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  • 1.
    Anslan, Sten
    et al.
    Univ Tartu, Inst Ecol & Earth Sci, 14A Ravila, EE-50411 Tartu, Estonia..
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Inst Ecol & Earth Sci, 14A Ravila, EE-50411 Tartu, Estonia.
    Tedersoo, Leho
    Univ Tartu, Nat Hist Museum, 14A Ravila, EE-50411 Tartu, Estonia..
    Seasonal and annual variation in fungal communities associated with epigeic springtails (Collembola spp.) in boreal forests2018In: Soil Biology and Biochemistry, ISSN 0038-0717, E-ISSN 1879-3428, Vol. 116, p. 245-252Article in journal (Refereed)
    Abstract [en]

    Soil fauna mediate nutrient cycling through engineering physical properties and altering microbial commtmities in soil. Collembola is one of the most abundant groups of soil fauna, which regulates microbial communities by consumption and dispersal. The spatial structure of associations between Collembola and soil microbes have been described in several studies, but temporal variation of these associations remains unclear. Using high throughput sequencing, we studied the fungal communities on Collembola (Entomobiya nivalis, Orchesella flavescens, Pogonognathellus longicornis) body surface, gut and their immediate habitat (topsoil samples) in four seasons across three years. The soil samples were characterized by fairly uniform relative abundance of saprotrophic and mycorrhizal fungi, whereas collembolans were associated mostly with saprotrophs. The structure of fungal communities from all substrate types exhibited comparable patterns of temporal distance decay of shnilarity. Unlike in soil, fungal richness and composition in Collembola body and gut samples exhibited seasonal and annual variation, with a significant interaction term, indicating low predictability. These results reflect spatial and temporal plasticity of the fungal communities associated with epigeic Collembola, indicating the high adaptability of collembolans to available conditions. We found that the Collembola associations with fungi (including diet) did not vary among the studied epigeic Collembola species. The detected high diversity of fungi associated with Collembola suggests that dispersal by arthropod vectors may represent a powerful alternative to aerial dispersal of fungal propagules.

  • 2. Anslan, Sten
    et al.
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Tedersoo, Leho
    Temporal changes in fungal communities associated with guts and appendages of Collembola as based on culturing and high-throughput sequencing2016In: Soil Biology and Biochemistry, ISSN 0038-0717, E-ISSN 1879-3428, Vol. 96, p. 152-159Article in journal (Refereed)
    Abstract [en]

    Due to high abundance and feeding habits, invertebrates are of great importance for shaping microbial communities at the fine scale. Springtails (Collembola) that feed on fungal spores and mycelia may contribute to dispersal through carrying fungal propagules in their guts or on their appendages. The Collembola–fungal associations are mainly investigated by microscopy or culturing techniques, which allow identify only fungi that have distinctive morphological characteristics or that can be cultured in vitro. Here we identified the Collembola-associated fungi on the body surface and in the gut content using both culturing and high-throughput sequencing (HTS) methods. We studied three epigeic Collembola species found on the Norway spruce dominated forest stands throughout the vegetation period – Entomobrya nivalisOrchesella flavescens andPogonognathellus longicornis. We discovered over 1200 fungal operational taxonomic units (OTUs), i.e. the proxies for species, based on 97% sequence similarity of the ITS2 subregion of ribosomal DNA. Most of the fungi were saprotrophs, but we detected also mycorrhizal, parasitic and lichenized fungi. Season was the most important factor affecting fungal richness and composition, especially on body surface. Although the data matrix revealed significant effect of substrate, we were unable to detect the significant fungal community differences between body surface and gut samples of conspecifics. There were no significant differences among studied epigeic Collembola species in the preference for fungal diet. Our study demonstrates that collembolans associate with a broader range of fungi than previously observed and thus potentially play an important role in enhancing fungal colonization through dispersal activities.

  • 3. Baker, Kate L.
    et al.
    Langenheder, Silke
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Nicol, Graeme W.
    Ricketts, Dean
    Killham, Kenneth S.
    Campell, Colin D.
    Prosser, James I.
    Environmental and spatial characterisation of microbial community composition to inform sampling strategies2009In: Soil Biology and Biochemistry, ISSN 0038-0717, E-ISSN 1879-3428, Vol. 41, no 11, p. 2292-2298Article in journal (Refereed)
    Abstract [en]

