PCR products from the TE-Display analysis shows that Pokey inserts into both coding and noncoding regions of the genome. However, there is no obvious similarity among sequences downstream of the TTAA Pokey insertion site.