A new species ofCortinarius sect.Sericeocybe from Japan

Cortinarius prunicola sp. nov., found in orchards and plantations ofPrunus mume, is described and illustrated. It is characterized by its dry and violet-white carpophores, unpleasant odor, and its close association withP. mume in spring and early summer. The differences betweenC. prunicola and similar species are briefly discussed.     

Coniochaeta prunicola �� first record for Slovakia and Europe

This study reports the first record of Coniochaeta on Laurocerasus officinalis Roem. from the Nitra district. This is the first record of Coniochaeta for Slovakia and also for Europe. The fungus Coniochaeta prunicola Damm & Crous (Coniochaetales, Sordariomycetes, Ascomycota) was isolated from damaged leaves and twigs of host trees. Morphological analyses demonstrate that Coniochaeta prunicola and Coniochaeta velutina are distinct species.     

The transfer of <Emphasis Type="Italic">Desmos caudatus</Emphasis> C. E. C. Fisch. (Annonaceae) to <Emphasis Type="Italic">Meiogyne</Emphasis>

Desmos caudatus C. E. C. Fisch. (Annonaceae), a species of small tree known only from a couple of collections from the south of Burma, is transferred to Meiogyne. This is the first record of the genus from Burma.     

Miricatena prunicola (Hyphomycetes), a new genus and species causing leaf spots of Prunus serotina in the UK

A fungus causing conspicuous leaf spots of Prunus serotina was recently collected in Surrey, UK. It proved to represent an undescribed species which also cannot be referred to any known genus. The species is described as Miricatena prunicola gen. et sp. nov.     

Chemical constituents of the plants of the genus <Emphasis Type="Italic">Cleistanthus</Emphasis> and their biological activity

Chemical examinations of Cleistanthus collinus Roxb., a poisonous tree from India, and Cleistanthus patulus Muell. Arg. have resulted in isolation of a number of arylnaphthalide lignans and their glycosides as well as some furofuranoid lignans. While Cleistanthus gracilis Hook. f. from Thailand afforded an unusual glucoside of 2-β-hydroxy-8-azabicyclo-(5,0,2)-4β, 9β-epoxynona-5,7-diene, C. schlechteri from South Africa was the first reported source of the pimarane diterpenes. Cleistanthin A and cleistanthin B, diphyllin glycosides isolated from C. collinus were reported to exhibit cytotoxicity on several cancer cell lines. Cleistanthin A was found to cause DNA strand breaks and induce apoptosis in cultured cells while cleistanthin B caused G1 arrest and induced apoptosis in mammalian cells.     

Efficient Evergreen Plant Regeneration of <i>Cinnamomum japonicum</i> Sieb. through <i>in vitro</i> Organogenesis

Cinnamomum japonicum Sieb. is an excellent roadside tree and medicinal tree species with considerable ornamental and economic value. In this study, we successfully developed a large-scale micropropagation protocol for C. japonicum for the first time. Sterilized shoots were excised and used as explants for shoot induction on several basal media, supplemented with different concentrations of plant growth regulators (PGRs), such as Thidiazuron (TDZ), N⁶ -Benzyladenine (6-benzylaminopurine) (BA), α-naphthaleneacetic acid (NAA) and Gibberellic acid (GA₃). After comparison, the most efficient medium for shoot regeneration was 1/2 Murashige and Skoog (MS) medium containing 0.5 mg L^–1 BA, 0.05 mg L^–1 NAA and 0.2 mg L^–1 GA₃, which resulted in an average number of induced shoots per explant and shoot length of 5.2 and 1.62 cm at 28 d, respectively. Then, elongated adventitious shoots were transferred to induce roots. 86.7% of shoots was able to root on 1/2 MS medium supplemented with 0.5 mg L^–1 NAA and 0.1 mg L^–1 BA. The earliest rooting time observed was after 21 d and the average root length was up to 3.3 cm after 28 d. Our study shows that C. japonicum can be successfully regenerated through de novo organogenesis, which lays a foundation for future transformation research on this tree.     

