Soil fungi invest into asexual sporulation under resource scarcity,but trait spaces of individual isolates are unique

During the last few decades, a plethora of sequencing studies provided insight into fungal community composition under various environmental conditions. Still, the mechanisms of species assembly and fungal spread in soil remain largely unknown. While mycelial growth patterns are studied extensively, the abundant formation of asexual spores is often overlooked, though representing a substantial part of the fungal life cycle relevant for survival and dispersal. Here, we explore asexual sporulation (spore abundance, size and shape) in 32 co-occurring soil fungal isolates under varying resource conditions, to answer the question whether resource limitation triggers or inhibits fungal investment into reproduction. We further hypothesized that trade-offs exist in fungal investment towards growth, spore production and size. The results revealed overall increased fungal investment into spore production under resource limitations; however, effect sizes and response types varied strongly among fungal isolates. Such isolate-specific effects were apparent in all measured traits, resulting in unique trait spaces of individual isolates. This comprehensive dataset also elucidated variability in sporulation strategies and trade-offs with fungal growth and reproduction under resource scarcity, as only predicted by theoretical models before. The observed isolate-specific strategies likely underpin mechanisms of co-existence in this diverse group of saprobic soil fungi.     

A shift from exploitation to interference competition with increasing density affects population and community dynamics

Intraspecific competition influences population and community dynamics and occurs via two mechanisms. Exploitative competition is an indirect effect that occurs through use of a shared resource and depends on resource availability. Interference competition occurs by obstructing access to a resource and may not depend on resource availability. Our study tested whether the strength of interference competition changes with protozoa population density. We grew experimental microcosms of protozoa and bacteria under different combinations of protozoan density and basal resource availability. We then solved a dynamic predator–prey model for parameters of the functional response using population growth rates measured in our experiment. As population density increased, competition shifted from exploitation to interference, and competition was less dependent on resource levels. Surprisingly, the effect of resources was weakest when competition was the most intense. We found that at low population densities, competition was largely exploitative and resource availability had a large effect on population growth rates, but the effect of resources was much weaker at high densities. This shift in competitive mechanism could have implications for interspecific competition, trophic interactions, community diversity, and natural selection. We also tested whether this shift in the mechanism of competition with protozoa density affected the structure of the bacterial prey community. We found that both resources and protozoa density affected the structure of the bacterial prey community, suggesting that competitive mechanism may also affect trophic interactions.     

Hyphal growth and colony expansion

Several generations of soil microbiologists and plant pathologists have attempted to unravel the microbial composition, population dynamics and various life-sustaining processes in the soil. However, until recently, this basic resource for plant growth and nutrient recycling has to a large extent remained a black box. Studies have been made of the behavior of individual microorganisms or their population dynamics, but the relationship between the growth of individual organisms or parts of organisms (such as fungal hyphae) and that of populations and communities has been largely unknown. In particular, the spread of fungal colonies in soil has been an enigma, but now Bailey et al . (pp. 000–000 in this issue) have clearly demonstrated that spatial behavior of Rhizoctonia colonies can switch from finite to invasive expansion dependent on the non-linear relationship between the distance among substrate particles and the probability of colonization.     

Mathematical modeling of regulatory mechanisms in yeast colony development

In the present study, yeast colony development serves as a model system to study growth of fungal populations with negligible nutrient and signal transport within the mycelium. Mathematical simulations address the question whether colony development is governed by diffusional limitation of nutrients. A hybrid one-dimensional cellular automaton model was developed that describes growth of discrete cells based upon microscopic interaction rules in a continuous field of nutrient and messenger. The model is scaled for the geometry of the experimental setup, cell size, growth- and substrate uptake rates. Therefore, calculated cell density profiles and nutrient distributions can be compared to experimental results and the model assumptions can be verified. In the physiologically relevant parameter range, simulations show an exponentially declining cell density along the median axis of the colonies in case of a diffusion limited growth scenario. These results are in good agreement with cell density profiles obtained in cultivations of the yeast Candida boidinii with glucose as the limiting carbon source but stand in contrast to the constant cell density profile estimated for Yarrowia lipolytica grown under the same conditions. While from the comparison of experimental results and simulations a diffusion limited growth mechanism is proposed for glucose limited C. boidinii colonies, this hypothesis is rejected for the growth of Y. lipolytica. As an alternative, a quorum sensing model was developed that can explain the evolution of constant cell density profiles based on the effect of a not further characterized unstable or volatile messenger.     

