Summer temperature increase has distinct effects on the ectomycorrhizal fungal communities of moist tussock and dry tundra in Arctic Alaska

Arctic regions are experiencing the greatest rates of climate warming on the planet and marked changes have already been observed in terrestrial arctic ecosystems. While most studies have focused on the effects of warming on arctic vegetation and nutrient cycling, little is known about how belowground communities, such as fungi root‐associated, respond to warming. Here, we investigate how long‐term summer warming affects ectomycorrhizal (ECM) fungal communities. We used Ion Torrent sequencing of the rDNA internal transcribed spacer 2 (ITS2) region to compare ECM fungal communities in plots with and without long‐term experimental warming in both dry and moist tussock tundra. Cortinarius was the most OTU‐rich genus in the moist tundra, while the most diverse genus in the dry tundra was Tomentella. On the diversity level, in the moist tundra we found significant differences in community composition, and a sharp decrease in the richness of ECM fungi due to warming. On the functional level, our results indicate that warming induces shifts in the extramatrical properties of the communities, where the species with medium‐distance exploration type seem to be favored with potential implications for the mobilization of different nutrient pools in the soil. In the dry tundra, neither community richness nor community composition was significantly altered by warming, similar to what had been observed in ECM host plants. There was, however, a marginally significant increase in OTUs identified as ECM fungi with the medium‐distance exploration type in the warmed plots. Linking our findings of decreasing richness with previous results of increasing ECM fungal biomass suggests that certain ECM species are favored by warming and may become more abundant, while many other species may go locally extinct due to direct or indirect effects of warming. Such compositional shifts in the community might affect nutrient cycling and soil organic C storage.     

Broad host range plasmids can invade an unexpectedly diverse fraction of a soil bacterial community

Conjugal plasmids can provide microbes with full complements of new genes and constitute potent vehicles for horizontal gene transfer. Conjugal plasmid transfer is deemed responsible for the rapid spread of antibiotic resistance among microbes. While broad host range plasmids are known to transfer to diverse hosts in pure culture, the extent of their ability to transfer in the complex bacterial communities present in most habitats has not been comprehensively studied. Here, we isolated and characterized transconjugants with a degree of sensitivity not previously realized to investigate the transfer range of IncP- and IncPromA-type broad host range plasmids from three proteobacterial donors to a soil bacterial community. We identified transfer to many different recipients belonging to 11 different bacterial phyla. The prevalence of transconjugants belonging to diverse Gram-positive Firmicutes and Actinobacteria suggests that inter-Gram plasmid transfer of IncP-1 and IncPromA-type plasmids is a frequent phenomenon. While the plasmid receiving fractions of the community were both plasmid- and donor- dependent, we identified a core super-permissive fraction that could take up different plasmids from diverse donor strains. This fraction, comprising 80% of the identified transconjugants, thus has the potential to dominate IncP- and IncPromA-type plasmid transfer in soil. Our results demonstrate that these broad host range plasmids have a hitherto unrecognized potential to transfer readily to very diverse bacteria and can, therefore, directly connect large proportions of the soil bacterial gene pool. This finding reinforces the evolutionary and medical significances of these plasmids.     

iDynoMiCS: next-generation individual-based modelling of biofilms

Individual-based modelling of biofilms accounts for the fact that individual organisms of the same species may well be in a different physiological state as a result of environmental gradients, lag times in responding to change, or noise in gene expression, which we have become increasingly aware of with the advent of single-cell microbiology. But progress in developing and using individual-based modelling has been hampered by different groups writing their own code and the lack of an available standard model. We therefore set out to merge most features of previous models and incorporate various improvements in order to provide a common basis for further developments. Four improvements stand out: the biofilm pressure field allows for shrinking or consolidating biofilms; the continuous-in-time extracellular polymeric substances excretion leads to more realistic fluid behaviour of the extracellular matrix, avoiding artefacts; the stochastic chemostat mode allows comparison of spatially uniform and heterogeneous systems; and the separation of growth kinetics from the individual cell allows condition-dependent switching of metabolism. As an illustration of the model's use, we used the latter feature to study how environmentally fluctuating oxygen availability affects the diversity and composition of a community of denitrifying bacteria that induce the denitrification pathway under anoxic or low oxygen conditions. We tested the hypothesis that the existence of these diverse strategies of denitrification can be explained solely by assuming that faster response incurs higher costs. We found that if the ability to switch metabolic pathways quickly incurs no costs the fastest responder is always the best. However, if there is a trade-off where faster switching incurs higher costs, then there is a strategy with optimal response time for any frequency of environmental fluctuations, suggesting that different types of denitrifying strategies win in different environments. In a single environment, biodiversity of denitrifiers is higher in biofilms than chemostats, higher with than without costs and higher at intermediate frequency of change. The highly modular nature of the new computational model made this case study straightforward to implement, and reflects the sort of novel studies that can easily be executed with the new model.     