Independent origins of tetraploid cryptic species in the fern <Emphasis Type="Italic">Ceratopteris thalictroides</Emphasis>

Ceratopteris thalictroides (L.) Brongn is a tetraploid fern species that contains at least three cryptic species, the south, the north and the third type. In this study we combined data from both chloroplast DNA (cpDNA) and nuclear DNA sequences of three diploid species and three cryptic species of C. thalictroides to unravel the origin of the cryptic species, particularly of the reticulate relationships among the diploid and tetraploid taxa in the genus Ceratopteris. Of the three diploid species examined, C. cornuta had cpDNA identical to that of the tetraploid third type plants, and this diploid species is a possible maternal ancestor of the tetraploid third type. Analysis of the homologue of the Arabidopsis thaliana LEAFY gene (CLFY1) identified ten alleles in the genus Ceratopteris, with six alleles found in C. thalictroides. The unrooted tree of the CLFY1 gene revealed four clusters. Each cryptic species showed fixed heterozygosity at the CLFY1 locus and had two alleles from different clusters of the CLFY1 tree. Consideration of the cpDNA sequences, CLFY1 genotypes of the cryptic species and CLFY1 gene tree in concert suggested that the cryptic species of C. thalictroides had originated through independent allopolyploidization events involving C. cornuta and two unknown hypothetical diploid species.     

Inhibition of <Emphasis Type="Italic">Pichia stipitis</Emphasis> fermentation of hydrolysates from olive tree cuttings

The ethanolic fermentation of liquid fractions (hydrolysates) issued from dilute acid pre-treatment of olive tree biomass by Pichia stipitis is reported for the first time. On the one side, P. stipitis has been reported as the most promising naturally occurring C5 fermenting microorganism; on the other side, olive tree biomass is a renewable, low cost, and lacking of alternatives agricultural residue especially abundant in Mediterranean countries. The study was performed in two steps. First, the fermentation performance of P. stipitis was evaluated on a fermentation medium also containing the main inhibitors found in these hydrolysates (acetic acid, formic acid, and furfural), as well as glucose and xylose as carbon sources. The effect of inhibitors, individually or in a mixture, on kinetic and yield parameters was calculated. In a second step, hydrolysates obtained from 1% (w/w) sulfuric acid pre-treatment of olive tree biomass at 190°C for 10 min were used as a real fermentation medium with the same microorganism. Due to inhibition, effective fermentation required dilution of the hydrolysate and either overliming or activated charcoal treatment. Results show that ethanol yields obtained from hydrolysates, ranging from 0.35 to 0.42 g/g, are similar to those from synthetic medium, although the process proceeds at lower rates. Inhibiting compounds affect the fermentation performance in a synergistic way. Furfural is rapidly assimilated by the yeast; acetic acid and formic acid concentrations decrease slowly during the process. Activated charcoal or overliming detoxification improve the fermentability of diluted hydrolysates.     

Revisiting the Molecular Evolutionary History of <Emphasis Type="Italic">Shigella</Emphasis> spp.

The theory that Shigella is derived from multiple independent origins of Escherichia coli (Pupo et al. 2000) has been challenged by recent findings that the virulence plasmids (VPs) and the chromosomes share a similar evolutionary history (Escobar-Paramo et al. 2003), which suggests that an ancestral VP entered an E. coli strain only once, which gave rise to Shigella spp. In an attempt to resolve these conflicting theories, we constructed three phylogenetic trees in this study: a robust chromosomal tree using 23 housekeeping genes from 46 strains of Shigella and enteroinvasive E. coli (EIEC), a chromosomal tree using 4 housekeeping genes from 19 EcoR strains and 46 Shigella/EIEC strains, and a VP tree using 5 genes outside of the VP cell-entry region from 38 Shigella/EIEC strains. Both chromosomal trees group Shigella into three main clusters and five outliers, and strongly suggest that Shigella has multiple origins within E. coli. Most strikingly, the VP tree shows that the VPs from two main Shigella clusters, C1 and C2, are more closely related, which contradicts the chromosomal trees that place C2 and C3 next to each other but C1 at a distance. Additionally, we have identified a complete tra operon of the F-plasmid in the genome sequence of an EIEC strain and found that two other EIEC strains are also likely to possess a complete tra operon. All lines of evidence support an alternative multiorigin theory that transferable diverse ancestral VPs entered diverse origins of E. coli multiple times during a prolonged period of time, resulting in Shigella species with diverse genomes but similar pathogenic properties. Electronic Supplementary Material Electronic Supplementary material is available for this article at and accessible for authorised users. [Reviewing Editor: Dr. Martin Kreitman] Jian Yang and Huan Nie contributed equally to this work.     

