Current knowledge of Chytridiomycota diversity in Northern Europe and future research needs

Chytridiomycota is the most species-rich phylum of basal lineage fungi involved in vital processes in both terrestrial and aquatic ecosystems. Still, the diversity and richness of this group remains cryptic. In Northern Europe, few species have been recorded despite the numerous intact lake systems covering this region. Recent classifications of early diverging fungal lineages differ considerably on the diversity of chytrid species and their taxonomic placement. Here, we present the current knowledge of the Chytridiomycota diversity within Northern Europe by using the Global Biodiversity Information Facility (GBIF) data and compare how this diversity distributes across two recently proposed classification systems. Furthermore, we illustrate how various sampling types are influencing the recorded classification levels. Lastly, we discuss how metabarcoding has contributed to the overall understanding of the Chytridiomycota diversity in revealing the “dark matter fungi”, and we point out future research needs in the field of aquatic mycology in the Nordic region.acceptedVersio

Diversity and community composition of root-associated fungi explored by high throughput sequencing

Interactions between plant roots and fungi are well known from most terrestrial ecosystems. Mycorrhizal association is the most prominent plant-fungi interaction, where the fungal partners increase the water and nutrient uptake of their host plants. This symbiosis might be especially important in marginal habitats like arctic and alpine environments. The structure, diversity and spatial patterns of the root-associated fungal communities are to a large extent unknown due to previous methodological limitations. The main objective in this thesis was to implement high throughput DNA sequencing to assess the community structure, richness and spatial distribution of root-associated fungal communities in arctic and alpine environments. We focused on one host plant species, namely the ectomycorrhizal herb Bistorta vivipara. Its small and condensed root system enabled us to analyze the entire fungal assemblages associated with individual root systems, using 454 pyrosequencing of ITS1 and/or ITS2 amplicons. All the five studies included in this thesis revealed that the most prominent fungal groups were well-known ectomycorrhizal fungi such as Agaricales, Sebacinales and Thelephorales. Furthermore, ascomycete fungi of the order Helotiales were also recovered frequently across all root systems. Although a high patchiness in fungal community composition generally was observed, some systematic compositional changes along gradients were observed. In a 2x2 m2 local scale study, a spatial autocorrelation was observed at small scales (<0.34 m). Furthermore, a significant compositional difference was observed between the rootassociated fungal communities and adjacent soil fungal communities. Along two primary succession gradients in arctic and alpine areas, a systematic compositional shift was observed. The fungal richness increased along the chronosequences towards the climax vegetation. In a biogeographic survey, where the root-associated fungi were analyzed across Svalbard, a compositional shift was observed that was associated with the latitudinal gradient. Moreover, the fungal richness increased westwards in the more climatic favorable habitats. Overall, the different studies indicate that stochastic processes, possibly related to aerial spore dispersal, are important during fungal community establishment. The conducted studies exemplify that high throughput sequencing is a powerful approach for analyzing complex microbial communities

Habitat Protection Approaches Facilitate Conservation of Overlooked Fungal Diversity–A Case Study From the Norwegian Coastal Heathland System

European coastal heathlands are distinct ecosystems shaped by land use tradition and they have experienced an 80% area reduction from their historical maximum. These mosaics of mires and wind exposed patches have ericaceous shrub dominated vegetation, and soils within coastal heathlands are characterized by low pH and high levels of recalcitrant debris. Using a culture-based approach with molecular identification of isolates, we characterized root-associated fungal communities of six ericaceous species in eight heathland localities along Norway’s western coast. Site-level alpha diversity ranged from 21-38 OTUs, while the total estimated gamma diversity for culturable heathland root fungi was 190-231 OTUs. Most species recovered are previously reported at low abundance in Norway, suggesting the biodiversity in this community is underreported, rather than novel for science. The fungi recovered were primarily Ascomycota, specifically endophytic Phialocephala, and Pezicula, and no host specificity was observed in the communities. The fungal communities exhibited high turnover and low nestedness, both between ericaceous hosts and across heathland sites. We observed no spatial patterns in fungal betadiversity, and this heterogeneity may be a product of the unique historic land use practices at each locality creating a distinct mycofloral “fingerprint”. Robust diversity estimates will be key for managing fungal biodiversity in coastal heathlands. Our results indicate that sampling schemes that maximize the number of host plants sampled per site, rather than the number of cultures per plant yield improved alpha diversity estimates. Similarly, gamma diversity estimates are improved by maximizing the total number of localities sampled, rather than increasing the number of plants sampled per locality. We argue that while the current protected status of coastal heathland habitats and restoration efforts have knock-on effects for the conservation of fungal biodiversity, fungi have a vital functional role in the ecosystem and holistic conservation plans that consider fungal biodiversity would be beneficial. coastal heathland, mycoflora, conservation, diversity, ericaceous fungi, root associated fungipublishedVersio

