Peeking through a frosty window: molecular insights into the communities of Arctic soil fungi

Thesis (Ph.D.) University of Alaska Fairbanks, 2013Fungi are thought to be one of the most diverse groups of organisms in the Arctic. They drive mineral and energy cycles and influence the occurrence of other organisms as mutualists (mycorrhizae, endophytes, lichens), decomposers and pathogens. Nevertheless, information on fungal biodiversity and distribution patterns in relation to environments across the Arctic is still sparse. Molecular methods were used to examine the diversity and community structures of ectomycorrhizal fungi (EMF) associated with two principal arctic host plants, Salix aretica and Dryas integrifolia, as well as total soil fungal communities of adjacent disturbed and undisturbed areas of patterned-ground features across the five bioclimatic subzones (A-E) of the North American Arctic. Key findings include the following: (1) More diverse fungal communities had been observed than previously known. These communities encompass nearly all fungal phyla and included all fungal guilds. However, a few species-rich fungal families dominated these fungal communities. (2) Surprisingly, species richness did not decline with latitude. (3) The most abundant fungal taxa were widely distributed in and beyond the Arctic. Yet root (EMF) and soil fungal communities showed niche preferences in regard to bioclimatic subzones. Furthermore, disturbed and undisturbed patterned ground features harbored different soil fungal communities with the exception of the coldest subzone A. In contrast, EMF community composition was not affected by host plant identity. (4) Fungal communities in the warmest subzone E were distinct from the other arctic subzones and the majority of taxa matched fungi from the boreal forest. (5) Key drivers of fungal community and guild composition along the bioclimatic gradient included regional climate, p.H as well as vegetation composition and productivity across the subzones. At the local scale of patterned-ground features, fungal communities were correlated with vegetation composition and microclimate. With a warming climate, I would expect an enhanced colonization of patterned-ground features by vascular plants that would then affect fungal community structure not only at the species level, but also at the level of fungal guilds. In particular I would expect increases in fungi that are symbiotic with plants and a northward shift of both plant and fungal taxa.Chapter 1. General introduction -- 1.1. References -- Chapter 2. Peeking through a frosty window : molecular insights into the ecology of Arctic soil fungi -- 2.1. Abstract -- 2.2. Introduction -- 2.3. Arctic soil : an extreme environment -- 2.4. Arctic soil fungal diversity -- 2.5. Fungal distribution patterns in Arctic soils -- 2.6. Responses of Arctic soil fungi to climate change -- 2.7. Adaptations of soil fungi to Arctic environments -- 2.8. Future challenges in Arctic soil mycology -- 2.9. Acknowledgements -- 2.10. References -- Chapter 3. Distribution and drivers of ectomycorrhizal fungal communities and across the North American Arctic -- 3.1. Abstract -- 3.2. Introduction -- 3.3. Material and methods -- 3.3.1. Study area -- 3.3.2. Sampling and processing -- 3.3.3. Molecular analysis -- 3.3.4. RFLP screening -- 3.3.5. Cloning and sequencing -- 3.3.6. Bioinformatics & statistical analysis -- 3.3.7. OTU clustering and alignment -- 3.3.8. Nomenclature -- 3.3.9. Ordination analysis -- 3.3.10 Diversity analysis -- 3.4. Results -- 3.4.1. EMF diversity in the Arctic -- 3.4.2. Patterns of EMF communities -- 3.4.3. Drivers of EMF community structure -- 3.5. Discussion -- 3.5.1. EMF diversity in the Arctic -- 3.5.2. Large scale EMF community patterns in the Arctic -- 3.5.3. Factors shaping EMF communities -- 3.6. Acknowledgements -- 3.7. References -- 3.8. Figures -- 3.9. Tables -- 3.10. Appendices -- 3.11. Supporting information -- Chapter 4. Rich and cold : diversity, distribution and drivers of fungi in patterned-ground ecosystems of the North American Arctic -- 4.1. Abstract -- 4.2. Introduction -- 4.3. Material and methods -- 4.3.1. Study areas and patterned ground features -- 4.3.2. Sampling and processing -- 4.3.3. Molecular analysis -- 4.3.4. Bioinformatics -- 4.3.4.1. Sequence clean up -- 4.3.4.2. Diversity analysis -- 4.3.4.3. Ordination analysis -- 4.3.4.4. Distribution of OTUs -- 4.4. Results -- 4.4.1. Fungal divesity in the Arctic -- 4.4.2. Species richness along the latitudinal gradient -- 4.4.3. Community structure across the bioclimatic subzones -- 4.4.4. Fungal community structure within patterned-ground complexes -- 4.4.5. Drivers of fungal community structure -- 4.5. Discussion -- 4.5.1. Fungal diversity in Arctic soils (general description) -- 4.5.2. Large-scale fungal community patterns in the Arctic -- 4.5.2.1. Wide distribution of Arctic fungi -- 4.5.2.2. Fungal species richness along latitudinal gradient -- 4.5.2.3. Community structures and environmental drivers -- 4.6. Conclusions -- 4.7. Acknowledgements -- 4.8. References -- 4.9. Figures -- 4.10. Tables -- 4.11. Supporting information -- Chapter 5. Conclusions -- 5.1. Fungal diversity 5.2. Fungal distribution -- 5.3. Key drivers of fungal communities in the Arctic -- 5.4. Future work -- 5.5. A fungal 'outlook' -- 5.6. References

