Evidence of adaptive tolerance to nickel in isolates of Cenococcum geophilum from serpentine soils

Selection for metal-tolerant ecotypes of ectomycorrhizal (ECM) fungi has been reported in instances of metal contamination of soils as a result of human activities. However, no study has yet provided evidence that natural metalliferous soils, such as serpentine soils, can drive the evolution of metal tolerance in ECM fungi. We examined in vitro Ni tolerance in isolates of Cenococcum geophilum from serpentine and non-serpentine soils to assess whether isolates from serpentine soils exhibited patterns consistent with adaptation to elevated levels of Ni, a typical feature of serpentine. A second objective was to investigate the relationship between Ni tolerance and specific growth rates (μ) among isolates to increase our understanding of possible tolerance/growth trade-offs. Isolates from both soil types were screened for Ni tolerance by measuring biomass production in liquid media with increasing Ni concentrations, so that the effective concentration of Ni inhibiting fungal growth by 50% (EC₅₀) could be determined. Isolates of C. geophilum from serpentine soils exhibited significantly higher tolerance to Ni than non-serpentine isolates. The mean Ni EC₅₀ value for serpentine isolates (23.4 μg ml⁻¹) was approximately seven times higher than the estimated value for non-serpentine isolates (3.38 μg ml⁻¹). Although there was still a considerable variation in Ni sensitivity among the isolates, none of the serpentine isolates had EC₅₀ values for Ni within the range found for non-serpentine isolates. We found a negative correlation between EC₅₀ and μ values among isolates (r = −0.555). This trend, albeit only marginally significant (P = 0.06), indicates a potential trade-off between tolerance and growth, in agreement with selection against Ni tolerance in “normal” habitats. Overall, these results suggest that Ni tolerance arose among serpentine isolates of C. geophilum as an adaptive response to Ni exposure in serpentine soils. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Local and microscale distributions of Cenococcum geophilum in soils of coastal pine forests

To clarify the local and microscale distribution patterns of Cenococcum geophilum at soil surfaces in coastal pine forests, we collected soil samples in Pinus thunbergii stands. To investigate the local distribution of C. geophilum, five soil samples were collected randomly to obtain roots of P. thunbergii at four study sites. To examine the microscale distribution of fungi, 19 soil samples were collected from a 5 × 5 m quadrat at a minimum interval of 15 cm. Ectomycorrhizas of P. thunbergii were examined and identified morphologically. C. geophilum mycorrhizas were retrieved from all the sites at the local scale and from all sampling points within a site at the microscale. The occurrence frequency of C. geophilum ectomycorrhizas ranged from 20.0 to 62.6 % at the sites studied. These results suggest that C. geophilum is the dominant ectomycorrhizal fungus and is distributed ubiquitously in coastal pine forests of Japan.     

Effects of Pisolithus tinctorius and Cenococcum geophilum inoculation on pine in copper-contaminated soil to enhance phytoremediation

We used Pisolithus tinctorius and Cenococcum geophilum to determine the copper (Cu) resistance of ectomycorrhizal (ECM) fungi and their potential for improving phytoremediation of Cu-contaminated soil by Chinese red pine (Pinus tabulaeformis). The results showed that nutrient accumulation in C. geophilum mycelium was significantly lower under higher Cu concentrations in the soil, which was not observed in P. tinctorius. Meanwhile, P. tinctorius exhibited greater Cu tolerance than C. geophilum. Inoculation with ECM fungi significantly improved the growth of pine shoots planted in polluted soil in pot experiments (p < 0.01). The total accumulated Cu in pine seedlings planted in Cu-contaminated soil increased by 72.8% and 113.3% when inoculated with P. tinctorius and C. geophilum, respectively, indicating that ECM fungi may help their host to phytoextract heavy metals. Furthermore, the majority of the total absorbed metals remained in the roots, confirming the ability of ECM fungi to promote heavy metal phytostabilization. There were no differences between the effects of the two fungi in helping the host stabilize and absorb Cu, even though they have different Cu tolerances. Inoculation with ECM fungi can benefit plant establishment in polluted environments and assist plants with phytoremediating heavy-metal-contaminated soils.     

