| 1. |
- Zamora, Juan Carlos, et al.
(författare)
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Considerations and consequences of allowing DNA sequence data as types of fungal taxa
- 2018
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Ingår i: IMA Fungus. - : INT MYCOLOGICAL ASSOC. - 2210-6340 .- 2210-6359. ; 9:1, s. 167-185
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Tidskriftsartikel (refereegranskat)abstract
- Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
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| 2. |
- Corbett, Thomas, et al.
(författare)
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Organic carbon source controlled microbial olivine dissolution in small-scale flow-through bioreactors, for CO2 removal
- 2024
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Ingår i: NPJ MATERIALS DEGRADATION. - : Nature Publishing Group. - 2397-2106. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- The development of carbon dioxide removal methods, coupled with decreased CO2 emissions, is fundamental to achieving the targets outlined in the Paris Agreement limiting global warming to 1.5 degrees C. Here we are investigating the importance of the organic carbon feedstock to support silicate mineral weathering in small-scale flow through bioreactors and subsequent CO2 sequestration. Here, we combine two bacteria and two fungi, widely reported for their weathering potential, in simple flow through bioreactors (columns) consisting of forsterite and widely available, cheap organic carbon sources (wheat straw, bio-waste digestate of pig manure and biowaste, and manure compost), over six weeks. Compared to their corresponding abiotic controls, the inoculated straw and digestate columns release more total alkalinity (similar to 2 times more) and produce greater dissolved and solid inorganic carbon (29% for straw and 13% for digestate), suggesting an increase in CO2 sequestration because of bio-enhanced silicate weathering. Microbial biomass is higher in the straw columns compared to the digestate and manure compost columns, with a phospholipid fatty acid derived total microbial biomass 10 x greater than the other biotic columns. Scanning Electron Microscopy imaging shows the most extensive colonisation and biofilm formation on the mineral surfaces in the straw columns. The biotic straw and digestate columns sequester 50 and 14 mg C more than their abiotic controls respectively, while there is no difference in the manure columns. The selection of organic carbon sources to support microbial communities in the flow through bioreactors controlls the silicate weathering rates and CO2 sequestration.
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| 3. |
- Cheeke, Tanya, et al.
(författare)
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Dominant mycorrhizal association of trees alters carbon and nutrient cycling by selecting for microbial groups with distinct enzyme function
- 2017
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Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 214:1, s. 432-442
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Tidskriftsartikel (refereegranskat)abstract
- While it is well established that plants associating with arbuscular mycorrhizal (AM) and ectomycorrhizal (ECM) fungi cycle carbon (C) and nutrients in distinct ways, we have a limited understanding of whether varying abundance of ECM and AM plants in a stand can provide integrative proxies for key biogeochemical processes. We explored linkages between the relative abundance of AM and ECM trees and microbial functioning in three hardwood forests in southern Indiana, USA. Across each site's 'mycorrhizal gradient', we measured fungal biomass, fungal : bacterial (F : B) ratios, extracellular enzyme activities, soil carbon : nitrogen ratio, and soil pH over a growing season. We show that the percentage of AM or ECM trees in a plot promotes microbial communities that both reflect and determine the C to nutrient balance in soil. Soils dominated by ECM trees had higher F : B ratios and more standing fungal biomass than AM stands. Enzyme stoichiometry in ECM soils shifted to higher investment in extracellular enzymes needed for nitrogen and phosphorus acquisition than in C-acquisition enzymes, relative to AM soils. Our results suggest that knowledge of mycorrhizal dominance at the stand or landscape scale may provide a unifying framework for linking plant and microbial community dynamics, and predicting their effects on ecological function.
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| 4. |
- Cheeke, Tanya, et al.
(författare)
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Variation in hyphal production rather than turnover regulates standing fungal biomass in temperate hardwood forests
- 2021
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Ingår i: Ecology. - : John Wiley & Sons. - 0012-9658 .- 1939-9170. ; 102:3
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Tidskriftsartikel (refereegranskat)abstract
- Soil fungi link above- and belowground carbon (C) fluxes through their interactions with plants and contribute to C and nutrient dynamics through the production, turnover, and activity of fungal hyphae. Despite their importance to ecosystem processes, estimates of hyphal production and turnover rates are relatively uncommon, especially in temperate hardwood forests. We sequentially harvested hyphal ingrowth bags to quantify the rates of Dikarya (Ascomycota and Basidiomycota) hyphal production and turnover in three hardwood forests in the Midwestern United States, where plots differed in their abundance of arbuscular (AM)-vs. ectomycorrhizal (ECM)-associated trees. Hyphal production rates increased linearly with the percentage of ECM trees and annual production rates were 66% higher in ECM- than AM-dominated plots. Hyphal turnover rates did not differ across the mycorrhizal gradient (plots varying in their abundance of AM vs. ECM trees), suggesting that the greater fungal biomass in ECM-dominated plots relates to greater fungal production rather than slower fungal turnover. Differences in hyphal production across the gradient aligned with distinctly different fungal communities and activities. As ECM trees increased in dominance, fungi inside ingrowth bags produced more extracellular enzymes involved in degrading nitrogen (N)-bearing relative to C-bearing compounds, suggesting greater fungal (and possibly plant) N demand in ECM-dominated soils. Collectively, our results demonstrate that shifts in temperate tree species composition that result in changes in the dominant type of mycorrhizal association may have strong impacts on Dikarya hyphal production, fungal community composition and extracellular enzyme activity, with important consequences for soil C and N cycling.
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| 5. |
- Eshghi Sahraei, Shadi, et al.
