Ecological niche of <Emphasis Type="Italic">Cryptococcus neoformans</Emphasis> var. <Emphasis Type="Italic">grubii</Emphasis> and <Emphasis Type="Italic">Cryptococcus gattii</Emphasis> in decaying wood of trunk hollows of living trees in Jabalpur City of Central India

Cryptococcus neoformans var. grubii and C. gattii were repeatedly isolated from decaying wood of trunk hollows in living trees growing in Jabalpur City in Central India. The isolation of C.␣gattii has been reported from decayed wood inside trunk hollow of Tamarindus indica (15.6%), Mangifera indica (2.2%), Pithecolobium dulce (12.5%), Syzygium cumini (14%), and one from bark of S.␣cumini. C. n. var. grubii was isolated from decaying wood debris of T. indica (4.4%), M. indica (13.3%), Terminalia arjuna (25%), S. cumini (2%), Cassia fistula (4.5%), and two from bark of S. cumini. The two varieties never co-occurred in the same hollow. C. gattii and C. n. var. grubii isolates belonged to serotype B and serotype A respectively. The data strongly supported the colonization of the pathogen in␣decaying wood hollow of all six-tree species. Evidence of this was found by repeated isolation up to 820 days. P. dulce is being reported for the first time as natural habitat of C. gattii and T.␣arjuna and C. fistula as natural habitat for C. n. var. grubii. M. indica is being reported for the second time as the natural habitat of both varieties (C. n. var. grubii and C. gattii). The population density of these pathogens from decaying wood debris of various tree species ranged between 0.5 × 10³ cells/g and 6 × 10⁵ cells/g. The seasonal variation has been seen in isolation of this yeast. Our result further reinforce the recently emerging evidence that the natural habitat of C. n. var. grubii and C. gattii is more generalized.     

Latent infections of <Emphasis Type="Italic">Fomes fomentarius</Emphasis> in the xylem of European beech (<Emphasis Type="Italic">Fagus sylvatica</Emphasis>)

Fungal colonisation originating from endophytic thalli in wood of healthy European beech trees (Fagus sylvatica) was studied. Fungi were isolated from wood immediately after felling and after incubation for 8, 16 and 24 weeks under two different drying regimes. Two media were used to isolate fungi: malt extract agar with and without thiabendazol. Thiabendazol was added to inhibit non-basidiomycetes. The two drying regimes had no influence on the species composition of the recovered mycobiota and the frequency of isolation of these species. Mycelia of basidiomycetes except Coniophora puteana emerged only from wood samples inoculated onto malt extract agar containing thiabendazol. Only a few isolates were obtained from freshly cut wood, but a great number of isolates was recovered already after eight weeks of wood incubation. Four taxa accounted for 88 % of the total number of isolates: Hypoxylon fragiforme, Trichoderma spp., and the basidio-mycetes Coniophora puteana and Fomes fomentarius. The latter had not been considered an endophyte before. The isolates of F. fomentarius were made exclusively from the stem and some large diameter branches, which are the locations of its basidiocarps on dying trees. Every isolate of F. fomentarius was genetically different as revealed by tests for somatic compatibility. Advantages of the presumed endophytic strategy of F. fomentarius are discussed. Microscopic investigations showed a great number of hyphae within the cell lumina of vessels and a distinct wood degradation already after eight weeks of wood incubation.     

Fungal Communities in Decaying Sapwood and Heartwood of a Conifer <Emphasis Type="Italic">Keteleeria evelyniana</Emphasis>

Fungal communities in decaying sapwood and heartwood of K. evelyniana were demonstrated through construction of four 18 S rRNA gene libraries. The 210 sequenced clones were clustered into 11 subgroups, belonging to Basidiomycota (71.9%) and to Ascomycota (22.4%) and unclassified (1 subgroup; 5.7%). The heartwood displayed higher species richness than the sapwood. Basidiomycota were dominant in either the heartwood or the sapwood. Phylogenetically diverse Homobasidiomycetes were detected in the heartwood, contrary to the sapwood, where Heterobasidiomycetes were detected. Clones close to Spongipellis unicolor dominated in the heartwood (21 of 99 clones), while those close to Hydnochaete olivacea dominated in the sapwood (41 of 111 clones). The common species between the two parts were those related to S. unicolor, Calocera cornea, Debaryomyces hansenii, Davidiella tassiana, and Nomuraea rileyi and those from Chaetothyriomycetes.     

