Impact of white-rot fungi on numbers and community composition of bacteria colonizing beech wood from forest soil

White-rot fungi are important wood-decomposing organisms in forest ecosystems. Their ability to colonize and decompose woody resources may be strongly influenced by wood-inhabiting bacteria that grow on easily utilizable compounds e.g. oligomers of wood-polymers released by fungal enzymes. However, so far, it is not known how white-rot fungi deal with the presence of potential competing bacteria. Here, the effects of two white-rot fungi, Hypholoma fasciculare and Resinicium bicolor, on the numbers and composition of bacteria colonizing sterile beech wood blocks from forest soil are reported. Both total numbers (microscopic counts) and the numbers of cultivable wood-inhabiting bacteria were considerably lower in wood blocks that became colonized by the white-rot fungi than in control blocks. This points to the fungi out-competing the opportunistic bacteria. The presence of white-rot fungi resulted in a change in the relative abundance of families of cultivable bacteria in wood and also in a change of denaturing gradient gel electrophoresis patterns of directly amplified 16S rRNA gene fragments. Analysis of the bacterial community structure in soil adhering to exploratory mycelium (cords) indicated that fungal species-specific effects on bacterial community composition were also apparent in this fungal growth phase.     

Drought‐resistant fungi control soil organic matter decomposition and its response to temperature

Microbial‐mediated decomposition of soil organic matter (SOM) ultimately makes a considerable contribution to soil respiration, which is typically the main source of CO₂ arising from terrestrial ecosystems. Despite this central role in the decomposition of SOM, few studies have been conducted on how climate change may affect the soil microbial community and, furthermore, on how possible climate‐change induced alterations in the ecology of microbial communities may affect soil CO₂ emissions. Here we present the results of a seasonal study on soil microbial community structure, SOM decomposition and its temperature sensitivity in two representative Mediterranean ecosystems where precipitation/throughfall exclusion has taken place during the last 10 years. Bacterial and fungal diversity was estimated using the terminal restriction fragment length polymorphism technique. Our results show that fungal diversity was less sensitive to seasonal changes in moisture, temperature and plant activity than bacterial diversity. On the other hand, fungal communities showed the ability to dynamically adapt throughout the seasons. Fungi also coped better with the 10 years of precipitation/throughfall exclusion compared with bacteria. The high resistance of fungal diversity to changes with respect to bacteria may open the controversy as to whether future ‘drier conditions’ for Mediterranean regions might favor fungal dominated microbial communities. Finally, our results indicate that the fungal community exerted a strong influence over the temporal and spatial variability of SOM decomposition and its sensitivity to temperature. The results, therefore, highlight the important role of fungi in the decomposition of terrestrial SOM, especially under the harsh environmental conditions of Mediterranean ecosystems, for which models predict even drier conditions in the future.     

喀斯特森林常见树种倒木分解对土壤真菌群落组成及分布规律的影响

倒木是森林生态系统的重要组分,其分解调控着土壤的养分循环,同时也影响着土壤微生物群落结构。但目前鲜见关于倒木分解对土壤微生物群落影响方面的报道。选取贵州茂兰喀斯特常绿落叶阔叶混交林中处于轻、中和重度腐烂等级的狭叶润楠（Machilus rehderi）、枫香（Liquidambar formosana）、青冈栎（Cyclobalanopsis glauca）和圆果化香（Platycarya longipes）4种常见树种倒木为研究对象,以距倒木外围的3个不同水平距离（10cm、30cm和50cm）的土壤样品为实验材料,分析倒木树种、腐烂等级和距离对土壤真菌种类及多样性的影响。结果表明：1）喀斯特森林4种树种倒木所影响土壤真菌群落在门级分类上主要为子囊菌门、担子菌门和毛霉门,优势属有Mortierella spp.、Phlebia spp.、Pluteus spp.和Chaetomium spp.等;2）倒木的树种对土壤真菌群落相对丰度的影响有差异,圆果化香倒木下的土壤真菌丰富度Chao1指数显著高于青冈栎;3）随腐烂程度加深,4种树种倒木下的土壤真菌群落多样性呈显著增加趋势;4）土壤真菌群落丰度随着距倒木距离的增大（10-50cm）变化明显,如狭叶润楠影响的Pluteus spp.、Mortierella spp.和Ganoderma spp.,枫香的Chaetomium spp.,圆果化香的Mortierella spp.和青冈栎的Phlebia spp.和Oliveonia spp.等。本研究量化了喀斯特森林倒木所影响的土壤真菌群落组成及分布规律,在一定程度上为倒木分解与土壤微生物群落之间的作用机制的深入探索提供了科学依据。     