(författare)
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Effects of operational taxonomic unit inference methods on soil microeukaryote community analysis using long‐read metabarcoding
- 2022
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Ingår i: Ecology and Evolution. - : John Wiley & Sons. - 2045-7758. ; 12:3
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Tidskriftsartikel (refereegranskat)abstract
- Long amplicon metabarcoding has opened the door for phylogenetic analysis of the largely unknown communities of microeukaryotes in soil. Here, we amplified and sequenced the ITS and LSU regions of the rDNA operon (around 1500 bp) from grassland soils using PacBio SMRT sequencing. We tested how three different methods for generation of operational taxonomic units (OTUs) effected estimated richness and identified taxa, and how well large-scale ecological patterns associated with shifting environmental conditions were recovered in data from the three methods. The field site at Kungsängen Nature Reserve has drawn frequent visitors since Linnaeus's time, and its species rich vegetation includes the largest population of Fritillaria meleagris in Sweden. To test the effect of different OTU generation methods, we sampled soils across an abrupt moisture transition that divides the meadow community into a Carex acuta dominated plant community with low species richness in the wetter part, which is visually distinct from the mesic-dry part that has a species rich grass-dominated plant community including a high frequency of F. meleagris. We used the moisture and plant community transition as a framework to investigate how detected belowground microeukaryotic community composition was influenced by OTU generation methods. Soil communities in both moisture regimes were dominated by protists, a large fraction of which were taxonomically assigned to Ciliophora (Alveolata) while 30%–40% of all reads were assigned to kingdom Fungi. Ecological patterns were consistently recovered irrespective of OTU generation method used. However, different methods strongly affect richness estimates and the taxonomic and phylogenetic resolution of the characterized community with implications for how well members of the microeukaryotic communities can be recognized in the data.
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| 6. |
- Eshghi Sahraei, Shadi, et al.
(författare)
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Whole genome analyses based on single, field collected spores of the arbuscular mycorrhizal fungus Funneliformis geosporum
- 2022
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Ingår i: Mycorrhiza. - : Springer. - 0940-6360 .- 1432-1890. ; 32:5-6, s. 361-371
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Tidskriftsartikel (refereegranskat)abstract
- Arbuscular mycorrhizal (AM) fungi are ubiquitous mutualistic symbionts of most terrestrial plants and many complete their lifecycles underground. Whole genome analysis of AM fungi has long been restricted to species and strains that can be maintained under controlled conditions that facilitate collection of biological samples. There is some evidence suggesting that AM fungi can adapt to culture resulting in phenotypic and possibly also genotypic changes in the fungi. In this study, we used field isolated spores of AM fungi and identified them as Funneliformis geosporum based on morphology and phylogenetic analyses. We separately assembled the genomes of two representative spores using DNA sequences of 19 and 22 individually amplified nuclei. The genomes were compared with previously published data from other members of Glomeraceae including two strains of F. mosseae. No significant differences were observed among the species in terms of gene content, while the single nucleotide polymorphism density was higher in the strains of F. geosporum than in the strains of F. mosseae. In this study, we demonstrate that it is possible to sequence and assemble genomes from AM fungal spores sampled in the field, which opens up the possibility to include uncultured AM fungi in phylogenomic and comparative genomic analysis and to study genomic variation in natural populations of these important plant symbionts.
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| 7. |
- Finlay, Roger, et al.
(författare)
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Reviews and syntheses : Biological weathering and its consequences at different spatial levels - from nanoscale to global scale
- 2020
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Ingår i: Biogeosciences. - : Copernicus GmbH. - 1726-4170 .- 1726-4189. ; 17:6, s. 1507-1533
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Forskningsöversikt (refereegranskat)abstract
- Plant nutrients can be recycled through microbial decomposition of organic matter but replacement of base cations and phosphorus, lost through harvesting of biomass/biofuels or leaching, requires de novo supply of fresh nutrients released through weathering of soil parent material (minerals and rocks). Weathering involves physical and chemical processes that are modified by biological activity of plants, microorganisms and animals. This article reviews recent progress made in understanding biological processes contributing to weathering. A perspective of increasing spatial scale is adopted, examining the consequences of biological activity for weathering from nanoscale interactions, through in vitro and in planta microcosm and meso-cosm studies, to field experiments, and finally ecosystem and global level effects. The topics discussed include the physical alteration of minerals and mineral surfaces; the composition, amounts, chemical properties, and effects of plant and microbial secretions; and the role of carbon flow (including stabilisation and sequestration of C in organic and inorganic forms). Although the predominant focus is on the effects of fungi in forest ecosystems, the properties of biofilms, including bacterial interactions, are also discussed. The implications of these biological processes for modelling are discussed, and we attempt to identify some key questions and knowledge gaps, as well as experimental approaches and areas of research in which future studies are likely to yield useful results. A particular focus of this article is to improve the representation of the ways in which biological processes complement physical and chemical processes that mobilise mineral elements, making them available for plant uptake. This is necessary to produce better estimates of weathering that are required for sustainable management of forests in a post-fossil-fuel economy. While there are abundant examples of nanometre- and micrometre-scale physical interactions between microorganisms and different minerals, opinion appears to be divided with respect to the quantitative significance of these observations for overall weathering. Numerous in vitro experiments and microcosm studies involving plants and their associated microorganisms suggest that the allocation of plant-derived carbon, mineral dissolution and plant nutrient status are tightly coupled, but there is still disagreement about the extent to which these processes contribute to field-scale observations. Apart from providing dynamically responsive pathways for the allocation of plant-derived carbon to power dissolution of minerals, mycorrhizal mycelia provide conduits for the long-distance trans-portation of weathering products back to plants that are also quantitatively significant sinks for released nutrients. These mycelial pathways bridge heterogeneous substrates, reducing the influence of local variation in C : N ratios. The production of polysaccharide matrices by biofilms of interacting bacteria and/or fungi at interfaces with mineral surfaces and roots influences patterns of production of antibiotics and quorum sensing molecules, with concomitant effects on microbial community structure, and the qualitative and quantitative composition of mineral-solubilising compounds and weathering products. Patterns of carbon allocation and nutrient mobilisation from both organic and inorganic substrates have been studied at larger spatial and temporal scales, including both ecosystem and global levels, and there is a generally wider degree of acceptance of the systemic effects of microorganisms on patterns of nutrient mobilisation. Theories about the evolutionary development of weathering processes have been advanced but there is still a lack of information connecting processes at different spatial scales. Detailed studies of the liquid chemistry of local weathering sites at the micrometre scale, together with upscaling to soil-scale dissolution rates, are advocated, as well as new approaches involving stable isotopes.
