Ectomycorrhizal Fungal Protein Degradation Ability Predicted by Soil Organic Nitrogen Availability

In temperate and boreal forest ecosystems, nitrogen (N) limitation of tree metabolism is alleviated by ectomycorrhizal (ECM) fungi. As forest soils age, the primary source of N in soil switches from inorganic (NH4 (+) and NO3 (-)) to organic (mostly proteins). It has been hypothesized that ECM fungi adapt to the most common N source in their environment, which implies that fungi growing in older forests would have greater protein degradation abilities. Moreover, recent results for a model ECM fungal species suggest that organic N uptake requires a glucose supply. To test the generality of these hypotheses, we screened 55 strains of 13 Suillus species with different ecological preferences for their in vitro protein degradation abilities. Suillus species preferentially occurring in mature forests, where soil contains more organic matter, had significantly higher protease activity than those from young forests with low-organic-matter soils or species indifferent to forest age. Within species, the protease activities of ecotypes from soils with high or low soil organic N content did not differ significantly, suggesting resource partitioning between mineral and organic soil layers. The secreted protease mixtures were strongly dominated by aspartic peptidases. Glucose addition had variable effects on secreted protease activity; in some species, it triggered activity, but in others, activity was repressed at high concentrations. Collectively, our results indicate that protease activity, a key ectomycorrhizal functional trait, is positively related to environmental N source availability but is also influenced by additional factors, such as carbon availability.

The Microbiome of Pinus muricata Ectomycorrhizae: Community Assemblages, Fungal Species Effects, and Burkholderia as Important Bacteria in Multipartnered Symbioses

Bacteria have been observed to grow with fungi, and those that associate with ectomycorrhizal fungi have often been thought of as symbionts that may either increase or decrease ectomycorrhizal formation rate or provide other unaccounted benefits. To explore this symbiosis from a community ecology perspective, we sampled ectomycorrhizal root tips over a 3-year period and used 454 pyrosequencing to identify the bacteria that live inside the ectomycorrhizal root tips. The results showed that fungal community composition within the same soil core and fungal taxonomic identity had a stronger effect on bacterial community composition than sample year or site. Members of the Burkholderiales and Rhizobiales were most highly represented, reflecting many previous reports of these bacteria in association with fungi. The repeated occurrences of these two bacterial orders suggest that they may be symbiotic with their fungal hosts, although the nature of such mechanisms, be it symbiotic diazotrophy or otherwise, remains to be thoroughly tested.

Antibiotic dosing in obesity: the search for optimum dosing strategies

Global obesity has nearly doubled and is now a common occurrence in high-income and developing countries. The World Health Organization estimates that more than 1.4 billion adults are obese. Although the prevalence of obesity is increasing over the last decades, pharmacokinetic evaluations are still conducted in individuals with a body weight of approximately 70 kg. Morbid obesity is associated with several pathophysiological changes that can profoundly affect drug distribution and clearance. There are currently no specific dosing recommendations for antibiotics in obese patients, making dosing suggestions primarily based on pharmacokinetic characteristics of the medications and dosing recommendations in other disease states. Understanding of the pharmacokinetic alterations and maximum doses of antibiotics safely used is paramount to appropriate treatment in the obese population.

Towards a unified paradigm for sequence-based identification of fungi

The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for the exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference data set and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized stable way. Here, we report on progress in these regards through further development of the UNITE database (http://unite.ut.ee) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g. Hymenoscyphus pseudoalbidus|GU586904|SH133781.05FU), and their taxonomic and ecological annotations were corrected as far as possible through a distributed, third-party annotation effort. We introduce the term 'species hypothesis' (SH) for the taxa discovered in clustering on different similarity thresholds (97-99%). An automatically or manually designated sequence is chosen to represent each such SH. These reference sequences are released (http://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and in the QIIME pipeline. The system and the data will be updated automatically as the number of public fungal ITS sequences grows. We invite everybody in the position to improve the annotation or metadata associated with their particular fungal lineages of expertise to do so through the new Web-based sequence management system in UNITE.