High temporal resolution tracing of photosynthate carbon from the tree canopy to forest soil microorganisms

Half of the biological activity in forest soils is supported by recent tree photosynthate, but no study has traced in detail this flux of carbon from the canopy to soil microorganisms in the field. Using (13)CO(2), we pulse-labelled over 1.5 h a 50-m(2) patch of 4-m-tall boreal Pinus sylvestris forest in a 200-m(3) chamber. Tracer levels peaked after 24 h in soluble carbohydrates in the phloem at a height of 0.3 m, after 2-4 d in soil respiratory efflux, after 4-7 d in ectomycorrhizal roots, and after 2-4 d in soil microbial cytoplasm. Carbon in the active pool in needles, in soluble carbohydrates in phloem and in soil respiratory efflux had half-lives of 22, 17 and 35 h, respectively. Carbon in soil microbial cytoplasm had a half-life of 280 h, while the carbon in ectomycorrhizal root tips turned over much more slowly. Simultaneous labelling of the soil with (15)NH(+)(4) showed that the ectomycorrhizal roots, which were the strongest sinks for photosynthate, were also the most active sinks for soil nitrogen. These observations highlight the close temporal coupling between tree canopy photosynthesis and a significant fraction of soil activity in forests.     

Insight into the temperature sensitivity of forest litter decomposition and soil enzymes in subtropical forest in China

Aims With the continuing increase in the impact of human activities on ecosystems, ecologists are increasingly interested in understanding the effects of high temperature on litter decomposition since litter decomposition and the accompanying release of nutrients and carbon dioxide are key processes in ecosystem nutrient cycling and carbon flux. This study was conducted to evaluate the temperature sensitivity of forest litter decomposition and soil enzymes during litter decomposition in subtropical forest in China.Methods Two dominant litter types were chosen from Zijin Mountain in China: Quercus acutissima leaves from a broadleaf forest (BF) and Pinus massoniana needles from a coniferous forest (CF). The litter samples were incubated in soil microcosms at ambient control temperature (20°C) and 10°C warmer. During a 5-month incubation, chemical composition of litter samples, litter mass losses, and related soil enzyme activities were determined.Important findings Three main results were found: (i) high temperature accelerated decomposition rates of both litter types, and the temperature sensitivities of litter decomposition for BF leaves and that for CF needles are equivalent basically, (ii) high temperature enhanced soil enzyme activities in the two forest types, and the temperature sensitivities of polyphenol oxidase were significantly higher than those of the other soil enzymes and (iii) the temperature sensitivities of nitrate reductase were significantly higher in the CF soil than in the BF soil, while there was no significant difference in the temperature sensitivities of the other soil enzymes between BF and CF. As a long-term consequence, the high-temperature-induced acceleration of litter decomposition rates in these subtropical forests may cause carbon stored belowground to be transferred in the atmosphere, which may alter the balance between carbon uptake and release, and then alter the global carbon cycle in the coming decades.     

Leaf litter fungi in a Central Amazonian forest: the influence of rainfall,soil and topography on the distribution of fruiting bodies