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| 8. |
- Furneaux, Brendan R., et al.
(författare)
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Both ectomycorrhizal tree diversity and soil characteristics structure ectomycorrhizal mushroom communities, and production in Sudanian savanna woodlands
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Ectomycorrhiza (ECM) are a symbiosis between plant and fungi where the plant get nutrients and other benefits from the fungi while the fungi get energy rich carbon compounds from the plant.Many ECM fungi form fleshy fruitbodies, including many choice edible mushrooms.Sudanian savanna woodlands are a tropical ecosystem that has a large proportion of ECM trees, but is under severe threat due to human activities.Based on three mushroom seasons of biweekly frutingbody collection we analyze the environmental factors driving the structure of the ECM community, including: composition, diversity, richness and biomass production.As wild edible mushrooms are an important food supplement in the region, we also analyzed the community structure of local choice edibles specifically.Different types of factors have been shown to influence different systems so we consequently take a comprehensive approach to what environmental factors are investigated, including ECM tree community structure, microclimate, and soil characteristics.We find that the spatial variation in ECM fungal community structure within our study area is larger than the variation in ECM fungal community structure of the study area between years.The richness of ECM host trees influenced all aspects of the spatial community structure, with a positive effect on diversity, richness, and biomass production.Microclimate also had an affect on all aspects of the community structure, but the relative importance of soil temperature and soil moisture varied.Soil characteristics were the strongest correlates of species diversity and richness, as well as biomass production, with soil nitrogen levels found to have a negative effect while phosphorus had a positive effect.Soil characteristicss were not found to be important to species composition, but this may be due to lack of statistical power, since the sampling size was lower for these factors than the others.Despite our comprehensive measurements, most of the spatial variation was not explained by any of the included factors.This variation may be due to unmeasured environmental, individual, or population level factors.
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| 9. |
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| 10. |
- Furneaux, Brendan R., et al.
(författare)
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Long- and short-read metabarcoding technologies reveal similar spatiotemporal structures in fungal communities
- 2021
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Ingår i: Molecular Ecology Resources. - : John Wiley & Sons. - 1755-098X .- 1755-0998. ; 21:6, s. 1833-1849
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Tidskriftsartikel (refereegranskat)abstract
- Fungi form diverse communities and play essential roles in many terrestrial ecosystems, yet there are methodological challenges in taxonomic and phylogenetic placement of fungi from environmental sequences. To address such challenges, we investigated spatiotemporal structure of a fungal community using soil metabarcoding with four different sequencing strategies: short-amplicon sequencing of the ITS2 region (300-400 bp) with Illumina MiSeq, Ion Torrent Ion S5 and PacBio RS II, all from the same PCR library, as well as long-amplicon sequencing of the full ITS and partial LSU regions (1200-1600 bp) with PacBio RS II. Resulting community structure and diversity depended more on statistical method than sequencing technology. The use of long-amplicon sequencing enables construction of a phylogenetic tree from metabarcoding reads, which facilitates taxonomic identification of sequences. However, long reads present issues for denoising algorithms in diverse communities. We present a solution that splits the reads into shorter homologous regions prior to denoising, and then reconstructs the full denoised reads. In the choice between short and long amplicons, we suggest a hybrid approach using short amplicons for sampling breadth and depth, and long amplicons to characterize the local species pool for improved identification and phylogenetic analyses.
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| 11. |
- George, T. S., et al.
(författare)
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Organic phosphorus in the terrestrial environment : a perspective on the state of the art and future priorities
- 2018
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Ingår i: Plant and Soil. - : Springer Netherlands. - 0032-079X .- 1573-5036. ; 427:1-2, s. 191-208
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Tidskriftsartikel (refereegranskat)abstract
- Background: The dynamics of phosphorus (P) in the environment is important for regulating nutrient cycles in natural and managed ecosystems and an integral part in assessing biological resilience against environmental change. Organic P (P-o) compounds play key roles in biological and ecosystems function in the terrestrial environment being critical to cell function, growth and reproduction.Scope: We asked a group of experts to consider the global issues associated with P-o in the terrestrial environment, methodological strengths and weaknesses, benefits to be gained from understanding the P-o cycle, and to set priorities for P-o research.Conclusions: We identified seven key opportunities for P-o research including: the need for integrated, quality controlled and functionally based methodologies; assessment of stoichiometry with other elements in organic matter; understanding the dynamics of P-o in natural and managed systems; the role of microorganisms in controlling P-o cycles; the implications of nanoparticles in the environment and the need for better modelling and communication of the research. Each priority is discussed and a statement of intent for the P-o research community is made that highlights there are key contributions to be made toward understanding biogeochemical cycles, dynamics and function of natural ecosystems and the management of agricultural systems.
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| 12. |
- Kalsoom Khan, Faheema, et al.
