龙南钾矿区常见蕨类植物可培养内生真菌的多样性

植物内生真菌作为一类特殊的微生物资源,与宿主在长期的生态系统演化过程中形成了互惠共生关系,通过多样化途径来增强植物体的营养生理和抗性机能,对宿主植物产生多种有益生物学作用,在植物演替过程中具有重要的生态学意义。这种特殊微生物资源近年来倍受关注,而利用植物-真菌共生体强化植物在矿区逆境中生长,提高矿区生物修复效率是一个新的研究热点。为探明钾矿区不同蕨类植物内生真菌的物种多样性、群落组成以及生态分布规律,该研究以芒萁、狗脊、禾秆蹄盖蕨、海金沙、华中铁角蕨、井栏边草和乌蕨等植物为材料,采用组织分离、形态学鉴定等方法,对其内生真菌多样性进行分析。结果表明:从7种植物中共分离获得377株内生真菌,总分离率在2.50%~4.52%之间。经鉴定377个菌株隶属于链格孢属、曲霉属、枝孢菌属和轮枝孢属等25个分类单元,其中链格孢属、曲霉属、枝孢菌属和轮枝孢属等在所有被调查蕨类植物中都有分布,为优势属,共计为185株,占总株数的49.07%,但它们在每种植物的分布存在明显差异;7种蕨类植物内生真菌总定植率为叶高于根状茎(P0.05),多样性指数在0.502~0.867之间,但每种植物及其不同组织部位的内生真菌定植率和多样性指数存在一定的差异;从相似性分析来看,同一个钾矿区不同蕨类植物内生真菌菌群之间的相似性程度较低,相似性系数在0.189~0.587之间。该研究结果不仅丰富了植物内生真菌种质资源,而且为进一步开展植物内生真菌强化宿主植物在钾矿区生长适应机制的研究奠定了基础。     

A meta‐analysis of temperature sensitivity as a microbial trait

Traits‐based approaches in microbial ecology provide a valuable way to abstract organismal interaction with the environment and to generate hypotheses about community function. Using macromolecular rate theory (MMRT), we recently identified that temperature sensitivity can be characterized as a distinct microbial trait. As temperature is fundamental in controlling biological reactions, variation in temperature sensitivity across communities, organisms, and processes has the potential to vastly improve understanding of microbial response to climate change. These microbial temperature sensitivity traits include the heat capacity (), temperature optimum (T_opt), and point of maximum temperature sensitivity (TS_max), each of which provide unique insights about organismal response to changes in temperature. In this meta‐analysis, we analyzed the distribution of these temperature sensitivity traits from bacteria, fungi, and mixed communities across a variety of biological systems (e.g., soils, oceans, foods, wastewater treatment plants) in order to identify commonalities in temperature responses across these diverse organisms and reaction rates. Our analysis of temperature sensitivity traits from over 350 temperature response curves reveals a wide distribution of temperature sensitivity traits, with T_opt and TS_max well within biological relevant temperatures. We find that traits vary significantly depending on organism type, microbial diversity, source environment, and biological process, with higher temperature sensitivity found in fungi than bacteria and in less diverse systems. Carbon dioxide production was found to be less temperature sensitive than denitrification, suggesting that changes in temperature will have a potentially larger impact on nitrogen‐related processes. As climate changes, these results have important implications for basic understanding of the temperature sensitivity of biological reactions and for ecological understanding of species’ trait distributions, as well as for improved treatment of temperature sensitivity in models.     

Characterization of microbial contamination in United States Air Force aviation fuel tanks

