Long-term spatiotemporal dynamics in a mountain birch (Betula pubescens ssp. czerepanovii) forest in south-east Norway.

Mountain birch forest covers large areas in Eurasia, and their ecological resilience provides important ecosystem services to human societies. This study describes long-term stand dynamics based on permanent plots in the upper mountain birch belt in SE Norway. We also present forest line changes over a period of 70 years. Inventories were conducted in 1931, 1953, and 2007. Overall, there were small changes from 1931 up to 1953 followed by a marked increase in biomass and dominant height of mountain birch throughout the period from 1953 to 2007. In addition, the biomass of spruce (Picea abies) and the number of plots with spruce present doubled. The high mortality rate of larger birch stems and large recruitment by sprouting since the 1960s reveal recurrent rejuvenation events after the earlier outbreak of the autumnal moth (Epirrita autumnata). Our results demonstrate both a high stem turnover in mountain birch and a great ability to recover after disturbances. This trend is interpreted as regrowth after a moth attack, but also long-term and time-lagged responses due to slightly improved growth conditions. An advance of the mountain birch forest line by 0.71 m year-1 from 1937 to 2007 was documented, resulting in a total reduction of the alpine area by 12%. Most of the changes in the forest line seem to have taken place after 1960. Regarding silviculture methods in mountain birch, a dimension cutting of larger birch trees with a cutting interval of c. 60 years seems to be a sustainable alternative for mimicking natural processes.

Biotic threats for 23 major non-native tree species in Europe.

For non-native tree species with an origin outside of Europe a detailed compilation of enemy species including the severity of their attack is lacking up to now. We collected information on native and non-native species attacking non-native trees, i.e. type, extent and time of first observation of damage for 23 important non-native trees in 27 European countries. Our database includes about 2300 synthesised attack records (synthesised per biotic threat, tree and country) from over 800 species. Insects (49%) and fungi (45%) are the main observed biotic threats, but also arachnids, bacteria including phytoplasmas, mammals, nematodes, plants and viruses have been recorded. This information will be valuable to identify patterns and drivers of attacks, and trees with a lower current health risk to be considered for planting. In addition, our database will provide a baseline to which future impacts on non-native tree species could be compared with and thus will allow to analyse temporal trends of impacts.

Gap formation and dynamics after long-term steady state in an old-growth Picea abies stand in Norway: Above- and belowground interactions.

Stand dynamics and the gap initiation prior to gap formation are not well-understood because of its long-term nature and the scarcity of late-successional stands. Reconstruction of such disturbance is normally based on historical records and dendroecological methods. We investigated gap initiation and formation at the fine-scale stand level in the old-growth reserve of Karlshaugen in Norway. Given its long-term conservation history, and thorough mapping in permanent marked plots with spatially referenced trees, it provides an opportunity to present stand development before, during, and after gap formation. Late-successional decline in biomass was recorded after more than 50 years of close to steady state. Gaps in the canopy were mainly created by large old trees that had been killed by spruce bark beetles. Snapping by wind was the main reason for treefall. Long-term dominance of Norway spruce excluded downy birch and Scots pine from the stand. Comparisons of the forest floor soil properties between the gap and nongap area showed significantly higher concentrations of plant available Ca within the gap area. Plant root simulator (PRS™) probes showed significantly higher supply rates for Ca and Mg, but significantly lower K for the gap compared to the nongap area. Soil water from the gap area had significantly higher C:N ratios compared to the nongap area. Fine-scale variation with increasing distance to logs indicated that CWD is important for leaking of DOC and Ca. Our long-term study from Karlshaugen documents gap dynamics after more than 50 years of steady state and a multiscale disturbance regime in an old-growth forest. The observed disturbance dynamic caused higher aboveground and belowground heterogeneity in plots, coarse woody debris, and nutrients. Our study of the nutrient levels of the forest floor suggest that natural gaps of old-growth forest provide a long-lasting biogeochemical feedback system particularly with respect to Ca and probably also N. Norway spruce trees near the gap edge responded with high plasticity to reduced competition, showing the importance of the edge zone as hot spots for establishing heterogeneity, but also the potential for carbon sequestration in old-growth forest.

The purine efflux pump PbuE in Bacillus subtilis modulates expression of the PurR and G-box (XptR) regulons by adjusting the purine base pool size.

