Active microbial ecosystem in glacier basal ice fuelled by iron and silicate comminution-derived hydrogen.

The basal zone of glaciers is characterized by physicochemical properties that are distinct from firnified ice due to strong interactions with underlying substrate and bedrock. Basal ice (BI) ecology and the roles that the microbiota play in biogeochemical cycling, weathering, and proglacial soil formation remain poorly described. We report on basal ice geochemistry, bacterial diversity (16S rRNA gene phylogeny), and inferred ecological roles at three temperate Icelandic glaciers. We sampled three physically distinct basal ice facies (stratified, dispersed, and debris bands) and found facies dependent on biological similarities and differences; basal ice character is therefore an important sampling consideration in future studies. Based on a high abundance of silicates and Fe-containing minerals and, compared to earlier BI literature, total C was detected that could sustain the basal ice ecosystem. It was hypothesized that C-fixing chemolithotrophic bacteria, especially Fe-oxidisers and hydrogenotrophs, mutualistically support associated heterotrophic communities. Basal ice-derived rRNA gene sequences corresponding to genera known to harbor hydrogenotrophic methanogens suggest that silicate comminution-derived hydrogen can also be utilized for methanogenesis. PICRUSt-predicted metabolism suggests that methane metabolism and C-fixation pathways could be highly relevant in BI, indicating the importance of these metabolic routes. The nutrients and microbial communities release from melting basal ice may play an important role in promoting pioneering communities establishment and soil development in deglaciating forelands.

Arbuscular Mycorrhizal Fungi Alter the Community Structure of Ammonia Oxidizers at High Fertility via Competition for Soil NH4.

Nitrification represents a central process in the cycling of nitrogen (N) which in high-fertility habitats can occasionally be undesirable. Here, we explore how arbuscular mycorrhiza (AM) impacts nitrification when N availability is not limiting to plant growth. We wanted to test which of the mechanisms that have been proposed in the literature best describes how AM influences nitrification. We manipulated the growth settings of Plantago lanceolata so that we could control the mycorrhizal state of our plants. AM induced no changes in the potential nitrification rates or the estimates of ammonium oxidizing (AO) bacteria. However, we could observe a moderate shift in the community of ammonia-oxidizers, which matched the shift we saw when comparing hyphosphere to rhizosphere soil samples and mirrored well changes in the availability of ammonium in soil. We interpret our results as support that it is competition for N that drives the interaction between AM and AO. Our experiment sheds light on an understudied interaction which is pertinent to typical management practices in agricultural systems.

Neutral variation does not predict immunogenetic variation in the European grayling (Thymallus thymallus)-implications for management.

Preservation of genetic diversity is critical to successful conservation, and there is increasing demand for the inclusion of ecologically meaningful genetic information in management decisions. Supportive breeding programmes are increasingly implemented to combat declines in many species, yet their effect on adaptive genetic variation is understudied. This is despite the fact that supportive breeding may interfere with natural evolutionary processes. Here, we assessed the performance of neutral and adaptive markers (major histocompatibility complex; MHC) to inform management of European grayling (Thymallus thymallus), which routinely involves supplementation of natural populations with hatchery-reared fish (stocking). This study is the first to characterize MH II DAA and DAB loci in grayling and to investigate immune genetic variation in relation to management practice in this species. High-throughput Illumina sequencing of "introduced," "stocked native" and "non-stocked native" populations revealed significantly higher levels of allelic richness and heterozygosity for MH markers than microsatellites exclusively in non-stocked native populations. Likewise, significantly lower differentiation at the MH II than for microsatellites was apparent when considering non-stocked native populations, but not stocked populations. We developed a simulation model to test the effects of relaxation of selection during the early life stage within captivity. Dependent on the census population size and stocking intensity, there may be long-term effects of stocking on MH II, but not neutral genetic diversity. This is consistent with our empirical results. This study highlights the necessity for considering adaptive genetic variation in conservation decisions and raises concerns about the efficiency of stocking as a management practice.

Not All that Is Solid Melts into Air? Care-Experienced Young People, Friendship and Relationships in the 'Digital Age'.

