Ivika Ostonen

PlutoF—a Web Based Workbench for Ecological and Taxonomic Research, with an Online Implementation for Fungal ITS Sequences

DNA sequences accumulating in the International Nucleotide Sequence Databases (INSD) form a rich source of information for taxonomic and ecological meta-analyses. However, these databases include many erroneous entries, and the data itself is poorly annotated with metadata, making it difficult to target and extract entries of interest with any degree of precision. Here we describe the web-based workbench PlutoF, which is designed to bridge the gap between the needs of contemporary research in biology and the existing software resources and databases. Built on a relational database, PlutoF allows remote-access rapid submission, retrieval, and analysis of study, specimen, and sequence data in INSD as well as for private datasets though web-based thin clients. In contrast to INSD, PlutoF supports internationally standardized terminology to allow very specific annotation and linking of interacting specimens and species. The sequence analysis module is optimized for identification and analysis of environmental ITS sequences of fungi, but it can be modified to operate on any genetic marker and group of organisms. The workbench is available at http://plutof.ut.ee.

Revisiting ectomycorrhizal fungi of the genus Alnus: differential host specificity, diversity and determinants of the fungal community.

Actinorhizal plants, including those of the genus Alnus (alders; Betulaceae), and their nitrogen-fixing bacterial symbionts rely on mycorrhizal fungi for phosphorus and other mineral nutrients. To date, alders are known to associate with only 20-30 species of ectomycorrhizal fungi which are highly host-specific. This study aimed to determine the species richness and the relative importance of host species, soil and site variables on the community composition of Alnus-associated ectomycorrhizal fungi on root tips. Using rDNA internal transcribed spacer (ITS) and large subunit (LSU) sequence analysis, 40 species of putatively ectomycorrhizal fungi were identified from seven sites dominated by Alnus incana or Alnus glutinosa. Alnicola spp. and Tomentella aff. sublilacina were most prevalent in all sites. Species of the /pseudotomentella, /inocybe, /peziza michelii-peziza succosa, /genea-humaria, /pachyphloeus-amylascus, /helvella-tuber and /tarzetta-geopyxis lineages were recorded as natural symbionts of alders for the first time. All basidiomycetes were specific to Alnus, whereas four out of seven Pezizales spp. (ascomycetes) were nonspecific. The complex of soil variables and geographical (site) effect drives the community composition of ectomycorrhizal fungi in alder forests. Alder-associated fungi have independently evolved and subsequently radiated in several ectomycorrhizal lineages, indicating frequent and persistent host shifts after the divergence of Alnus and Betula.

The role of soil conditions in fine root ecomorphology in Norway spruce (Picea abies (L.) Karst.)

The present study is an attempt to investigate the pattern of morphological variability of the short roots of Norway spruce (Picea abies (L.) Karst.) growing in different soils. Five root parameters – diameter, length and dry weight of the root tip, root density (dry weight per water-saturated volume) and specific root area (absorbing area of dry weight unit) were studied with respect to 11 soil characteristics using CANOCO RDA analysis. The investigation was conducted in seven study areas in Estonia differing in site quality class and soil type. Ten root samples per study area were collected randomly from the forest floor and from the 20 cm soil surface layer. Eleven soil parameters were included in the study: humus content, specific soil surface area, field capacity, soil bulk density, pH (KCl and H2O dilutions), N and Ca concentrations, Ca/Al and C/N ratios, and the decomposition rate of fine roots (<2 mm dia.). Root morphological characteristics most strongly related to the measured soil characteristics in the different sites were specific root area, root density and diameter of the short roots, the means varying from 29 to 42 m2 kg−1, from 310 to 540 kg m−3 and from 0.26 to 0.32 mm, respectively; root density being most sensitive. The most favourable site and soil types resulting in fine roots with morphological characteristics for optimizing nutrient uptake (e.g. low short root density and high specific root area) were Umbric Luvisol (Oxalis), Dystric Gleysol (Oxalis) and Gleyic Luvisol (Hepatica). These soil types correspond to highly productive natural forest stands of Norway spruce in Estonia. All measured soil variables explained 28% of total variance of the root characteristics. The most important variables related to root morphology were the humus content, field capacity and specific soil surface area.

Ectomycorrhizal root tips in relation to site and stand characteristics in Norway spruce and Scots pine stands in boreal forests