(författare)
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Naming the untouchable - environmental sequences and niche partitioning as taxonomical evidence in fungi
- 2020
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Ingår i: IMA Fungus. - : BMC. - 2210-6340 .- 2210-6359. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Due to their submerged and cryptic lifestyle, the vast majority of fungal species are difficult to observe and describe morphologically, and many remain known to science only from sequences detected in environmental samples. The lack of practices to delimit and name most fungal species is a staggering limitation to communication and interpretation of ecology and evolution in kingdom Fungi. Here, we use environmental sequence data as taxonomical evidence and combine phylogenetic and ecological data to generate and test species hypotheses in the class Archaeorhizomycetes (Taphrinomycotina, Ascomycota). Based on environmental amplicon sequencing from a well-studied Swedish pine forest podzol soil, we generate 68 distinct species hypotheses of Archaeorhizomycetes, of which two correspond to the only described species in the class. Nine of the species hypotheses represent 78% of the sequenced Archaeorhizomycetes community, and are supported by long read data that form the backbone for delimiting species hypothesis based on phylogenetic branch lengths. Soil fungal communities are shaped by environmental filtering and competitive exclusion so that closely related species are less likely to co-occur in a niche if adaptive traits are evolutionarily conserved. In soil profiles, distinct vertical horizons represent a testable niche dimension, and we found significantly differential distribution across samples for a well-supported pair of sister species hypotheses. Based on the combination of phylogenetic and ecological evidence, we identify two novel species for which we provide molecular diagnostics and propose names. While environmental sequences cannot be automatically translated to species, they can be used to generate phylogenetically distinct species hypotheses that can be further tested using sequences as ecological evidence. We conclude that in the case of abundantly and frequently observed species, environmental sequences can support species recognition in the absences of physical specimens, while rare taxa remain uncaptured at our sampling and sequencing intensity.
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| 13. |
- Kluting, Kerri, et al.
(författare)
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Forest Fire Influence on Tomicus piniperda-Associated Fungal Communities and Phloem Nutrient Availability of Colonized Pinus sylvestris
- 2023
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Ingår i: Microbial Ecology. - : Springer. - 0095-3628 .- 1432-184X. ; 86:1, s. 224-239
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Tidskriftsartikel (refereegranskat)abstract
- Forest fire is known to positively affect bark beetle populations by providing fire-damaged trees with impaired defenses for infestation. Tomicus piniperda, the common pine shoot beetle, breeds and lays eggs under the bark of stressed pine trees and is considered a serious forest pest within its native range. Wood-colonizing fungi have been hypothesized to improve substrate quality and detoxify tree defensive chemistry to indirectly facilitate tree colonization by beetles. While some bark beetle species form symbiotic associations with fungi and actively vector their partners when colonizing new trees, T. piniperda does not have mycangia or body hairs for specific vectoring of fungi. To explore the T. piniperda-associated fungal community for signs of specific association, we used ITS metabarcoding to separately characterize fungal communities associated with surface and gut of male and female beetles. We also characterized the temporal changes in fungal community and nutrient status of pine phloem with and without beetle galleries. Sampling was performed 2 years after a natural forest fire and included both burnt and unburnt sites. In our study system, we find that forest fire significantly impacts the fungal community composition associated with T. piniperda and that fire may also indirectly change nutrient availability in phloem to beetle galleries. We conclude that T. piniperda can vector fungi to newly colonized trees but the absence of positive effects on substrate quality and minimal effects of sex indicate that vectoring of associated fungal communities is not a strategy associated with the T. piniperda life cycle.
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| 14. |
- Kluting, Kerri
(författare)
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Fungal molecular ecology in boreal forests and challenges associated with unidentified environmental DNA sequences
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Many fungi are characteristically difficult to observe and collect, making the process of documenting the world’s fungal diversity challenging. The vast majority of fungal species are undescribed. The use of DNA sequencing technologies has revolutionized the study of fungal diversity by facilitating the detection of new species, the investigation of community structure and dynamics, and the elucidation of evolutionary relationships. In this dissertation, I focus on filling in some of the many gaps in our understanding of fungal diversity and community ecology in boreal pine forests through the use of DNA sequence data. In the first half of this thesis, a metabarcoding approach is used to study the composition of fungal communities found in the soil of a Lithuanian coastal pine forest and in association with the bark beetle Tomicus piniperda in Swedish pine forests. In the second half, two different approaches are taken to describe taxa detected in environmental DNA. In paper I, I demonstrate how soil microhabitats, defined based on mineral vs organic soil type and root presence or absence, vary with respect to a suite of abiotic factors and shape fungal community composition belowground. These microhabitats support functionally and taxonomically distinct fungal communities and support the overall fungal diversity of the site through niche variation. In paper II, the relationships between a) the fungal communities found on and in bark beetles from forests that have been affected by forest fire and forests that have not, b) pine phloem that has been colonized by bark beetles and phloem that has not at two different post-colonization time points, and c) phloem chemical nutrients are described. In paper III, the diversity of species within the fungal class Archaeorhizomycetes in the soil of a Swedish pine forest was studied, and two new species are described using an integrative taxonomic approach that relies on environmental DNA sequence data as taxonomical evidence. Finally, in paper IV, a new class is described to accommodate a lineage previously detected in environmental DNA, and its first known species is described based on isolates collected during the study of paper III, one of which serves as the type specimen.
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| 15. |
- Kluting, Kerri L., et al.
(författare)
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Another dark taxon comes to light: Eludereomycetes, class nov. (Pucciniomycotina, Basidiomycota), and its first known living representative, Eluderea minerophilus, gen. et sp. nov.