Bacteria and fungi, isolated from United States Air Force (USAF) aviation fuel samples, were identified by gas chromatograph fatty acid methyl ester (GC-FAME) profiling and 16S or 18S rRNA gene sequencing. Thirty-six samples from 11 geographically separated USAF bases were collected. At each base, an above-ground storage tank, a refueling truck, and an aircraft wing tank were sampled at the lowest sample point, or sump, to investigate microbial diversity and dispersion within the fuel distribution chain. Twelve genera, including four Bacillus species and two Staphylococcus species, were isolated and identified. Bacillus licheniformis, the most prevalent organism isolated, was found at seven of the 11 bases. Of the organisms identified, Bacillus sp., Micrococcus luteus, Sphinogmonas sp., Staphylococcus sp., and the fungus Aureobasidium pullulans have previously been isolated from aviation fuel samples. The bacteria Pantoea ananatis, Arthrobacter sp., Alcaligenes sp., Kocuria rhizophilia, Leucobacter komagatae, Dietza sp., and the fungus Discophaerina fagi have not been previously reported in USAF aviation fuel. Only at two bases were the same organisms isolated from all three sample points in the fuel supply distribution chain. Isolation of previously undocumented organisms suggests either, changes in aviation fuel microbial community in response to changes in aviation fuel composition, additives and biocide use, or simply, improvements in isolation and identification techniques.     

Architectural and growth traits differ in effects on performance of clonal plants: an analysis using a field-parameterized simulation model

Individual traits are often assumed to be linked in a straightforward manner to plant performance and processes such as population growth, competition and community dynamics. However, because no trait functions in isolation in an organism, the effect of any one trait is likely to be at least somewhat contingent on other trait values. Thus, to the extent that the suite of trait values differs among species, the magnitude and even direction of correlation between values of any particular trait and performance is likely to differ among species. Working with a group of clonal plant species, we assessed the degree of this contingency and therefore the extent to which the assumption of simple and general linkages between traits and performance is valid. To do this, we parameterized a highly calibrated, spatially explicit, individual‐based model of clonal plant population dynamics and then manipulated one trait at a time in the context of realistic values of other traits for each species. The model includes traits describing growth, resource allocation, response to competition, as well as architectural traits that determine spatial spread. The model was parameterized from a short‐term (3 month) experiment and then validated with a separate, longer term (two year) experiment for six clonal wetland sedges, Carex lasiocarpa, Carex sterilis, Carex stricta, Cladium mariscoides, Scirpus acutus and Scirpus americanus. These plants all co‐occur in fens in southeastern Michigan and represent a spectrum of clonal growth forms from strong clumpers to runners with long rhizomes. Varying growth, allocation and competition traits produced the largest and most uniform responses in population growth among species, while variation in architectural traits produced responses that were smaller and more variable among species. This is likely due to the fact that growth and competition traits directly affect mean ramet size and number of ramets, which are direct components of population biomass. In contrast, architectural and allocation traits determine spatial distribution of biomass; in the long run, this also affects population size, but its net effect is more likely to be mediated by other traits. Such differences in how traits affect plant performance are likely to have implications for interspecific interactions and community structure, as well as on the interpretation and usefulness of single trait optimality models.     

罗汉果内生真菌多样性研究

该文采用传统形态学方法结合r DNA-ITS序列分析,对我国重要药用植物罗汉果中的内生真菌进行了鉴定并研究其多样性。结果表明:采用组织培养法从罗汉果健康植株中共分离得到150株内生真菌,包括罗汉果中雌株的内生真菌96株、雄株的内生真菌54株。122株内生真菌经形态学结合r DNA-ITS序列分析鉴定为9个属,均归属为子囊菌门,包含座囊菌纲(Dothideomycetes)和子囊菌纲(Sordariomycetes)。其中,座囊菌纲(Dothideomycetes)真菌包含3科、3属;子囊菌纲(Sordariomycetes)真菌包含6科、6属。优势属为刺盘孢属(Colletotrichum)和镰刀菌属(Fusarium)。罗汉果雌、雄植株不同组织中内生真菌的定殖率及分离率的变化规律均不相同,雌株中以根中内生真菌的定殖率和分离率最高,叶片中的最低;在雄株中以叶片中的定殖率和分离率最高,根中的最低。不同菌株在雌、雄两种植株的不同组织中的分布均不同,结合内生真菌群落组成的相似性比较结果,表明部分内生真菌对罗汉果雌株和雄株,以及同一植株中的不同组织均具有偏好性。不同组织中内生真菌的多样性指数在...     