Variations in ectomycorrhizal (EcM) short root tips of Norway spruce (Picea abies (L.) Karst.) and Scots pine (Pinus sylvestris L.) in 16 stands throughout Finland were studied, and their relationships with latitude, organic layer C:N ratio, temperature sum and foliage biomass were determined. There were no significant differences in EcM root tip frequency (number per milligram of fine roots) or root tip mass between tree species or between northern and southern sites. The EcM root tip number per unit area of the organic layer plus the 0-30 cm mineral soil layer varied between 0.8 and 2.4 million per m(2) for Norway spruce and between 0.7 and 2.9 million per m(2) for Scots pine, and it was higher in the northern Scots pine stands than in the southern Scots pine stands. Over 80% of the EcM root tips of both species were in the organic layer and the upper 0-10 cm mineral soil layer. We related EcM root tips to foliage mass because these two components are the most important functional units in boreal tree physiology. Both species, especially the Scots pine trees, had more EcM root tips in relation to foliage mass in northern Finland than in southern Finland. Scots pine trees had more EcM root tips in relation to foliage mass than Norway spruce in the same climatic region. The EcM root tip:foliage biomass ratio of Norway spruce was positively related to the C:N ratio in the organic layer, whereas that of Scots pine was negatively related to the temperature sum. The number of EcM root tips per milligram of fine root biomass was constant, implying that trees of both species increase nutrient uptake by increasing fine root production and hence their total number of EcM tips and the area of soil occupied by mycelia. Both tree species responded to nitrogen (N) deficiency by maintaining more EcM tips per foliage unit, and this may be related to a higher proportion of N uptake in an organic form.

Reed canary grass cultivation mitigates greenhouse gas emissions from abandoned peat extraction areas

We studied the impact of reed canary grass (RCG) cultivation on greenhouse gas emission in the following sites of an abandoned peat extraction area in Estonia: a bare soil (BS) site, a nonfertilized Phalaris (nfP) plot, a fertilized Phalaris (fP) plot, and a natural bog (NB) and a fen meadow (FM) as reference areas. The C balance and global warming potential (GWP) were estimated by measuring CO2, CH4, and N2O emissions and aboveground and belowground biomass variations. The high CO2 flux from the nfP and fP sites and the low CO2 emission from the BS are due to the enhancement of mineralization by plant growth on planted sites and inhibited mineralization by the recalcitrant C of BS. The NB site emitted 24 kg CH4 ha−1 yr−1, whereas the almost zero CH4 emission from the Phalaris plots and the BS site was due to the high S concentration in peat, which probably inhibited methanogenesis. The N2O flux varied from <0.1 kg on the Phalaris plots and the NB to 2.64 kg N2O ha−1 yr−1 on the FM. The highest yield of RCG was obtained in autumn (13.9 t and 8.0 t dw ha−1 on the fP and nfP, respectively). By spring, the biomass yield on the fP and nfP plot was 12.7 and 7.9 t dw ha−1, respectively. The C balance of nfP and fP plots was negative in comparison to the BS (−3322, −5983, and 2504 kg CO2 ha−1 yr−1, respectively). This indicates that the cultivation of RCG transformed them from a net source of C into a net sink of C. The GWP for the fP and nfP sites was −5981 and −3885 kg CO2 eq ha−1 yr−1, respectively. The BS site had a total GWP of 2544 kg CO2 eq ha−1 yr−1.

Morphological plasticity of ectomycorrhizal short roots in Betula sp and Picea abies forests across climate and forest succession gradients: its role in changing environments

Morphological plasticity of ectomycorrhizal (EcM) short roots (known also as first and second order roots with primary development) allows trees to adjust their water and nutrient uptake to local environmental conditions. The morphological traits (MTs) of short-living EcM roots, such as specific root length (SRL) and area, root tip frequency per mass unit (RTF), root tissue density, as well as mean diameter, length, and mass of the root tips, are good indicators of acclimation. We investigated the role of EcM root morphological plasticity across the climate gradient (48–68°N) in Norway spruce (Picea abies (L.) Karst) and (53–66°N) birch (Betula pendula Roth., B. pubescens Ehrh.) forests, as well as in primary and secondary successional birch forests assuming higher plasticity of a respective root trait to reflect higher relevance of that characteristic in acclimation process. We hypothesized that although the morphological plasticity of EcM roots is subject to the abiotic and biotic environmental conditions in the changing climate; the tools to achieve the appropriate morphological acclimation are tree species-specific. Long-term (1994–2010) measurements of EcM roots morphology strongly imply that tree species have different acclimation-indicative root traits in response to changing environments. Birch EcM roots acclimated along latitude by changing mostly SRL [plasticity index (PI) = 0.60], while spruce EcM roots became adjusted by modifying RTF (PI = 0.68). Silver birch as a pioneer species must have a broader tolerance to environmental conditions across various environments; however, the mean PI of all MTs did not differ between early-successional birch and late-successional spruce. The differences between species in SRL, and RTF, diameter, and length decreased southward, toward temperate forests with more favorable growth conditions. EcM root traits reflected root-rhizosphere succession across forest succession stages.