The circumstances of those who are, or have been, in the care system may augment concern about their use of mobile phones and the internet, but little is specifically known about such use. Presenting findings from an exploratory study which investigated the experiences and views of six care leavers and four looked after children, this paper considers their social contact via mobile phones and the internet. Exploration of the study data is located alongside wider empirical findings around internet use and critical consideration of theoretical insights from the work of Bauman, Castells and LaMendola. Participants' reported use of digital media was not substantially different to that of their peer group: their core virtual networks had significant overlap with their core offline networks and social contact via digital media could provide welcome, if limited and individualised, social support. The most prominent difficulty arising from the use of these media was forms of verbal abuse by those known to the young people offline. While the centrality of digital technology within young people's lives influenced the way they communicated, underlying issues within their social relationships reflected greater similarity with a pre-digital age than has sometimes been suggested.

Bacterial and fungal communities in a degraded ombrotrophic peatland undergoing natural and managed re-vegetation.

The UK hosts 15-19% of global upland ombrotrophic (rain fed) peatlands that are estimated to store 3.2 billion tonnes of carbon and represent a critical upland habitat with regard to biodiversity and ecosystem services provision. Net production is dependent on an imbalance between growth of peat-forming Sphagnum mosses and microbial decomposition by microorganisms that are limited by cold, acidic, and anaerobic conditions. In the Southern Pennines, land-use change, drainage, and over 200 years of anthropogenic N and heavy metal deposition have contributed to severe peatland degradation manifested as a loss of vegetation leaving bare peat susceptible to erosion and deep gullying. A restoration programme designed to regain peat hydrology, stability and functionality has involved re-vegetation through nurse grass, dwarf shrub and Sphagnum re-introduction. Our aim was to characterise bacterial and fungal communities, via high-throughput rRNA gene sequencing, in the surface acrotelm/mesotelm of degraded bare peat, long-term stable vegetated peat, and natural and managed restorations. Compared to long-term vegetated areas the bare peat microbiome had significantly higher levels of oligotrophic marker phyla (Acidobacteria, Verrucomicrobia, TM6) and lower Bacteroidetes and Actinobacteria, together with much higher ligninolytic Basidiomycota. Fewer distinct microbial sequences and significantly fewer cultivable microbes were detected in bare peat compared to other areas. Microbial community structure was linked to restoration activity and correlated with soil edaphic variables (e.g. moisture and heavy metals). Although rapid community changes were evident following restoration activity, restored bare peat did not approach a similar microbial community structure to non-eroded areas even after 25 years, which may be related to the stabilisation of historic deposited heavy metals pollution in long-term stable areas. These primary findings are discussed in relation to bare peat oligotrophy, re-vegetation recalcitrance, rhizosphere-microbe-soil interactions, C, N and P cycling, trajectory of restoration, and ecosystem service implications for peatland restoration.

UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi.

Identification of ectomycorrhizal (ECM) fungi is often achieved through comparisons of ribosomal DNA internal transcribed spacer (ITS) sequences with accessioned sequences deposited in public databases. A major problem encountered is that annotation of the sequences in these databases is not always complete or trustworthy. In order to overcome this deficiency, we report on UNITE, an open-access database. UNITE comprises well annotated fungal ITS sequences from well defined herbarium specimens that include full herbarium reference identification data, collector/source and ecological data. At present UNITE contains 758 ITS sequences from 455 species and 67 genera of ECM fungi. UNITE can be searched by taxon name, via sequence similarity using blastn, and via phylogenetic sequence identification using galaxie. Following implementation, galaxie performs a phylogenetic analysis of the query sequence after alignment either to pre-existing generic alignments, or to matches retrieved from a blast search on the UNITE data. It should be noted that the current version of UNITE is dedicated to the reliable identification of ECM fungi. The UNITE database is accessible through the URL http://unite.zbi.ee

Suillus bovinus glutamine synthetase gene organization, transcription and enzyme activities in the Scots pine mycorrhizosphere developed on forest humus.

• Glutamine synthetase (GS) expression and activity is of central importance for cellular ammonium assimilation and recycling. Thus, a full characterization of this enzyme at the molecular level is of critical importance for a better understanding of nitrogen (N) assimilation in the mycorrhizal symbiosis. • Genomic and cDNA libraries of Suillus bovinus were constructed to isolate the GS gene, glnA, and corresponding cDNAs. The transcription initiation site was identified and transcription and enzyme activities were characterized in pure culture mycelium and mycorrhiza, and extramatrical mycelium samples harvested from Scots pine-Suillus bovinus microcosms grown on forest humus. • Pure culture mycelium, mycorrhiza and extramatrical mycelium all exhibited equivalent levels of GS transcription, translation and enzyme activities. However, levels of transcription and enzyme activity did not correlate as a large majority of detectable transcripts showed specific 5'-end truncation. • Our data suggest that GS is constitutively expressed and not directly affected by environmental conditions of the symbiotic N uptake. Any changes in the intracellular ammonium level are most likely handled by regulatory flexibility of GS at enzyme level.

