In vitro evidence of root colonization suggests ecological versatility in the genus Mycena.

The root-associated habit has evolved on numerous occasions in different fungal lineages, suggesting a strong evolutionary pressure for saprotrophic fungi to switch to symbiotic associations with plants. Species within the ubiquitous, saprotrophic genus Mycena are frequently major components in molecular studies of root-associated fungal communities, suggesting that an evaluation of their trophic status is warranted. Here, we report on interactions between a range of Mycena species and the plant Betula pendula. In all, 17 Mycena species were inoculated onto B. pendula seedlings. Physical interactions between hyphae and fine roots were examined using differential staining and fluorescence microscopy. Physiological interactions were investigated using 14 C and 32 P to show potential transfer between symbionts. All Mycena species associated closely with fine roots, showing hyphal penetration into the roots, which in some cases were intracellular. Seven species formed mantle-like structures around root tips, but none formed a Hartig net. Mycena pura and Mycena galopus both enhanced seedling growth, with M. pura showing significant transfer of 32 P to the seedlings. Our results support the view that several Mycena species can associate closely with plant roots and some may potentially occupy a transitional state between saprotrophy and biotrophy.

A single ectomycorrhizal plant root system includes a diverse and spatially structured fungal community.

Although only a relatively small proportion of plant species form ectomycorrhizae with fungi, it is crucial for growth and survival for a number of widespread woody plant species. Few studies have attempted to investigate the fine scale spatial structure of entire root systems of adult ectomycorrhizal (EcM) plants. Here, we use the herbaceous perennial Bistorta vivipara to map the entire root system of an adult EcM plant and investigate the spatial structure of its root-associated fungi. All EcM root tips were sampled, mapped and identified using a direct PCR approach and Sanger sequencing of the internal transcribed spacer region. A total of 32.1% of all sampled root tips (739 of 2302) were successfully sequenced and clustered into 41 operational taxonomic units (OTUs). We observed a clear spatial structuring of the root-associated fungi within the root system. Clusters of individual OTUs were observed in the younger parts of the root system, consistent with observations of priority effects in previous studies, but were absent from the older parts of the root system. This may suggest a succession and fragmentation of the root-associated fungi even at a very fine scale, where competition likely comes into play at different successional stages within the root system.

Primary succession of Bistorta vivipara (L.) Delabre (Polygonaceae) root-associated fungi mirrors plant succession in two glacial chronosequences.

Glacier chronosequences are important sites for primary succession studies and have yielded well-defined primary succession models for plants that identify environmental resistance as an important determinant of the successional trajectory. Whether plant-associated fungal communities follow those same successional trajectories and also respond to environmental resistance is an open question. In this study, 454 amplicon pyrosequencing was used to compare the root-associated fungal communities of the ectomycorrhizal (ECM) herb Bistorta vivipara along two primary succession gradients with different environmental resistance (alpine versus arctic) and different successional trajectories in the vascular plant communities (directional replacement versus directional non-replacement). At both sites, the root-associated fungal communities were dominated by ECM basidiomycetes and community composition shifted with increasing time since deglaciation. However, the fungal community's successional trajectory mirrored the pattern observed in the surrounding plant community at both sites: the alpine site displayed a directional-replacement successional trajectory, and the arctic site displayed a directional-non-replacement successional trajectory. This suggests that, like in plant communities, environmental resistance is key in determining succession patterns in root-associated fungi. The need for further replicated study, including in other host species, is emphasized.

Arctic fungal communities associated with roots of Bistorta vivipara do not respond to the same fine-scale edaphic gradients as the aboveground vegetation.

Soil conditions and microclimate are important determinants of the fine-scale distribution of plant species in the Arctic, creating locally heterogeneous vegetation. We hypothesize that root-associated fungal (RAF) communities respond to the same fine-scale environmental gradients as the aboveground vegetation, creating a coherent pattern between aboveground vegetation and RAF. We explored how RAF communities of the ectomycorrhizal (ECM) plant Bistorta vivipara and aboveground vegetation structure of arctic plants were affected by biotic and abiotic variables at 0.3-3.0-m scales. RAF communities were determined using pyrosequencing. Composition and spatial structure of RAF and aboveground vegetation in relation to collected biotic and abiotic variables were analysed by ordination and semi-variance analyses. The vegetation was spatially structured along soil C and N gradients, whereas RAF lacked significant spatial structure. A weak relationship between RAF community composition and the cover of two ECM plants, B. vivipara and S. polaris, was found, and RAF richness increased with host root length and root weight. Results suggest that the fine-scale spatial structure of RAF communities of B. vivipara and the aboveground vegetation are driven by different factors. At fine spatial scales, neighbouring ECM plants may affect RAF community composition, whereas soil nutrients gradients structure the vegetation.

