| 1. |
- Dawson, S. K., et al.
(författare)
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Fungal trait-environment relationships in wood-inhabiting communities of boreal forest patches
- 2024
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Ingår i: Functional Ecology. - : Wiley. - 0269-8463 .- 1365-2435.
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Tidskriftsartikel (refereegranskat)abstract
- Fungal traits can provide a mechanistic understanding of how wood-inhabiting fungi interact with their environment and how that influences community assembly in deadwood. However, fungal trait exploration is relatively new and almost no studies measure fungal traits in their environment. In this study we tested species- and trait-environment relationships in reproducing fungal communities inhabiting 571 Norway spruce (Picea abies) logs in 55 isolated forest patches (0.1–9.9 ha) of different naturalness types, located in Northern boreal Sweden. The studied patches were (1) semi-natural set-aside patches within highly managed landscapes, or (2) old-growth natural patches located in an unmanaged landscape. We tested species and trait relationships to deadwood substrate and forest patch variables. We measured mean fruit body size and density for each of the 19 species within communities. Traits assembled in relation to log decay stage and forest patch naturalness, illustrating the important role of deterministic environmental filtering in shaping reproducing wood-inhabiting fungal communities. Early decay stage communities had larger, less dense, annual fruiting bodies of half-resupinate type and were more often white-rot fungi. Species rich mid-decay stage communities had mixed trait assemblages with more long lived perennial fruit bodies of intermediate size, and both brown- and white-rot fungi equally represented. Finally, late decay stage communities had smaller, denser and perennial fruit bodies, more often of the brown-rot type. The relationships between the studied traits and decay stages were similar in both set-aside and natural patches. However, set-aside semi-natural patches in highly managed landscapes more frequently supported species with smaller, perennial and resupinate fruit bodies compared to natural patches in an unmanaged landscape. Synthesis. We found that log decay stage was the primary driver of fungal community assembly of species and traits in isolated forest patches. Our results suggest that decay stage filters four reproduction traits (fruit body density, size, lifespan and type) and one resource-use trait (white or brown rot). Our results highlights, for the first time, that communities with diverse fungal reproductive traits are maintained foremost across all deadwood decay stages under different forest naturalness conditions. Read the free Plain Language Summary for this article on the Journal blog.
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| 2. |
- Engelbrecht Clemmensen, Karina, et al.
(författare)
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Roots and associated fungi drive long-term carbon sequestration in boreal forest
- 2013
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 339:6127, s. 1615-1618
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Tidskriftsartikel (refereegranskat)abstract
- Boreal forest soils function as a terrestrial net sink in the global carbon cycle. The prevailing dogma has focused on aboveground plant litter as a principal source of soil organic matter. Using C-14 bomb-carbon modeling, we show that 50 to 70% of stored carbon in a chronosequence of boreal forested islands derives from roots and root-associated microorganisms. Fungal biomarkers indicate impaired degradation and preservation of fungal residues in late successional forests. Furthermore, 454 pyrosequencing of molecular barcodes, in conjunction with stable isotope analyses, highlights root-associated fungi as important regulators of ecosystem carbon dynamics. Our results suggest an alternative mechanism for the accumulation of organic matter in boreal forests during succession in the long-term absence of disturbance.
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| 3. |
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| 4. |
- Graco-Roza, Caio, et al.