The need to re-investigate the nature of homoplastic characters: an ontogenetic case study of the 'bracteoles' in Atripliceae (Chenopodiaceae)

Background and Aims

Within Chenopodioideae, Atripliceae have been distinguished by two bracteoles enveloping the female flowers/fruits, whereas in other tribes flowers are described as ebracteolate with persistent perianth. Molecular phylogenetic hypotheses suggest ‘bracteoles’ to be homoplastic. The origin of the bracteoles was explained by successive inflorescence reductions. Flower reduction was used to explain sex determination. Therefore, floral ontogeny was studied to evaluate the nature of the bracteoles and sex determination in Atripliceae.

Methods

Inflorescences of species of Atriplex, Chenopodium, Dysphania and Spinacia oleracea were investigated using light microscopy and scanning electron microscopy.

Key Results

The main axis of the inflorescence is indeterminate with elementary dichasia as lateral units. Flowers develop centripetally, with first the formation of a perianth primordium either from a ring primordium or from five individual tepal primordia fusing post-genitally. Subsequently, five stamen primordia originate, followed by the formation of an annular ovary primordium surrounding a central single ovule. Flowers are either initially hermaphroditic remaining bisexual and/or becoming functionally unisexual at later stages, or initially unisexual. In the studied species of Atriplex, female flowers are strictly female, except in A. hortensis. In Spinacia, female and male flowers are unisexual at all developmental stages. Female flowers of Atriplex and Spinacia are protected by two accrescent fused tepal lobes, whereas the other perianth members are absent.

Conclusions

In Atriplex and Spinacia modified structures around female flowers are not bracteoles, but two opposite accrescent tepal lobes, parts of a perianth persistent on the fruit. Flowers can achieve sexuality through many different combinations; they are initially hermaphroditic, subsequently developing into bisexual or functionally unisexual flowers, with the exception of Spinacia and strictly female flowers in Atriplex, which are unisexual from the earliest developmental stages. There may be a relationship between the formation of an annular perianth primordium and flexibility in floral sex determination.     

Floral development of Hydrocera and Impatiens reveals evolutionary trends in the most early diverged lineages of the Balsaminaceae

Background and Aims

Balsaminaceae consist of two genera, the monospecific Hydrocera and its species-rich sister Impatiens. Although both genera are seemingly rather similar in overall appearance, they differ in ecology, distribution range, habitat preference and morphology. Because morphological support for the current molecular phylogenetic hypothesis of Impatiens is low, a developmental study is necessary in order to obtain better insights into the evolutionary history of the family. Therefore, the floral development of H. triflora and I. omeiana was investigated, representing the most early-diverged lineage of Impatiens, and the observations were compared with the literature.

Methods

Flowers at all developmental stages were examined using scanning electron microscopy and light microscopy.

Key results

In Hydrocera, two whorls of five free perianth primordia develop into a less zygomorphic perianth compared with its sister genus. The androecial cap originates from five individual stamen primordia. Post-genital fusion of the upper parts of the filaments result in a filament ring below the anthers. The anthers fuse forming connivent anther-like units. The gynoecium of Hydrocera is pentamerous; it is largely synascidiate in early development. Only then is a symplicate zone formed resulting in style and stigmas. In I. omeiana, the perianth is formed as in Hydrocera. Five individual stamen primordia develop into five stamens, of which the upper part of the filaments converge with each other. The gynoecium of I. omeiana is tetramerous; it appears annular in early development.

Conclusions

Comparison of the present results with developmental data from the literature confirms the perianth morphocline hypothesis in which a congenital fusion of the parts of the perianth results in a shift from pentasepalous to trisepalous flowers. In addition, the development of the androecial cap and the gynoecium follows several distinct ontogenetic sequences within the family.     

Pseudomonad swarming motility is restricted to a narrow range of high matric water potentials

Using a novel experimental system that allows control of the matric potential of an agar slab, we explored the hydration conditions under which swarming motility is possible. If there is recognition that this physical parameter is a key determinant of swarming, it is usually neither controlled nor measured rigorously but only manipulated through proxies, namely, the agar concentration and the drying time of "soft" agar plates (swarming plates). We contend that this not only obscures the biophysical mechanisms underlying swarming but also impedes a full assessment of its clinical and environmental significances. Our results indicate that swarming motility is restricted to a narrow range of high matric water potentials in the three pseudomonads tested (Pseudomonas sp. DSS73, Pseudomonas syringae B728a, and Pseudomonas aeruginosa PA14). The threshold below which no swarming was observed was about -0.45 kPa for the first and about -0.1 kPa for the latter two. Above the threshold, the expansion rate of DSS73 swarms increased exponentially with the matric potential. Mutants deficient in surfactant production were totally or partially unable to expand rapidly on the surface of the agar slab. Our results thus suggest that swarming motility in pseudomonads is restricted to (micro)sites where ambient humidity is very high (relative humidity of >99.99%). The spatiotemporal occurrence of such sites is limited in many types of terrestrial environments.