Respiration activity of ectomycorrhizas from Cenococcum geophilum and Lactarius sp. in relation to soil water potential in five beech forests

Forest trees are involved in root symbioses with hundreds of species of ectomycorrhizal fungi which constitute functional guilds able to improve the water and mineral nutrition of host trees. In temperate ecosystems, water shortage is a main factor limiting tree vitality. To assess how soil water conditions affected the physiological state of beech (Fagus silvatica L.) ectomycorrhizal roots, we monitored glucose respiration of two ectomycorrhizal types (Lactarius sp. and Cenococcum geophilum) during two complete growing seasons. Five stands of contrasting soil conditions were chosen in north-eastern France. The top soil horizons were equipped with micropsychrometers for measuring water potential and temperature. Glucose respiration on individual ectomycorrhizas was measured in vitro by trapping [¹⁴C]-CO₂ from radiolabelled glucose. For soil water potential <-0.2 MPa, the potential respiration activity of C. geophilumectomycorrhizas was significantly less altered than that of Lactariussp. ectomycorrhizas, indicating that C. geophilumis more likely than Lactariussp. to maintain the physiological integrity of beech roots facing drought stress.     

Random distribution pattern and non-adaptivity of genome size in a highly variable population of Festuca pallens

BACKGROUND AND AIMS: The spatial and statistical distribution of genome sizes and the adaptivity of genome size to some types of habitat, vegetation or microclimatic conditions were investigated in a tetraploid population of Festuca pallens. The population was previously documented to vary highly in genome size and is assumed as a model for the study of the initial stages of genome size differentiation. METHODS: Using DAPI flow cytometry, samples were measured repeatedly with diploid Festuca pallens as the internal standard. Altogether 172 plants from 57 plots (2.25 m(2)), distributed in contrasting habitats over the whole locality in South Moravia, Czech Republic, were sampled. The differences in DNA content were confirmed by the double peaks of simultaneously measured samples. KEY RESULTS: At maximum, a 1.115-fold difference in genome size was observed. The statistical distribution of genome sizes was found to be continuous and best fits the extreme (Gumbel) distribution with rare occurrences of extremely large genomes (positive-skewed), as it is similar for the log-normal distribution of the whole Angiosperms. Even plants from the same plot frequently varied considerably in genome size and the spatial distribution of genome sizes was generally random and unautocorrelated (P > 0.05). The observed spatial pattern and the overall lack of correlations of genome size with recognized vegetation types or microclimatic conditions indicate the absence of ecological adaptivity of genome size in the studied population. CONCLUSIONS: These experimental data on intraspecific genome size variability in Festuca pallens argue for the absence of natural selection and the selective non-significance of genome size in the initial stages of genome size differentiation, and corroborate the current hypothetical model of genome size evolution in Angiosperms (Bennetzen et al., 2005, Annals of Botany 95: 127-132).     

The impact of transposable elements on eukaryotic genomes: From genome size increase to genetic adaptation to stressful environments

Transposable elements (TEs) are present in roughly all genomes. These mobile DNA sequences are able to invade genomes and their impact on genome evolution is substantial. The mobility of TEs can induce the appearance of deleterious mutations, gene disruption and chromosome rearrangements, but transposition activity also has positive aspects and the mutational activities of TEs contribute to the genetic diversity of organisms. This short review aims to give a brief overview of the impact TEs may have on animal and plant genome structure and expression, and the relationship between TEs and the stress response of organisms, including insecticide resistance.     

Cell size does not always correspond to genome size: phylogenetic analysis in geckos questions optimal DNA theories of genome size evolution

At higher taxonomic levels, a significant correlation between genome size (GS) and erythrocyte size (ES) has been reported for many taxa. Under optimal DNA theories, several mechanisms presuming a causative link between GS and ES have been proposed to explain this seemingly general pattern. The correlation between GS and ES has been rarely tested among closely related organisms within an explicit phylogenetic framework. Eyelid geckos (family Eublepharidae) serve as a proper group to conduct such an analysis. We used flow cytometry to measure GS in 15 forms of eublepharids and conducted a phylogenetic reconstruction of GS and ES to test the successiveness of evolutionary shifts in these traits. Most parsimoniously, there were two independent increases and two decreases in GS during the evolution of eublepharids. Nevertheless, changes in GS and ES were not phylogenetically associated in a manner predicted by optimal DNA theories. Our results question the generality of causative bonds between DNA content and cell size and demonstrate that cell size cannot always serve as a proxy of GS. We suggest there is no need to expect a direct causative link between GS and ES to explain the correlation between GS and cell size at higher taxonomic levels. Such a correlation can be explained by simple mechanistic constraints and a combination of the population-genetic model of genome complexity with cell-size-metabolic rate relationship.     

Recombinant rearrangements of bacterial genome and adaptation to the environment]

The rearrangement of bacterial chromosomes induced by intragenomic recombination is considered. The role of stochastic and programmed genome rearrangements in bacterial adaptation to the environment and in cell differentiation is discussed.     