桃儿七茎叶组织内生真菌多样性

通过用两种传统培养基(PDA、SDA)分离方法对5个自然野生分布的桃儿七群落(分布于青海省、甘肃省和四川省)茎叶组织内的内生真菌多样性进行研究,并用形态学与分子生物学的方法鉴定菌株。实验结果显示,720个茎叶组织块中共分离到141株内生真菌。依据真菌在培养基上的形态初步划分为52个分类单元,经鉴定归属于19属,其中茎组织中16属叶组织中6属,桃儿七茎叶组织中的真菌优势属为拟青霉属,相对分离频率为26.34%。5个采样点间内生真菌的香浓维纳多样性指数为0.71—1.41,Sorenson相似性系数为0.13—0.50,定殖率为14.58%—28.47%。通过对PDA、SDA两种培养基以及茎、叶组织的定殖率进行统计,结果显示:PDA(17.50%)SDA(21.67%),茎(29.72%)叶(9.44%)。研究结果表明,桃儿七茎叶组织中内生真菌的多样性较低,不同采样点间宿主植物内内生真菌群落的相似性较低,真菌群落结构存在差异。研究为进一步扩大从桃儿七中筛选产鬼臼毒素等活性物质内生真菌提供了一种新的思路。     

施磷对干旱胁迫下箭竹根际土壤养分及微生物群落的影响

以箭竹及其根际土壤作为研究对象,采用两因素随机区组实验,设置2种水分处理（正常浇水和干旱胁迫）和2种施磷量处理（施磷和不施磷）,探究施磷对干旱胁迫下箭竹根际土壤养分及微生物群落结构和多样性的影响。结果表明：（1）干旱胁迫显著降低了箭竹根际土壤中微生物量碳、可溶性有机氮和有效磷的含量,虽对箭竹根际土壤微生物群落的多样性无显著影响,但显著降低了箭竹根际土壤中总PLFA（phospholipid fatty acid contents）的含量和真菌、细菌、革兰氏阳性菌与革兰氏阴性菌的PLFA含量以及革兰氏阳性菌/革兰氏阴性菌的PLFA比值,显著改变了箭竹根际土壤微生物群落结构,结果显著降低了箭竹的生物量。（2）施磷显著增加了受旱箭竹根际土壤中微生物量碳和有效磷的含量,虽大体上对受旱箭竹根际土壤微生物群落的多样性无显著影响,但显著增加了受旱箭竹根际土壤中总PLFA和真菌PLFA的含量,并在一定程度上增加了细菌、革兰氏阳性菌、革兰氏阴性菌和放线菌的PLFA含量以及革兰氏阳性菌/革兰氏阴性菌和真菌/细菌的PLFA比值,也在一定程度上改善了受旱箭竹根际土壤微生物群落结构,从而改善受旱箭竹的生长。（3）主成分分析表明,干旱对箭竹根际土壤微生物群落结构的影响显著,而施磷的影响不明显。（4）相关分析发现,箭竹根际土壤微生物群落结构与箭竹根际土壤微生物量碳、可溶性有机氮及箭竹生物量呈显著正相关。综上,干旱降低了箭竹根际土壤养分含量和微生物生物量,改变了箭竹根际土壤微生物群落结构,抑制了箭竹的生长;施磷能增加受旱箭竹根际土壤养分含量和微生物生物量,改善受旱箭竹根际土壤微生物群落结构,进而改善受旱箭竹的生长。     

Growth rates of rhizosphere microorganisms depend on competitive abilities of plants and N supply

Abstract

Plant‐microbial interactions under N‐limiting conditions are governed by competitive abilities of plants for N. Our study aimed to examine how two plant species of strawberry, Fragaria vesca L. (native species) and Duchesnea indica (Andrews) Focke (an invasive plant in central Europe), growing in intra‐specific and inter‐specific competition alter the functions of rhizosphere microorganisms in dependence on N availability. By intra‐specific competition at low N level, a 2.4‐fold slower microbial‐specific growth rate was observed under D. indica characterized by smaller root biomass and lower N content in roots compared with F. vesca. By inter‐specific competition of both plants at low N level, microbial growth rates were similar to those for D. indica indicating that plants with stronger competitive abilities for N controls microbial community in the rhizosphere. Since a high N level smoothed the differences between plant species in root and microbial biomass as well as in microbial growth rates under both intra‐specific and inter‐specific competition, we conclude that competitive abilities of plant species were crucial for microbial growth in the rhizosphere only under N imitation.     