Isothiocyanates inhibit fungal pathogens of potato in in vitro assays

Aims

This study aimed to examine the effects of seven different isothiocyanates against the growth and development of three important soil borne potato pathogens, (Colletotrichum coccodes, Rhizoctonia solani and Helminthosporium solani).

Methods

The study was carried out using an agar diffusion assay. The radial growth of fungal pathogens grown on agar containing different ITCs at a range of concentrations was compared to that of growth on control agar plates that did not contain ITCs.

Results

Results varied depending on the specific isothiocyanate incorporated into the agar. They ranged from those which showed a significant effect on fungal growth to those which appeared to have little or no effect. Where a suppressive effect was observed, due to the presence of the isothiocyanate, fungal colony growth decreased as the concentration of the incorporated isothiocyanate increased.

Conclusions

Results from this study indicate that fungal growth can be inhibited by exposure to ITCs. However the results observed are specific to the ITC structure and exposure concentration.     

神农架国家公园林线过渡带土壤真菌多样性

林线过渡带是陆地生态系统对气候变化响应的敏感区域,研究林线过渡带土壤真菌的群落结构和形成机制,对于预测气候变化对土壤养分循环和维持陆地生态系统功能的影响具有重要意义。利用Illumina高通量测序技术分析了神农架国家公园林线上下的灌木林和针叶林的土壤真菌群落结构和多样性。结果表明,在真菌物种组成上,两种植被类型的土壤优势菌门、属和种类不同,针叶林和灌木林的优势菌门分别是担子菌门(Basidiomycota)和接合菌门(Zygomycota)。除趋势对应分析(DCA)和不相似性检验(Dissimilarity test)表明两种林型的土壤真菌群落结构组成存在显著差异,且针叶林土壤真菌Shannon指数、Chao值和Richness指数均显著(P0.05)高于灌木林。典范对应分析(CCA)和Mantel检验显示土壤真菌群落结构与土壤p H、植物多样性、土壤温度和土壤湿度存在显著相关性。因此,林线过渡带上下的土壤真菌群落结构和多样性存在显著差异,土壤p H、植物多样性、土壤湿度和土壤温度可能是影响土壤真菌群落结构的重要因素。     

Modelling the growth of Trichoderma virens with limited sampling of digital images

AIMS: Using limited digital image sampling, a model of fungal growth in soil that considers both hyphal production and lysis was constructed for two strains of Trichoderma virens over a range of four temperatures. MATERIALS AND METHODS: A growth model was developed by fitting the radial cross sectional data with a modified form of the Ratkowsky equation to determine maximum growth rate and a modified Arrhenius equation to determine maximal rate of decrease in area covered by mycelia. The parameters obtained from a combined equation were then verified by using the data obtained from the whole colony to determine the appropriateness of the model. CONCLUSIONS: Using a limited data set and a combination of the Ratkowsky and Arrhenius equations, the mycelial coverage of the T. virens colony was determined, relating microscopic hyphal growth to macroscopic colony growth. This model was sufficiently robust to predict growth across four temperatures for a genetically modified and wild-type strain of T. virens. SIGNIFICANCE AND IMPACT OF STUDY: By using simple assumptions for the increase and eventual decline in fungal growth on a resource-limited medium, this model constructs an initial framework onto which additional parameters such as nutrient consumption could be incorporated for prediction of fungal growth.     

Cellular automata simulations of fungal growth on solid substrates

Growth of filamentous fungi on the surface of cereal grains is a critical aspect of solid substrate fermentation (SSF). Numerous mathematical models have been developed to describe various aspects of fungal growth in SSF. These models consider hyphal geometry and nutrient availability as determinants of colony morphology and fungal physiological state. This work describes the use of cellular automata (CA) as an alternative method of modeling fungal growth. CA models reliant on a very limited set of rules or "knowledge base" display a rich array of behaviors that mimic fungal growth. By incorporating probablistic growth rules into CA models, colony characteristics such as biomass accumulation rate, colony radial growth rate, mycelial density and fungal differentiation are readily generated.     