(författare)
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Distance decay 2.0 – A global synthesis of taxonomic and functional turnover in ecological communities
- 2022
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Ingår i: Global Ecology and Biogeography. - : Wiley. - 1466-822X .- 1466-8238. ; 31:7, s. 1399-1421
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Tidskriftsartikel (refereegranskat)abstract
- Aim: Understanding the variation in community composition and species abundances (i.e., beta-diversity) is at the heart of community ecology. A common approach to examine beta-diversity is to evaluate directional variation in community composition by measuring the decay in the similarity among pairs of communities along spatial or environmental distance. We provide the first global synthesis of taxonomic and functional distance decay along spatial and environmental distance by analysing 148 datasets comprising different types of organisms and environments.Location: Global.Time period: 1990 to present.Major taxa studied: From diatoms to mammals.Method: We measured the strength of the decay using ranked Mantel tests (Mantel r) and the rate of distance decay as the slope of an exponential fit using generalized linear models. We used null models to test whether functional similarity decays faster or slower than expected given the taxonomic decay along the spatial and environmental distance. We also unveiled the factors driving the rate of decay across the datasets, including latitude, spatial extent, realm and organismal features.Results: Taxonomic distance decay was stronger than functional distance decay along both spatial and environmental distance. Functional distance decay was random given the taxonomic distance decay. The rate of taxonomic and functional spatial distance decay was fastest in the datasets from mid-latitudes. Overall, datasets covering larger spatial extents showed a lower rate of decay along spatial distance but a higher rate of decay along environmental distance. Marine ecosystems had the slowest rate of decay along environmental distances.Main conclusions: In general, taxonomic distance decay is a useful tool for biogeographical research because it reflects dispersal-related factors in addition to species responses to climatic and environmental variables. Moreover, functional distance decay might be a cost-effective option for investigating community changes in heterogeneous environments.
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| 5. |
- Hamis, S., et al.
(författare)
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Spatial cumulant models enable spatially informed treatment strategies and analysis of local interactions in cancer systems
- 2023
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Ingår i: Journal of Mathematical Biology. - : Springer Nature. - 0303-6812 .- 1432-1416. ; 86:5
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Tidskriftsartikel (refereegranskat)abstract
- Theoretical and applied cancer studies that use individual-based models (IBMs) have been limited by the lack of a mathematical formulation that enables rigorous analysis of these models. However, spatial cumulant models (SCMs), which have arisen from theoretical ecology, describe population dynamics generated by a specific family of IBMs, namely spatio-temporal point processes (STPPs). SCMs are spatially resolved population models formulated by a system of differential equations that approximate the dynamics of two STPP-generated summary statistics: first-order spatial cumulants (densities), and second-order spatial cumulants (spatial covariances). We exemplify how SCMs can be used in mathematical oncology by modelling theoretical cancer cell populations comprising interacting growth factor-producing and non-producing cells. To formulate model equations, we use computational tools that enable the generation of STPPs, SCMs and mean-field population models (MFPMs) from user-defined model descriptions (Cornell et al. Nat Commun 10:4716, 2019). To calculate and compare STPP, SCM and MFPM-generated summary statistics, we develop an application-agnostic computational pipeline. Our results demonstrate that SCMs can capture STPP-generated population density dynamics, even when MFPMs fail to do so. From both MFPM and SCM equations, we derive treatment-induced death rates required to achieve non-growing cell populations. When testing these treatment strategies in STPP-generated cell populations, our results demonstrate that SCM-informed strategies outperform MFPM-informed strategies in terms of inhibiting population growths. We thus demonstrate that SCMs provide a new framework in which to study cell-cell interactions, and can be used to describe and perturb STPP-generated cell population dynamics. We, therefore, argue that SCMs can be used to increase IBMs' applicability in cancer research.
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| 6. |
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| 7. |
- Ovaskainen, O., et al.
(författare)
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Combining high-throughput sequencing with fruit body surveys reveals contrasting life-history strategies in fungi
- 2013
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Ingår i: Isme Journal. - : Springer Science and Business Media LLC. - 1751-7362 .- 1751-7370. ; 7:9, s. 1696-1709
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Tidskriftsartikel (refereegranskat)abstract
- Before the recent revolution in molecular biology, field studies on fungal communities were mostly confined to fruit bodies, whereas mycelial interactions were studied in the laboratory. Here we combine high-throughput sequencing with a fruit body inventory to study simultaneously mycelial and fruit body occurrences in a community of fungi inhabiting dead wood of Norway spruce. We studied mycelial occurrence by extracting DNA from wood samples followed by 454-sequencing of the ITS1 and ITS2 regions and an automated procedure for species identification. In total, we detected 198 species as mycelia and 137 species as fruit bodies. The correlation between mycelial and fruit body occurrences was high for the majority of the species, suggesting that high-throughput sequencing can successfully characterize the dominating fungal communities, despite possible biases related to sampling, PCR, sequencing and molecular identification. We used the fruit body and molecular data to test hypothesized links between life history and population dynamic parameters. We show that the species that have on average a high mycelial abundance also have a high fruiting rate and produce large fruit bodies, leading to a positive feedback loop in their population dynamics. Earlier studies have shown that species with specialized resource requirements are rarely seen fruiting, for which reason they are often classified as red-listed. We show with the help of high-throughput sequencing that some of these species are more abundant as mycelium in wood than what could be expected from their occurrence as fruit bodies.
