Highly competitive fungi manipulate bacterial communities in decomposing beech wood (Fagus sylvatica).
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ABSTRACT:
SUBMITTER: Johnston SR
PROVIDER: S-EPMC6301287 | biostudies-literature | 2019 Feb
REPOSITORIES: biostudies-literature
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Project description:Deadwood decomposition and other environmental processes mediated by microbial communities are generally studied with composite sampling strategies, where deadwood is collected from multiple locations in a large volume, that produce an average microbial community. In this study, we used amplicon sequencing to compare fungal and bacterial communities sampled with either traditional, composite samples, or small, 1 cm3 cylinders from a discrete location within decomposing European beech (Fagus sylvatica L.) tree trunks. We found that bacterial richness and evenness is lower in small samples when compared to composite samples. There was no significant difference in fungal alpha diversity between different sampling scales, suggesting that visually defined fungal domains are not restricted to a single species. Additionally, we found that composite sampling may obscure variation in community composition and this affects the understanding of microbial associations that are detected. For future experiments in environmental microbiology, we recommend that scale is explicitly considered as a factor and properly selected to correspond with the questions asked. Studies of microbial functions or associations may require samples to be collected at a finer scale than is currently practised.
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Project description:Background:The European beech is arguably the most important climax broad-leaved tree species in Central Europe, widely planted for its valuable wood. Here, we report the 542 Mb draft genome sequence of an up to 300-year-old individual (Bhaga) from an undisturbed stand in the Kellerwald-Edersee National Park in central Germany. Findings:Using a hybrid assembly approach, Illumina reads with short- and long-insert libraries, coupled with long Pacific Biosciences reads, we obtained an assembled genome size of 542 Mb, in line with flow cytometric genome size estimation. The largest scaffold was of 1.15 Mb, the N50 length was 145 kb, and the L50 count was 983. The assembly contained 0.12% of Ns. A Benchmarking with Universal Single-Copy Orthologs (BUSCO) analysis retrieved 94% complete BUSCO genes, well in the range of other high-quality draft genomes of trees. A total of 62,012 protein-coding genes were predicted, assisted by transcriptome sequencing. In addition, we are reporting an efficient method for extracting high-molecular-weight DNA from dormant buds, by which contamination by environmental bacteria and fungi was kept at a minimum. Conclusions:The assembled genome will be a valuable resource and reference for future population genomics studies on the evolution and past climate change adaptation of beech and will be helpful for identifying genes, e.g., involved in drought tolerance, in order to select and breed individuals to adapt forestry to climate change in Europe. A continuously updated genome browser and download page can be accessed from beechgenome.net, which will include future genome versions of the reference individual Bhaga, as new sequencing approaches develop.
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Project description:During the growing season, trees allocate photoassimilates to increase their aboveground woody biomass in the stem (ABIstem). This 'carbon allocation' to structural growth is a dynamic process influenced by internal and external (e.g., climatic) drivers. While radial variability in wood formation and its resulting structure have been intensively studied, their variability along tree stems and subsequent impacts on ABIstem remain poorly understood. We collected wood cores from mature trees within a fixed plot in a well-studied temperate Fagus sylvatica L. forest. For a subset of trees, we performed regular interval sampling along the stem to elucidate axial variability in ring width (RW) and wood density (ρ), and the resulting effects on tree- and plot-level ABIstem. Moreover, we measured wood anatomical traits to understand the anatomical basis of ρ and the coupling between changes in RW and ρ during drought. We found no significant axial variability in ρ because an increase in the vessel-to-fiber ratio with smaller RW compensated for vessel tapering towards the apex. By contrast, temporal variability in RW varied significantly along the stem axis, depending on the growing conditions. Drought caused a more severe growth decrease, and wetter summers caused a disproportionate growth increase at the stem base compared with the top. Discarding this axial variability resulted in a significant overestimation of tree-level ABIstem in wetter and cooler summers, but this bias was reduced to ~2% when scaling ABIstem to the plot level. These results suggest that F. sylvatica prioritizes structural carbon sinks close to the canopy when conditions are unfavorable. The different axial variability in RW and ρ thereby indicates some independence of the processes that drive volume growth and wood structure along the stem. This refines our knowledge of carbon allocation dynamics in temperate diffuse-porous species and contributes to reducing uncertainties in determining forest carbon fixation.