Escape to the high canopy—thermal deficiency causes niche expansion in a forest‐floor ant

The small formicoxenine ant Temnothorax saxonicus was known from about 40 localities in Central Europe nesting in anorganic substrates on floor of xerothermous forests whereas investigations of 198 tree canopies in 19 forest sites of the same region provided no indication for arboreal nesting or foraging. We present the first evidence for canopy‐nesting populations of T. saxonicus on old Quercus trees in 3 sites having maximum calibrated topsoil temperatures of 17.9 ± 0.3 °C which were significantly (P < 0.007) lower than 22.8 ± 2.0 °C measured in 5 sites with ground‐nesting populations. The thermal deficit on forest floor inhibits brood development in ground nests and caused a moving to canopy were maximum calibrated temperatures of the, now wooden, substrates are at least 26.1 °C for the whole canopy and 30.8 °C in more sun‐exposed spots. T. saxonicus competed here successfully with the obligatory canopy ants T. affinis and T. corticalis. The distributional data of this rope‐climbing study support former results that highest nest densities of small arboreal ants occur in temperate climate over the entire canopy mantle of single trees situated in open land or in park‐like environments but occur in the top of the canopy in tree stands with high degree of canopy closure.     

The mycobiome of Australian tree hollows in relation to the Cryptococcus gattii and C. neoformans species complexes

Cryptococcosis is a fungal infection caused by members of the Cryptococcus gattii and C. neoformans species complexes. The C. gattii species complex has a strong environmental association with eucalypt hollows (particularly Eucalyptus camaldulensis), which may present a source of infection. It remains unclear whether a specific mycobiome is required to support its environmental survival and growth. Conventional detection of environmental Cryptococcus spp. involves culture on differential media, such as Guizotia abyssinica seed agar. Next‐generation sequencing (NGS)‐based culture‐independent identification aids in contextualising these species in the environmental mycobiome. Samples from 23 Australian tree hollows were subjected to both culture‐ and amplicon‐based metagenomic analysis to characterize the mycobiome and assess relationships between Cryptococcus spp. and other fungal taxa. The most abundant genera detected were Coniochaeta, Aspergillus, and Penicillium, all being commonly isolated from decaying wood. There was no correlation between the presence of Cryptococcus spp. in a tree hollow and the presence of any other fungal genus. Some differences in the abundance of numerous taxa were noted in a differential heat tree comparing samples with or without Cryptococcus‐NGS reads. The study expanded the known environmental niche of the C. gattii and C. neoformans species complexes in Australia with detections from a further five tree species. Discrepancies between the detection of Cryptococcus spp. using culture or NGS suggest that neither is superior per se and that, rather, these methodologies are complementary. The inherent biases of amplicon‐based metagenomics require cautious interpretation of data through consideration of its biological relevance.     

Diameter Growth of Juvenile Trees after Gap Formation in a Bolivian Rain Forest: Responses are Strongly Species‐specific and Size‐dependent