    Soil physicochemical properties and microbial communities are highly heterogeneous and vary widely over spatial scales, necessitating careful consideration of sampling strategies to provide representative and reproducible soil samples across field sites. To achieve this, the study aimed to establish appropriate sampling methodology and to determine links between the variability of parameters, utilising two sampling strategies. The first (design 1) involved extracting 25 cores from random locations throughout the field and pooling them into five sets of five cores. The second (design 2) involved a further 25 cores within five 1 m2 sub-plots. Sub-samples from each sub-plot were pooled in order to determine between and within sub-plot variability. All samples were analysed independently and as pooled sub-samples. Results indicate that pooling spatially separated samples significantly reduced the variability in pH, compared to individual samples. Pooling samples from a small area resulted in lower within sub-plot variability than between sub-plots for pH and bacterial community composition assessed by terminal-restriction fragment length polymorphism analysis. Following multivariate statistical analysis, a large amount of variation in community composition was explained by soil pH, which is remarkable given the relatively small size of the sampling area and minor differences in pH. Moisture content was also important in determining bacterial communities in the random design (design 1). In the 1 m2 sub-plot design (design 2), the spatial location of the plots explained a large degree of the variation in bacterial community composition between plots, which was due to spatial autocorrelation of pH and possible additional environmental parameters. This study emphasises the importance of sampling design for obtaining representative samples from soil.

  • 4. Clarholm, Marianne
    et al.
    Skyllberg, Ulf
    Rosling, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Organic acid induced release of nutrients from metal-stabilized soil organic matter - The unbutton model2015In: Soil Biology and Biochemistry, ISSN 0038-0717, E-ISSN 1879-3428, Vol. 84, p. 168-176Article, review/survey (Refereed)
    Abstract [en]

    Processes of soil organic matter (SOM) stabilization and the reverse, destabilization of SOM resulting in subsequent release and mobilization of nutrients from SOM, remain largely unresolved. The perception of SOM as supramolecular aggregates built of low molecular mass biomolecules is currently emerging. Polyvalent metal cations contribute to SOM tertiary structure by bridging functional groups of such molecules (Simpson et al., 2002). The strong bond to metals protects high quality organic material from being immediately accessed and decomposed. Here we propose a three-step process by which low molecular mass organic acids (LMMOAs) and hydrolytic enzymes act in series to destabilize SOM supramolecules to release organic nitrogen (N) and phosphorus (P) for local hyphal and root uptake. Complexation of the stabilizing metals by fungal-released LMMOA gives fungal-root consortia direct access to organic substrates of good quality. Because of their small sizes and carboxyl group configuration, citric and oxalic acids are the most effective LMMOAs forming stable complexes with the main SOM bridging metals Ca and Al in SOM. Citrate, forming particularly strong complexes with the trivalent cations Al and Fe, is dominant in soil solutions of low-productive highly acidic boreal forest soils where mycorrhizal associations with roots are formed predominantly by fungi with hydrophobic hyphal surfaces. In these systems mycelia participate in the formation of N-containing SOM with a significant contribution from strong Al bridges. In less acidic soils of temperate forests, including calcareous influenced soils, SOM is stabilized predominantly by Ca bridges. In such systems mycorrhizal fungi with more hydrophilic surfaces dominate, and oxalic acid, forming strong bidentate complexes with Ca, is the most common LMMOA exuded. A plant-fungus driven biotic mechanism at the supramolecular aggregate level (10(3)-10(5) Da) resolves micro-spatial priming of SOM, where the destabilization step is prerequisite for subsequent release of nutrients. (C) 2015 Elsevier Ltd. All rights reserved.

  • 5. Enwall, Karin
    et al.
    Nyberg, Karin
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Stenström, John
    Hallin, Sara
    Long-Term impact of fertilization on activity and composition of bacterial communities and metabolic guilds in agricultural soil2007In: Soil Biology and Biochemistry, ISSN 0038-0717, E-ISSN 1879-3428, Vol. 39, no 1, p. 106-115Article in journal (Refereed)
    Abstract [en]

    To explore long-term impact of organic and inorganic fertilizers on microbial communities, we targeted both the total bacterial community and the autotrophic ammonia oxidizing bacteria (AOB) in soil from six treatments at an experimental field site established in 1956: cattle manure, sewage sludge, Ca(NO3)2, (NH4)2SO4, unfertilized and unfertilized without crops. All plots, except the bare fallows, were cropped with maize. Effects on activity were assessed by measuring the basal respiration and substrate induced respiration (SIR) rates, and the potential activity of the AOB. To determine the bacterial community composition, 16S rRNA genes were used to fingerprint total soil communities by terminal restriction fragment length polymorphism analysis and AOB communities by denaturing gradient gel electrophoresis. The fertilization regimes had clear effects on both activity and composition of the soil communities. Basal respiration and r, which was kinetically derived as the exponentially growing fraction of the SIR-response, correlated well with the soil organic C content (r=0.93 and 0.66, respectively). Soil pH ranged from 3.97 to 6.26 in the treatments and was found to be an important factor influencing all microbial activities. pH correlated negatively with the ratio between basal respiration and SIR (r=0.90), indicating a decreased efficiency of heterotrophic microorganisms to convert organic carbon into microbial biomass in the most acid soils with pH 3.97 and 4.68 ((NH4)2SO4 and sewage sludge fertilized plots, respectively). The lowest SIR and ammonia oxidation rates were also found in these treatments. In addition, these treatments exhibited individually different community fingerprints, showing that pH affected the composition of AOB and total bacterial communities. The manure fertilized plots harbored the most diverse AOB community and the pattern was linked to a high potential ammonia oxidation activity. Thus, the AOB community composition appeared to be more strongly linked to the activity than the total bacterial communities were, likely explained by physiological differences in the populations present.