Not poles apart: Antarctic soil fungal communities show similarities to those of the distant Arctic

Antarctica's extreme environment and geographical isolation offers a useful platform for testing the relative roles of environmental selection and dispersal barriers influencing fungal communities. The former process should lead to convergence in community composition with other cold environments, such as those in the Arctic. Alternatively, dispersal limitations should minimise similarity between Antarctica and distant northern landmasses. Using high-throughput sequencing, we show that Antarctica shares significantly more fungi with the Arctic, and more fungi display a bipolar distribution, than would be expected in the absence of environmental filtering. In contrast to temperate and tropical regions, there is relatively little endemism, and a strongly bimodal distribution of range sizes. Increasing southerly latitude is associated with lower endemism and communities increasingly dominated by fungi with widespread ranges. These results suggest that micro-organisms with well-developed dispersal capabilities can inhabit opposite poles of the Earth, and dominate extreme environments over specialised local specie

Exploring the symbiont diversity of ancient western redcedars: arbuscular mycorrhizal fungi of long-lived hosts

Arbuscular mycorrhizal fungi (AMF) are globally distributed, monophyletic root symbionts with ancient origins. Their contribution to carbon cycling and nutrient dynamics is ecologically important, given their obligate association with over 70% of vascular plant species. Current understanding of AMF species richness and community structure is based primarily on studies of grasses, herbs, and agricultural crops, typically in disturbed environments. Few studies have considered AMF interactions with long-lived woody perennial species in undisturbed ecosystems. Here we examined AMF communities associated with roots and soils of young, mature, and old western redcedar (Thuja plicata) at two sites in the old-growth temperate rainforests of British Columbia. Due to the unique biology of AMF, community richness and structure were assessed using a conservative, clade-based approach. We found 91 AMF OTUs across all samples, with significantly greater AMF richness in the southern site, but no differences in richness along the host chronosequence at either site. All host age classes harboured AMF communities that were overdispersed (more different to each other than expected by chance), with young tree communities most resembling old tree communities. A comparison with similar clade richness data obtained from the literature indicates that western redcedar AMF communities are as rich as those of grasses, tropical trees, and palms. Our examination of undisturbed temperate old growth rainforests suggests that priority effects, rather than succession, are an important aspect of AMF community assembly in this ecosystem

A communal catalogue reveals Earth’s multiscale microbial diversity

Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity

A communal catalogue reveals Earth's multiscale microbial diversity

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.Peer reviewe

Spatial patterns of arctic tundra vegetation properties on different soils along the Eurasia Arctic Transect, and insights for a changing Arctic

Vegetation properties of arctic tundra vary dramatically across its full latitudinal extent, yet few studies have quantified tundra ecosystem properties across latitudinal gradients with field-based observations that can be related to remotely sensed proxies. Here we present data from field sampling of six locations along the Eurasia Arctic Transect in northwestern Siberia. We collected data on the aboveground vegetation biomass, the normalized difference vegetation index (NDVI), and the leaf area index (LAI) for both sandy and loamy soil types, and analyzed their spatial patterns. Aboveground biomass, NDVI, and LAI all increased with increasing summer warmth index (SWI—sum of monthly mean temperatures > 0 °C), although functions differed, as did sandy vs. loamy sites. Shrub biomass increased non-linearly with SWI, although shrub type biomass diverged with soil texture in the southernmost locations, with greater evergreen shrub biomass on sandy sites, and greater deciduous shrub biomass on loamy sites. Moss biomass peaked in the center of the gradient, whereas lichen biomass generally increased with SWI. Total aboveground biomass varied by two orders of magnitude, and shrubs increased from 0 g m−2 at the northernmost sites to >500 g m−2 at the forest-tundra ecotone. Current observations and estimates of increases in total aboveground and shrub biomass with climate warming in the Arctic fall short of what would represent a 'subzonal shift' based on our spatial data. Non-vascular (moss and lichen) biomass is a dominant component (>90% of the photosynthetic biomass) of the vegetation across the full extent of arctic tundra, and should continue to be recognized as crucial for Earth system modeling. This study is one of only a few that present data on tundra vegetation across the temperature extent of the biome, providing (a) key links to satellite-based vegetation indices, (b) baseline field-data for ecosystem change studies, and (c) context for the ongoing changes in arctic tundra vegetation.Non peer reviewe