Proportion of fungal mantle, cortex and stele of ectomycorrhizas in Picea abies (L.) Karst. in different soils and site conditions

Anatomical variability of ectomycorrhizal short roots in Norway spruce (Picea abies (L.) Karst) stands was investigated in five stands differing in site quality class (Ia–V) and soil type. Ten root samples per stand were randomly collected from the forest floor and the subsequent 20 cm soil layer. Thin transverse or axial sections (5 μm) of randomly taken short roots were examined by light microscopy (AXIOPHOT; magnification 200–800×). All analyzed short root tips of Norway spruce in different stands were colonized by ectomycorrhizal fungi. Thickness of the mantle (Tmantle) and cortex (Tcortex) and diameter of the root (Droot) were measured in four crossing radial directions for transverse sections and in two radial directions for axial sections. The proportions of the mantle (PSmantle), cortex (PScortex) and stele (PSstele) of the root cross-sectional area (CSA) were calculated. Mean Tmantle and Tcortex varied from 16.5 ± 0.6 to 29 ± 1.3 μm and 83.9 ± 1.7 to 108.4 ± 2.4 μm, respectively; significant differences between stands were found. The number of cell rows in the cortex (4–6) did not vary between different stands, thus thickness of cortex depended on cell size. Mean PSmantle, PScortex and PSstele of the root CSA varied from 17.7 to 28.1%, from 58.9 to 66.9%, and from 13.4 to 15.8%, respectively. No differences between stands were revealed in mean CSA ratio of cortex and stele. It can be concluded that irrespective of big differences in soil and site conditions, including the influence of fungal symbionts, a 4:1 relation on a CSA basis between the cortex and stele is inherent to Norway spruce.

Reuse potential of phosphorus-rich filter materials from subsurface flow wastewater treatment filters for forest soil amendment

The aim of this study was to test P-enriched filter materials from a wastewater treatment experiment regarding their fertilizing efficiency in pot experiments with silver birch (Betula pendula Roth.) seedlings. Tested materials included hydrated calcium-rich oil shale ash and well-mineralised peat. A mixture of peat and hydrated ash demonstrated the best results: seedlings grown on that mixture had the highest P concentration and an optimal N:P:K ratio in leaves. Hydrated ash has a low concentration of heavy metals and almost the same composition as common lime fertilizers. The hydrated ash sediment and its combination with well-mineralised peat enriched with phosphorus in wastewater treatment filters are promising materials for forest soil fertilization.

Geothermal ecosystems as natural climate change experiments : The ForHot research site in Iceland as a case study

This article describes how natural geothermal soil temperature gradients in Iceland have been used to study terrestrial ecosystem responses to soil warming. The experimental approach was evaluated at three study sites in southern Iceland; one grassland site that has been warm for at least 50 years (GO), and another comparable grassland site (GN) and a Sitka spruce plantation (FN) site that have both been warmed since an earthquake took place in 2008. Within each site type, five ca. 50 m long transects, with six permanent study plots each, were established across the soil warming gradients, spanning from unwarmed control conditions to gradually warmer soils. It was attempted to select the plots so the annual warming levels would be ca. +1, +3, +5, +10 and +20 °C within each transect. Results of continuous measurements of soil temperature (Ts) from 2013-2015 revealed that the soil warming was relatively constant and followed the seasonal Ts cycle of the unwarmed control plots. Volumetric water content in the top 5 cm of soil was repeatedly surveyed during 2013-2016. The grassland soils were wetter than the FN soils, but they had sometimes some significant warming-induced drying in the surface layer of the warmest plots, in contrast to FN. Soil chemistry did not show any indications that geothermal water had reached the root zone, but soil pH did increase somewhat with warming, which was probably linked to vegetation changes. As expected, the potential decomposition rate of organic matter increased significantly with warming. It was concluded that the natural geothermal gradients at the ForHot sites in Iceland offered realistic conditions for studying terrestrial ecosystem responses to warming with minimal artefacts.

Elevated air humidity affects hydraulic traits and tree size but not biomass allocation in young silver birches (Betula pendula)

As changes in air temperature, precipitation, and air humidity are expected in the coming decades, studies on the impact of these environmental shifts on plant growth and functioning are of major importance. Greatly understudied aspects of climate change include consequences of increasing air humidity on forest ecosystems, predicted for high latitudes. The main objective of this study was to find a link between hydraulic acclimation and shifts in trees’ resource allocation in silver birch (Betula pendula Roth) in response to elevated air relative humidity (RH). A second question was whether the changes in hydraulic architecture depend on tree size. Two years of application of increased RH decreased the biomass accumulation in birch saplings, but the biomass partitioning among aboveground parts (leaves, branches, and stems) remained unaffected. Increased stem Huber values (xylem cross-sectional area to leaf area ratio) observed in trees under elevated RH did not entail changes in the ratio of non-photosynthetic to photosynthetic tissues. The reduction of stem–wood density is attributable to diminished mechanical load imposed on the stem, since humidified trees had relatively shorter crowns. Growing under higher RH caused hydraulic conductance of the root system (KR) to increase, while KR (expressed per unit leaf area) decreased and leaf hydraulic conductance increased with tree size. Saplings of silver birch acclimate to increasing air humidity by adjusting plant morphology (live crown length, slenderness, specific leaf area, and fine-root traits) and wood density rather than biomass distribution among aboveground organs. The treatment had a significant effect on several hydraulic properties of the trees, while the shifts were largely associated with changes in tree size but not in biomass allocation.