Fungi are important components of tropical ecosystems, especially in the recycling of nutrients. However, there is little information on how fungal diversity is structured at scales suitable to plan their conservation. We tested if the distribution of fruiting bodies of litter fungi was random in the landscape (over 25 km²) in a tropical evergreen forest in Central Amazonia. We used linear regressions to evaluate the influence of rainfall, soil characteristics and topography on morphospecies richness and composition. Fungi were collected twice in thirty 0.25 × 250 m plots. Short-term rainfall was represented by the cumulative rainfall in the three days before each plot was surveyed. Plots were classified in two groups based on cumulative rainfall. Clay content in soil and rainfall influenced morphospecies richness, but responses to edaphic factors depended on rainfall. Wetter periods apparently decreased limiting moisture conditions in higher areas, allowing fungal activity and fruiting body production. Morphospecies composition was influenced by clay content, but influence on fungi was probably indirect as clay content was correlated with altitude, plant community and nitrogen availability. Our results suggest that the species of litter fungi are not randomly distributed in the landscape. Furthermore, they indicate that it is viable to conduct mesoscale evaluations of fungal diversity, if the temporal and spatial variation and their interaction are taken into account.     

Presence and distribution of insect-associated and entomopathogenic fungi in a temperate pine forest soil: An integrated approach

For decades entomopathogenic fungi have garnered interest as possible alternatives to chemical pesticides. However, their ecology outside of agroecosystems demands further study. We assessed the diversity and abundance of entomopathogenic and insect-associated fungi at a loblolly pine forest in North Carolina, USA using culture-dependent and next-generation sequencing libraries. Fungi were isolated using Galleria mellonella larvae, as well as from soil dilutions plated on a selective medium. Isolates were identified using Sanger sequencing of the ITS and LSU rRNA gene regions, and represented 36 OTUs including Metarhizium, Lecanicillium, and Paecilomyces. Additionally, we assessed the chitinolytic potential of isolates and found widespread, variable ability to degrade chitin within and between genera. Phylogenetic analyses resolved several isolates to genus, with some forming clades with other insect-associated taxa, as well as with fungi associated with plant tissues. Saprophytes were widely distributed in soil, while entomopathogens were less abundant and present primarily in the top two cm of the soil. The similarity between culture-dependent and next-generation sequencing results demonstrates that both methods can be used concurrently in this system to study the ecology of entomopathogenic fungi.     

Restoration of belowground fungal communities in reclaimed landscapes of the Canadian boreal forest

The trajectory of forests establishing on reclaimed oil sands mines in the Canadian boreal forest is uncertain. Soil microbes, namely mycorrhizal fungi, partly underlie successional trajectories of plant communities, yet their role in restoration is often overlooked. Here, we tested the relative importance of common management tools used in restoration—species planted and soil placement—on the recovery of ectomycorrhizal fungal communities over 4 years. Importantly, we further compared the community assembly of fungi on reclaimed landscapes to that in reference ecosystems disturbed to different degrees. This latter test addresses whether disturbance intensity is more important than common management interventions to restore fungal communities in these ecosystems. Three main findings emerged. (1) The effect of tree species planted and soil placement on ectomycorrhizal fungal communities establishing on reclaimed landscapes was dynamic through time. (2) Disturbances that remove or disrupt the organic layer of soils substantially affect the composition of ectomycorrhizal fungal communities. (3) Shifts in the community composition of ectomycorrhizal fungi were driven to a greater extent by disturbance severity than either tree species planted or soil placement.     

Neighboring trees regulate the root‐associated pathogenic fungi on the host plant in a subtropical forest

Root‐associated fungi and host‐specific pathogens are major determinants of species coexistence in forests. Phylogenetically related neighboring trees can strongly affect the fungal community structure of the host plant, which, in turn, will affect the ecological processes. Unfortunately, our understanding of the factors influencing fungal community composition in forests is still limited. In particular, investigation of the relationship between the phytopathogenic fungal community and neighboring trees is incomplete. In the current study, we tested the host specificity of members of the root‐associated fungal community collected from seven tree species and determined the influence of neighboring trees and habitat variation on the composition of the phytopathogenic fungal community of the focal plant in a subtropical evergreen forest. Using high‐throughput sequencing data with respect to the internal transcribed spacer (ITS) region, we characterized the community composition of the root‐associated fungi and found significant differences with respect to fungal groups among the seven tree species. The density of conspecific neighboring trees had a significantly positive influence on the relative abundance of phytopathogens, especially host‐specific pathogens, while the heterospecific neighbor density had a significant negative impact on the species richness of host‐specific pathogens, as well as phytopathogens. Our work provides evidence that the root‐associated phytopathogenic fungi of a host plant depend greatly on the tree neighbors of the host plant.     