Low host specificity of root-associated fungi at an Arctic site.

In High Arctic ecosystems, plant growth and reproduction are limited by low soil moisture and nutrient availability, low soil and air temperatures, and a short growing season. Mycorrhizal associations facilitate plant nutrient acquisition and water uptake and may therefore be particularly ecologically important in nutrition-poor and dry environments, such as parts of the Arctic. Similarly, endophytic root associates are thought to play a protective role, increasing plants' stress tolerance, and likely have an important ecosystem function. Despite the importance of these root-associated fungi, little is known about their host specificity in the Arctic. We investigated the host specificity of root-associated fungi in the common, widely distributed arctic plant species Bistorta vivipara, Salix polaris and Dryas octopetala in the High Arctic archipelago Svalbard. High-throughput sequencing of the internal transcribed spacer 1 (ITS1) amplified from whole root systems generated no evidence of host specificity and no spatial autocorrelation within two 3 m × 3 m sample plots. The lack of spatial structure at small spatial scales indicates that Common Mycelial Networks (CMNs) are rare in marginal arctic environments. Moreover, no significant differences in fungal OTU richness were observed across the three plant species, although their root system characteristics (size, biomass) differed considerably. Reasons for lack of host specificity could be that association with generalist fungi may allow arctic plants to more rapidly and easily colonize newly available habitats, and it may be favourable to establish symbiotic relationships with fungi possessing different physiological attributes.

Substantial compositional turnover of fungal communities in an alpine ridge-to-snowbed gradient.

The main gradient in vascular plant, bryophyte and lichen species composition in alpine areas, structured by the topographic gradient from wind-exposed ridges to snowbeds, has been extensively studied. Tolerance to environmental stress, resulting from wind abrasion and desiccation towards windswept ridges or reduced growing season due to prolonged snow cover towards snowbeds, is an important ecological mechanism in this gradient. The extent to which belowground fungal communities are structured by the same topographic gradient and the eventual mechanisms involved are less well known. In this study, we analysed variation in fungal diversity and community composition associated with roots of the ectomycorrhizal plant Bistorta vivipara along the ridge-to-snowbed gradient. We collected root samples from fifty B. vivipara plants in ten plots in an alpine area in central Norway. The fungal communities were analysed using 454 pyrosequencing analyses of tag-encoded ITS1 amplicons. A distinct gradient in the fungal community composition was found that coincided with variation from ridge to snowbeds. This gradient was paralleled by change in soil content of carbon, nitrogen and phosphorus. A large proportion (66%) of the detected 801 nonsingleton operational taxonomic units (OTUs) were ascomycetes, while basidiomycetes dominated quantitatively (i.e. with respect to number of reads). Numerous fungal OTUs, many with taxonomic affinity to Sebacinales, Cortinarius and Meliniomyces, showed distinct affinities either to ridge or to snowbed plots, indicating habitat specialization. The compositional turnover of fungal communities along the gradient was not paralleled by a gradient in species richness.

Microsatellite markers for Bistorta vivipara (Polygonaceae).

PREMISE OF THE STUDY: Using genomic shotgun 454 sequencing, 50 candidate microsatellite markers were targeted for the arctic-alpine polyploid perennial herb Bistorta vivipara to distinguish between individual genets and ramets within a population. METHODS AND RESULTS: Out of the 50 markers, 31 were polymorphic for seven test samples. We have developed a multiplex protocol for 16 of these microsatellite markers. CONCLUSIONS: Our results show that the microsatellite markers provide a powerful tool for the research on genetic variation of B. vivipara.

Microsatellite markers for Hylocomium splendens (Hylocomiaceae).

PREMISE OF THE STUDY: The perennial feather moss Hylocomium splendens is one of the most widely distributed and common bryophytes in the Northern Hemisphere and has, because of its capacity to grow under a wide range of environmental conditions, been used as a biomonitor for atmospheric metal deposition in Europe. METHODS AND RESULTS: We present a multiplex approach for the analysis of 14 microsatellite markers tested on 194 H. splendens gametophytes. Ten of the markers are developed recently, and are presented for the first time in this paper, whereas four were previously developed but have not been used for population genetic investigations. CONCLUSIONS: The microsatellite markers reported here will provide a powerful tool for further research on population genetic structure in H. splendens.

Fine-scale diversity patterns in belowground microbial communities are consistent across kingdoms.