Utilizing pigment-producing fungi to add commercial value to American beech (<Emphasis Type="Italic">Fagus grandifolia</Emphasis>)

American beech (Fagus grandifolia) is an abundant, underutilized tree in certain areas of North America, and methods to increase its market value are of considerable interest. This research utilized pigment-producing fungi to induce color in American beech to potentially establish its use as a decorative wood. Wood samples were inoculated with Trametes versicolor, Xylaria polymorpha, Inonotus hispidus, and Arthrographis cuboidea to induce fungal pigmentation. Black pigmentation (T. versicolor, X. polymorpha, I. hispidus) was sporadic, occurred primarily on the surfaces of the heartwood, but not internally. Pink pigmentation (A. cuboidea) occurred throughout all of the tested beech samples, but was difficult to see in the heartwood due to the darker color of the wood. To increase the visibility of the pink stain, beech blocks were pretreated with T. versicolor for 4 weeks before being inoculated with A. cuboidea. This method significantly increased the saturation of the pink stain on both beech heartwood and sapwood, creating coloration similar to that found on sugar maple. This value-adding process should be particularly effective for small-scale wood pigmentation, and should help establish a market for this currently underutilized wood species.     

Differences in patterns of cell death between ray parenchyma cells and ray tracheids in the conifers <Emphasis Type="Italic">Pinus densiflora</Emphasis> and <Emphasis Type="Italic">Pinus rigida</Emphasis>

Differences in patterns of cell death between ray parenchyma cells and ray tracheids in the conifers Pinus densiflora and Pinus rigida were clarified. Differentiation and cell death of ray tracheids occurred successively and both were related to the distance from the cambium. In this respect, they resembled those of longitudinal tracheids. Thus, the cell death of short-lived ray tracheids could be characterized as time-dependent programmed cell death. In contrast, ray parenchyma cells survived for several years or more, and no successive cell death occurred, even within a single radial line of cells in a ray. Thus, the features of death of the ray parenchyma cells were different from those of ray tracheids. Cell death occurred early in ray parenchyma cells that were in contact with ray tracheids. The initiation of secondary wall thickening occurred earlier in ray parenchyma cells that were in contact with ray tracheids in Pinus densiflora than in others. In addition, localized thickening of secondary walls occurred only in ray parenchyma cells that were in contact with ray tracheids in Pinus rigida. Moreover, no polyphenols were evident in such cells in either species. Therefore, ray parenchyma cells that were in contact with ray tracheids appeared not to play a role in the formation of heartwood extractives. Our observations indicate that short-lived ray tracheids might affect the pattern of differentiation and, thus, the functions of neighboring long-lived ray parenchyma cells in conifers.     

Molecular evolution of paclitaxel biosynthetic genes <Emphasis Type="Italic">TS</Emphasis> and <Emphasis Type="Italic">DBAT</Emphasis> of <Emphasis Type="Italic">Taxus</Emphasis> species