Compartmentalized microbial composition, oxygen gradients and nitrogen fixation in the gut of Odontotaenius disjunctus

Coarse woody debris is an important biomass pool in forest ecosystems that numerous groups of insects have evolved to take advantage of. These insects are ecologically important and represent useful natural analogs for biomass to biofuel conversion. Using a range of molecular approaches combined with microelectrode measurements of oxygen, we have characterized the gut microbiome and physiology of Odontotaenius disjunctus, a wood-feeding beetle native to the eastern United States. We hypothesized that morphological and physiological differences among gut regions would correspond to distinct microbial populations and activities. In fact, significantly different communities were found in the foregut (FG), midgut (MG)/posterior hindgut (PHG) and anterior hindgut (AHG), with Actinobacteria and Rhizobiales being more abundant toward the FG and PHG. Conversely, fermentative bacteria such as Bacteroidetes and Clostridia were more abundant in the AHG, and also the sole region where methanogenic Archaea were detected. Although each gut region possessed an anaerobic core, micron-scale profiling identified radial gradients in oxygen concentration in all regions. Nitrogen fixation was confirmed by (15)N2 incorporation, and nitrogenase gene (nifH) expression was greatest in the AHG. Phylogenetic analysis of nifH identified the most abundant transcript as related to Ni-Fe nitrogenase of a Bacteroidetes species, Paludibacter propionicigenes. Overall, we demonstrate not only a compartmentalized microbiome in this beetle digestive tract but also sharp oxygen gradients that may permit aerobic and anaerobic metabolism to occur within the same regions in close proximity. We provide evidence for the microbial fixation of N2 that is important for this beetle to subsist on woody biomass.

The Helvella lacunosa species complex in western North America: cryptic species, misapplied names and parasites

Based on morphology, fungal species have been considered widespread and as a result names of species from Europe or eastern North America were applied to species in western North America. However, DNA sequences have shown that many western taxa are different from their European counterparts; one such case is presented here. Comparisons of ITS and LSU rDNA sequences from ectomycorrhizal root tips and ascomata of specimens identified as Helvella lacunosa from North America, Europe and Asia revealed that the taxa from western North America and Mexico formed a well supported clade different from the eastern North American, European and Asian taxa. Within this western North American clade there are at least four taxa. Here we describe two of these western taxa as new species: Helvella vespertina and Helvella dryophila. Helvella vespertina is a bigger version of H. lacunosa, is variable in hymenial color and shape and forms ectomycorrhizae with conifers; it fruits typically Oct-Jan. Helvella dryophila is characterized by a dark almost black, squat pileus, a light stipe when young, medium size and forms ectomycorrhizae with Quercus species; it fruits Jan-Jun. Due to insufficient material, the two other Helvella taxa are discussed but not formally described here. We also examined the Hypomyces and other mycoparasites associated with the ascomata of Helvella species and discuss misleadingly labeled sequences in public databases.

Selective breeding in fish and conservation of genetic resources for aquaculture

To satisfy increasing demands for fish as food, progress must occur towards greater aquaculture productivity whilst retaining the wild and farmed genetic resources that underpin global fish production. We review the main selection methods that have been developed for genetic improvement in aquaculture, and discuss their virtues and shortcomings. Examples of the application of mass, cohort, within family, and combined between-family and within-family selection are given. In addition, we review the manner in which fish genetic resources can be lost at the intra-specific, species and ecosystem levels and discuss options to best prevent this. We illustrate that fundamental principles of genetic management are common in the implementation of both selective breeding and conservation programmes, and should be emphasized in capacity development efforts. We highlight the value of applied genetics approaches for increasing aquaculture productivity and the conservation of fish genetic resources.

