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Dive into the research topics where Håvard Kauserud is active.

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Featured researches published by Håvard Kauserud.


New Phytologist | 2013

Fungal community analysis by high-throughput sequencing of amplified markers – a user's guide

Björn D. Lindahl; R. Henrik Nilsson; Leho Tedersoo; Kessy Abarenkov; Tor Carlsen; Rasmus Kjøller; Urmas Kõljalg; Taina Pennanen; Søren Rosendahl; Jan Stenlid; Håvard Kauserud

Novel high-throughput sequencing methods outperform earlier approaches in terms of resolution and magnitude. They enable identification and relative quantification of community members and offer new insights into fungal community ecology. These methods are currently taking over as the primary tool to assess fungal communities of plant-associated endophytes, pathogens, and mycorrhizal symbionts, as well as free-living saprotrophs. Taking advantage of the collective experience of six research groups, we here review the different stages involved in fungal community analysis, from field sampling via laboratory procedures to bioinformatics and data interpretation. We discuss potential pitfalls, alternatives, and solutions. Highlighted topics are challenges involved in: obtaining representative DNA/RNA samples and replicates that encompass the targeted variation in community composition, selection of marker regions and primers, options for amplification and multiplexing, handling of sequencing errors, and taxonomic identification. Without awareness of methodological biases, limitations of markers, and bioinformatics challenges, large-scale sequencing projects risk yielding artificial results and misleading conclusions.


Science | 2011

The Plant Cell Wall–Decomposing Machinery Underlies the Functional Diversity of Forest Fungi

Daniel C. Eastwood; Dimitrios Floudas; Manfred Binder; Andrzej Majcherczyk; Patrick Schneider; Andrea Aerts; Fred O. Asiegbu; Scott E. Baker; Kerrie Barry; Mika Bendiksby; Melanie Blumentritt; Pedro M. Coutinho; Dan Cullen; Ronald P. de Vries; Allen C. Gathman; Barry Goodell; Bernard Henrissat; Katarina Ihrmark; Håvard Kauserud; Annegret Kohler; Kurt LaButti; Alla Lapidus; José L. Lavín; Yong-Hwan Lee; Erika Lindquist; Walt W. Lilly; Susan Lucas; Emmanuelle Morin; Claude Murat; José A. Oguiza

Comparative genomic analysis of “dry rot” fungus shows both convergent evolution and divergence among fungal decomposers. Brown rot decay removes cellulose and hemicellulose from wood—residual lignin contributing up to 30% of forest soil carbon—and is derived from an ancestral white rot saprotrophy in which both lignin and cellulose are decomposed. Comparative and functional genomics of the “dry rot” fungus Serpula lacrymans, derived from forest ancestors, demonstrated that the evolution of both ectomycorrhizal biotrophy and brown rot saprotrophy were accompanied by reductions and losses in specific protein families, suggesting adaptation to an intercellular interaction with plant tissue. Transcriptome and proteome analysis also identified differences in wood decomposition in S. lacrymans relative to the brown rot Postia placenta. Furthermore, fungal nutritional mode diversification suggests that the boreal forest biome originated via genetic coevolution of above- and below-ground biota.


Molecular Ecology Resources | 2013

ITS1 versus ITS2 as DNA metabarcodes for fungi

Rakel Blaalid; Surendra Kumar; Rolf Henrik Nilsson; Kessy Abarenkov; Paul M. Kirk; Håvard Kauserud

The nuclear ribosomal Internal Transcribed Spacer ITS region is widely used as a DNA metabarcoding marker to characterize the diversity and composition of fungal communities. In amplicon pyrosequencing studies of fungal diversity, one of the spacers ITS1 or ITS2 of the ITS region is normally used. In this methodological study we evaluate the usability of ITS1 vs. ITS2 as a DNA metabarcoding marker for fungi. We analyse three data sets: two comprising ITS1 and ITS2 sequences of known taxonomic affiliations and a third comprising ITS1 and ITS2 environmental amplicon pyrosequencing data. Clustering analyses of sequences with known taxonomy using the bioinformatics pipeline ClustEx revealed that a 97% similarity cut‐off represent a reasonable threshold for estimating the number of known species in the data sets for both ITS1 and ITS2. However, no single threshold value worked well for all fungi at the same time within the curated UNITE database, and we found that the Operational Taxonomic Unit (OTU) concept is not easily translated into the level of species because many species are distributed over several clusters. Clustering analyses of the 134 692 ITS1 and ITS2 pyrosequences using a 97% similarity cut‐off revealed a high similarity between the two data sets when it comes to taxonomic coverage. Although some groups are under‐ or unrepresented in the two data sets due to, e.g. primer mismatches, our results indicate that ITS1 and ITS2 to a large extent yield similar results when used as DNA metabarcodes for fungi.