Growth of ectomycorrhizal mycelia and composition of soil microbial communities in oak forest soils along a nitrogen deposition gradient

Deciduous forests may respond differently from coniferous forests to the anthropogenic deposition of nitrogen (N). Since fungi, especially ectomycorrhizal (EM) fungi, are known to be negatively affected by N deposition, the effects of N deposition on the soil microbial community, total fungal biomass and mycelial growth of EM fungi were studied in oak-dominated deciduous forests along a nitrogen deposition gradient in southern Sweden. In-growth mesh bags were used to estimate the production of mycelia by EM fungi in 19 oak stands in the N deposition gradient, and the results were compared with nitrate leaching data obtained previously. Soil samples from 154 oak forest sites were analysed regarding the content of phospholipid fatty acids (PLFAs). Thirty PLFAs associated with microbes were analysed and the PLFA 18:2ω6,9 was used as an indicator to estimate the total fungal biomass. Higher N deposition (20 kg N ha⁻¹ y⁻¹ compared with 10 kg N ha⁻¹ y⁻¹) tended to reduce EM mycelial growth. The total soil fungal biomass was not affected by N deposition or soil pH, while the PLFA 16:1ω5, a biomarker for arbuscular mycorrhizal (AM) fungi, was negatively affected by N deposition, but also positively correlated to soil pH. Other PLFAs positively affected by soil pH were, e.g., i14:0, a15:0, 16:1ω9, a17:0 and 18:1ω7, while some were negatively affected by pH, such as i15:0, 16:1ω7t, 10Me17:0 and cy19:0. In addition, N deposition had an effect on the PLFAs 16:1ω7c and 16:1ω9 (negatively) and cy19:0 (positively). The production of EM mycelia is probably more sensitive to N deposition than total fungal biomass according to the fungal biomarker PLFA 18:2ω6,9. Low amounts of EM mycelia covaried with increased nitrate leaching, suggesting that EM mycelia possibly play an important role in forest soil N retention at increased N input.     

Changes in organic matter composition of forest soil treated with a large amount of urea to promote ammonia fungi and the abilities of these fungi to decompose organic matter

Organic matter composition (lignin, holocellulose, 50% (v/v) methanol extract, water-soluble carbohydrate (WSC) and phenolics (WSP), petroleum ether extract, and ash) of A₀ layer soil treated with 700 g/m² of urea to promote ammonia fungi was investigated in a Japanese red pine (Pinus densiflora) forest. Nine species of fungi were found during the study period of 18 months after the treatment. Of these, seven species belong to the ammonia fungi. WSC content of the treated soil was lower than that of the control. Methanol extract content increased initially after the treatment, then decreased to below the control level. There were no consistent differences in other components between the treated plot and the control. The abilities to decompose cellulose, lignin, chitin, protein and lipid in 18 strains in 10 species of the ammonia fungi were also screened. Cellulose was not lysed byPseudombrophila deerata, Hebeloma spp. andLaccaria bicolor. Strong lignolytic activity was shown byLyophyllum tylicolor, Coprinus echinosporus andP. deerata. Chitin was decomposed byAmblyosporium botrytis, L. tylicolor, C. echinosporus andHebeloma vinosophyllum. All strains possessed proteolytic and lipolytic activities. Supply of glucose to the culture media resulted in weaker enzyme activities except for lignolytic ability.     

The response of forest floor vegetation and tree regeneration to deer exclusion and disturbance in a riparian deciduous forest,central Japan