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Project description:European beech (Fagus sylvatica L.) adapts to local growing conditions to enhance its performance. In response to variations in climatic conditions, beech trees adjust leaf phenology, cambial phenology, and wood formation patterns, which result in different tree-ring widths (TRWs) and wood anatomy. Chronologies of tree ring width and vessel features [i.e., mean vessel area (MVA), vessel density (VD), and relative conductive area (RCTA)] were produced for the 1960-2016 period for three sites that differ in climatic regimes and spring leaf phenology (two early- and one late-flushing populations). These data were used to investigate long-term relationships between climatic conditions and anatomical features of four quarters of tree-rings at annual and intra-annual scales. In addition, we investigated how TRW and vessel features adjust in response to extreme weather events (i.e., summer drought). We found significant differences in TRW, VD, and RCTA among the selected sites. Precipitation and maximum temperature before and during the growing season were the most important climatic factors affecting TRW and vessel characteristics. We confirmed differences in climate-growth relationships between the selected sites, late flushing beech population at Idrija showing the least pronounced response to climate. MVA was the only vessel trait that showed no relationship with TRW or other vessel features. The relationship between MVA and climatic factors evaluated at intra-annual scale indicated that vessel area in the first quarter of tree-ring were mainly influenced by climatic conditions in the previous growing season, while vessel area in the second to fourth quarters of tree ring width was mainly influenced by maximum temperature and precipitation in the current growing season. When comparing wet and dry years, beech from all sites showed a similar response, with reduced TRW and changes in intra-annual variation in vessel area. Our findings suggest that changes in temperature and precipitation regimes as predicted by most climate change scenarios will affect tree-ring increments and wood structure in beech, yet the response between sites or populations may differ.
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Project description:European beech (Fagus sylvatica L.) forests provide multiple essential ecosystem goods and services. The projected climatic conditions for the current century will significantly affect the vitality of European beech. The expected impact of climate change on forest ecosystems will be potentially stronger in southeast Europe than on the rest of the continent. Therefore, our aim was to use the long-term monitoring data of crown vitality indicators in Croatia to identify long-term trends, and to investigate the influence of current and previous year climate conditions and available site factors using defoliation (DEF) and defoliation change (ΔDEF) as response variables. The results reveal an increasing trend of DEF during the study period from 1996 to 2017. In contrast, no significant trend in annual ΔDEF was observed. The applied linear mixed effects models indicate a very strong influence of previous year drought on ΔDEF, while climate conditions have a weak or insignificant effect on DEF. The results suggest that site factors explain 25 to 30% DEF variance, while similar values of conditional and marginal R2 show a uniform influence of drought on ΔDEF. These results suggest that DEF represents the accumulated impact of location-specific stressful environmental conditions on tree vitality, while ΔDEF reflects intense stress and represents the current or recent status of tree vitality that could be more appropriate for analysing the effect of climate conditions on forest trees.
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Project description:Fungi are important members of soil microbial communities with a crucial role in biogeochemical processes. Although soil fungi are known to be highly diverse, little is known about factors influencing variations in their diversity and community structure among forests dominated by the same tree species but spread over different regions and under different managements. We analyzed the soil fungal diversity and community composition of managed and unmanaged European beech dominated forests located in three German regions, the Schwäbische Alb in Southwestern, the Hainich-Dün in Central and the Schorfheide Chorin in the Northeastern Germany, using internal transcribed spacer (ITS) rDNA pyrotag sequencing. Multiple sequence quality filtering followed by sequence data normalization revealed 1655 fungal operational taxonomic units. Further analysis based on 722 abundant fungal OTUs revealed the phylum Basidiomycota to be dominant (54%) and its community to comprise 71.4% of ectomycorrhizal taxa. Fungal community structure differed significantly (p?0.001) among the three regions and was characterized by non-random fungal OTUs co-occurrence. Soil parameters, herbaceous understory vegetation, and litter cover affected fungal community structure. However, within each study region we found no difference in fungal community structure between management types. Our results also showed region specific significant correlation patterns between the dominant ectomycorrhizal fungal genera. This suggests that soil fungal communities are region-specific but nevertheless composed of functionally diverse and complementary taxa.
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Project description:Beech (Fagus sylvatica), a dominant forest species in Central Europe, competes for nitrogen with soil microbes and suffers from N limitation under dry conditions. We hypothesized that ectomycorrhizal communities and the free-living rhizosphere microbes from beech trees from sites with two contrasting climatic conditions exhibit differences in N acquisition that contribute to differences in host N uptake and are related to differences in host belowground carbon allocation. To test these hypotheses, young trees from the natural regeneration of two genetically similar populations, one from dryer conditions (located in an area with a southwest exposure [SW trees]) and the other from a cooler, moist climate (located in an area with a northeast exposure [NE trees]), were transplanted into a homogeneous substrate in the same environment and labeled with (13)CO2 and (15)NH4 (+). Free-living rhizosphere microbes were characterized by marker genes for the N cycle, but no differences between the rhizospheres of SW or NE trees were found. Lower (15)N enrichment was found in the ectomycorrhizal communities of the NE tree communities than the SW tree communities, whereas no significant differences in (15)N enrichment were observed for nonmycorrhizal root tips of SW and NE trees. Neither the ectomycorrhizal communities nor the nonmycorrhizal root tips originating from NE and SW trees showed differences in (13)C signatures. Because the level of (15)N accumulation in fine roots and the amount transferred to leaves were lower in NE trees than SW trees, our data support the suggestion that the ectomycorrhizal community influences N transfer to its host and demonstrate that the fungal community from the dry condition was more efficient in N acquisition when environmental constraints were relieved. These findings highlight the importance of adapted ectomycorrhizal communities for forest nutrition in a changing climate.