Molecular Ecology | 2012

Changes in the root-associated fungal communities along a primary succession gradient analysed by 454 pyrosequencing

Rakel Blaalid; Tor Carlsen; Surendra Kumar; Rune Halvorsen; Karl Inne Ugland; Giovanni Fontana; Håvard Kauserud

We investigated changes in the root‐associated fungal communities associated with the ectomycorrhizal herb Bistorta vivipara along a primary succession gradient using 454 amplicon sequencing. Our main objective was to assess the degree of variation in fungal richness and community composition as vegetation cover increases along the chronosequence. Sixty root systems of B. vivipara were sampled in vegetation zones delimited by dated moraines in front of a retreating glacier in Norway. We extracted DNA from rinsed root systems, amplified the ITS1 region using fungal‐specific primers and analysed the amplicons using 454 sequencing. Between 437 and 5063 sequences were obtained from each root system. Clustering analyses using a 98.5% sequence similarity cut‐off yielded a total of 470 operational taxonomic units (OTUs), excluding singletons. Between eight and 41 fungal OTUs were detected within each root system. Already in the first stage of succession, a high fungal diversity was present in the B. vivipara root systems. Total number of OTUs increased significantly along the gradient towards climax vegetation, but the average number of OTUs per root system stayed unchanged. There was a high patchiness in distribution of fungal OTUs across root systems, indicating that stochastic processes to a large extent structure the fungal communities. However, time since deglaciation had impact on the fungal community structure, as a systematic shift in the community composition was observed along the chronosequence. Ectomycorrhizal basidiomycetes were the dominant fungi in the roots of B. vivipara, when it comes to both number of OTUs and number of sequences.


Molecular Ecology | 2012

New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems

Laura Saskia Epp; Sanne Boessenkool; Eva Bellemain; James Haile; Alfonso Esposito; Tiayyba Riaz; Christer Erséus; Vladimir I. Gusarov; Mary E. Edwards; Arild Johnsen; Hans K. Stenøien; Kristian Hassel; Håvard Kauserud; Nigel G. Yoccoz; Kari Anne Bråthen; Pierre Taberlet; Eric Coissac; Christian Brochmann

Metabarcoding approaches use total and typically degraded DNA from environmental samples to analyse biotic assemblages and can potentially be carried out for any kinds of organisms in an ecosystem. These analyses rely on specific markers, here called metabarcodes, which should be optimized for taxonomic resolution, minimal bias in amplification of the target organism group and short sequence length. Using bioinformatic tools, we developed metabarcodes for several groups of organisms: fungi, bryophytes, enchytraeids, beetles and birds. The ability of these metabarcodes to amplify the target groups was systematically evaluated by (i) in silico PCRs using all standard sequences in the EMBL public database as templates, (ii) in vitro PCRs of DNA extracts from surface soil samples from a site in Varanger, northern Norway and (iii) in vitro PCRs of DNA extracts from permanently frozen sediment samples of late‐Pleistocene age (∼16 000–50 000 years bp) from two Siberian sites, Duvanny Yar and Main River. Comparison of the results from the in silico PCR with those obtained in vitro showed that the in silico approach offered a reliable estimate of the suitability of a marker. All target groups were detected in the environmental DNA, but we found large variation in the level of detection among the groups and between modern and ancient samples. Success rates for the Pleistocene samples were highest for fungal DNA, whereas bryophyte, beetle and bird sequences could also be retrieved, but to a much lesser degree. The metabarcoding approach has considerable potential for biodiversity screening of modern samples and also as a palaeoecological tool.


BMC Plant Biology | 2010

High diversity of root associated fungi in both alpine and arctic Dryas octopetala.