Measuring ectomycorrhizal fungal dispersal: macroecological patterns driven by microscopic propagules

Dispersal plays a prominent role in most conceptual models of community assembly. However, direct measurement of dispersal across a whole community is difficult at ecologically relevant spatial scales. For cryptic organisms, such as fungi and bacteria, the scale and importance of dispersal limitation has become a major point of debate. We use an experimental island biogeographic approach to measure the effects of dispersal limitation on the ecological dynamics of an important group of plant symbionts, ectomycorrhizal fungi. We manipulated the isolation of uncolonized host seedlings across a natural landscape and used a range of molecular techniques to measure the dispersal rates of ectomycorrhizal propagules and host colonization. Some species were prolific dispersers, producing annual spore loads on the order of trillions of spores per km(2). However, fungal propagules reaching host seedlings decreased rapidly with increasing distance from potential spore sources, causing a concomitant reduction in ectomycorrhizal species richness, host colonization and host biomass. There were also strong differences in dispersal ability across species, which correlated well with the predictable composition of ectomycorrhizal communities associated with establishing pine forest. The use of molecular tools to measure whole community dispersal provides a direct confirmation for a key mechanism underlying island biogeography theory and has the potential to make microbial systems a model for understanding the role of dispersal in ecological theory.

Response to pegylated interferon and ribavirin in Asian American patients with chronic hepatitis C genotypes 1 vs 2/3 vs 6

Chronic hepatitis C is generally underappreciated in Asian Americans, and most pivotal studies were conducted in western countries and only included a small numbers of Asian patients. Our goal was to examine and compare treatment outcomes in these patients with genotypes 1 vs 2/3 vs 6. We performed a retrospective cohort study of 167 consecutive treatment-naïve Asian American patients treated with pegylated interferon (PEG IFN) plus ribavirin (RBV) at two community clinics in Northern California from 12/00 to 1/08. Primary outcome was sustained virological response rate by intention-to-treat analysis. The overall completion rate was 76%, and treatment adherence (completion of ≥ 75-80% PEG IFN + RBV dose for ≥ 75-80% of intended duration) was 74%. Significant depression was noted in only 4% of patients. Sustained virologic response in patients with genotype 6 treated for 48 weeks was similar to that seen in those with genotype 2/3 (74%vs 75%, P = 0.89) and significantly higher than those with genotype 1 (74%vs 49%, P = 0.016). On multivariate analysis inclusive of sex, age, body mass index (≤ 25 vs > 25) and viral load, only treatment adherence and genotype (2/3 and 6 treated for 48 weeks) were found to be significant predictors of sustained virologic response. We conclude that significant depression is rare in Asian American patients (4%). Patients with genotype 6 treated for 48 weeks appear to have a similar treatment response rate as patients with genotype 2/3 and a significantly higher response rate than those with genotype 1.

Décrypthon grid - grid resources dedicated to neuromuscular disorders

Thanks to the availability of computational grids and their middleware, a seamless access to computation and storage resources is provided to application developers and scientists. The Décrypthon project is one example of such a high performance platform. In this paper, we present the architecture of the platform, the middleware developed to facilitate access to several servers deployed in France, and the data center for integrating large biological datasets over multiple sites, supported by a new query language and integration of various tools. The SM2PH project represents an example of a biological application that exploits the capacities of the Décrypthon grid. The goal of SM2PH is a better understanding of mutations involved in human monogenic diseases, their impact on the 3D structure of the protein and the subsequent consequences for the pathological phenotypes.

Inoculum potential of Rhizopogon spores increases with time over the first 4 yr of a 99-yr spore burial experiment

In disturbed or pioneer settings, spores and sclerotia of ectomycorrhizal fungi serve as the necessary inoculum for establishment of ectomycorrhizal-dependent trees. Yet, little is known about the persistence of these propagules through time. Here, live field soil was inoculated with known quantities of basidiospores from four pine-associated species of Rhizopogon; these samples were then buried in retrievable containers, and pine seedling bioassays of serially diluted spore samples were used to measure spore viability. In the first 4 yr, no evidence of loss of spore viability was found in the four Rhizopogon species tested, but all four species exhibited dormancy in which a maximum of 1-8% of their spores were initially receptive to pine roots. There were some differences between species in overall inoculum potential of their spores, but all species broke dormancy at a statistically similar rate. This result provides evidence for spore dormancy in a common ectomycorrhizal genus, but it also precludes our ability to estimate the longevity of the spores accurately. Nevertheless these results, coupled with the observed patterns of Rhizopogon spore banks, suggest that at least decade-long durations are likely. As this experiment progresses, the true longevity of the spores will eventually be revealed.