Comparative activity and functional ecology of permafrost soils and lithic niches in a hyper‐arid polar desert

Permafrost in the high elevation McMurdo Dry Valleys of Antarctica ranks among the driest and coldest on Earth. Permafrost soils appear to be largely inhospitable to active microbial life, but sandstone lithic microhabitats contain a trophically simple but functional cryptoendolithic community. We used metagenomic sequencing and activity assays to examine the functional capacity of permafrost soils and cryptoendolithic communities in University Valley, one of the most extreme regions in the Dry Valleys. We found metagenomic evidence that cryptoendolithic microorganisms are adapted to the harsh environment and capable of metabolic activity at in situ temperatures, possessing a suite of stress response and nutrient cycling genes to fix carbon under the fluctuating conditions that the sandstone rock would experience during the summer months. We additionally identified genes involved in microbial competition and cooperation within the cryptoendolithic habitat. In contrast, permafrost soils have a lower richness of stress response genes, and instead the metagenome is enriched in genes involved with dormancy and sporulation. The permafrost soils also have a large presence of phage genes and genes involved in the recycling of cellular material. Our results underlie two different habitability conditions under extreme cold and dryness: the permafrost soil which is enriched in traits which emphasize survival and dormancy, rather than growth and activity; and the cryptoendolithic environment that selects for organisms capable of growth under extremely oligotrophic, arid and cold conditions. This study represents the first metagenomic interrogation of Antarctic permafrost and polar cryptoendolithic microbial communities.     

When to cut your losses: Dispersal allocation in an asexual filamentous fungus in response to competition

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细菌铁载体拮抗植物病原真菌及促生作用研究进展

铁载体是微生物在缺铁条件下分泌的小分子有机化合物,以获取铁元素维持其生长。细菌分泌的铁载体在拮抗植物病原菌和促进植物生长方面具有重要作用。本文总结了细菌铁载体拮抗植物病原真菌的营养和生态位竞争、诱导植物诱导性系统抗性、扰乱病原菌铁稳态的机制,以及促进植物生长的作用,以解释细菌分泌的铁载体在多功能微生物菌剂研制中的重要作用。     

Priming and memory of stress responses in organisms lacking a nervous system

Experience and memory of environmental stimuli that indicate future stress can prepare (prime) organismic stress responses even in species lacking a nervous system. The process through which such organisms prepare their phenotype for an improved response to future stress has been termed ‘priming’. However, other terms are also used for this phenomenon, especially when considering priming in different types of organisms and when referring to different stressors. Here we propose a conceptual framework for priming of stress responses in bacteria, fungi and plants which allows comparison of priming with other terms, e.g. adaptation, acclimation, induction, acquired resistance and cross protection. We address spatial and temporal aspects of priming and highlight current knowledge about the mechanisms necessary for information storage which range from epigenetic marks to the accumulation of (dormant) signalling molecules. Furthermore, we outline possible patterns of primed stress responses. Finally, we link the ability of organisms to become primed for stress responses (their ‘primability’) with evolutionary ecology aspects and discuss which properties of an organism and its environment may favour the evolution of priming of stress responses.     

Initial colonization,community assembly and ecosystem function: fungal colonist traits and litter biochemistry mediate decay rate

Priority effects are an important ecological force shaping biotic communities and ecosystem processes, in which the establishment of early colonists alters the colonization success of later‐arriving organisms via competitive exclusion and habitat modification. However, we do not understand which biotic and abiotic conditions lead to strong priority effects and lasting historical contingencies. Using saprotrophic fungi in a model leaf decomposition system, we investigated whether compositional and functional consequences of initial colonization were dependent on initial colonizer traits, resource availability or a combination thereof. To test these ideas, we factorially manipulated leaf litter biochemistry and initial fungal colonist identity, quantifying subsequent community composition, using neutral genetic markers, and community functional characteristics, including enzyme potential and leaf decay rates. During the first 3 months, initial colonist respiration rate and physiological capacity to degrade plant detritus were significant determinants of fungal community composition and leaf decay, indicating that rapid growth and lignolytic potential of early colonists contributed to altered trajectories of community assembly. Further, initial colonization on oak leaves generated increasingly divergent trajectories of fungal community composition and enzyme potential, indicating stronger initial colonizer effects on energy‐poor substrates. Together, these observations provide evidence that initial colonization effects, and subsequent consequences on litter decay, are dependent upon substrate biochemistry and physiological traits within a regional species pool. Because microbial decay of plant detritus is important to global C storage, our results demonstrate that understanding the mechanisms by which initial conditions alter priority effects during community assembly may be key to understanding the drivers of ecosystem‐level processes.     