Effect of natamycin on the enumeration, genetic structure and composition of bacterial community isolated from soils and soybean rhizosphere

Natamycin is commonly used to control fungal growth on agar media used for bacterial enumeration or strain isolation. However, there is no conclusive report on the possible effect of this antibiotic on bacterial growth or on the diversity of the recovered soil bacteria. Therefore, the possible effects of natamycin on the numbers of bacteria isolated at 12 degrees C from three different soils and soybean rhizosphere soil were investigated using natamycin concentrations ranging from 0 to 200 mg l(-1). Our results demonstrate that natamycin concentrations, which inhibit the growth of fungi on the media, have a small but significant inhibitory effect on the number of bacterial colony forming units. A natamycin concentration of 50-200 mg l(-1) is required for an efficient control of fungal growth on media in our experimental conditions depending on the soil type. Bacterial community structure was assessed on culturable cells (cells washed from enumeration plates: plate-wash approach) obtained at 12 degrees C from soybean rhizosphere soil by performing Ribosomal Intergenic Spacer Analysis (RISA) fingerprinting. We demonstrate that all natamycin concentrations used alter the structure of the recovered, culturable bacterial community, compared to control without natamycin. Using ARDRA (amplification of the 16S rDNA gene and restriction analysis) genotyping of individual isolates, some differences were observed between the bacterial isolates obtained in the presence or absence of natamycin. Bacterial isolates recovered in the presence of natamycin are more tolerant (maximal growth rate and lag phase) to this compound than those isolated without natamycin, indicating a possible selection of resistant strains. Therefore, high concentration of natamycin cannot be used for isolation of bacterial strains with the aim of studying biodiversity and could bias a selection of strains for practical applications.     

接种木霉菌对黄瓜幼苗生长和根际土壤AM真菌侵染的影响

在盆栽试验中分别接种3株长枝木霉菌株Trichoderma longibrachiatum MF-1、MF-2和MF-3,以不接种木霉菌处理作为对照,研究木霉菌接种对土著AM真菌和黄瓜幼苗生长的影响。结果表明,菌株MF-1和MF-2显著提高了AM真菌侵染率和根外菌丝密度,与对照相比,AM真菌侵染率分别提高了26.85%和54.66%,根外菌丝密度分别是对照的3.94和3.76倍。接种菌株MF-2使植株地上部生物量显著提高了39.07%。菌株MF-3显著提高土壤pH和土壤有效磷含量。Pearson相关分析发现,添加木霉菌后,AM真菌侵染率与根外菌丝密度和孢子密度均呈显著正相关关系,土壤pH与植株地上部生物量和土壤有效磷含量均呈显著正相关关系。研究表明,3株长枝木霉与土著AM真菌的联合作用效果有明显差异,菌株MF-1和MF-2显著促进AM真菌生长,菌株MF-2更有利于黄瓜幼苗生长,而菌株MF-3主要改善土壤pH和有效磷含量。将几种木霉菌复合应用,有助于达到联合促生和改善土壤环境的综合效果。     

Plant traits determine the phylogenetic structure of arbuscular mycorrhizal fungal communities

Functional diversity in ecosystems has traditionally been studied using aboveground plant traits. Despite the known effect of plant traits on the microbial community composition, their effects on the microbial functional diversity are only starting to be assessed. In this study, the phylogenetic structure of arbuscular mycorrhizal (AM) fungal communities associated with plant species differing in life cycle and growth form, that is, plant life forms, was determined to unravel the effect of plant traits on the functional diversity of this fungal group. The results of the 454 pyrosequencing showed that the AM fungal community composition differed across plant life forms and this effect was dependent on the soil collection date. Plants with ruderal characteristics tended to associate with phylogenetically clustered AM fungal communities. By contrast, plants with resource‐conservative traits associated with phylogenetically overdispersed AM fungal communities. Additionally, the soil collected in different seasons yielded AM fungal communities with different phylogenetic dispersion. In summary, we found that the phylogenetic structure, and hence the functional diversity, of AM fungal communities is dependent on plant traits. This finding adds value to the use of plant traits for the evaluation of belowground ecosystem diversity, functions and processes.     