Marit Markussen Bjorbækmo; Tor Carlsen; Anne K. Brysting; Trude Vrålstad; Klaus Høiland; Karl Inne Ugland; József Geml; Trond Schumacher; Håvard Kauserud

BackgroundDryas octopetala is a widespread dwarf shrub in alpine and arctic regions that forms ectomycorrhizal (ECM) symbiotic relationships with fungi. In this study we investigated the fungal communities associated with roots of D. octopetala in alpine sites in Norway and in the High Arctic on Svalbard, where we aimed to reveal whether the fungal diversity and species composition varied across the Alpine and Arctic regions. The internal transcribed spacer (ITS) region of nuclear ribosomal DNA was used to identify the fungal communities from bulk root samples obtained from 24 plants.ResultsA total of 137 operational taxonomic units (OTUs) were detected (using 97% similarity cut off during sequence clustering) and well-known ECM genera such as Cenococcum, Cortinarius, Hebeloma, Inocybe and Tomentella occurred frequently. There was no decrease in fungal diversity with increasing latitude. The overall spatial heterogeneity was high, but a weak geographical structuring of the composition of OTUs in the root systems was observed. Calculated species accumulation curves did not level off.ConclusionsThis study indicates that the diversity of fungi associated with D. octopetala does not decrease in high latitude arctic regions, which contrasts observations made in a wide spectrum of other organism groups. A high degree of patchiness was observed across root systems, but the fungal communities were nevertheless weakly spatially structured. Non-asymptotical species accumulation curves and the occurrence of a high number of singletons indicated that only a small fraction of the fungal diversity was detected.


Journal of Microbiological Methods | 2012

Environmental microbiology through the lens of high-throughput DNA sequencing: synopsis of current platforms and bioinformatics approaches

Ramiro Logares; Thomas Hendricus Augustus Haverkamp; Surendra Kumar; Anders Lanzén; Christopher Quince; Håvard Kauserud

The incursion of High-Throughput Sequencing (HTS) in environmental microbiology brings unique opportunities and challenges. HTS now allows a high-resolution exploration of the vast taxonomic and metabolic diversity present in the microbial world, which can provide an exceptional insight on global ecosystem functioning, ecological processes and evolution. This exploration has also economic potential, as we will have access to the evolutionary innovation present in microbial metabolisms, which could be used for biotechnological development. HTS is also challenging the research community, and the current bottleneck is present in the data analysis side. At the moment, researchers are in a sequence data deluge, with sequencing throughput advancing faster than the computer power needed for data analysis. However, new tools and approaches are being developed constantly and the whole process could be depicted as a fast co-evolution between sequencing technology, informatics and microbiologists. In this work, we examine the most popular and recently commercialized HTS platforms as well as bioinformatics methods for data handling and analysis used in microbial metagenomics. This non-exhaustive review is intended to serve as a broad state-of-the-art guide to researchers expanding into this rapidly evolving field.


New Phytologist | 2011

Towards standardization of the description and publication of next‐generation sequencing datasets of fungal communities

R. Henrik Nilsson; Leho Tedersoo; Björn D. Lindahl; Rasmus Kjøller; Tor Carlsen; Christopher Quince; Kessy Abarenkov; Taina Pennanen; Jan Stenlid; Thomas D. Bruns; Karl-Henrik Larsson; Urmas Kõljalg; Håvard Kauserud

Bonfante P, Genre A. 2008. Plants and arbuscular mycorrhizal fungi: an evolutionary-developmental perspective. Trends in Plant Science 13: 492–498. Bonfante P, Selosse MA. 2010. A glimpse into the past of land plants and of their mycorrhizal affairs: from fossils to evo-devo. New Phytologist 186: 267–270. Boullard B. 1979. Considerations sur la symbiose fongique chez les pteridophytes. Syllogeus 19: 1–58. Brachmann A, Parniske M. 2006. The most widespread symbiosis on Earth. PLoS Biology 4: e239. Brundrett MC. 2002. Coevolution of roots and mycorrhizas of land plants. New Phytologist 154: 275–304. Brundrett MC. 2004. Diversity and classification of mycorrhizal associations. Biological Reviews 78: 473–495. Koltai H, Kapulnik Y, Eds. 2010. Arbuscular mycorrhizas: physiology and function, 2nd edn. Dordrecht, the Netherlands: Springer. Parniske M. 2008. Arbuscular mycorrhiza: the mother of plant root endosymbioses. Nature Reviews: Microbiology 6: 763–775. Phillips TL, DiMichele WA. 1992. Comparative ecology and life-history biology of arborescent lycopsids in Late Carboniferous swamps of Euramerica. Annals of the Missouri Botanical Garden 79: 560–588. Pressel S, Bidartondo MI, Ligrone R, Duckett JG. 2010. Fungal symbioses in bryophytes: new insights in the twenty first century. Phytotaxa 9: 238–253. Rothwell GW, Erwin DM. 1985. The rhizomorphic apex of Paurodendron; implications for homologies among the rooting organs of Lycopsida. American Journal of Botany 72: 86–98. Stewart WN. 1947. A comparative study of stigmarian appendages and Isoetes roots. American Journal of Botany 34: 315–324. Strullu-Derrien C, Rioult JP, Strullu DG. 2009. Mycorrhizas in Upper Carboniferous Radiculites-type cordaitalean rootlets. New Phytologist 182: 561–564. Strullu-Derrien C, Strullu DG. 2007. Mycorrhization of fossil and living plants. Comptes Rendus Palevol 6: 483–494. Stubblefield SP, Rothwell GW. 1981. Embryology and reproductive biology of Bothrodendrostrobus mundus (Lycopsida). American Journal of Botany 68: 625–634. Sudová R, Rydlová J, Ctvrtlı́ková M, Havránek P, Adamec L 2011. The incidence of arbuscular mycorrhiza in two submerged Isoëtes species. Aquatic Botany 94: 183–187. Taber RA, Trappe JM. 1982. Vesicular-arbuscular mycorrhiza in rhizomes, scale-like leaves, roots, and xylem of ginger. Mycologia 74: 156–161. Taylor TN, Taylor EL, Krings M. 2009. Paleobotany. The biology and evolution of fossil plants, 2nd edn. New York, NY, USA: Elsevier ⁄ Academic Press. Wagner CA, Taylor TN. 1981. Evidence for endomycorrhizae in Pennsylvanian age plant fossils. Science 212: 562–563. Winther JL, Friedman WE. 2008. Arbuscular mycorrhizal associations in Lycopodiaceae. New Phytologist 177: 790–801.