Habitat Protection Approaches Facilitate Conservation of Overlooked Fungal Diversity–A Case Study From the Norwegian Coastal Heathland System

European coastal heathlands are distinct ecosystems shaped by land use tradition and they have experienced an 80% area reduction from their historical maximum. These mosaics of mires and wind exposed patches have ericaceous shrub dominated vegetation, and soils within coastal heathlands are characterized by low pH and high levels of recalcitrant debris. Using a culture-based approach with molecular identification of isolates, we characterized root-associated fungal communities of six ericaceous species in eight heathland localities along Norway’s western coast. Site-level alpha diversity ranged from 21-38 OTUs, while the total estimated gamma diversity for culturable heathland root fungi was 190-231 OTUs. Most species recovered are previously reported at low abundance in Norway, suggesting the biodiversity in this community is underreported, rather than novel for science. The fungi recovered were primarily Ascomycota, specifically endophytic Phialocephala, and Pezicula, and no host specificity was observed in the communities. The fungal communities exhibited high turnover and low nestedness, both between ericaceous hosts and across heathland sites. We observed no spatial patterns in fungal betadiversity, and this heterogeneity may be a product of the unique historic land use practices at each locality creating a distinct mycofloral “fingerprint”. Robust diversity estimates will be key for managing fungal biodiversity in coastal heathlands. Our results indicate that sampling schemes that maximize the number of host plants sampled per site, rather than the number of cultures per plant yield improved alpha diversity estimates. Similarly, gamma diversity estimates are improved by maximizing the total number of localities sampled, rather than increasing the number of plants sampled per locality. We argue that while the current protected status of coastal heathland habitats and restoration efforts have knock-on effects for the conservation of fungal biodiversity, fungi have a vital functional role in the ecosystem and holistic conservation plans that consider fungal biodiversity would be beneficial. coastal heathland, mycoflora, conservation, diversity, ericaceous fungi, root associated fungipublishedVersio

A benefit-cost analysis framework for prioritization of control programs for well-established invasive alien species

nvasive alien species (IAS) are identified as a major threat to biodiversity and ecosystem services. While early detection and control programs to avoid establishments of new alien species can be very cost-effective, control costs for well-established species can be enormous. Many of these well-established species constitute severe or high ecological impact and are thus likely to be included in control programs. However, due to limited funds, we need to prioritize which species to control according to the gains in ecological status and human well-being compared to the costs. Benefit-Cost Analysis (BCA) provides such a tool but has been hampered by the difficulties in assessing the overall social benefits on the same monetary scale as the control costs. In order to overcome this obstacle, we combine a non-monetary benefit assessment tool with the ecosystem service framework to create a benefit assessment in line with the welfare economic underpinnings of BCA. Our simplified BCA prioritization tool enables us to conduct rapid and cheap appraisals of large numbers of invasive species that the Norwegian Biodiversity Information Centre has found to cause negative ecological impacts. We demonstrate this application on 30 well-established invasive alien vascular plant species in Norway. Social benefits are calculated and aggregated on a benefit point scale for six impact categories: four types of ecosystem services (supporting, provisioning, regulating and cultural), human health and infrastructure impacts. Total benefit points are then compared to the total control costs of programs aiming at eradicating individual IAS across Norway or in selected vulnerable ecosystems. Although there are uncertainties with regards to IAS population size, benefits assessment and control program effectiveness and costs; our simplified BCA tool identified six species associated with robust low cost-benefit ratios in terms of control costs (in million USD) per benefit point. As a large share of public funds for eradication of IAS is currently spent on control programs for other plant species, we recommend that the environmental authorities at all levels use our BCA prioritization tool to increase the social benefits of their limited IAS control budgets. In order to maximize the net social benefits of IAS control programs, environmental valuation studies of their ecosystem service benefits are needed.publishedVersio

Reindeer carcasses provide foraging habitat for insectivorous birds of the alpine tundra