ITS probe development for specific detection of Rhizoctonia spp. and Suillus bovinus based on Southern blot and liquid hybridization-fragment length polymorphism.

Development of specific DNA probes targeting rDNA internal transcribed spacer (ITS-1 or -2) sequences is described for the detection of strains representing uninucleate and binucleate Rhizoctonia spp. and Suillus bovinus. Discriminatory taxon/species-specific target sequences were identified following full length ITS sequence alignment of the test fungal sequences and those of other root associated pathogenic or mycorrhizal fungi. Both long (124-151 bp) and shorter (20-25 bp) probes were generated for assessment in Southern dot blot and liquid hybridization ITS capture-fragment length polymorphism assays. Fungal genomic DNA was presented as the target in dot blot protocols using the longer DIG (digoxigenin) labelled probes whilst the shorter 3' biotin-labelled oligonucleotide probes were hybridized to PCR amplified full length ITS (ITS1-5.8S-ITS2) in both dot blot and liquid hybridization assays. The optimal hybridization temperatures for dot blot detection also produced maximal target specific signals in the liquid hybridization protocol. The latter protocol was found to be more discriminatory as target fungi were detected on the basis of combined probe hybridization-ITS capture and 5' Cy-5 labelled ITS length polymorphism analysis (+/- 5 bp) following denaturing sequencing gel electrophoresis in a ALFexpress DNA sequencer.

Nested PCR detection of Archaea in defined compartments of pine mycorrhizospheres developed in boreal forest humus microcosms.

Archaea colonising defined compartments of Scots pine Suillus bovinus or Paxillus involutus mycorrhizospheres developed in forest humus-containing microcosms were investigated by nested polymerase chain reaction (PCR), cloning, restriction fragment length polymorphism (RFLP) and sequencing. Archaea representing six RFLP groups were detected in the system. Sequence analysis of clones representing the different RFLP types confirmed the presence of novel Finnish forest soil Crenarchaeota. Archaeal sequences were identified from mycorrhizas of both P. involutus and S. bovinus, at the margins of the external mycelium and in uncolonised humus but not from non-mycorrhizal short roots. Fungal and compartment-specific crenarchaeal occupation of mycorrhizospheres is discussed in relation to bacterial community distribution in similar systems.

An unknown mechanism promotes somatic incompatibility in Ceratobasidium bicorne.

Strains of Ceratobasidium bicorne (anamorph uninucleate Rhizoctonia), causing root dieback in nursery-grown conifer seedlings, were fruited in the laboratory and the pairing interactions among sibling, single-basidiospore progeny were investigated. No mating reactions were observed. Instead, a high frequency of somatic incompatibility was observed in progeny pairings, indicated by a killing reaction in hyphal anastomosis and by formation of a demarcation line. The F1 progeny also could be fruited, and the level of somatic incompatibility within the F2 progeny remained high, even if lower than in the F1 progeny. The interaction types in pairings within a family of progeny were similar in all respects to those between field isolates, indicating that the species is homothallic. The uninucleate condition of vegetative cells and the basidial characteristics would indicate homokaryotic fruiting, but the possibility of pseudohomothallism remains. We currently are not able to provide an explanation for the mechanism promoting somatic incompatibility in this species, but it seems likely that the classic heterogenic model of somatic incompatibility recognized in basidiomycetes is not applicable here. Alternative mechanisms are discussed.

Divergent arbuscular mycorrhizal fungal communities colonize roots of Pulsatilla spp. in boreal Scots pine forest and grassland soils.

