Dynamics of a bloom of halophilic archaea in the Dead Sea

After a period of more than ten years in which bacterial and algal community sizes were extremely small, a dense bloom of halophilic archaea developed in the upper 5–10 m of the Dead Sea water column in the summer of 1992. The development of this bloom followed a dilution of the upper water layer by winter rainfloods, which enabled the development of a short-lived dense bloom of the unicellular green alga Dunaliella parva. The dense archaeal community (up to 3.5 × 10⁷ cells m1^–1 in June 1992) imparted a red coloration to the Dead Sea, due to its high content of bacterioruberin. Bacteriorhodopsin was not detected. High levels of potential heterotrophic activity were associated with the bloom, as measured by the incorporation of labeled organic substrates. After the decline of the algal bloom, archaeal numbers in the lake decreased only little, and most of the community was still present at the end of 1993. The amount of carotenoid pigment per cell, however, decreased 2–3-fold between June 1992 and August 1993. No new algal and archaeal blooms developed after the winter floods of 1992–1993, in spite of the fact that salinity values in the surface layer were sufficiently low to support a new algal bloom. A remnant of the 1992 Dunaliella bloom maintained itself at the lower end of the pycnocline at depths between 7 and 13 m (September 1992–August 1993). Its photosynthetic activity was small, and very little stimulation of archaeal growth and activity was associated with this algal community.     

Leaf and canopy responses to elevated CO2 in a pine forest under free-air CO2 enrichment

Physiological responses to elevated CO₂ at the leaf and canopy-level were studied in an intact pine (Pinus taeda) forest ecosystem exposed to elevated CO₂ using a free-air CO₂ enrichment (FACE) technique. Normalized canopy water-use of trees exposed to elevated CO₂ over an 8-day exposure period was similar to that of trees exposed to current ambient CO₂ under sunny conditions. During a portion of the exposure period when sky conditions were cloudy, CO₂-exposed trees showed minor (7%) but significant reductions in relative sap flux density compared to trees under ambient CO₂ conditions. Short-term (minutes) direct stomatal responses to elevated CO₂ were also relatively weak (5% reduction in stomatal aperture in response to high CO₂ concentrations). We observed no evidence of adjustment in stomatal conductance in foliage grown under elevated CO₂ for nearly 80 days compared to foliage grown under current ambient CO₂, so intrinsic leaf water-use efficiency at elevated CO₂ was enhanced primarily by direct responses of photosynthesis to CO₂. We did not detect statistical differences in parameters from photosynthetic responses to intercellular CO₂ (A _net-C _i curves) for Pinus taeda foliage grown under elevated CO₂ (550 mol mol^–1) for 50–80 days compared to those for foliage grown under current ambient CO₂ from similar-sized reference trees nearby. In both cases, leaf net photosynthetic rate at 550 mol mol^–1 CO₂ was enhanced by approximately 65% compared to the rate at ambient CO₂ (350 mol mol^–1). A similar level of enhancement under elevated CO₂ was observed for daily photosynthesis under field conditions on a sunny day. While enhancement of photosynthesis by elevated CO₂ during the study period appears to be primarily attributable to direct photosynthetic responses to CO₂ in the pine forest, longer-term CO₂ responses and feedbacks remain to be evaluated.     

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.     

Translocation from nuclei to cytoplasm is necessary for anti A‐PCD activity and turnover of the Type II IAP BcBir1

Type II inhibitors of apoptosis (IAPs) belong to a subgroup of IAP‐related proteins. While IAPs are restricted to animals, Type II IAPs are found in other phyla, including fungi. BcBir1, a Type II IAP from Botrytis cinerea has anti apoptotic‐like programmed cell death (A‐PCD) activity, which is important for pathogenicity of this fungus. Here we report on the role of sub‐cellular localization of BcBir1 in protein turnover and anti A‐PCD activity. Expression of BcBir1 in Saccharomyces cerevisiae had no effect on sensitivity of the yeast cells to A‐PCD‐inducing conditions, whereas expression of a truncated N' part reduced sensitivity of the cells to these conditions. The full‐length BcBir1 protein was detected only in the yeast nucleus, whereas the N' part was observed both in the nucleus and cytoplasm. In B. cinerea, BcBir1 was mainly nuclear under optimal conditions, whereas under A‐PCD‐inducing conditions it shuttled to the cytoplasm and then it was completely degraded. Collectively, our results show that anti A‐PCD activity of BcBir1 occurs in the cytoplasm, the C′ end mediates regulation of steady state level of BcBir1 in the nucleus, and the N' end mediates anti A‐PCD activity as well as fast degradation of BcBir1 in the cytoplasm.     

hfAIM: A reliable bioinformatics approach for in silico genome-wide identification of autophagy-associated Atg8-interacting motifs in various organisms

Most of the proteins that are specifically turned over by selective autophagy are recognized by the presence of short Atg8 interacting motifs (AIMs) that facilitate their association with the autophagy apparatus. Such AIMs can be identified by bioinformatics methods based on their defined degenerate consensus F/W/Y-X-X-L/I/V sequences in which X represents any amino acid. Achieving reliability and/or fidelity of the prediction of such AIMs on a genome-wide scale represents a major challenge. Here, we present a bioinformatics approach, high fidelity AIM (hfAIM), which uses additional sequence requirements—the presence of acidic amino acids and the absence of positively charged amino acids in certain positions—to reliably identify AIMs in proteins. We demonstrate that the use of the hfAIM method allows for in silico high fidelity prediction of AIMs in AIM-containing proteins (ACPs) on a genome-wide scale in various organisms. Furthermore, by using hfAIM to identify putative AIMs in the Arabidopsis proteome, we illustrate a potential contribution of selective autophagy to various biological processes. More specifically, we identified 9 peroxisomal PEX proteins that contain hfAIM motifs, among which AtPEX1, AtPEX6 and AtPEX10 possess evolutionary-conserved AIMs. Bimolecular fluorescence complementation (BiFC) results verified that AtPEX6 and AtPEX10 indeed interact with Atg8 in planta. In addition, we show that mutations occurring within or nearby hfAIMs in PEX1, PEX6 and PEX10 caused defects in the growth and development of various organisms. Taken together, the above results suggest that the hfAIM tool can be used to effectively perform genome-wide in silico screens of proteins that are potentially regulated by selective autophagy. The hfAIM system is a web tool that can be accessed at link: http://bioinformatics.psb.ugent.be/hfAIM/.     

Relationships between foliage and conducting xylem in Picea abies (L.) Karst.

Summary The relationship of leaf biomass and leaf area to the conductive area of stems and branches was investigated in Picea abies. A total of 30 trees were harvested to determine if these relationships were different in different crown zones and in trees growing with and without competition for light. Two methods were compared. In the first, data were accumulated from crown zones situated at the top of trees to the bottom; in the second, data were used from individual crown zones. The results indicated that the latter method is much more sensitive in detecting differences in the relationship of leaf biomass or leaf area to conductive area. The analysis also indicated that ratios such as leaf area/sapwood area are frequently size-dependent. This size-dependency can in some cases result in the differences being abscured, but more often leads to the false impression that the relationship between the variables changes. The relationship between leaf biomass and leaf area and conductive area of stems or branches was different in different crown zones and under different growth conditions. The slopes of these regressions appear to increase with decreasing transpirational demand and decrease with increasing hydraulic conductivity. The intercepts are probably related to the amount of identified sapwood actually involved in water conductance.