The belowground environment is heterogeneous and complex at fine spatial scales. Physical structures, biotic components and abiotic conditions create a patchwork mosaic of potential niches for microbes. Questions remain about mechanisms and patterns of community assembly belowground, including: Do fungal and bacterial communities assemble differently? How do microbes reach the roots of host plants? Within a 4 m2 plot in alpine vegetation, high throughput sequencing of the 16S (bacteria) and ITS1 (fungal) ribosomal RNA genes was used to characterise microbial community composition in roots and adjacent soil of a viviparous host plant (Bistorta vivipara). At fine spatial scales, beta-diversity patterns in belowground bacterial and fungal communities were consistent, although compositional change was greater in bacteria than fungi. Spatial structure and distance-decay relationships were also similar for bacteria and fungi, with significant spatial structure detected at <50 cm among root- but not soil-associated microbes. Recruitment of root microbes from the soil community appeared limited at this sampling and sequencing depth. Possible explanations for this include recruitment from low-abundance populations of soil microbes, active recruitment from neighbouring plants and/or vertical transmission of symbionts to new clones, suggesting varied methods of microbial community assembly for viviparous plants. Our results suggest that even at relatively small spatial scales, deterministic processes play a significant role in belowground microbial community structure and assembly.

Using Prokaryotes for Carbon Capture Storage.

Geological storage of CO2 is a fast-developing technology that can mitigate rising carbon emissions. However, there are environmental concerns with the long-term storage and implications of a leak from a carbon capture storage (CCS) site. Traditional monitoring lacks clear protocols and relies heavily on physical methods. Here, we discuss the potential of biotechnology, focusing on microbes with a natural ability to utilize and assimilate CO2 through different metabolic pathways. We propose the use of natural microbial communities for CCS monitoring and CO2 utilization, and, with examples, demonstrate how synthetic biology may maximize CO2 uptake within and above storage sites. An integrated physical and biological approach, combined with metagenomics data and biotechnological advances, will enhance CO2 sequestration and prevent large-scale leakages.

Different bacterial communities in ectomycorrhizae and surrounding soil.

Several eukaryotic symbioses have shown to host a rich diversity of prokaryotes that interact with their hosts. Here, we study bacterial communities associated with ectomycorrhizal root systems of Bistorta vivipara compared to bacterial communities in bulk soil using pyrosequencing of 16S rRNA amplicons. A high richness of Operational Taxonomic Units (OTUs) was found in plant roots (3,571 OTUs) and surrounding soil (3,476 OTUs). The community composition differed markedly between these two environments. Actinobacteria, Armatimonadetes, Chloroflexi and OTUs unclassified at phylum level were significantly more abundant in plant roots than in soil. A large proportion of the OTUs, especially those in plant roots, presented low similarity to Sanger 16S rRNA reference sequences, suggesting novel bacterial diversity in ectomycorrhizae. Furthermore, the bacterial communities of the plant roots were spatially structured up to a distance of 60 cm, which may be explained by bacteria using fungal hyphae as a transport vector. The analyzed ectomycorrhizae presents a distinct microbiome, which likely influence the functioning of the plant-fungus symbiosis.

Microsatellite markers show decreasing diversity but unchanged level of clonality in Dryas octopetala (Rosaceae) with increasing latitude.

PREMISE OF THE STUDY: Average arctic temperatures have increased at almost twice the global average in the past 100 years. Most studies on biodiversity along latitudinal gradients have focused on species richness or genetic diversity at lower latitudes, and only a few studies have inferred genetic diversity within a species along a latitudinal gradient at higher latitudes, even though these areas might be most affected by recent climate changes. Here, intraspecific genetic diversity of the arctic-alpine Dryas octopetala (Rosaceae) is studied along a latitudinal gradient to test the hypotheses that genetic diversity decreases and vegetative clonal growth increases with latitude. • METHODS: Ten microsatellite markers have been developed for D. octopetala and analyzed with population genetic methods in five populations along a latitudinal transect spanning from 59.0°N to 79.9°N. • KEY RESULTS: The nine microsatellites that were used in the final analyses resulted in a resolution high enough to distinguish between ramets while providing useful information at a larger geographical scale. Three genetic clusters were indicated, a southern Norway group, a northern Norway group, and a Svalbard group, with corresponding decreasing genetic diversity. No trend was found with regard to clonality along the gradient. • CONCLUSIONS: The newly developed microsatellite markers provide a useful tool for further genetic studies of D. octopetala and its close relatives, addressing population structure as well as phylogeographic patterns. The results of this study support the hypothesis of decreasing genetic diversity with increasing latitude, which may have implications for future adaptability to climate change.