Mating group size and evolutionarily stable pattern of sexuality in barnacles

Barnacles, marine crustaceans, have various patterns of sexuality depending on species including simultaneous hermaphroditism, androdioecy (hermaphrodites and dwarf males), and dioecy (females and dwarf males). We develop a model that predicts the pattern of sexuality in barnacles by two key environmental factors: (i) food availability and (ii) the fraction of larvae that settle on the sea floor. Populations in the model consist of small individuals and large ones. We calculate the optimal resource allocation toward male function, female function and growth for small and large barnacles that maximizes each barnacle's lifetime reproductive success using dynamic programming. The pattern of sexuality is defined by the combination of the optimal resource allocations. In our model, the mating group size is a dependent variable and we found that sexuality pattern changes with the food availability through the mating group size: simultaneous hermaphroditism appears in food-rich environments, where the mating group size is large, protandric simultaneous hermaphroditism appears in intermediate food environments, where the mating group size also takes intermediate value, the other sexuality patterns, androdioecy, dioecy, and sex change are observed in food-poor environments, where the mating group size is small. Our model is the first one where small males can control their growth to large individuals, and hence has ability to explain a rich spectrum of sexual patterns found in barnacles.     

Genetic diversity and differential in vitro responses to Ni in <Emphasis Type="Italic">Cenococcum geophilum</Emphasis> isolates from serpentine soils in Portugal

Amplified fragment length polymorphism (AFLP) analysis was used to investigate the genetic diversity in isolates of the ectomycorrhizal fungus Cenococcum geophilum from serpentine and non-serpentine soils in Portugal. A high degree of genetic diversity was found among C. geophilum isolates; AFLP fingerprints showed that all the isolates were genetically distinct. We also assessed the in vitro Ni sensitivity in three serpentine isolates and one non-serpentine isolate. Only the non-serpentine isolate was significantly affected by the addition of Ni to the growth medium. At 30 microg g(-1) Ni, radial growth rate and biomass accumulation decreased to 73.3 and 71.6% of control, respectively, a highly significant inhibitory effect. Nickel at this concentration had no significant inhibitory effect on serpentine isolates, and so the fitness of serpentine isolates, as evaluated by radial growth rate and biomass yield, is likely unaffected by Ni in the field. In all isolates, the Ni concentration in the mycelia increased with increasing Ni concentration in the growth medium, but two profiles of Ni accumulation were identified. One serpentine isolate showed a linear trend of Ni accumulation. At the highest Ni exposure, the concentration of Ni in the mycelium of this isolate was in the hyperaccumulation range for Ni as defined for higher plants. In the remaining isolates, Ni accumulation was less pronounced and seems to approach a plateau at 30 microg g(-1) Ni. Because two profiles of Ni accumulation emerged among our Ni-insensitive serpentine isolates, this result suggests that different Ni detoxification pathways may be operating. The non-serpentine isolate whose growth was significantly affected by Ni was separated from the other isolates in the genetic analysis, suggesting a genetic basis for the Ni-sensitivity trait. This hypothesis is further supported by the fact that all isolates were maintained on medium without added Ni to avoid carry-over effects. However, because AFLP analysis failed to distinguish between serpentine and non-serpentine isolates, we cannot conclude that Ni insensitivity among our serpentine isolates is due to evolutionary adaptation. Screening a larger number of isolates, from different geographical origins and environments, should clarify the relationships between genetic diversity, morphology, and physiology in this important species.     

Inter- and intramolecular recombinations in the cucumber mosaic virus genome related to adaptation to alstroemeria

In four distinct alstroemeria-infecting cucumber mosaic virus (CMV) isolates, additional sequences of various lengths were present in the 3' nontranslated regions of their RNAs 2 and 3, apparently the result of intra- and intermolecular recombination events. Competition experiments revealed that these recombined RNA 2 and 3 segments increased the biological fitness of CMV in alstroemeria.     

Variation in genome size of argasid and ixodid ticks

The suborder Ixodida includes many tick species of medical and veterinary importance, but little is known about the genomic characteristics of these ticks. We report the first study to determine genome size in two species of Argasidae (soft ticks) and seven species of Ixodidae (hard ticks) using flow cytometry analysis of fluorescent stained nuclei. Our results indicate a large haploid genome size (1C>1000 Mbp) for all Ixodida with a mean of 1281 Mbp (1.31+/-0.07 pg) for the Argasidae and 2671 Mbp (2.73+/-0.04 pg) for the Ixodidae. The haploid genome size of Ixodes scapularis was determined to be 2262 Mbp. We observed inter- and intra-familial variation in genome size as well as variation between strains of the same species. We explore the implications of these results for tick genome evolution and tick genomics research.     