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Project description:Samples of beech (Fagus sylvatica) leaves were taken from the time of leaf emergence until leaf fall. They were extracted with boiling aqueous ethanol and the residues analysed for their acetyl-group content and their content of sugars released by acid hydrolysis. The accumulation of acetyl groups closely paralled that of xylose, and the two were present in approximately equimolecular proportions, except during the period of leaf expansion, when the acetyl-group/xylose ratio exceeded 3:2. The galactose present in each leaf reached a maximum as leaf expansion ceased and then declined during the period of rapid xylose accumulation. The results are discussed in relation to the known association of acetyl groups with xylans and pectic substancesand to the disappearance of constituents during cell-wall maturation.
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Project description:Biochar (BC) soil amendments could partially counteract soil carbon (C) stock decrease in broad-leaved forests in Italy; however, its effects on the growth of representative tree species-Fagus sylvatica L. and Quercus cerris L.-has not yet been addressed. We examine whether seed germination and growth of these species are affected by addition of BC obtained from deciduous broadleaf trees. Seeds were left to germinate in greenhouse conditions under three different BC amendments: 0% (control), 10% and 20% (v/v). Seedlings were then subjected to controlled conditions under the same BC percentage. Biochar effects on seed germination were assessed measuring germination time and percentage, while effects on photosynthesis were assessed using leaf chlorophyll content (mg/m2) and photosynthetic efficiency (FV/FM). Plant growth was estimated by recording leaf number, longest leaf length and plant height. Biochar treatments had no negative effects on germination and early growth stage of the two species. Positive effects were found on the chlorophyll content of both species (ca. +8%) regardless of the treatment and on the leaf number (+30%), leaf length (+14%) and plant height (+48%) of Q. cerris (only with 10% BC). Biochar applications seem, therefore, a suitable method for increasing broad-leaved forest C stock in Italy.
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Project description:Glucans like cellulose and starch are a major source of carbon for decomposer food webs, especially during early- and intermediate-stages of decomposition. Litter quality has previously been suggested to notably influence decomposition processes as it determines the decomposability of organic material and the nutrient availability to the decomposer community. To study the impact of chemical and elemental composition of resources on glucan decomposition, a laboratory experiment was carried out using beech (Fagus sylvatica, L.) litter from four different locations in Austria, differing in composition (concentration of starch, cellulose and acid unhydrolyzable residue or AUR fraction) and elemental stoichiometry (C:N:P ratio). Leaf litter was incubated in mesocosms for six months in the laboratory under controlled conditions. To investigate the process of glucan decomposition and its controls, we developed an isotope pool dilution (IPD) assay using (13)C-glucose to label the pool of free glucose in the litter, and subsequently measured the dilution of label over time. This enabled us to calculate gross rates of glucose production through glucan depolymerization, and glucose consumption by the microbial community. In addition, potential activities of extracellular cellulases and ligninases (peroxidases and phenoloxidases) were measured to identify effects of resource chemistry and stoichiometry on microbial enzyme production. Gross rates of glucan depolymerization and glucose consumption were highly correlated, indicating that both processes are co-regulated and intrinsically linked by the microbial demand for C and energy and thereby to resource allocation to enzymes that depolymerize glucans. At early stages of decomposition, glucan depolymerization rates were correlated with starch content, indicating that starch was the primary source for glucose. With progressing litter decomposition, the correlation with starch diminished and glucan depolymerization rates were highly correlated to cellulase activities, suggesting that cellulose was the primary substrate for glucan depolymerization at this stage of decomposition. Litter stoichiometry did not affect glucan depolymerization or glucose consumption rates early in decomposition. At later stages, however, we found significant negative relationships between glucan depolymerization and litter C:N and AUR:N ratio and a positive relationship between glucan depolymerization and litter N concentration. Litter C:N and C:P ratios were negatively related to cellulase, peroxidase and phenoloxidase activities three and six months after incubation, further corroborating the importance of resource stoichiometry for glucan depolymerization after the initial pulse of starch degradation.
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