Functional consequences of nutrient translocation in mycelial fungi

Fungi are of fundamental importance for plant and microbial nutrition with primary roles in decomposition and nutrient recycling. They also have great potential for use in areas of biotechnology such as bioremediation of organic and inorganic pollutants and biocontrol of plant pathogens. In all these contexts, environmental heterogeneity has a strong influence on growth and function. A large class of fungi overcome the difficulties encountered in such environments by the mechanism of translocation which results in the internal redistribution of nutrients within the fungal mycelium. In this paper, we use a combination of experimental techniques and mathematical modelling to examine fungal growth in general, and in particular, translocation in the common soil saprophytic fungus Rhizoctonia solani. A detailed mathematical model is presented where translocation is considered to have both diffusive and metabolically-driven components. A calibration experiment provided the necessary parameter values. Growth experiments were compared with model solutions and thus we provide strong evidence that diffusion is the dominant mechanism for translocation in homogeneous environments. In heterogeneous environments, we conclude that diffusion is still vital for exploration, i.e. the expansion of the fungal network into the surrounding area. However, we also conclude that localized resources may be utilized faster if energy is invested, i.e. when exploitation of the fungal microenvironment is enhanced by metabolically driven translocation.     

Fungal community composition in neotropical rain forests: the influence of tree diversity and precipitation

Plant diversity is considered one factor structuring soil fungal communities because the diversity of compounds in leaf litter might determine the extent of resource heterogeneity for decomposer communities. Lowland tropical rain forests have the highest plant diversity per area of any biome. Since fungi are responsible for much of the decomposition occurring in forest soils, understanding the factors that structure fungi in tropical forests may provide valuable insight for predicting changes in global carbon and nitrogen fluxes. To test the role of plant diversity in shaping fungal community structure and function, soil (0-20?cm) and leaf litter (O horizons) were collected from six established 1-ha forest census plots across a natural plant diversity gradient on the Isthmus of Panama. We used 454 pyrosequencing and phospholipid fatty acid analysis to evaluate correlations between microbial community composition, precipitation, soil nutrients, and plant richness. In soil, the number of fungal taxa increased significantly with increasing mean annual precipitation, but not with plant richness. There were no correlations between fungal communities in leaf litter and plant diversity or precipitation, and fungal communities were found to be compositionally distinct between soil and leaf litter. To directly test for effects of plant species richness on fungal diversity and function, we experimentally re-created litter diversity gradients in litter bags with 1, 25, and 50 species of litter. After 6?months, we found a significant effect of litter diversity on decomposition rate between one and 25 species of leaf litter. However, fungal richness did not track plant species richness. Although studies in a broader range of sites is required, these results suggest that precipitation may be a more important factor than plant diversity or soil nutrient status in structuring tropical forest soil fungal communities.     

Endophytic fungus fine‐tunes the persistence strategy of its alpine host grass in response to soil resource levels

An understanding of hereditary endophytic fungi, and the effects on grass persistence strategies (i.e. relative investment in sexual reproduction and vegetative growth) under natural conditions may help to predict how some alpine ecosystems will respond to environmental change. Grass persistence and endophyte maintenance in host populations are closely related, but could become independent due to endophyte loss mechanisms. We used native grass and endophyte populations to test the hypothesis that fungal endophytes manipulate grass persistence strategies to secure endophyte maintenance in plant populations. Two conditions were required to verify this hypothesis: 1) the fungus caused alterations in host plant strategies; and 2) plant phenotypic changes induced by the fungal endophyte increased endophyte transmission. We compared symbiotic (S) and non‐symbiotic (NS) persistence strategies of Festuca eskia (Poaceae), an alpine grass infected by the asexual form of the fungal endophyte Epichloë festucae. We characterised endophyte transmission efficiency, and described vegetative growth and sexual reproduction in a field population that naturally supports approximately 50% S plants. We built a demographic model to estimate plant vegetative growth rates. A correlation between plant persistence strategy, and fungal maintenance was evaluated by increasing soil resource levels. Under natural conditions, S and NS plants exploited different persistence strategies in the same population; S plants exhibited greater vegetative growth than their NS counterparts, while maintaining the same reproductive output. In response to higher soil resource levels, S plants shifted in persistence strategies and phenology, whereas NS plants maintained the same strategies. Therefore, results suggested the fungal endophyte fine‐tuned host persistence strategies according to soil resource level. Finally, we found no direct relationship between the changes induced by fungal endophyte and endophyte transmission. Consequently, fungal endophytes affected host persistence strategies, but did not directly increase endophyte transmission.     