Evolutionary patterns of sequence divergence were analyzed in genes from the conifer genus Taxus (yew), encoding paclitaxel biosynthetic enzymes taxadiene synthase (TS) and 10-deacetylbaccatin III-10β-O-acetyltransferase (DBAT). N-terminal fragments of TS, full-length DBAT and internal transcribed spacer (ITS) were amplified from 15 closely related Taxus species and sequenced. Premature stop codons were not found in TS and DBAT sequences. Codon usage bias was not found, suggesting that synonymous mutations are selectively neutral. TS and DBAT gene trees are not consistent with the ITS tree, where species formed monophyletic clades. In fact, for both genes, alleles were sometimes shared across species and parallel amino acid substitutions were identified. While both TS and DBAT are, overall, under purifying selection, we identified a number of amino acids of TS under positive selection based on inference using maximum likelihood models. Positively selected amino acids in the N-terminal region of TS suggest that this region might be more important for enzyme function than previously thought. Moreover, we identify lineages with significantly elevated rates of amino acid substitution using a genetic algorithm. These findings demonstrate that the pattern of adaptive paclitaxel biosynthetic enzyme evolution can be documented between closely related Taxus species, where species-specific taxane metabolism has evolved recently.     

Heartwood extractives and lignin content of different larch species (<Emphasis Type="Italic">Larix </Emphasis>sp.) and relationships to brown-rot decay-resistance

The extractive content of lignin and the brown-rot decay-resistance against Coniophora puteana and Poria placenta were studied in larch heartwood from different species and origin (Larix decidua var. decidua, L. decidua var. sudetica, L. kaempferi , L. × eurolepis). The study material consisted of 106 trees from a 39-year old provenance trial in France. The hot-water-soluble extractives were very variable (from5.66% to 20.50% of dry weight), but there was no significant variation between the investigated species and origins. In contrast, acetone extractives, the total amount of phenolics and lignin showed significant differences. The concentration of phenolics and lignin was significantly higher in L. kaempferi and in L. × eurolepis than in L. decidua. The total phenolics content was strongly correlated with decay-resistance in all investigated larch origins. A higher concentration of phenolics goes hand in hand with higher decay resistance and phenolics might therefore be a promising parameter to rapidly evaluate the level of decay-resistance in larch.     

Limitations of <Emphasis Type="Italic">Neoseiulus baraki</Emphasis> and <Emphasis Type="Italic">Proctolaelaps bickleyi</Emphasis> as control agents of <Emphasis Type="Italic">Aceria guerreronis</Emphasis>

Several predatory mites have been found in association with the coconut mite, Aceria guerreronis Keifer, in northeast Brazil. However, the latter still causes damage to coconut in that region. The objectives of this work were to compare the frequencies of occurrence of Neoseiulus (Phytoseiidae) and Proctolaelaps (Melicharidae) species on standing and aborted coconuts in coastal Pernambuco State, northeast Brazil and to analyze their possible limitations as control agents of the coconut mite, based on evaluations of the restrictions they may have to access the microhabitat inhabited by the pest and their functional and reproductive responses to increasing densities of the latter. Neoseiulus baraki (Athias-Henriot) was found mostly on standing coconuts whereas Proctolaelaps bickleyi (Bram) was found mostly on aborted coconuts. Measurements of the entrance to the microhabitat occupied by the coconut mite, between the bracts and the subjacent fruit surface, showed that this different pattern of predator prevalence could be related to predator sizes, although other environmental factors could not be disregarded. Progressively higher predation rate of N. baraki was observed up to an experimental density that corresponded to 1,200 coconut mites per fruit, which is close to the average number determined in northeast Brazil, reducing slightly afterwards. Predation rate of P. bickleyi reduced consistently but slightly with increasing prey densities, but in absolute values, rates were always much higher than determined for N. baraki. The excessively high killing capacity of P. bickleyi, probably related to its high feeding requirement, may be detrimental in terms of stability. In fact, such high requirement for food suggests that P. bickleyi might not have a strong relation with the coconut mite and that the latter may not be its main food source under natural conditions. It is concluded that body sizes of both predators and the exceedingly high feeding requirement of P. bickleyi may limit their performance as control agents of the coconut mite.     