We evaluated growth responses to gap formation for juvenile individuals of three canopy rain forest species: Peltogyne cf. heterophylla, Clarisia racemosa and Cedrelinga catenaeformis. Gaps were formed during selective logging operations 7 yr before sampling in a Bolivian rain forest. We collected wood samples for tree‐ring analyses at different distances to the stump (<10, 10–40 and >40 m) and from trees with different diameters (5–30 cm diameter at breast height [dbh]). Tree‐rings width was measured in at least two radii and converted to average diameter growth. Changes in 7‐yr median diameter growth before and after selective logging were analyzed. Diameter growth rates significantly increased by 0.7–0.8 mm/yr after gap formation for P. heterophylla and C. catenaeformis, but not for C. racemosa. We applied a multiple regression analysis to explain variation in growth responses of P. heterophylla and C. catenaeformis by distance to logging gap and tree size. For P. heterophylla we found that growth increase occurring close to logging gaps was strongest for large juvenile trees (20–25 cm dbh) and almost absent in small juveniles. For C. catenaeformis, variation in growth responses was not related to tree size or distance to gaps. Our results show that growth responses to gap formation strongly differ across species and tree sizes. This finding calls for caution in the interpretation of growth releases in tree‐ring series, as gap formation does not necessarily invoke growth responses and if such growth responses occur, their strength is species‐ and size specific.     

Tree‐ring stable isotopes record the impact of a foliar fungal pathogen on CO2 assimilation and growth in Douglas‐fir

Swiss needle cast (SNC) is a fungal disease of Douglas‐fir (Pseudotsuga menziesii) that has recently become prevalent in coastal areas of the Pacific Northwest. We used growth measurements and stable isotopes of carbon and oxygen in tree‐rings of Douglas‐fir and a non‐susceptible reference species (western hemlock, Tsuga heterophylla) to evaluate their use as proxies for variation in past SNC infection, particularly in relation to potential explanatory climate factors. We sampled trees from an Oregon site where a fungicide trial took place from 1996 to 2000, which enabled the comparison of stable isotope values between trees with and without disease. Carbon stable isotope discrimination (Δ¹³C) of treated Douglas‐fir tree‐rings was greater than that of untreated Douglas‐fir tree‐rings during the fungicide treatment period. Both annual growth and tree‐ring Δ¹³C increased with treatment such that treated Douglas‐fir had values similar to co‐occurring western hemlock during the treatment period. There was no difference in the tree‐ring oxygen stable isotope ratio between treated and untreated Douglas‐fir. Tree‐ring Δ¹³C of diseased Douglas‐fir was negatively correlated with relative humidity during the two previous summers, consistent with increased leaf colonization by SNC under high humidity conditions that leads to greater disease severity in following years.     

Examining the response of needle carbohydrates from Siberian larch trees to climate using compound‐specific δ13C and concentration analyses

Little is known about the dynamics of concentrations and carbon isotope ratios of individual carbohydrates in leaves in response to climatic and physiological factors. Improved knowledge of the isotopic ratio in sugars will enhance our understanding of the tree ring isotope ratio and will help to decipher environmental conditions in retrospect more reliably. Carbohydrate samples from larch (Larix gmelinii) needles of two sites in the continuous permafrost zone of Siberia with differing growth conditions were analysed with the Compound‐Specific Isotope Analysis (CSIA). We compared concentrations and carbon isotope values (δ¹³C) of sucrose, fructose, glucose and pinitol combined with phenological data. The results for the variability of the needle carbohydrates show high dynamics with distinct seasonal characteristics between and within the studied years with a clear link to the climatic conditions, particularly vapour pressure deficit. Compound‐specific differences in δ¹³C values as a response to climate were detected. The δ¹³C of pinitol, which contributes up to 50% of total soluble carbohydrates, was almost invariant during the whole growing season. Our study provides the first in‐depth characterization of compound‐specific needle carbohydrate isotope variability, identifies involved mechanisms and shows the potential of such results for linking tree physiological responses to different climatic conditions.     