In Bacillus subtilis, the expression of genes encoding enzymes and other proteins involved in purine de novo synthesis and salvage is affected by purine bases and phosphoribosylpyrophosphate (PRPP). The transcription of the genes belonging to the PurR regulon is negatively regulated by the PurR protein and PRPP. The expression of the genes belonging to the G-box (XptR) regulon, including the pbuE gene, is negatively regulated by a riboswitch-controlled transcription termination mechanism. The G-box regulon effector molecules are hypoxanthine and guanine. pbuE encodes a purine base efflux pump and is now recognized as belonging to a third purine regulon. The expression of the pbuE gene is positively regulated by a riboswitch that recognizes adenine. Here we show that the expression of pbuE'-lacZ transcriptional fusions are induced by adenine to the highest extent in mutants which do not express a functional PbuE pump. In a mutant defective in the metabolism of adenine, the ade apt mutant, we found a high intracellular level of adenine and constitutive high levels of PbuE. A growth test using a purine auxotroph provided further evidence for the role of PbuE in lowering the intracellular concentration of purine bases, including adenine. Purine analogs also affect the expression of pbuE, which might be of importance for the protection against toxic analogs. In a mutant that overexpresses PbuE, the expression of genes belonging to the PurR regulon was increased. Our findings provide further evidence for important functions of the PbuE protein, such as acting as a pump that lowers the purine base pool and affects the expression of the G-box and PurR regulons, including pbuE itself, and as a pump involved in protection against toxic purine base analogs.

CtaG is required for formation of active cytochrome c oxidase in Bacillus subtilis.

The Gram-positive bacterium Bacillus subtilis contains two respiratory oxidases of the haem-copper superfamily: cytochrome aa(3), which is a quinol oxidase, and cytochrome caa(3), which is a cytochrome c oxidase. Cytochrome c oxidase uniquely contains a di-copper centre, Cu(A). B. subtilis CtaG is a membrane protein encoded by the same gene cluster as that which encodes the subunits of cytochrome c oxidase. The role of B. subtilis CtaG and orthologous proteins present in many other Gram-positive bacteria has remained unexplored. The sequence of CtaG is unrelated to that of CtaG/Cox11p of proteobacteria and eukaryotic cells. This study shows that B. subtilis CtaG is essential for the formation of active cytochrome caa(3) but is not required for assembly of the core subunits I and II with haem in the membrane and it has no role in the synthesis of active cytochrome aa(3). B. subtilis YpmQ, a homologue to Sco1p of eukaryotic cells, is also a membrane-bound cytochrome c oxidase-specific assembly factor. Properties of CtaG- and YpmQ-deficient mutants were compared. Cells lacking YpmQ showed a low cytochrome c oxidase activity and this defect was suppressed by the supplementation of the growth medium with copper ions. It has previously been proposed that YpmQ/Sco1p is involved in synthesis of the Cu(A) centre. The results of this study are consistent with this proposal but the exact role of YpmQ in assembly of cytochrome c oxidase remains to be elucidated.

Definition of a second Bacillus subtilis pur regulon comprising the pur and xpt-pbuX operons plus pbuG, nupG (yxjA), and pbuE (ydhL).

In Bacillus subtilis expression of genes or operons encoding enzymes and other proteins involved in purine synthesis is affected by purine bases and nucleosides in the growth medium. The genes belonging to the PurR regulon (purR, purA, glyA, guaC, pbuO, pbuG, and the pur, yqhZ-folD, and xpt-pbuX operons) are controlled by the PurR repressor, which inhibits transcription initiation. Other genes are regulated by a less-well-described transcription termination mechanism that responds to the presence of hypoxanthine and guanine. The pur operon and the xpt-pbuX operon, which were studied here, are regulated by both mechanisms. We isolated two mutants resistant to 2-fluoroadenine in which the pur operon and the xpt-pbuX operon are expressed at increased levels in a PurR-independent manner. The mutations were caused by deletions that disrupted a potential transcription terminator structure located immediately upstream of the ydhL gene. The 5' part of the ydhL leader region contained a 63-nucleotide (nt) sequence very similar to the 5' ends of the leaders of the pur and xpt-pbuX operons. Transcripts of these regions may form a common tandem stem-loop secondary structure. Two additional genes with potential leader regions containing the 63-nt sequence are pbuG, encoding a hypoxanthine-guanine transporter, and yxjA, which was shown to encode a purine nucleoside transporter and is renamed nupG. Transcriptional lacZ fusions and mutations in the 63-nt sequence encoding the possible secondary structures provided evidence that expression of the pur and xpt-pbuX operons and expression of the ydhL, nupG, and pbuG genes are regulated by a common mechanism. The new pur regulon is designated the XptR regulon. Except for ydhL, the operons and genes were negatively regulated by hypoxanthine and guanine. ydhL was positively regulated. The derived amino acid sequence encoded by ydhL (now called pbuE) is similar to the amino acid sequences of metabolite efflux pumps. When overexpressed, PbuE lowers the sensitivity to purine analogs. Indirect evidence indicated that PbuE decreases the size of the internal pool of hypoxanthine. This explains why the hypoxanthine- and guanine-regulated genes are expressed at elevated levels in a mutant that overexpresses pbuE.