Prevalence of <Emphasis Type="Italic">Wolbachia</Emphasis> Infection in <Emphasis Type="Italic">Bemisia tabaci</Emphasis>

Wolbachia are obligate intracellular bacteria present in reproductive tissues of many arthropod species. It has been reported that few silverleafing populations of Bemisia tabaci were positive for Wolbachia, whereas non-silverleafing populations were more likely infected with Wolbachia and all that infect B. tabaci are Wolbachia belonging to supergroup B. However, current detection methods were shown to be not sensitive enough to uncover all infections. Herein, a protocol based on polymerase chain reaction–restriction fragment length polymorphism analysis of Wolbachia 16S ribosomal DNA is presented. A systematic survey for the prevalence of Wolbachia infection in natural populations of B. tabaci using this method revealed that (1) all populations of B. tabaci tested positive for Wolbachia and the overall infection rate reached 80.5% (293 positives in 364 tests); (2) both single infection and superinfection existed within individual whiteflies tested; and (3) silverleafing populations of B. tabaci most likely harbored A Wolbachia as single infection, whereas non-silverleafing populations tend to carry B Wolbachia as superinfection. It is clear that the Wolbachia infection pattern is closely related to the genetic races of B. tabaci, and the infection frequencies are apparently much higher than those described previously. This study shows that detection methods can significantly influence estimation of Wolbachia infection. It is supposed that Wolbachia may be acting as a biotic agent promoting rapid differentiation and speciation of B. tabaci. This is the most systematic survey of Wolbachia infection within B. tabaci.     

New species of <Emphasis Type="Italic">Moristroma</Emphasis> (Ascomycetes) and phylogenetic position of the genus

The loculoascomycete Moristroma quercinum sp. nov. and Moristroma japonicum sp. nov. are described from Northern Europe (Denmark, Lithuania, Sweden) and Japan, respectively. M. quercinum is reported from wood of Quercus robur and Q. petraea, and M. japonicum is reported from wood of Quercus mongolica var. grossoserrata. Ascostromata of both species were found on hard heartwood of attached or shed branches. The two new species differ from the type species of the genus, M. polysporum, by the presence of pycnidia, and by the size of ascostromata, asci and ascospores. Drawings illustrate ascostromata, pycnidia, asci, hamathecium and ascospores of the two new species. A phylogenetic analysis suggests that Moristroma belongs to the Chaetothyriomycetes, rather than to the Dothideomycetes as previously suggested.     

Post-pollination hybridization barriers in <Emphasis Type="Italic">Nicotiana</Emphasis> section <Emphasis Type="Italic">Alatae</Emphasis>

Nicotiana section Alatae contains eight species with variable flower sizes and morphologies. Section members readily hybridize in the glasshouse, but no hybrids have been observed in natural sympatric and parapatric populations. To investigate interspecific crossing relationships with respect to mechanisms preventing hybridization, all members of section Alatae were intercrossed in a complete diallel. We found positive correlation between the pistil length of the pollen donor and interspecific seed set relative to the conspecific cross. Pollen tube growth rate and pollen donor pistil length were positively correlated as well. Furthermore, pollen from short-pistil members of section Alatae could only grow a maximum distance proportional to, but greater than, their own pistil lengths. Our results show that pollen tube growth capacity (i.e., rate and distance), provides a hybridization barrier in long-pistil species × short-pistil species crosses. We also found another hybridization barrier not specifically related to pollen tube growth capacity in short-pistil species × long-pistil species. Taken together, these barriers can generally be described by a ‘pistil-length mismatch’ rule; in section Alatae, pollen has the most success fertilizing ovules from species with pistil lengths similar to their own. This rule could contribute to hybridization barriers in Section Alatae because the species display dramatically different pistil lengths. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Localization of ferruginol,a diterpene phenol,in <Emphasis Type="Italic">Cryptomeria japonica</Emphasis> heartwood by time-of-flight secondary ion mass spectrometry