The response of forest floor vegetation and regeneration of major treespecies to deer exclusion in a riparian forest were studied for 3 years withtheinteractive effects of natural disturbances. At the start of this study, deerdensity had quickly increased to a fairly high level (29–31 individualskm^–2) during the last decade and had severely reduced theamount of forest floor vegetation in the study area. Dwarf bamboos, which weredominant before, had almost diminished from the forest floor. During the studyperiod, aboveground biomass increased steadily but species diversity did notchange much in the exclosures. Outside the exclosures, the seedlings of alltreespecies were damaged greatly by deer browsing, especially the taller ones. Deerbrowsing had little effect on the emergence of tree seedlings, but deertrampling might have accelerated emergence indirectly by disturbing the soilsurface for some species. Differences in plant responses were also observed fordeer browsing and the presence of dwarf bamboo that strongly inhibits therecruitment of tree seedlings. The nine major species were classified intothreegroups according to the response of seedlings to deer browsing and disturbance.Group 1 consists of the species whose seedling survival is affected bybrowsing,but seldom by disturbances (Phellodendron amurense,Kalopanax pictus, Quercus crispulaandMalus toringo). Groups 2 and 3 consist of species adaptedto tree-fall disturbance (Betula spp.) and ripariandisturbance (Alnus hirsuta var.sibirica, Ulmus davidiana var.japonica, Populus maximowiczii andSalix sachalinensis), respectively, and seedling survivalof these two groups is principally affected by light conditions. The effect ofdeer browsing on seedling survival and growth was greater for Group 2 than forGroup 3.     

Seasonal changes in the contribution of root respiration to total soil respiration in a cool-temperate deciduous forest

A trenching method was used to determine the contribution of root respiration to soil respiration. Soil respiration rates in a trenched plot (R _trench) and in a control plot (R _control) were measured from May 2000 to September 2001 by using an open-flow gas exchange system with an infrared gas analyser. The decomposition rate of dead roots (R _D) was estimated by using a root-bag method to correct the soil respiration measured from the trenched plots for the additional decaying root biomass. The soil respiration rates in the control plot increased from May (240–320 mg CO₂ m^–2 h^–1) to August (840–1150 mg CO₂ m^–2 h^–1) and then decreased during autumn (200–650 mg CO₂ m^–2 h^–1). The soil respiration rates in the trenched plot showed a similar pattern of seasonal change, but the rates were lower than in the control plot except during the 2 months following the trenching. Root respiration rate (R _r) and heterotrophic respiration rate (R _h) were estimated from R _control, R _trench, and R _D. We estimated that the contribution of R _r to total soil respiration in the growing season ranged from 27 to 71%. There was a significant relationship between R _h and soil temperature, whereas R _r had no significant correlation with soil temperature. The results suggest that the factors controlling the seasonal change of respiration differ between the two components of soil respiration, R _r and R _h.     

Response of fine roots to an experimental gap in a boreal Picea abies forest

We examined the initial response of the quantity and distribution of fine roots to the creation of an experimental canopy gap with a diameter of 50 m in a mature managed Norway spruce forest. Under the canopy, the fine root length densities of trees, shrubs, and grasses and herbs were 3207, 707 and 2738 m m^–2, respectively. The fine root biomass of trees, shrubs, and grasses and herbs were 182, 47 and 52 g m^–2, respectively. Two growing seasons after gap creation hardly any fine tree roots were found in the middle part of the gap. The living tree roots in the gap edge zone were mainly located within a 5-m distance from the standing edge trees. The indices developed here to show the influence of trees on fine root lenght density clearly revealed the effect of the vicinity of living trees on fine root lenght density. The root densities of grasses, herbs and dwarf shrubs did not show a clear response to gap creation despite the increase of their foliage. Our results suggest that in boreal spruce forests a gap disturbance creates a distinct tree root gap and that the gap edge trees do not extend their root systems rapidly into the formed root gap.     

Comparing tropical forest tree size distributions with the predictions of metabolic ecology and equilibrium models

Tropical forests vary substantially in the densities of trees of different sizes and thus in above-ground biomass and carbon stores. However, these tree size distributions show fundamental similarities suggestive of underlying general principles. The theory of metabolic ecology predicts that tree abundances will scale as the −2 power of diameter. Demographic equilibrium theory explains tree abundances in terms of the scaling of growth and mortality. We use demographic equilibrium theory to derive analytic predictions for tree size distributions corresponding to different growth and mortality functions. We test both sets of predictions using data from 14 large-scale tropical forest plots encompassing censuses of 473 ha and > 2 million trees. The data are uniformly inconsistent with the predictions of metabolic ecology. In most forests, size distributions are much closer to the predictions of demographic equilibrium, and thus, intersite variation in size distributions is explained partly by intersite variation in growth and mortality.     