Proceedings of the Royal Society of London B: Biological Sciences | 2010

Climate change and spring-fruiting fungi

Håvard Kauserud; Einar Heegaard; Mikhail A. Semenov; Lynne Boddy; Rune Halvorsen; Leif Chr. Stige; Tim H. Sparks; Alan C. Gange; Nils Chr. Stenseth

Most macrofungi produce ephemeral fruit bodies during autumn but some have adapted to spring fruiting. In this study, temporal changes in the time of spring fruiting in Norway and the UK during 1960–2007 have been investigated by statistical analyses of about 6000 herbarium and field records, covering 34 species. Nearly 30 per cent of the temporal variation in fruiting could be ascribed to spatial and species-specific effects. Correcting for these effects, linear trends towards progressively earlier fruiting were detected during the entire period in both Norway and the UK, with a change in average fruiting day of 18 days over the study period. Early fruiting was correlated with high winter temperatures in both countries, indicating that the observed phenological changes are likely due to earlier onset of spring. There were also significant correlations between climatic conditions in one year and timing of fruiting the following year, indicating that below-ground mycelia are influenced by climatic conditions over a longer time period before fruiting. Fruiting dates were, however, not strictly related to changes in vernal accumulated thermal time. Our results indicate that global warming has lead to progressively earlier fruiting of spring fungi in northwest Europe during the last half century.


Molecular Ecology | 2005

Multiple gene genealogies and AFLPs suggest cryptic speciation and long-distance dispersal in the basidiomycete Serpula himantioides (Boletales).

Håvard Kauserud; Øyvind Stensrud; Cony Decock; Kamran Shalchian-Tabrizi; Trond Schumacher

Serpula himantioides (Boletales, Basidiomycota) produces thin resupinate basidiocarps on dead coniferous wood worldwide and causes damage in buildings as well. In this study, we present evidence for the existence of at least three phylogenetically defined cryptic species (referred to as Sib I–III) within the morphospecies S. himantioides, a conclusion based on analyses of sequence data from four DNA regions and amplified fragment length polymorphisms (AFLPS). A low degree of shared sequence polymorphisms was observed among the three lineages indicating a long‐lasting separation. The AFLPs revealed two additional subgroups within Sib III. Results from mating studies were consistent with the molecular data. In Sib III, no correspondence between genetic and geographical distance was observed among isolates worldwide, presumably reflecting recent dispersal events. Our results indicate that at least two of the lineages (Sib II and Sib III) have wide sympatric distributions. A population genetic analysis of Sib III isolates, scoring sequence polymorphisms as codominant SNP markers, indicates that panmictic conditions exist in the Sib III group. This study supports the view that cryptic speciation is a common phenomenon in basidiomycete fungi and that phylogenetic species recognition can be a powerful inference to detect cryptic species. Furthermore, this study shows that AFLP data are a valuable supplement to DNA sequence data in that they may detect a finer level of genetic variation.

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Rune Halvorsen

American Museum of Natural History

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Einar Heegaard

Norwegian Forest and Landscape Institute

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Ulf Büntgen

University of Cambridge

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Mikael Ohlson

Norwegian University of Life Sciences

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