Five novel Candida species in insect-associated yeast clades isolated from Neuroptera and other insects

Ascomycete yeasts are found commonly in the guts of basidioma-feeding beetles but little is known about their occurrence in the gut of other insects. In this study we isolated 95 yeasts from the gut of adult insects in five neuropteran families (Neuroptera: Corydalidae, Chrysopidae, Ascalaphidae, Mantispidae and Hemerobiidae) and a roach (Blattodea: Blattidae). Based on DNA sequence comparisons and other taxonomic characteristics, they were identified as more than 15 species of Saccharomycetes as well as occasional Cryptococcus-like basidiomycete yeasts. Yeast species such as Lachancea fermentati, Lachancea thermotolerans and Hanseniaspora vineae were isolated repeatedly from the gut of three species of corydalids, suggesting a close association of these species and their insect hosts. Among the yeasts isolated in this study 12 were identified as five novel Candida species that occurred in three phylogenetically distinct clades. Molecular phylogenetic analyses showed that Candida chauliodes sp. nov. (NRRL Y-27909T) and Candida corydali sp. nov. (NRRL Y-27910T) were sister taxa in the Candida albicans/ Lodderomyces elongisporus clade. Candida dosseyi sp. nov. (NRRL Y-27950T) and Candida blattae sp. nov. (NRRL Y-27698T) were sister taxa in the Candida intermedia clade. Candida ascalaphidarum sp. nov. (NRRL Y-27908T) fell on a basal branch in a clade containing Candida membranifaciens and many other insect-associated species. Descriptions of these novel yeast species are provided as well as discussion of their ecology in relation to their insect hosts.

Yeasts isolated from plant-associated beetles and other insects: seven novel Candida species near Candida albicans

Yeasts related to Candida albicans were isolated from the digestive tracts of beetles in eight families and various orders of insects such as earwigs, crickets, and roaches, most of which were caught at light traps or in a few cases directly from plant materials. Based on comparisons of DNA sequences and other taxonomic characteristics, a total of 41 isolates were identified as Candida orthopsilosis, Candida pseudorhagii, Candida maltosa, Candida parapsilosis, Candida tropicalis, Candida neerlandica, Lodderomyces elongisporus, and seven new Candida species. The new species and type strains are designated as Candida gigantensis NRRL Y-27736T, Candida bohiensis NRRL Y-27737T, Candida alai NRRL Y-27739T, Candida buenavistaensis NRRL Y-27734T, Candida frijolesensis NRRL Y-48060T, Candida labiduridarum NRRL Y-27940T, and Candida tetrigidarum NRRL Y-48142T. A phylogeny based on SSU and LSU rRNA gene sequences indicated that most of the new species were closely related to members of the C. albicans/L. elongisporus clade, such as C. albicans, Candida dulbliniensis, C. neerlandica, Candida chauliodes, and Candida corydali. Candida alai was placed near this clade, but no closely related sister taxon was identified. The ecology of the insect-associated yeasts is discussed and compared with the results from other studies.

A yeast clade near Candida kruisii uncovered: nine novel Candida species associated with basidioma-feeding beetles