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Only a small fraction of the world’s fungi is described, and the large number of unnamed fungal sequences from environmental DNA serves as a significant complication for taxonomic identification in metabarcoding studies. There are several deeply diverged fungal lineages—some hypothesized to represent class and order ranks—currently known only by environmental DNA sequences that represent them. Here, we describe a previously unidentified fungal culture as the first living representative of one of these lineages (previously referred to as ‘clade GS25’, hypothesized as an early diverging lineage sister to the Pucciniomycotina, Basidiomycota) and present its sequenced genome. We used a phylogenomic approach to test the placement and taxonomic rank of this lineage. We formally describe the first known species in Eludereomycetes, class nov. (Pucciniomycotina, Basidiomycota): Eluderea minerophilus, gen. et sp. nov. This species was isolated from Pinus sylvestris roots collected from a Swedish pine forest, where previously published environmental sequencing data from the site indicate that it is almost exclusively found in the deeper mineral soil horizons. Our analysis shows that the most closely related described species to E. minerophilus likely belongs to the Classiculomycetes, a class within the Pucciniomycotina that is morphologically, molecularly, and ecologically distinct from the Eludereomycetes. Identification of a living representative for this lineage previously detected in environmental DNA, ‘clade GS25’, and describing it as a new species was a somewhat serendipitous discovery made possible in part due to characteristics of two previously published studies. We call attention to some of these aspects and propose a set of practices that could be adopted by the research community to help facilitate more connections between living fungus and environmental DNA sequence. The use of such practices would in turn help to alleviate some of the complications associated with unidentified fungal DNA sequences in reference databases and contribute towards a more complete understanding of fungal diversity.
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| 16. |
- Kluting, Kerri L., et al.
(författare)
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Distribution patterns of fungal taxa and inferred functional traits reflect the non-uniform vertical stratification of soil microhabitats in a coastal pine forest
- 2019
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Ingår i: FEMS Microbiology Ecology. - : Oxford University Press (OUP). - 0168-6496 .- 1574-6941. ; 95:11
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Tidskriftsartikel (refereegranskat)abstract
- In boreal systems, soil profiles typically consist of distinct stratified horizons, with organic layers at the surface overlying deeper mineral horizons providing microhabitat variation along a depth gradient, and vertical stratification of fungal communities along such soil profiles is commonly observed. We studied fungal community structure in a coastal pine forest along a gradient of decreasing influence from the coast. In this system, the vertical stratification pattern of soil microhabitats (defined here as organic, mineral with roots and mineral without roots: O, MR and MN, respectively) is non-uniform; organic horizons are sometimes buried under drifting sand dunes. Our results show that soil microhabitats are distinct with respect to physiochemical characteristics, community composition and OTU richness. While community composition was partly related to depth and distance from the coastal forest edge, microhabitat appeared to have the strongest influence. A closer inspection of the OTUs with the highest relative sequence abundance within each microhabitat revealed that microhabitats support functionally distinct fungal communities with respect to trophic mode and growth morphology. These results suggest that in coastal pine forests, variation in soil microhabitats contributes to the high fungal diversity found belowground and may play an important role in optimizing nutrient cycling.
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| 17. |
- Kluting, Kerri L., et al.
(författare)
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Forest fire influence on Tomicus piniperda-associated fungal communities and phloem nutrient availability of colonized Pinus sylvestris
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Forest fire is known to positively affect bark beetle populations by providing fire-damaged trees with impaired defenses for infestation. Tomicus piniperda, the common pine shoot beetle, breeds and lays eggs under the bark of stressed pine trees and is considered a serious forest pest within its native range. Wood-colonizing fungi have been hypothesized to improve substrate quality and detoxify tree defensive chemistry to indirectly facilitate tree colonization by beetles. While some bark beetle species form symbiotic associations with beneficial fungi and actively vector their partners when colonizing new trees, T. piniperda does not have mycangia or body hairs for specific vectoring of fungi. To explore the T. piniperda-associated fungal community for signs of specific association, we used ITS metabarcoding to separately characterize fungal communities associated with surface and gut of male and female beetles. We also characterized the temporal changes in fungal community and nutrient status of pine phloem with and without beetle galleries. Sampling was performed two years after a natural forest fire and included both burnt and unburnt sites.In our study system, we find that forest fire significantly impacts the fungal community composition associated with T. piniperda and that fire may also indirectly change nutrient availability in phloem to beetle galleries. We conclude that T. piniperda can vector fungi to newly colonized trees but the absence of positive effects on substrate quality and minimal effects of sex indicate that vectoring of associated fungal communities is not a strategy associated with the T. piniperda life cycle.
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| 18. |
- Meidl, Peter, et al.
(författare)
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Soil fungal communities of ectomycorrhizal dominated woodlands across West Africa
- 2021
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Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 81, s. 45-68
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Tidskriftsartikel (refereegranskat)abstract
- Forests and woodlands in the West African Guineo-Sudanian transition zone contain many tree species that form symbiotic interactions with ectomycorrhizal (ECM) fungi. These fungi facilitate plant growth by increasing nutrient and water uptake and include many fruiting body-forming fungi, including some edible mushrooms. Despite their importance for ecosystem functioning and anthropogenic use, diversity and distribution of ECM fungi is severely under-documented in West Africa. We conducted a broad regional sampling across five West African countries using soil eDNA to characterize the ECM as well as the total soil fungal community in gallery forests and savanna woodlands dominated by ECM host tree species. We subsequently sequenced the entire ITS region and much of the LSU region to infer a phylogeny for all detected soil fungal species. Utilizing a long read sequencing approach allows for higher taxonomic resolution by using the full ITS region, while the highly conserved LSU gene allows for a more accurate higher-level assignment of species hypotheses, including species without ITS-based taxonomy assignments. We detect no overall difference in species richness between gallery forests and woodlands. However, additional gallery forest plots and more samples per plot would have been needed to firmly conclude this pattern. Based on both abundance and richness, species from the families Russulaceae and Inocybaceae dominate the ECM fungal soil communities across both vegetation types. The community structure of both total soil fungi and ECM fungi was significantly influenced by vegetation types and showed strong correlation within plots. However, we found no significant difference in fungal community structure between samples collected adjacent to different host tree species within each plot. We conclude that within plots, the fungal community is structured more by the overall ECM host plant community than by the species of the individual host tree that each sample was collected from.