Transcription analysis of the Bacillus subtilis PucR regulon and identification of a cis-acting sequence required for PucR-regulated expression of genes involved in purine catabolism.

The PucR protein of Bacillus subtilis has previously been suggested to regulate the expression of 15 genes, pucABCDE, pucFG, pucH, pucI, pucJKLM, pucR, and gde, all of which encode proteins involved in purine catabolism. When cells are grown under nitrogen-limiting conditions, the expression of these genes is induced and intermediary compounds of the purine catabolic pathway affect this expression. By using pucR deletion mutants, we have found that PucR induces the expression of pucFG, pucH, pucI, pucJKLM, and gde while it represses the expression of pucR and pucABCDE. Deletions in the promoters of the five induced operons and genes combined with bioinformatic analysis suggested a conserved upstream activating sequence, 5'-WWWCNTTGGTTAA-3', now named the PucR box. Potential PucR boxes overlapping the -35 and -10 regions of the pucABCDE promoter and located downstream of the pucR transcription start point were also found. The positions of these PucR boxes are consistent with PucR acting as a negative regulator of pucABCDE and pucR expression. Site-directed mutations in the PucR box upstream of pucH and pucI identified positions that are essential for the induction of pucH and pucI expression, respectively. Mutants with decreased pucH or increased pucR expression obtained from a library of clones containing random mutations in the pucH-to-pucR intercistronic region all contained mutations in or near the PucR box. The induction of pucR expression under nitrogen-limiting conditions was found to be mediated by the global nitrogen-regulatory protein TnrA. In other gram-positive bacteria, we have found open reading frames that encode proteins similar to PucR located next to other open reading frames encoding proteins with similarity to purine catabolic enzymes. Hence, the PucR homologues are likely to exert the same function in other gram-positive bacteria as PucR does in B. subtilis.

Bacillus subtilis guanine deaminase is encoded by the yknA gene and is induced during growth with purines as the nitrogen source.

Bacillus subtilis can utilize the purine bases adenine, hypoxanthine and xanthine as nitrogen sources. The utilization of guanine as a nitrogen source is reported here. The first step is the deamination of guanine to xanthine catalysed by guanine deaminase (GDEase). To isolate mutants defective in GDEase activity, a collection of mutant strains was screened for strains unable to use guanine as a nitrogen source. The strain BFA1819 (yknA) showed the expected phenotype and no GDEase activity could be detected in this strain. A new name for yknA, namely gde, is proposed. The gde gene encodes a 156 amino acid polypeptide and was preceded by a promoter sequence that is recognized by the sigma(A) form of RNA polymerase. High levels of GDEase were found in cells grown with purines and intermediary compounds of the purine catabolic pathway as nitrogen sources. Allantoic acid, most likely, is a low molecular mass inducer molecule. The level of GDEase was found to be subjected to global nitrogen control exerted by the GlnA/TnrA-dependent signalling pathway. The two regulatory proteins of this pathway, TnrA and GlnR, indirectly and positively affected gde expression. This is the first instance of a gene whose expression is positively regulated by GlnR. The GDEase amino acid sequence shows no homology with the mammalian enzyme. In agreement with this are the different physiological roles for the two enzymes.

The yexA gene product is required for phosphoribosylformylglycinamidine synthetase activity in Bacillus subtilis.

The yexA gene encodes an 84 amino acid reading frame; in Bacillus subtilis it is positioned between the purC and purQ genes of the purine biosynthetic operon. Disruption of yexA resulted in a purine-auxotrophic phenotype. When yexA was expressed in trans it was able to complement a yexA mutation. Growth experiments and enzyme analysis of yexA mutant strains revealed a defective phosphoribosylformylglycinamidine synthetase (FGAM synthetase). In the organisms in which FGAM synthetase has been studied a single polypeptide is responsible for activity. In some organisms two separate genes - in B. subtilis the purL and purQ genes - encode polypeptides with similarity to the N-terminal and the C-terminal region, respectively, of the single-polypeptide FGAM synthetase. Thus, active FGAM synthetase in B. subtilis requires the yexA gene product in addition to the purL and purQ gene products. Open reading frames with sequence similarity to yexA are found in other Gram-positive organisms, in a cyanobacterium and in methanogenic archaea. The designation purS is proposed for this novel function in purine biosynthesis in B. subtilis.