First Environmental Isolations of <Emphasis Type="Italic">Cryptococcus neoformans</Emphasis> and <Emphasis Type="Italic">Cryptococcus gattii</Emphasis> in Tunisia and Review of Published Studies on Environmental Isolations in Africa

Cryptococcus neoformans and Cryptococcus gattii are pathogenic yeasts that cause cryptococcosis. These fungi were commonly associated with pigeon droppings and plant materials. The habitat of these pathogens has not been yet studied in Tunisia, although the ecology of these yeasts must be elucidated in order to establish surveillance programs and to prevent infections. The aim of this survey was to recover C. neoformans and C. gattii environmental isolates from pigeon droppings and plant materials in different areas of Sfax region, Tunisia. Nine hundred and fifty samples from leaves, wood, flowers, fruits and soil around trunk bases of 40 almond (Prunus dulcis) and 60 eucalyptus trees were collected as well as 250 pigeon droppings samples from different sites: buildings (n = 150), houses (n = 50) and zoo (n = 50). The identification of Cryptococcus neoformans complex was confirmed using the ID32C auxanogram panel (BioMérieux, Marcy l’Etoile, France); species were determined by multiplex PCR using the CN70 and CN49 primers, and mating type was determined by PCR. C. neoformans was recovered from 26 specimens of pigeon droppings (10.4%). This yeast was obtained more frequently from dry droppings (9.2%) than from moist droppings (1.2%). The mating type was determined. All the 31 environmental strains of C. neoformans and C. gattii were MATα. Out of 700 samples tested from 100 trees, only 5 isolates of Cryptococcus neoformans species complex were recovered (0.6%), two isolates of C. gattii and one isolate of C. neoformans were recovered from the wood of E. camaldulensis trees, and only two isolates of C. gattii were recovered from the wood of almond trees (Prunus dulcis Mill. var. zaaf and var. achek). These two Tunisian almond tree varieties were recorded for the first time in Africa as hosts for C. gattii. These results add new information to the ecology and epidemiology of C. neoformans species complex in Tunisia.     

Carbon concentration in structures of <i>Arctostaphylos pungens</i> HBK: An alternative CO₂ sink in forests

Arctostaphylos pungens HBK is a dominant species with increasing abundance and distribution in chaparral ecosystems as a result of range management and, possibly, changes in climate. The value of this species for carbon (C) sequestration is unknown, and the standard 50% C out of total tree biomass is used as an approximate value. In this study, we aim to determine the C concentration of the primary components of A. pungens. The total C expressed as a percentage of biomass was determined with a Solids TOC Analyzer. We found the C concentration to vary among components. Leaves exhibited the highest C concentration (51.70%). Roots (46.11%), stems (47.30%), fruits (47.89%) and twigs (48.40%) had similar C concentration. These results provided superior estimates of C concentration, and reliable information concerning the potential use of A. pungens in climate-change mitigation programs.     

Comparative nutrient economy,stable isotopes,and related adaptive traits in <Emphasis Type="Italic">Picea rubens</Emphasis>, <Emphasis Type="Italic">Picea mariana</Emphasis>, and their hybrids

Nutrient- and water economy-related traits in plants have significant implications for growth and fitness. We explored, examined, and compared nutrient concentrations, use efficiencies, assimilation, and informative isotopic elements in a seedling provenance experiment, and in seedling and mature tree controlled-cross hybrid experiments of red spruce (RS) (Picea rubens Sarg.) and black spruce (BS) (P. mariana (Mill.) BSP). Provenance experiment results showed RS had consistently lower carbon (C) and nitrogen (N) concentrations, and N assimilation ratio (NAR), but higher N-use efficiency (NUE), C:N ratio, water-use efficiency (WUE), and needle calcium (Ca) and magnesium (Mg) concentrations than BS. The hybrid seedling experiment showed similar results and additive inheritance for needle N, C:N ratio, NAR, Ca, and Mg, evident by a near-linear progression from one species to the other. Within both species, seedling height showed a negative relationship with needle N and a positive relationship with NUE. However, across hybrid indices, seedling height showed a positive relationship with needle N and a negative relationship with NUE. Also across hybrid indices, seedling height showed a negative relationship to Ca and C:N, and a positive relationship with NAR and ¹³C discrimination (without hybrid 25). Mature tree hybrid experiment results were similar to those of the seedling experiment, but with a dampening of differences caused by low nutrient availability and possibly age effects. The similarity was not true for ¹³C discrimination as mature tree height showed a strong negative relationship to ¹³C discrimination, indicating that BS had greater WUE. The reversal is most probably caused by the large difference in water availability.