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| 19. |
- Montoliu-Nerin, Merce, et al.
(författare)
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Building de novo reference genome assemblies of complex eukaryotic microorganisms from single nuclei
- 2020
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- The advent of novel sequencing techniques has unraveled a tremendous diversity on Earth. Genomic data allow us to understand ecology and function of organisms that we would not otherwise know existed. However, major methodological challenges remain, in particular for multicellular organisms with large genomes. Arbuscular mycorrhizal (AM) fungi are important plant symbionts with cryptic and complex multicellular life cycles, thus representing a suitable model system for method development. Here, we report a novel method for large scale, unbiased nuclear sorting, sequencing, and de novo assembling of AM fungal genomes. After comparative analyses of three assembly workflows we discuss how sequence data from single nuclei can best be used for different downstream analyses such as phylogenomics and comparative genomics of single nuclei. Based on analysis of completeness, we conclude that comprehensive de novo genome assemblies can be produced from six to seven nuclei. The method is highly applicable for a broad range of taxa, and will greatly improve our ability to study multicellular eukaryotes with complex life cycles.
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| 20. |
- Montoliu-Nerin, Merce
(författare)
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Genomics of Arbuscular Mycorrhizal Fungi : Expanding knowledge, one assembly at a time
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Most life forms that inhabit Earth today are still unknown or are difficult to study. Accessing their DNA can give us information of their biology, ecology, and evolution, even when unculturable. The research here presented focused on method development for genomic research of non-model organisms. Paper I and II contributed to a comprehensive expansion of the genomic data available in arbuscular mycorrhizal (AM) fungi, an essential group of plant symbionts. While paper III and IV focused on the analysis of the generated genomic data. Paper I presents the development of a workflow that allows for DNA sequencing and assembling of AM fungal genomes, from as little as one single spore, by sorting and individually amplifying and sequencing nuclei. In paper II, the novel workflow was utilized to expand genomic data on AM fungi, by generating de novo genome assemblies from 22 different taxa. The evolutionary relationships within the group was also explored. In paper III possible genetic differences between nuclei of individual AM fungal organisms was examined, following the hypothesis of their sole reproductive asexual mode. Our results suggest low levels of genetic variation within the studied taxa. We also located genes involved in mating recognition, supporting earlier observations of a possible hitherto unknown sexual stage in AM fungal life cycle. Paper IV explores an important component that affects genomic architecture, the so-called transposable elements (TEs), which are selfish genetic elements that have the ability to move and multiply within the genome. These elements must be analyzed carefully, as we found that a significant part of what is initially classified as unknown repeat sequences are, in fact, not TEs, but genes from the fungus itself, that appear in many copies. We confirm that AM fungi contain a high proportion of TEs in their genomes. Furthermore, analyzing the evolutionary history of these genera, we observe a link with the existence of a possible control mechanism in the genus Rhizophagus. Our novel workflow and the comprehensive taxon sampling go beyond a few model organisms to bring the diverse monophyletic lineage of AM fungi fully into the genomic era.
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| 21. |
- Montoliu-Nerin, Merce, et al.
(författare)
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In-depth Phylogenomic Analysis of Arbuscular Mycorrhizal Fungi Based on a Comprehensive Set of de novo Genome Assemblies
- 2021
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Ingår i: Frontiers in Fungal Biology. - : Frontiers Media S.A.. - 2673-6128. ; 2
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Tidskriftsartikel (refereegranskat)abstract
- Morphological characters and nuclear ribosomal DNA (rDNA) phylogenies have so far been the basis of the current classifications of arbuscular mycorrhizal (AM) fungi. Improved understanding of the evolutionary history of AM fungi requires extensive ortholog sampling and analyses of genome and transcriptome data from a wide range of taxa. To circumvent the need for axenic culturing of AM fungi we gathered and combined genomic data from single nuclei to generate de novo genome assemblies covering seven families of AM fungi. We successfully sequenced the genomes of 15 AM fungal species for which genome data was not previously available. Comparative analysis of the previously published Rhizophagus irregularis DAOM197198 assembly confirm that our novel workflow generates genome assemblies suitable for phylogenomic analysis. Predicted genes of our assemblies, together with published protein sequences of AM fungi and their sister clades, were used for phylogenomic analyses. We evaluated the phylogenetic placement of Glomeromycota in relation to its sister phyla (Mucoromycota and Mortierellomycota), and found no support to reject a polytomy. Finally, we explored the phylogenetic relationships within Glomeromycota. Our results support family level classification from previous phylogenetic studies, and the polyphyly of the order Glomerales with Claroideoglomeraceae as the sister group to Glomeraceae and Diversisporales.
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| 22. |
- Montoliu-Nerin, Merce, 1991-, et al.