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) was applied to the investigation of heartwood extractives in Sugi (Cryptomeria japonica). Sugi heartwood tissue generated secondary ions that were not produced from sapwood tissue by TOF-SIMS. Among the peculiar ions generated from heartwood, two positive ions of m/z 285 and 301 were remarkable due to their appearance in a larger mass range and with a high intensity. These two ions were not generated from heartwood tissue preextracted with n-hexane, and the n-hexane extract of Sugi heartwood produced both ions. Gas chromatography-mass spectrometry of the n-hexane extract demonstrated that ferruginol, a diterpene phenol, the molecular weight of which is 286, constituted one of the predominant constituents of the extract. Authentic ferruginol also generated both ions by TOF-SIMS. The molecular formula of the m/z 285 ion generated from Sugi heartwood tissue was estimated to be C₂₀H₂₉O, which corresponds well with that of ferruginol, i.e. C₂₀H₃₀O, by peak identification. All these results strongly suggest that the m/z 285 ion generated from Sugi heartwood tissue originated significantly from ferruginol in Sugi heartwood. By TOF-SIMS imaging, the m/z 285 ion was detected uniformly in the tracheid cell walls, in the cell walls of the axial parenchyma cells and ray parenchyma cells, and also inside these parenchyma cells. These results indicate that ferruginol was distributed almost evenly in Sugi heartwood tissue.     

Identification of genes differentially expressed in cauliflower associated with resistance to <Emphasis Type="Italic">Xanthomonas campestris</Emphasis> pv. <Emphasis Type="Italic">campestris</Emphasis>

Black rot, caused by Xanthomonas campestris pv. campestris (Pammel) Dowson (Xcc), is one of the most damaging diseases of cauliflower and other crucifers. In order to investigate the molecular resistance mechanisms and to find the genes related to black rot resistance in cauliflower, a suppression subtractive hybridization (SSH) cDNA library was constructed using resistant line C712 and its susceptible near-isogenic line C731 as tester and driver, respectively. A total of 280 clones were obtained from the library by reverse northern blotting. Sequencing analysis and homology searching showed that these clones represent 202 unique sequences. The library included many defense/disease-resistant related genes, such as plant defensin gene PDF1.2, lipid transfer protein, thioredoxin h. Gene expression profiles of 12 genes corresponding to different functional categories were monitored by real-time RT-PCR. The results showed that the expression induction of these genes in the susceptible line C712 in response to Xcc was quicker and more intense, while in C731 the reaction was delayed and limited. Our results imply that these up-regulated genes might be involved in cauliflower responses against Xcc infection. Information obtained from this study could be used to understand the molecular mechanisms of disease response in cauliflower under Xcc stress.     

A new methanol assimilating yeast, <Emphasis Type="Italic">Ogataea</Emphasis><Emphasis Type="Italic">parapolymorpha</Emphasis>, the ascosporic state of <Emphasis Type="Italic">Candida</Emphasis><Emphasis Type="Italic">parapolymorpha</Emphasis>

Ogataea parapolymorpha sp. n. (NRRL YB-1982, CBS 12304, type strain), the ascosporic state of Candida parapolymorpha, is described. The species appears homothallic, assimilates methanol as is typical of most Ogataea species and forms hat-shaped ascospores in asci that become deliquescent. O. parapolymorpha is closely related to Ogataea angusta and Ogataea polymorpha. The three species can be resolved from gene sequence analyses but are unresolved from fermentation and growth reactions that are typically used for yeast identification. On the basis of multiple isolates, O. angusta is known only from California, USA, in association with Drosophila and Aulacigaster flies, O. parapolymorpha is predominantly associated with insect frass from trees in the eastern USA but O. polymorpha has been isolated from various substrates in the USA, Brazil, Spain and Costa Rica.     