  • 6.
    Martí, Magalí
    et al.
    Department of Thematic Studies – Environmental Change, Linköping University, SE-581 83 Linköping, Sweden.
    Juottonen, Heli
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Robroek, Bjorn J.M.
    Ecology and Biodiversity Group, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
    Yrjälä, Kim
    MEM-group, Department of Biosciences, University of Helsinki, FIN-00014 Helsinki, Finland.
    Danielsson, Åsa
    Department of Thematic Studies – Environmental Change, Linköping University, SE-581 83 Linköping, Sweden.
    Lindgren, Per-Eric
    Division of Medical Microbiology, Department of Clinical and Experimental Medicine, Linköping University, SE-581 85 Linköping, Sweden.
    Svensson, Bo H.
    Department of Thematic Studies – Environmental Change, Linköping University, SE-581 83 Linköping, Sweden.
    Nitrogen and methanogen community composition within and among three Sphagnum dominated peatlands in Scandinavia2015In: Soil Biology and Biochemistry, ISSN 0038-0717, E-ISSN 1879-3428, Vol. 81, p. 204-211Article in journal (Refereed)
    Abstract [en]

    Abstract Ombrotrophic raised bogs are nutrient poor acidic peatlands accumulating organic matter. They are widely spread on northern latitudes and are substantial sources of methane emissions to the atmosphere being of great concern from a climate change perspective. We investigated the methanogen community composition along microtopographic gradients within three bogs in Scandinavia, receiving different amounts of nitrogen precipitation. Methanogenic community analyses by terminal restriction fragment length polymorphism of the mcrA gene showed different profiles among the three sites, while no influence of the microtopographic gradients was observed. Peat temperature and dissolved organic carbon were the major edaphic variables explaining 38% of the variation of the methanogenic community diversity among the bogs. The family Methanoregulaceae (hydrogenotrophic methanogens) showed the largest relative proportion and highest activity in all three sites. Quantitative PCR of the mcrA gene and transcripts showed that the most northern site, receiving the lowest atmospheric nitrogen load, had significantly lower abundance and activity of methanogens (4.7 × 106 and 2.4 × 104 mcrA copies per gram of soil, respectively), compared to the most southern site (8.2 × 107 and 4.6 × 105 mcrA copies per gram of soil, respectively), receiving the highest nitrogen load. No patterns of the mcrA gene and transcript abundances were observed along the microtopography. The results indicated that the difference in occurrence of methanogens is mainly due to geoclimatological conditions rather than site intrinsic microtopographic variation. The study further suggests that environmental changes on the site intrinsic topography will not affect the methanogenic activity, while increasing average temperatures in Scandinavian ombrotrophic raised bogs might contribute to an increase of the methanogenic archaeal activity resulting in an increase of methane production.

  • 7.
    Peltoniemi, Krista
    et al.
    Natural Resources Institute Finland.
    Laiho, Raija
    Natural Resources Institute Finland.
    Juottonen, Heli
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Levente, Bodrossy
    CSIRO Oceans and Atmosphere.
    Kell, Dana K.
    Natural Resources Institute Finland.
    Minkkinen, Kari
    University of Helsinki, Department of Forest Sciences.
    Mäkiranta, Päivi
    Natural Resources Institute Finland.
    Mehtätalo, Lauri
    University of Eastern Finland, School of Computing.
    Penttilä, Timo
    Natural Resources Institute Finland.
    Siljanen, Henri M.P.
    University of Eastern Finland, Department of Environmental and Biosciences.
    Tuittila, Eeva-Stiina
    University of Eastern Finland, Department of Forest Sciences.
    Tuomivirta, Tero
    Natural Resources Institute Finland.
    Fritze, Hannu
    Natural Resources Institute Finland.
    Responses of methanogenic and methanotrophic communities to warming in varying moisture regimes of two boreal fens2016In: Soil Biology and Biochemistry, ISSN 0038-0717, E-ISSN 1879-3428, Vol. 97, p. 144-156Article in journal (Refereed)
    Abstract [en]