干扰对典型草原生态系统土壤净呼吸特征的影响

由于土地利用格局的改变和人类干扰活动的加剧,草地生态系统CO2排放与固定的平衡、碳循环特征以及碳储量越来越受到人们的重视。尤其是定量区分土壤净呼吸与土壤总呼吸量之间的比例关系,以及定量描述草地生态系统碳循环过程等方面的研究尚不够完善。以河北沽源的典型草原为研究对象,测定了火烧、灌溉、施肥、刈割干扰下的天然草地土壤净呼吸变化动态及其与主要控制因素之间的关系。结果表明:不同处理土壤净呼吸均表现出明显的季节性变化规律,变化趋势基本一致。火烧、灌溉和刈割处理分别比对照的土壤净呼吸通量降低了28.93%、16.25%和36.82%。土壤温度、土壤湿度与土壤净呼吸通量呈指数相关(P0.01)。对地上生物量、地下生物量、土壤有机碳含量和土壤全氮含量与土壤净呼吸之间进行逐步回归分析表明,土壤有机碳含量(SC)和土壤全氮含量(SN)是土壤净呼吸通量的主要影响因素。     

Local soil characteristics determine the microbial communities under forest understorey plants along a latitudinal gradient

The soil microbial community is essential for maintaining ecosystem functioning and is intimately linked with the plant community. Yet, little is known on how soil microbial communities in the root zone vary at continental scales within plant species. Here we assess the effects of soil chemistry, large-scale environmental conditions (i.e. temperature, precipitation and nitrogen deposition) and forest land-use history on the soil microbial communities (measured by phospholipid fatty acids) in the root zone of four plant species (Geum urbanum, Milium effusum, Poa nemoralis and Stachys sylvatica) in forests along a 1700 km latitudinal gradient in Europe.Soil microbial communities differed significantly among plant species, and soil chemistry was the main determinant of the microbial community composition within each plant species. Influential soil chemical variables for microbial communities were plant species-specific; soil acidity, however, was often an important factor. Large-scale environmental conditions, together with soil chemistry, only explained the microbial community composition in M. effusum and P. nemoralis. Forest land-use history did not affect the soil microbial community composition.Our results underpin the dominant role of soil chemistry in shaping microbial community composition variation within plant species at the continental scale, and provide insights into the composition and functionality of soil microbial communities in forest ecosystems.     

Observations and modeling of aboveground tree carbon stocks and fluxes following a bark beetle outbreak in the western United States

Bark beetle epidemics result in tree mortality across millions of hectares in North America. However, few studies have quantified impacts on carbon (C) cycling. In this study, we quantified the immediate response and subsequent trajectories of stand‐level aboveground tree C stocks and fluxes using field measurements and modeling for a location in central Idaho, USA that experienced an outbreak of mountain pine beetle (Dendroctonus ponderosae Hopkins). We measured tree characteristics in lodgepole pine (Pinus contorta) plots spanning a range of structure and mortality conditions. We then initialized the forest vegetation simulator, an individual tree‐based model, with these measurements and simulated the response of aboveground production of C fluxes as well as trajectories of C stocks and fluxes in the coming decades. Mountain pine beetles killed up to 52% of the trees within plots, with more larger trees killed. C stocks in lodgepole pine were reduced by 31–83% following the outbreak, and plot‐level C fluxes decreased 28–73%. Modeled C stocks increased nearly continuously following the infestation, recovering to preoutbreak levels in 25 years or less. Simulated aboveground tree C fluxes increased following the immediate postoutbreak decrease, then subsequently declined. Substantial variability of C stocks and fluxes among plots resulted from the number and size of killed and surviving trees. Our study illustrates that bark beetle epidemics alter forest C cycling unlike stand‐replacement wildfires or clear‐cut harvests, due in part to incomplete mortality coupled with the preference by beetles for larger trees. The dependency of postoutbreak C stocks and fluxes on stand structure suggests that C budget models and studies in areas experiencing mountain pine beetle disturbances need to include size distribution of trees for the most accurate results.