• Communities of arbuscular mycorrhizal (AM) fungi were characterized in roots of rare Pulsatilla patens and common P. pratensis native adults and seedlings grown in soils from Estonian boreal forest and grassland habitats. Since establishment of Pulsatilla species predominantly occurs in vegetation-free gaps, seedling baiting experiments were aimed at gap simulation. • The AM fungal small subunit ribosomal RNA gene (SSU rDNA) sequences amplified from roots were subjected to denaturing gradient gel electrophoresis (DGGE), cloning, restriction fragment length polymorphism (RFLP) grouping, sequence phylogenetic and multivariate analyses. • Nineteen identified sequence groups comprised 14 putative Glomus, two Acaulospora, two Scutellospora and one Gigaspora groupings. Four and six groupings, respectively, contained previously described species and root-derived AM fungal sequences. Sequence groups were identified in seedling roots that were more abundant in a grassland (Glomus sp. MO-G3) or a forest soil (Glomus spp. MO-G2 and MO-G5). • Our data showed site-dependent differences in AM fungal community composition, but we failed to identify AM fungi specifically or preferentially colonizing the rare plant species.

Multitrophic interactions between a Rhizoctonia sp. and mycorrhizal fungi affect Scots pine seedling performance in nursery soil.

• Interspecific variation in ectomycorrhizal fungal (ECMF) control of a root pathogenic uninucleate Rhizoctonia sp. (UnR) was identified in vitro and in planta. • Fungal-fungal and host-fungal interactions were assessed in direct confrontation and cell-free assays, the rhizosphere of Scots pine (Pinus sylvestris) seedling radicles and seedling mycorrhizospheres developed in N-limited nursery soil. • Isolates of Suillus bovinus inhibited UnR growth although no agar-diffusable fungicidal activity was detected. Presence of nonsymbiotic ECMF mycelia did not prevent UnR colonization of radicle apices and the onset of damping-off symptoms. Seedlings hosting S. bovinus mycorrhizas and extensive extramatrical mycelium showed vigorous and healthy shoot growth after a 168-d UnR challenge. Root biomass of Wilcoxina mikolae and Paxillus involutus colonized seedlings were negatively affected by both low soil nutrient status and UnR exposure. However, UnR was isolated from long and mycorrhizal short roots in all ECMF coinoculation treatments. • The differential responses highlight multitrophic host-fungal interaction dynamics that require further characterization in the development of 'efficient' UnR biological control solutions utilizing mycorrhizal fungal inoculants.

Heterogeneity of fungal and plant enzyme expression in intact Scots pine-Suillus bovinus and -Paxillus involutus mycorrhizospheres developed in natural forest humus.

Isozyme expression of nutrient-mobilizing and defence-related enzymes were examined in different functional components of intact Scots pine (Pinus sylvestris L.) ectomycorrhizal root systems developed in natural unsterilized forest humus. Scots pine seedlings colonized by Suillus bovinus (L. ex Fr.) O. Kuntze or Paxillus involutus (Batsch ex Fr.) strains were grown on humus in two-dimensional Perspex⌖ microcosms to allow development of complete ectomycorrhizal root systems. Soluble proteins from uncolonized short roots, whole mycorrhizal root tips or dissected mantle and core fractions, fungal strands and the outermost soil colonizing fine hyphae were subjected to native polyacrylamide gel electrophoresis and stained to detect esterase, acid phosphatase, peroxidase and different polyphenoloxidase isozyme activities. Tissue-specific esterase isozymes were detected in all components and most, including unique Hartig net isozymes, were of fungal origin. High fungal acid phosphatase activities were detected in mycorrhiza and fine hyphae of S. bovinus, supporting earlier findings of active phosphatase activity at the fungal interface in the Hartig net region and in the fine hyphal margins of extramatrical mycelium actively colonizing the humus. All compartments in the P. involutus mycorrhizosphere had weaker acid-phosphatase activities. Peroxidases formed a large part of the soluble-protein content in non-mycorrhizal short roots. The amount of peroxidases, on a tissue f. wt basis, was similar in mycorrhizal and non-mycorrhizal roots, but differential isozyme expression was detected, indicating a change in root peroxidase activities following mycorrhiza formation. The expression of DL-3,4-dihydroxyphenylalanine metabolizing polyphenol oxidase enzymes was reduced in mycorrhizas compared with non-mycorrhizal short roots. In the extramatrical mycelial components, fine hyphae expressed the highest polyphenoloxidase activity. P. involutus displayed some polyphenol-oxidizing isoenzymes not detected in S. bovinus systems. Laccase activity was not detected in the plant and fungal components examined. It is concluded that enzyme activities and isozyme expression are differentially regulated in the different functional components of Scots pine mycorrhizospheres.