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| 8. |
- Somervuo, P., et al.
(författare)
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Unbiased probabilistic taxonomic classification for DNA barcoding
- 2016
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 32:19, s. 2920-2927
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Tidskriftsartikel (refereegranskat)abstract
- Motivation: When targeted to a barcoding region, high-throughput sequencing can be used to identify species or operational taxonomical units from environmental samples, and thus to study the diversity and structure of species communities. Although there are many methods which provide confidence scores for assigning taxonomic affiliations, it is not straightforward to translate these values to unbiased probabilities. We present a probabilistic method for taxonomical classification (PROTAX) of DNA sequences. Given a pre-defined taxonomical tree structure that is partially populated by reference sequences, PROTAX decomposes the probability of one to the set of all possible outcomes. PROTAX accounts for species that are present in the taxonomy but that do not have reference sequences, the possibility of unknown taxonomical units, as well as mislabeled reference sequences. PROTAX is based on a statistical multinomial regression model, and it can utilize any kind of sequence similarity measures or the outputs of other classifiers as predictors. Results: We demonstrate the performance of PROTAX by using as predictors the output from BLAST, the phylogenetic classification software TIPP, and the RDP classifier. We show that PROTAX improves the predictions of the baseline implementations of TIPP and RDP classifiers, and that it is able to combine complementary information provided by BLAST and TIPP, resulting in accurate and unbiased classifications even with very challenging cases such as 50% mislabeling of reference sequences. Availability and implementation: Perl/R implementation of PROTAX is available at http://www.helsinki.fi/science/metapop/Software.htm. © 2016 The Author. Published by Oxford University Press. All rights reserved.
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| 9. |
- Sundell, J., et al.
(författare)
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Predation on two vole species by a shared predator: antipredatory response and prey preference
- 2008
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Ingår i: Population Ecology. - : Wiley. - 1438-3896 .- 1438-390X. ; 50:3, s. 257-266
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Tidskriftsartikel (refereegranskat)abstract
- In prey communities with shared predators, variation in prey vulnerability is a key factor in shaping community dynamics. Conversely, the hunting efficiency of a predator depends on the prey community structure, preferences of the predator and antipredatory behavioural traits of the prey. We studied experimentally, under seminatural field conditions, the preferences of a predator and the antipredatory responses of prey in a system consisting of two Myodes species of voles, the grey-sided vole (M. rufocanus Sund.) and the bank vole (M. glareolus Schreb.), and their specialist predator, the least weasel (Mustela nivalis nivalis L.). To quantify the preference of the weasels, we developed a new modelling framework that can be used for unbalanced data. The two vole species were hypothesised to have different habitat-dependent vulnerabilities. We created two habitats, open and forest, to provide different escape possibilities for the voles. We found a weak general preference of the weasels for the grey-sided voles over the bank voles, and a somewhat stronger preference specifically in open habitats. The weasels clearly preferred male grey-sided voles over females, whereas in bank voles, there was no difference. The activity of voles changed over time, so that voles increased their movements immediately after weasel introduction, but later adjusted their movements to times of lowered predation risk. Females that were more active had an elevated mortality risk, whereas in the case of males, the result was the opposite. We conclude that, in vulnerability to predation, the species- or habitat-specific characteristics of these prey species are playing a minor role compared to sex-specific characteristics.
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