The toolbox of Trichoderma spp. in the biocontrol of Botrytis cinerea disease

Botrytis cinerea is a necrotrophic fungal pathogen causing disease in many plant species, leading to economically important crop losses. So far, fungicides have been widely used to control this pathogen. However, in addition to their detrimental effects on the environment and potential risks for human health, increasing fungicide resistance has been observed in the B. cinerea population. Biological control, that is the application of microbial organisms to reduce disease, has gained importance as an alternative or complementary approach to fungicides. In this respect, the genus Trichoderma constitutes a promising pool of organisms with potential for B. cinerea control. In the first part of this article, we review the specific mechanisms involved in the direct interaction between the two fungi, including mycoparasitism, the production of antimicrobial compounds and enzymes (collectively called antagonism), and competition for nutrients and space. In addition, biocontrol has also been observed when Trichoderma is physically separated from the pathogen, thus implying an indirect systemic plant defence response. Therefore, in the second part, we describe the consecutive steps leading to induced systemic resistance (ISR), starting with the initial Trichoderma–plant interaction and followed by the activation of downstream signal transduction pathways and, ultimately, the defence response resulting in ISR (ISR‐prime phase). Finally, we discuss the ISR‐boost phase, representing the effect of ISR priming by Trichoderma spp. on plant responses after additional challenge with B. cinerea.     

Is plant genetic control of ectomycorrhizal fungal communities an untapped source of stable soil carbon in managed forests?

Background

Ectomycorrhizal (ECM) fungi provide one of the main pathways for carbon (C) to move from trees into soils, where these fungi make significant contributions to microbial biomass and soil respiration.

Scope

ECM fungal species vary significantly in traits that likely influence C sequestration, such that forest C sequestration potential may be driven in part by the existing community composition of ECM fungi. Moreover, accumulating experimental data show that tree genotypes differ in their compatibility with particular ECM fungal species, i.e. mycorrhizal traits of forest trees are heritable. Those traits are genetically correlated with other traits for which tree breeders commonly select, suggesting that selection for traits of interest, such as disease resistance or growth rate, could lead to indirect selection for or against particular mycorrhizal traits of trees in forest plantations.

Conclusions

Altogether, these observations suggest that selection of particular tree genotypes could alter the community composition of symbiotic ECM fungi in managed forests, with cascading effects on soil functioning and soil C sequestration.     

The trade-off between growth rate and yield in microbial communities and the consequences for under-snow soil respiration in a high elevation coniferous forest

Soil microbial respiration is a critical component of the global carbon cycle, but it is uncertain how properties of microbes affect this process. Previous studies have noted a thermodynamic trade-off between the rate and efficiency of growth in heterotrophic organisms. Growth rate and yield determine the biomass-specific respiration rate of growing microbial populations, but these traits have not previously been used to scale from microbial communities to ecosystems. Here we report seasonal variation in microbial growth kinetics and temperature responses (Q₁₀) in a coniferous forest soil, relate these properties to cultured and uncultured soil microbes, and model the effects of shifting growth kinetics on soil heterotrophic respiration (R_h). Soil microbial communities from under-snow had higher growth rates and lower growth yields than the summer and fall communities from exposed soils, causing higher biomass-specific respiration rates. Growth rate and yield were strongly negatively correlated. Based on experiments using specific growth inhibitors, bacteria had higher growth rates and lower yields than fungi, overall, suggesting a more important role for bacteria in determining R_h. The dominant bacteria from laboratory-incubated soil differed seasonally: faster-growing, cold-adapted Janthinobacterium species dominated in winter and slower-growing, mesophilic Burkholderia and Variovorax species dominated in summer. Modeled R_h was sensitive to microbial kinetics and Q₁₀: a sixfold lower annual R_h resulted from using kinetic parameters from summer versus winter communities. Under the most realistic scenario using seasonally changing communities, the model estimated R_h at 22.67 mol m⁻² year⁻¹, or 47.0% of annual total ecosystem respiration (R_e) for this forest.     