Quantitative genetics of growth and cryptic evolution of body size in an island population

While evolution occurs when selection acts on a heritable trait, empirical studies of natural systems have frequently reported phenotypic stasis under these conditions. We performed quantitative genetic analyses of weight and hindleg length in a free-living population of Soay sheep (Ovis aries) to test whether genetic constraints can explain previously reported stasis in body size despite evidence for strong positive directional selection. Genetic, maternal and environmental covariance structures were estimated across ontogeny using random regression animal models. Heritability increased with age for weight and hindleg length, though both measures of size were highly heritable across ontogeny. Genetic correlations among ages were generally strong and uniformly positive, and the covariance structures were also highly integrated across ontogeny. Consequently, we found no constraint to the evolution of larger size itself. Rather we expect size at all ages to increase in response to positive selection acting at any age. Consistent with expectation, predicted breeding values for age-specific size traits have increased over a twenty-year period, while maternal performance for offspring size has declined. Re-examination of the phenotypic data confirmed that sheep are not getting larger, but also showed that there are significant negative trends in size at all ages. The genetic evolution is therefore cryptic, with the response to selection presumably being masked at the phenotypic level by a plastic response to changing environmental conditions. Density-dependence, coupled with systematically increasing population size, may contribute to declining body size but is insufficient to completely explain it. Our results demonstrate that an increased understanding of the genetic basis of quantitative traits, and of how plasticity and microevolution can occur simultaneously, is necessary for developing predictive models of phenotypic change in nature.     

Homozygosity in a population of variable size and mutation rate

A formula is obtained for the probability that two genes at a single locus, sampled at random from a population at time t, are of particular types. The model assumed is a diffusion approximation to a neutral Wright-Fisher model in which mutation is not necessarily symmetric and the population size is a function of time. It is shown that for symmetric mutation in a population undergoing a step-function type bottleneck, homozygosity increases with decreasing population size. A formula is given for the distribution of the number of segregating sites occurring in two randomly sampled sequences of completely linked sites, with general mutation at a site and identical mutation structure between sites.We give similar results for a population of fixed size but for which the mutation rate is a function of time, and not necessarily symmetric. We confirm the intuitively clear effect that increasing the mutation rate decreases homozygosity.     

The genome of the xerotolerant mold Wallemia sebi reveals adaptations to osmotic stress and suggests cryptic sexual reproduction

Wallemia (Wallemiales, Wallemiomycetes) is a genus of xerophilic Fungi of uncertain phylogenetic position within Basidiomycota. Most commonly found as food contaminants, species of Wallemia have also been isolated from hypersaline environments. The ability to tolerate environments with reduced water activity is rare in Basidiomycota. We sequenced the genome of W. sebi in order to understand its adaptations for surviving in osmotically challenging environments, and we performed phylogenomic and ultrastructural analyses to address its systematic placement and reproductive biology. W. sebi has a compact genome (9.8 Mb), with few repeats and the largest fraction of genes with functional domains compared with other Basidiomycota. We applied several approaches to searching for osmotic stress-related proteins. In silico analyses identified 93 putative osmotic stress proteins; homology searches showed the HOG (High Osmolarity Glycerol) pathway to be mostly conserved. Despite the seemingly reduced genome, several gene family expansions and a high number of transporters (549) were found that also provide clues to the ability of W. sebi to colonize harsh environments. Phylogenetic analyses of a 71-protein dataset support the position of Wallemia as the earliest diverging lineage of Agaricomycotina, which is confirmed by septal pore ultrastructure that shows the septal pore apparatus as a variant of the Tremella-type. Mating type gene homologs were identified although we found no evidence of meiosis during conidiogenesis, suggesting there may be aspects of the life cycle of W. sebi that remain cryptic.     

Transposable elements and the evolution of genome size in eukaryotes

It is generally accepted that the wide variation in genome size observed among eukaryotic species is more closely correlated with the amount of repetitive DNA than with the number of coding genes. Major types of repetitive DNA include transposable elements, satellite DNAs, simple sequences and tandem repeats, but reliable estimates of the relative contributions of these various types to total genome size have been hard to obtain. With the advent of genome sequencing, such information is starting to become available, but no firm conclusions can yet be made from the limited data currently available. Here, the ways in which transposable elements contribute both directly and indirectly to genome size variation are explored. Limited evidence is provided to support the existence of an approximately linear relationship between total transposable element DNA and genome size. Copy numbers per family are low and globally constrained in small genomes, but vary widely in large genomes. Thus, the partial release of transposable element copy number constraints appears to be a major characteristic of large genomes.