Yeasts similar to Candida kruisii were isolated repeatedly from the digestive tracts of basidioma-feeding beetles, especially nitidulids inhabiting and feeding on a variety of agarics in the southeastern USA and Barro Colorado Island, Panama. Based on the identical sequences of the D1/D2 domains of the LSU rRNA gene (rDNA) and host beetle information, the isolates were grouped into 19 genotypes which varied from C. kruisii by up to 38 nucleotide differences in the D1/D2 region. Phylogenetic analysis of rDNA sequences and phenotypic traits placed the isolates in C. kruisii and in nine undescribed taxa. The new species and type strains are designated as Candida pallodes (NRRL Y-27653(T)), C. tritomae (NRRL Y-27650(T)), C. panamensis (NRRL Y-27657(T)), C. lycoperdinae (NRRL Y-27658(T)), C. atbi (NRRL Y-27651(T)), C. barrocoloradensis (NRRL Y-27934(T)), C. aglyptinia (NRRL Y-27935(T)), C. stri (NRRL Y-48063(T)), and C. gatunensis (NRRL Y-48064(T)). A phylogeny based on analysis of a combined database of sequences of SSU and LSU rDNA and the ITS region showed that the nine new species formed a novel sister clade to C. kruisii that was strongly supported by bootstrap analysis. Candida pallodes, C. tritomae, C. panamensis, and C. lycoperdinae formed one subclade, while C. atbi, C. barrocoloradensis, C. aglyptinia, C. stri, and C. gatunensis formed a second distinct subclade within the larger clade. Candida pallodes and C. atbi showed a strong host specificity to beetle species in the genus Pallodes (Coleoptera: Nitidulidae) collected from a variety of agarics. On the other hand, C. panamensis, C. tritomae, and C. lycoperdinae were associated with several unrelated beetles in Erotylidae, Scarabaeidae, Tenebrionidae, and Curculionidae as well as Lycoperdina ferruginea (Nitidulidae). Candida pallodes, C. tritomae, C. lycoperdinae, and C. atbi have been isolated repeatedly in the USA, while the other five new species have been found only at Barro Colorado Island, Panama.

Morphological and ecological similarities: wood-boring beetles associated with novel xylose-fermenting yeasts, Spathaspora passalidarum gen. sp. nov. and Candida jeffriesii sp. nov

Ascomycete yeasts that both ferment and assimilate xylose were reported previously as associates of insects living in woody substrates. Most notable have been reports of Pichia stipitis-like yeasts that are widely associated with the wood-boring beetle, Odontotaenius disjunctus (Coleoptera: Passalidae), in the eastern United States. Our continuing investigation of insect gut yeasts has lead to the discovery of two new xylose-fermenting yeasts that phylogenetic analysis places as sister taxa. The beetle hosts, O. disjunctus and Phrenapates bennetti (Coleoptera: Tenebrionidae), are similar in habitat and appearance, and the presence of similar gut yeasts is an additional common feature between them. Here we describe the new yeast genus Spathaspora, the type species S. passalidarum, and its sister taxon Candida jeffriesii and discuss their natural history, including a comparison with Pichia stipitis, another member of a guild of xylose-fermenting yeasts with similar metabolic traits. In addition a morphologically distinct yeast ascospore type is described for Spathaspora.

Communities of microbes that inhabit the changing hindgut landscape of a subsocial beetle

Microbes that have adopted endosymbiotic life styles not only have evolved to live in specialized habitats within living organisms, but the living habitats also have evolved to accommodate them. The hindgut of the passalid beetle (Odontotaenius disjunctus) is lined with a cuticle that undergoes dramatic topographic changes during the life cycle of the beetle. This manuscript addresses the changes that have been observed in time and space for the cuticular landscape of the hindgut as well as for the microbial communities within the hindgut. Microbial identity is based on morphology, culture, and extrapolation from previously reported passalid gut inhabitants.

Metschnikowia noctiluminum sp. nov., Metschnikowia corniflorae sp. nov., and Candida chrysomelidarum sp. nov., isolated from green lacewings and beetles