Molecular detection of <Emphasis Type="Italic">Rickettsia</Emphasis>, <Emphasis Type="Italic">Coxiella</Emphasis> and <Emphasis Type="Italic">Rickettsiella</Emphasis> DNA in three native Australian tick species

Three Australian native animal species yielded 60 samples composed of three indigenous ticks. Hosts included twelve koalas, two echidnas and one wombat from Victoria, and ticks were of the species Ixodes tasmani (n = 42), Bothriocroton concolor (n = 8) and B. auruginans (n = 10), respectively. PCR screening and sequencing detected a species of Coxiella, sharing closest sequence identity to C. burnetii (>98%), in all B. auruginans, as well as a species of Rickettsia, matching closest to R. massiliae, in 70% of the same samples. A genotype sharing closest similarity to Rickettsia bellii (>99%) was identified in three female B. concolor collected from one of the echidnas. Three samples of I. tasmani, taken from three koalas, yielded different genotypes of Rickettsiella. These results represent the first detection of the three genera in each tick species and identify a high level of previously undetected bacterial diversity in Australian ticks.     

Mitochondrial <Emphasis Type="Italic">cox</Emphasis>1 and plastid <Emphasis Type="Italic">rbc</Emphasis>L genes of <Emphasis Type="Italic">Gracilaria vermiculophylla</Emphasis> (Gracilariaceae,Rhodophyta)

The mitochondrial cytochrome c oxidase subunit I gene sequence was recently developed for DNA barcoding of red algal species. We determined the 1245 base pairs of the gene from 27 taxa of an agar-producing species, Gracilaria vermiculophylla, and putative relatives and compared the results with rbcL data from the same species. A total of 392 positions (31.5%) were variable, 282 positions (22.6%) were parsimoniously informative, and average sequence divergence was 13% in an ingroup. Within G. vermiculophylla, pairwise divergence of the gene was variable up to 11 bp (0.9%). Seven recognized haplotypes of cox1 tended to be geographically related. In the aligned 1386 bp of rbcL, three haplotypes were recognized. These results suggest that cox1 is a valuable molecular marker within species and will be very useful in haplotype analyses.     

Coexisting <Emphasis Type="Italic">Curtobacterium</Emphasis> Bacterium Promotes Growth of White-Rot Fungus <Emphasis Type="Italic">Stereum</Emphasis> sp.

White-rot basidiomycetes are the main decomposers of woody biomass in forest ecosystems. Little is known, however, about the interactions between white-rot fungi and other microorganisms in decayed wood. A wood-rotting fungus, Stereum sp. strain TN4F, was isolated from a fruit body, and its coexisting cultivable bacteria were isolated from its substrate; natural white-rot decayed wood. The effects of bacteria on fungal growth were examined by confrontational assay in vitro. A growth-promoting bacterium for this Stereum strain was identified as Curtobacterium sp. TN4W-19, using 16SrRNA sequencing. A confrontational assay revealed that Curtobacterium sp. TN4W-19 significantly promoted the mycelial growth of Stereum sp. TN4F in the direction of the bacterial colony, without direct contact between the mycelium and bacterial cells. This is the first report of a positive interaction between a white-rot fungus and a coexisting bacterial strain in vitro.     

Biochemical and molecular characterization of <Emphasis Type="Italic">Cronobacter</Emphasis> spp<Emphasis Type="Italic">.</Emphasis> (formerly <Emphasis Type="Italic">Enterobacter sakazakii</Emphasis>) isolated from foods

The aim of this study was to identify and characterize Cronobacter spp. isolated from a range of foods. A total of 71 Cronobacter strains were isolated from 602 foods in our laboratory. The highest contamination was observed in foods of plant origin, e.g. spices, teas, chocolate, nuts, pastries and vegetables. On the basis of genus and species identification performed using genus-specific PCR, 16S rRNA sequencing and AFLP genotyping, most of the strains belonged to Cronobacter sakazakii. Biochemical profiling by the tests included in API 20E, complemented with relevant additional tests, classified the strains into 13 biogroups. AFLP genotyping facilitated discrimination of six main groups at the 70% similarity level and strain grouping correlated clearly with species identification. Our results indicate that molecular typing by AFLP may be applied as a useful tool not only for direct comparison of Cronobacter isolates, providing traceability, but also for the reliable species classification. Moreover, tracing of these bacteria in a wider variety of foods should be important to enhance the knowledge of their transmission.