玫烟色拟青霉适温性及抗多菌灵特性的种内变异

在15 ℃～35 ℃的温度范围内比较测定了玫烟色拟青霉(Paecilomyces fumosoroseus) 6株野生菌的菌落生长、产孢量及孢子活力.结果显示,3个指标均以25 ℃左右最好,但同一温度下菌株间或同一菌株在不同温度下的差异显著, 菌株Pfr116和Pfr6206具有相对稳定优良的生长、产孢及活孢率性状.对不同浓度多菌灵对6株野生菌的菌落生长和单孢菌落形成的影响测定表明,菌株间存在较大差异.不同多菌灵浓度对单孢菌落形成的抑制率观察值可用逻辑斯蒂模型较好地拟合(r²≥0.90).用所获参数估计的最低禁菌浓度MIC值显示,Pfr4205和Pfr116对多菌灵表现为低抗性（MIC≤20.0 μg·ml^-1）;Pfr153、Pfr612和Pfr2175属于低水平中抗,MIC值仅略大于20 μg·ml^-1;而Pfr6206的MIC值高达93.5 μg·ml^-1,接近MIC>100 μg·ml^-1的高抗标准.因此,Pfr6206为适温性和抗多菌灵特性俱佳的菌株,可作为抗多菌灵和适应不同季节或地区的害虫生防菌剂的候选菌株.     

Regulation of Fusarium oxysporum population introduced into soil: the amoebal predation hypothesis

Abstract Inoculation of fungi into soil has been suggested for biological control of plant diseases. The aim of our work was to test the ability of protozoa to reduce the density of introduced fungal populations. The survival of Fusarium oxysporum in non-sterile soil was studied after introduction at densities of: 1 × 10⁴, 1 × 10⁶ and 5 × 10⁷ cfu/g soil. The dynamics of protozoa were also followed. The fungal populations remained close to the initial inoculation densities and did not induce the growth of indigenous protozoa. A bacterial population ( Enterobacter aerogenes ) was used to promote and stimulate the predatory activity of amoebae. Then, after simultaneous inoculation with bacteria and fungi, the density of protozoa increased but this had no effect on the fungal population, although some amoebae are able to feed on small fungal propagules such as conidia. The physiological state of Fusarium in soil and intraspecific competition seem to be more important in regulating introduced fungal populations than amoebal predation. We conclude that the regulation of bacterial and fungal populations in soil depend on different mechanisms.     

Afforestation alters community structure of soil fungi

Relatively little is known about the effect of afforestation on soil fungal communities. This study demonstrated that afforestation altered fungal community structure and that changes were correlated to pools of soil C. Pasture at three locations on the same soil type was afforested with Eucalyptus globulus or Pinus pinaster. The structure of fungal communities under the three land uses was measured after 13y using automated ribosomal intergenic spacer analysis (ARISA). Afforestation significantly altered the structure of fungal communities. The effect of location on the structure of fungal communities was limited to pasture soils; although these contained the same plant species, the relative composition of each species varied between locations. Differences in the structure of fungal communities between pasture, E. globulus and P. pinaster were significantly correlated with changes in the amount of total organic C and microbial biomass-C in soil. Afforestation of patches of agricultural land may contribute to conserving soil fungi in agricultural landscapes by supporting fungal communities with different composition to agricultural soils.     

长三角地区城市密度对碳排放绩效的影响效应与机制

城市密度是衡量城市各要素空间集聚程度的表征也是调控城市各要素资源分配效率的重要手段。过往主要围绕城市密度的物质形态测度来研究城市空间资源利用与环境问题,少有立足碳排放绩效的视角来研究城市密度的演变逻辑。立足生态效益中自然资源投入最小化与获得价值最大化的观点,从经济、社会、环境三个维度构建碳排放绩效综合评价指标,以长三角41个城市为例,基于标准差椭圆分析城市密度与碳排放绩效的时空演变及关联特征,采用地理加权回归模型与地理探测器相结合的方法,确定城市密度对碳排放绩效的影响效应及机制。结果表明:(1)城市密度与碳排放绩效均升高,城市密度增速减慢,而碳排放绩效增速加快;二者均呈东南-西北向发展且关联性不断增强。(2)城市密度分指标对碳排放绩效的影响效应存在时空差异,东南部多数城市各分指标影响系数增大且作用方向不变;西北部人口密度负向影响显著增强,经济密度的影响由负转正,而空间密度的影响由正转负。(3)城市密度与其他经济社会因素交互后对碳排放绩效产生影响,其中经济密度与产业结构协同作用对碳排放绩效的影响最大,且与因子独立作用相比,人口密度与其他影响因素的交互效应增幅最大。理清城市密度对碳排放绩效的影响效应及机制,可以为城市空间结构的合理优化提供依据。