(författare)
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In-depth phylogenomic analysis of Glomeromycota based on a comprehensive set of de novogenome assemblies
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Morphological characters and nuclear ribosomal DNA (rDNA) phylogenies have been the bases of the current classifications of arbuscular mycorrhizal (AM) fungi. Improved understanding of the AM fungi phylogeny will depend upon a more extensive ortholog sampling, resulting from a wider range of available whole genome sequences from a large set of taxa. To circumvent the need for axenic culturing of AM fungi we use single nuclei sequencing to generate de novogenome assemblies of AM fungi covering seven families of Glomeromycota. The predicted genes of these assemblies, together with the available protein sequences of AM fungi and sister clades, were used for phylogenomic analysis. We confirm that our novel workflow generates high quality genome assemblies suitable for phylogenomic analysis of AM fungi. Within the monophyletic phylum Glomeromycota, we identify three candidate topologies, in which the family Glomerales is recovered as polyphyletic in two of them. Our results support family level classification from previous phylogenetic studies using sequences of the rDNA operon. Our multi-locus analyses identify alternative evolutionary histories within this diverse phylum.
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| 23. |
- Rosling, Anna, 1974-, et al.
(författare)
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Archaeorhizomycetes : Patterns of Distribution and Abundance in Soil
- 2013
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Ingår i: Genomics of Soil- and Plant-Associated Fungi. - Heidelberg : Springer Berlin/Heidelberg. - 9783642393396 ; , s. 333-349
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Bokkapitel (refereegranskat)abstract
- Soil fungal ecology has developed tremendously with the introduction of environmental sequencing. The soil under our feet harbors great fungal diversity including species and even lineages of unknown identity. Beyond identification we can use environmental sequences to trace distribution patterns of species and lineages to better understand their life strategies and ecological roles. Environmental sequences provide the largest available source of information on the ecology of Archaeorhizomycetes, a class of globally distributed ubiquitous soil fungi for which there are no known fruiting structures and only two of over 250 estimated species have been cultured.The class was initially known as the Soil Clone Group 1 (SCG1) (Porter et al. 2008) based on environmental sequences from four diverse ecosystems and twelve published studies. Porter and co-workers highlighted two important features of the class Archaeorhizomycetes: its broad distribution across diverse ecosystems as well as its high species diversity within sites. When the class of Archaeorhizomycetes was formally described by Rosling et al. in 2011, thousands of ITS sequences were available in public databases. Based on meta-data associated with these sequences, ecosystem specificity and geographic distribution patterns emerged among several putative species, i.e. OTUs, within the class. In this chapter we expand upon earlier analyses of distribution by adding complementary datasets including environmental LSU and SSU sequences. Habitat specificity and geographic distribution are further analyzed using public and previously unpublished sequences from ten field studies in Alaska.
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| 24. |
- Rosling, Anna, 1974-, et al.
(författare)
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Evolutionary history of arbuscular mycorrhizal fungi and genomic signatures of obligate symbiosis
- 2024
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Ingår i: BMC Genomics. - : BioMed Central (BMC). - 1471-2164. ; 25:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: The colonization of land and the diversification of terrestrial plants is intimately linked to the evolutionary history of their symbiotic fungal partners. Extant representatives of these fungal lineages include mutualistic plant symbionts, the arbuscular mycorrhizal (AM) fungi in Glomeromycota and fine root endophytes in Endogonales (Mucoromycota), as well as fungi with saprotrophic, pathogenic and endophytic lifestyles. These fungal groups separate into three monophyletic lineages but their evolutionary relationships remain enigmatic confounding ancestral reconstructions. Their taxonomic ranks are currently fluid.Results: In this study, we recognize these three monophyletic linages as phyla, and use a balanced taxon sampling and broad taxonomic representation for phylogenomic analysis that rejects a hard polytomy and resolves Glomeromycota as sister to a clade composed of Mucoromycota and Mortierellomycota. Low copy numbers of genes associated with plant cell wall degradation could not be assigned to the transition to a plant symbiotic lifestyle but appears to be an ancestral phylogenetic signal. Both plant symbiotic lineages, Glomeromycota and Endogonales, lack numerous thiamine metabolism genes but the lack of fatty acid synthesis genes is specific to AM fungi. Many genes previously thought to be missing specifically in Glomeromycota are either missing in all analyzed phyla, or in some cases, are actually present in some of the analyzed AM fungal lineages, e.g. the high affinity phosphorus transporter Pho89.Conclusion: Based on a broad taxon sampling of fungal genomes we present a well-supported phylogeny for AM fungi and their sister lineages. We show that among these lineages, two independent evolutionary transitions to mutualistic plant symbiosis happened in a genomic background profoundly different from that known from the emergence of ectomycorrhizal fungi in Dikarya. These results call for further reevaluation of genomic signatures associated with plant symbiosis.
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| 25. |
- Sánchez-García, Marisol, et al.
(författare)
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Single nuclei sequencing reveals low levels of intra-organismal genomic variation across strains in the genus Claroideoglomus
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Arbuscular mycorrhizal (AM) fungi are important plant symbionts that propagate predominantly with multinucleate asexual spores formed below ground. The degree of intra-organismal genetic variation in AM fungi has been a long-standing topic of debate due to difficulties in generating high quality genome assemblies from most species in this phylum in combination with exceptionally high levels of rDNA polymorphism compared to other eukaryotes.In the AM fungi Claroideoglomus etunicatum, visualization of nuclei migration during spore formation has demonstrated that sporogenesis is random or sectorial, firmly rejecting false sporogenesis with one or two founding nuclei (Jany and Pawlowska, 2010). We thus expect the composition of nuclei in a single Claroideoglomusspore to reflect that of the entire organism when we study intra-organismal genetic variation of individual spores from three strains in the genus Claroideoglomus. The three strains are all within the luteum/claroideumspecies complex that cannot be phylogenetically resolved based on rRNA large subunit genes (Vankuren et al., 2013). From each strain we generated 24 single nuclei genome assemblies to identify rRNA gene variants and MAT locus in each nucleus. Then, we map the reads of each individual nucleus to two different reference assemblies and identify SNPs within and between nuclei from single spores using two different softwares for variant calling. We identify the mating type locus and characterized intra-organismal genetic diversity in each strain and explore patterns of recombination and shared variants across strains. Based on earlier studies in the genus Rhizophagus, we expect nuclei to be haploid and within spore allele frequency patterns to be explained by the number of MAT type alleles.