    Peatlands are one of the major sources of the powerful greenhouse gas methane (CH4). Our aim was to detect responses of methanogenic archaeal and methane-oxidizing bacterial (MOB) communities that control the methane (CH4) cycle to climatic warming. This study took place in two boreal fens three years after experimental warming in un-manipulated wet and drier regimes, thus simulating future climate scenarios. We determined active methanogen and MOB communities as transcripts of mcrA and pmoAgenes, along with the abundance of these genes, CH4 production and oxidation potentials, and in situ CH4 fluxes. Methanogenic community remained similar, although methanogen abundance decreased after warming. In the wet regime, this decrease resulted in a small but significant reduction on the potential CH4 production in such peat layers where the average production potential was high. Drying alone, however, reduced the potential CH4 production more than warming, and this impact was strong enough to mask the small warming impact in the drier regime. Warming did not affect the MOB community or the potential CH4 oxidation in the wet regime; however, type Ib MOB abundance decreased and MOB related to genus Methylocapsa became typical after warming in the drier regime of the southern fen. The in situ measured CH4 fluxes indicated similar patterns as potential measurements; both warming and drying reduced methane emissions, drying more than warming. These results indicate that methanogens and MOB may have different controlling patterns on CH4 fluxes when facing global warming. These patterns may further differ not only between moisture regimes, but inside the same habitat type, here boreal fen. Irrespective of this variation, the in situ CH4 fluxes still seem to respond similarly across sites.

  • 8.
    Zmudczynska-Skarbek, Katarzyna
    et al.
    Univ Gdansk, Fac Biol, Dept Vertebrate Ecol & Zool, Wita Stwosza 59, PL-80308 Gdansk, Poland..
    Barcikowski, Mateusz
    Univ Gdansk, Fac Biol, Dept Vertebrate Ecol & Zool, Wita Stwosza 59, PL-80308 Gdansk, Poland..
    Drobniak, Szymon M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Jagiellonian Univ, Inst Environm Sci, Gronostajowa 7, PL-30387 Krakow, Poland..
    Gwiazdowicz, Dariusz J.
    Poznan Univ Life Sci, Dept Forest Pathol, Wojska Polskiego 71, Poznan, Poland..
    Richard, Pierre
    Univ La Rochelle, CNRS, Littoral Environm & Soc, UMR 7266, 2 Rue Olympe Gouges, F-17000 La Rochelle, France..
    Skubala, Piotr
    Univ Silesia, Dept Ecol, Bankowa 9, PL-40007 Katowice, Poland..
    Stempniewicz, Lech
    Univ Gdansk, Fac Biol, Dept Vertebrate Ecol & Zool, Wita Stwosza 59, PL-80308 Gdansk, Poland..
    Transfer of ornithogenic influence through different trophic levels of the Arctic terrestrial ecosystem of Bjornoya (Bear Island), Svalbard2017In: Soil Biology and Biochemistry, ISSN 0038-0717, E-ISSN 1879-3428, Vol. 115, p. 475-489Article in journal (Refereed)
    Abstract [en]

    Despite widespread recognition of the crucial role seabirds play in the fertilization of nutrient-poor polar terrestrial ecosystems, no studies have attempted a concurrent analysis of the entire or large proportion of an ornithogenically-supported food web. The aim of the current study was to assess the significance of allochthonous nutrient enrichment of key elements of the Bjornoya (Svalbard) terrestrial ecosystem by investigating how different seabird species influenced the characteristics of soil, vegetation, and soil invertebrates (direct ornithogenic effects), and also how those characteristics were interrelated (indirect ornithogenic effects). We sampled in the vicinity of a little auk (Alle alle) colony, and in areas occupied by great skua (Stercorarius skua) and glaucous gull (Larus hyperboreus) nests. Our data demonstrate clear, multi-trophic-level, ornithogenic impacts across the terrestrial ecosystem, with most of the measured parameters of soil, vegetation and invertebrates being altered by proximity to bird nesting areas, though to varying degrees. The ornithogenic effects tended to weaken with increasing complexity of interactions between the ecosystem components, with progression through successive trophic levels. The clearest responses were observed for soil (higher nitrogen stable isotope ratio delta N-15, nitrogen and water content) and vegetation characteristics (higher delta N-15, N content and total cover, lower diversity and species number, and modified community composition). The responses seen in the invertebrate communities were less clear (community composition change), and were only apparent when major invertebrate groups were considered together and for the assumed decomposers: springtails and oribatid mites, while not in the case of predators (mesostigmatid mites and one spider species). There were also suggestions in the data that different seabird species may have different impacts on the surrounding environment, probably due to their different diet and nesting area topography. However, generally, the species of bird was a weaker factor than the presence of a seabird colony or nest itself.

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