On August of 2016, almost an entire herd (n = 323) of wild tundra reindeer (Rangifer tarandus) was killed by lightning on Hardangervidda in southern Norway. While conducting fieldwork for another study in 2017, we opportunistically registered the occurrence and behaviour of birds on carcasses from this mass die-off. Several passerine species other than corvids were observed actively foraging on arthropods, such as blowfly (Calliphoridae sp.) adults and larvae, which are typically associated with carcass decomposition. We quantified observations of those birds, and described their foraging behaviour at the carcass site. In decreasing order of abundance, five passerine species were observed taking arthropods at the site: Meadow Pipit (Anthus&nbsp;pratensis), Northern Wheatear (Oenanthe oenanthe), Common Reed Bunting (Emberiza schoeniclus), Bluethroat (Luscinia svecica,), and Lapland&nbsp;Bunting&nbsp;(Calcarius&nbsp;lapponicus). Systematic surveys of passerines utilizing carcass sites would further our understanding of how such resources may affect behaviour and life history of various bird species

Directed endozoochorous dispersal by scavengers facilitate sexual reproduction in otherwise clonal plants at cadaver sites

acceptedVersio

Designing a surveillance program for early detection of alien plants and insects in Norway

Naturalized species of alien plants and animals comprise < 3% of biodiversity recorded in Norway but have had major impacts on natural ecosystems through displacement of native species. Encroachment of alien species has been especially problematic for coastal sites close to transport facilities and urban areas with high density housing. The goal of our field project was to design and test a surveillance program for early detection of alien species of vascular plants and terrestrial insects at the first phase of establishment in natural areas. In our 3-year project (2018–2020), we sampled 60 study plots in three counties in the Oslofjord region of southern Norway. Study plots (6.25 ha) were selected by two criteria: manual selection based on expert opinion (27 plots) or by random selection based on weights from a hotspot analysis of occurrence of alien species (33 plots). Vascular plants were surveyed by two experienced botanists who found a total of 239 alien species of vascular plants in 95 rounds of surveys. Insects and other invertebrates were captured with a single Malaise trap per site, with 3–4 rounds of repeated sampling. We used DNA-metabarcoding to identify invertebrates based on DNA extractions from crushed insects or from the preservative media. Over 3500 invertebrate taxa were detected in 255 rounds of sampling. We recorded 20 alien species of known risk, and 115 species that were new to Norway, including several ‘doorknocker’ species identified by previous risk assessments. We modeled the probabilities of occupancy (ψ) and detection (p) with occupancy models with repeated visits by multiple observers (vascular plants) or multiple rounds of sampling (insects). The two probabilities covaried with risk category for alien organisms and both were low for species categorized as no known or low risk (range = 0.052–0.326) but were higher for species categorized as severe risk (range = 0.318–0.651)... Arthropods · DNA-metabarcoding · Early detection · Invasive · Invertebrates · Occupancy models · Rapid response · Study design · Vascular plantsDesigning a surveillance program for early detection of alien plants and insects in NorwaypublishedVersio

CLOTU: An online pipeline for processing and clustering of 454 amplicon reads into OTUs followed by taxonomic annotation

<p>Abstract</p> <p>Background</p> <p>The implementation of high throughput sequencing for exploring biodiversity poses high demands on bioinformatics applications for automated data processing. Here we introduce <smcaps>CLOTU</smcaps>, an online and open access pipeline for processing 454 amplicon reads. C<smcaps>LOTU</smcaps> has been constructed to be highly user-friendly and flexible, since different types of analyses are needed for different datasets.</p> <p>Results</p> <p>In <smcaps>CLOTU</smcaps>, the user can filter out low quality sequences, trim tags, primers, adaptors, perform clustering of sequence reads, and run <smcaps>BLAST</smcaps> against NCBInr or a customized database in a high performance computing environment. The resulting data may be browsed in a user-friendly manner and easily forwarded to downstream analyses. Although <smcaps>CLOTU</smcaps> is specifically designed for analyzing 454 amplicon reads, other types of DNA sequence data can also be processed. A fungal ITS sequence dataset generated by 454 sequencing of environmental samples is used to demonstrate the utility of <smcaps>CLOTU</smcaps>.</p> <p>Conclusions</p> <p>C<smcaps>LOTU</smcaps> is a flexible and easy to use bioinformatics pipeline that includes different options for filtering, trimming, clustering and taxonomic annotation of high throughput sequence reads. Some of these options are not included in comparable pipelines. C<smcaps>LOTU</smcaps> is implemented in a Linux computer cluster and is freely accessible to academic users through the Bioportal web-based bioinformatics service (<url>http://www.bioportal.uio.no</url>).</p