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| 26. |
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| 27. |
- Urbina, Hector, 1977-, et al.
(författare)
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Specificity in Arabidopsis thaliana recruitment of root fungal communities from soil and rhizosphere
- 2018
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Ingår i: Fungal Biology. - : Elsevier BV. - 1878-6146 .- 1878-6162. ; 122:4, s. 231-240
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Tidskriftsartikel (refereegranskat)abstract
- Biotic and abiotic conditions in soil pose major constraints on growth and reproductive success of plants. Fungi are important agents in plant soil interactions but the belowground mycobiota associated with plants remains poorly understood. We grew one genotype each from Sweden and Italy of the widely studied plant model Arabidopsis thaliana. Plants were grown under controlled conditions in organic topsoil local to the Swedish genotype, and harvested after ten weeks. Total DNA was extracted from three belowground compartments: endosphere (sonicated roots), rhizosphere and bulk soil, and fungal communities were characterized from each by amplification and sequencing of the fungal barcode region ITS2. Fungal species diversity was found to decrease from bulk soil to rhizosphere to endo-sphere. A significant effect of plant genotype on fungal community composition was detected only in the endosphere compartment. Despite A. thaliana being a non-mycorrhizal plant, it hosts a number of known mycorrhiza fungi in its endosphere compartment, which is also colonized by endophytic, pathogenic and saprotrophic fungi. Species in the Archaeorhizomycetes were most abundant in rhizosphere samples suggesting an adaptation to environments with high nutrient turnover for some of these species. We conclude that A. thaliana endosphere fungal communities represent a selected subset of fungi recruited from soil and that plant genotype has small but significant quantitative and qualitative effects on these communities.
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| 28. |
- van Creij, Jelle, et al.
(författare)
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Stochastic nuclear organization and host-dependent allele contribution in Rhizophagus irregularis
- 2023
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Ingår i: BMC Genomics. - : BioMed Central (BMC). - 1471-2164. ; 24:1
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundArbuscular mycorrhizal (AM) fungi are arguably the most important symbionts of plants, offering a range of benefits to their hosts. However, the provisioning of these benefits does not appear to be uniform among AM fungal individuals, with genetic variation between fungal symbionts having a substantial impact on plant performance. Interestingly, genetic variation has also been reported within fungal individuals, which contain millions of haploid nuclei sharing a common cytoplasm. In the model AM fungus, Rhizophagus irregularis, several isolates have been reported to be dikaryotes, containing two genetically distinct types of nuclei recognized based on their mating-type (MAT) locus identity. However, their extremely coenocytic nature and lack of a known single nucleus stage has raised questions on the origin, distribution and dynamics of this genetic variation.ResultsHere we performed DNA and RNA sequencing at the mycelial individual, single spore and single nucleus levels to gain insight into the dynamic genetic make-up of the dikaryote-like R. irregularis C3 isolate and the effect of different host plants on its genetic variation. Our analyses reveal that parallel spore and root culture batches can have widely variable ratios of two main genotypes in C3. Additionally, numerous polymorphisms were found with frequencies that deviated significantly from the general genotype ratio, indicating a diverse population of slightly different nucleotypes. Changing host plants did not show consistent host effects on nucleotype ratio's after multiple rounds of subculturing. Instead, we found a major effect of host plant-identity on allele-specific expression in C3.ConclusionOur analyses indicate a highly dynamic/variable genetic organization in different isolates of R. irregularis. Seemingly random fluctuations in nucleotype ratio's upon spore formation, recombination events, high variability of non-tandemly repeated rDNA sequences and host-dependent allele expression all add levels of variation that may contribute to the evolutionary success of these widespread symbionts.
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| 29. |
- Xu, Wenbo, et al.
(författare)
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Exploring genomic repeats in arbuscular mycorrhizal fungi
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Arbuscular mycorrhizal (AM) fungi are obligate root symbionts that form mutualistic associations with the majority of terrestrial plant species. Due to their submerged and obligate biotrophic lifestyle, access to pure tissue is limited and it was only in the last decade that the first genome of one of these important symbionts could be sequenced. Compared to other fungi, much of the AM genome is made up of repetitive genetic elements (repeats), ranging from ~30% in Rhizophagus irregularisto 60% in Gigaspora rosea. Repeats are expected to consist mainly of transposable elements (TEs), of these the Class II TEs, also known as DNA transposons, have been found to be especially abundant in AM fungi. Several strains of R. irregularishave been sequenced and 11% - 17% of the repeats were DNA TEs and in G. rosea, DNA transposons account for 12% of the total repeats. However, repeat annotation softwares cannot classify most repeats in genomes of AM fungi. For example, in R. irregularis(A1) 70% of the total repeats were not classified and 72% in G. rosea. In this study, we carefully examined the unclassified repeats and found that a considerable proportion (7% - 35%) were non-TE-repeats that encode proteins not related to TE activities but potentially code for interesting biological functions, like starch binding and ion exchange activity. Across the analyzed AM fungi, a potential TE-silencing protein complex known as PIWI (P-element Induced WImpy testis) was also identified among the unclassified repeats. In addition to identifying non-TE-repeats, we also developed a strategy for automated annotation of unclassified repeats using Pfam and custom Hidden Markov Model (HMM) searches. With this strategy, 44 repeats out of 460 unclassified repeats were annotated to superfamily levels in our focus species Claroideoglomus claroideum (SA101).
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