High-level classification of the Fungi and a tool for evolutionary ecological analyses

High-throughput sequencing studies generate vast amounts of taxonomic data. Evolutionary ecological hypotheses of the recovered taxa and Species Hypotheses are difficult to test due to problems with alignments and the lack of a phylogenetic backbone. We propose an updated phylum-and class-level fungal classification accounting for monophyly and divergence time so that the main taxonomic ranks are more informative. Based on phylogenies and divergence time estimates, we adopt phylum rank to Aphelidiomycota, Basidiobolomycota, Calcarisporiellomycota, Glomeromycota, Entomophthoromycota, Entorrhizomycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota and Olpidiomycota. We accept nine subkingdoms to accommodate these 18 phyla. We consider the kingdom Nucleariae (phyla Nuclearida and Fonticulida) as a sister group to the Fungi. We also introduce a perl script and a newick-formatted classification backbone for assigning Species Hypotheses into a hierarchical taxonomic framework, using this or any other classification system. We provide an example of testing evolutionary ecological hypotheses based on a global soil fungal data set.Peer reviewe

FungalTraits:A user-friendly traits database of fungi and fungus-like stramenopiles

The cryptic lifestyle of most fungi necessitates molecular identification of the guild in environmental studies. Over the past decades, rapid development and affordability of molecular tools have tremendously improved insights of the fungal diversity in all ecosystems and habitats. Yet, in spite of the progress of molecular methods, knowledge about functional properties of the fungal taxa is vague and interpretation of environmental studies in an ecologically meaningful manner remains challenging. In order to facilitate functional assignments and ecological interpretation of environmental studies we introduce a user friendly traits and character database FungalTraits operating at genus and species hypothesis levels. Combining the information from previous efforts such as FUNGuild and Fun(Fun) together with involvement of expert knowledge, we reannotated 10,210 and 151 fungal and Stramenopila genera, respectively. This resulted in a stand-alone spreadsheet dataset covering 17 lifestyle related traits of fungal and Stramenopila genera, designed for rapid functional assignments of environmental studies. In order to assign the trait states to fungal species hypotheses, the scientific community of experts manually categorised and assigned available trait information to 697,413 fungal ITS sequences. On the basis of those sequences we were able to summarise trait and host information into 92,623 fungal species hypotheses at 1% dissimilarity threshold

Distribution and drivers of ectomycorrhizal fungal communities across the North American Arctic

Ectomycorrhizal fungi (EMF) form symbioses with a few plant species that comprise a large fraction of the arctic vegetation. Despite their importance, the identity, abundance and distribution of EMF in the Arctic, as well as the key drivers controlling their community composition are poorly understood. In this study, we investigated the diversity and structure of EMF communities across a bioclimatic gradient spanning much of the North American Arctic. We collected roots from two principal arctic ectomycorrhizal host plants, Salix arctica and Dryas integrifolia, typically growing intermingled, at 23 locations stratified across the five bioclimatic subzones of the Arctic. DNA was extracted from ectomycorrhizal root tips and the ITS region was sequenced and phylogenetically analyzed. A total of 242 fungal Operational Taxonomic Units (OTUs) were documented, with 203 OTUs belonging to the Basidiomycota and 39 to the Ascomycota, exceeding the number of previously morphologically described EMF in the Arctic. EMF communities were dominated by a few common and species-rich families such as Thelephoraceae, Inocybaceae, Sebacinaceae, Cortinariaceae, and Pyronemataceae. Both host plants showed similar species richness, with 176 OTUs on Salix arctica and 154 OTUs on Dryas integrifolia. Host plant identity did not affect EMF community composition. The ten most abundant OTUs had a wide geographic distribution throughout the Arctic, and were also found in boreal, temperate and Mediterranean regions, where they were associated with a variety of hosts. Species richness did not decline with increasing latitude. However, EMF community structure changed gradually across the bioclimatic gradient with the greatest similarity between neighboring bioclimatic subzones and locations. EMF community structure was correlated with environmental factors at a regional scale, corresponding to a complex of glaciation history, geology, soil properties, plant productivity and climate. This is the first large-scale study of EMF communities across all five bioclimatic subzones of the North American Arctic, accompanied by an extensive set of environmental factors analyzed to date. While our study provides baseline data to assess shifts of plant and fungi distribution in response to climate change, it also suggests that with ongoing climate warming, EMF community composition may be affected by northward shifts of some taxa.Read More: http://www.esajournals.org/doi/abs/10.1890/ES12-00217.