Fourteen yeast isolates belonging to the Metschnikowia clade were isolated from the digestive tracts of lacewings (Neuroptera: Chrysopidae), soldier beetles and leaf beetles (Coleoptera: Cantharidae and Chrysomelidae), and a caddisfly (Trichoptera: Hydropsychidae). The insect hosts were associated with sugary substances of plants, a typical habitat for yeasts in this clade. Based on DNA sequence comparisons and phenetic characters, the yeasts were identified as Candida picachoensis, Candida pimensis, and four undescribed taxa. Among the undescribed taxa, three yeasts were distinguished from one another and from other described taxa by nucleotide differences in the ribosomal DNA repeat, which were sufficient to consider them as new species. Two of the novel yeast species are described as Metschnikowia noctiluminum (NRRL Y-27753(T)) and M. cornifloraespp. nov. (NRRL Y-27750(T)) based in part on production of needle-shaped ascospores, which are found in most Metschnikowia species. Sexual reproduction was not observed in the third new yeast, Candida chrysomelidarumsp. nov. (NRRL Y-27749(T)). A fourth isolate, NRRL Y-27752, was not significantly distinct from Metschnikowia viticola and Candida kofuensis to be described as a new species. Phylogenetic analysis of the D1/D2 loop sequences placed M. noctiluminum within the M. viticola clade, while C. chrysomelidarum was a sister taxon of Candida rancensis. Metschnikowia corniflorae was phylogenetically distinct from other new species and fell outside of the large-spored Metschnikowia group.

Nine new Candida species near C. membranifaciens isolated from insects

14 different yeasts were isolated from the gut of a variety of insects, including beetles, lacewings, fishflies, craneflies, and a cockroach. One of the yeasts was found both in the gut and on the body surface of a beetle larva. Based on ribosomal DNA sequence comparisons and phenotypic characters, the yeasts were identified as Candida membranifaciens, C. tenuis, Pichia nakazawae, and nine undescribed taxa in Saccharomycotina. All the undescribed taxa reproduced only asexually, and they fit within the limits of the polyphyletic genus Candida. The new species and their type strains are Candida blattariae NRRL Y-27703T, C. amphixiae NRRL Y-27704T, C. michaelii NRRL Y-27705T, C. cerambycidarum NRRL Y-27706T, C. gorgasii NRRL Y-27707T, C. endomychidarum NRRL Y-27708T, C. temnochilae NRRL Y-27763T, C. sinolaborantium NRRL Y-27765T, and C. lessepsii NRRL Y-27766T spp. nov. Phylogenetic analysis of combined small and large subunit ribosomal DNA sequences placed C. amphixiae, C. michaelii, C. cerambycidarum, C. gorgasii, C. endomychidarum, and C. lessepsii in a statistically well supported clade with C. blattariae, C. membranifaciens, C. friedrichii, and C. buinensis as sisters to the clade. The other two new taxa, C. temnochilae and C. sinolaborantium, formed an independent clade basal to the major clade containing C. membranifaciens and closely related taxa. C. sinolaborantium occurred in both Panama and the USA, but there were genetic differences between the isolates from the two places.

Responses in residual feed intake in lines of Large White pigs selected for growth rate on restricted feeding (measured on ad libitum individual feeding)

Residual feed intake (RFI) represents the deviation of the actual ad libitum food consumption of each animal from that predicted from combination of growth rate, backfat and metabolic body weight measurements. After 4 years of divergent selection of pigs in lines for either high or low postweaning growth rate on restricted feeding, the high line exhibited a significant reduction in RFI relative to the low line. This indicated, to some extents, a lower energy requirement for maintenance in the high than in the low line, possibly because of reduced physical activity of the animals. Estimates of genetical parameters showed that RFI was moderately heritable and those genetic correlations of RFI with carcass backfat and food conversion ratio were moderate to highly positive.

A novel antigenic variant of Canine parvovirus from a Vietnamese dog

Nine isolates of Canine parvovirus (CPV) were obtained from Vietnamese dogs and cats. One canine isolate showed a unique antigenic property which indicates a novel antigenic variant of CPV-2b when examined with hemagglutination inhibition tests using our monoclonal antibodies, 21C3 and 19D7, which were recently developed. This isolate had an amino acid substitution of residue 426, Asp to Glu, and the same substitution has recently been found in CPV from Italian dogs. This study first showed that such substitution caused an antigenic difference demonstrable by monoclonal antibodies and that a similar evolution may have occurred in CPV in Vietnam.