Evolution of fungal pathogens in domestic environments?

Specific indoor environments select for certain stress-tolerant fungi and can drive their evolution towards acquiring medically important traits. Here we review the current knowledge in this area of research, focussing on the so-called black yeasts. Many of these melanised stress-tolerant organisms originate in unusual ecological niches in nature, and they have a number of preadaptations that make them particularly suited for growth on human-made surfaces and substrates. Several pathogenic species have been isolated recently from various domestic habitats. We argue that in addition to enriching for - potentially - pathogenic species, the selection pressure and stress acting on microorganisms in indoor environments are driving their evolution towards acquiring the missing virulence factors and further enhancing their stress tolerance and pathogenic potential. Some of the polyextremotolerant fungi are particularly problematic: they can grow at elevated temperatures, and so they have a higher potential to colonise warm-blooded organisms. As several species of black fungi are already implicated in health problems of various kinds, their selection and possible evolution in human environments are of concern.     

Microbial stress priming: a meta‐analysis

Microbes have to cope with complex and dynamic environments, making it likely that anticipatory responses provide fitness benefits. Mild, previous stressors can prepare microbes (stress priming) to further and potentially damaging stressors (triggering). We here quantitatively summarize the findings from over 250 trials of 34 studies including bacteria and fungi, demonstrating that priming to stress has a beneficial impact on microbial survival. In fact, survival of primed microbes was about 10‐fold higher compared with that in non‐primed microbes. Categorical moderators related to microbial taxonomy and the kind of stress applied as priming or as triggering revealed significant differences of priming effect size among 14 different microbial species, 6 stress categories and stressor combination. We found that priming by osmotic, physiological and temperature stress had the highest positive effect sizes on microbial response. Cross‐protection was evident for physiological, temperature and pH stresses. Microbes are better prepared against triggering by oxidative, temperature and osmotic stress. Our finding of an overall positive mean effect of priming regardless of the microbial system and particular stressor provides unprecedentedly strong evidence of the broad ecological significance of microbial stress priming. These results further suggest that stress priming may be an important factor in shaping microbial communities.     

微生物物种多样性、群落构建与功能性状研究进展

微生物主要包括细菌、真菌、古菌、病毒等类群, 是地球上出现时间最早、分布最广泛、个体数量最多, 以及物种和基因多样性十分丰富的生物类群。为了适应各种生境, 微生物衍生出腐生、寄生、共生等多样的生存策略, 在生物地球化学循环、生态系统演替与稳定性、环境修复以及人类健康等方面发挥着重要作用。传统的微生物监测方法限制了我们对微生物多样性的认知; 但是, 近年来高通量测序技术和生物信息学的发展极大推动了微生物多样性的研究进展。本文概述了近年来在微生物多样性分布格局与维持、群落构建以及功能属性多样性的最新进展; 总结分析了细菌、古菌、真菌的多样性纬度分布格局及其驱动因子, 选择、扩散、成种、漂变等过程对细菌、古菌、真菌的群落构建的贡献, 以及细菌和真菌的形态、生理生化、生长繁殖、扩散、基因组等功能性状的多样性; 提出了未来微生物多样性研究的重要领域: 环境宏真菌组研究, 微生物多样性与生态系统多功能性的关系研究, 以及微生物互作网络的生态功能研究。     

Nontarget impacts of neonicotinoids on nectar-inhabiting microbes

Plant-systemic neonicotinoid (NN) insecticides can exert non-target impacts on organisms like beneficial insects and soil microbes. NNs can affect plant microbiomes, but we know little about their effects on microbial communities that mediate plant-insect interactions, including nectar-inhabiting microbes (NIMs). Here we employed two approaches to assess the impacts of NN exposure on several NIM taxa. First, we assayed the in vitro effects of six NN compounds on NIM growth using plate assays. Second, we inoculated a standardised NIM community into the nectar of NN-treated canola (Brassica napus) and assessed microbial survival and growth after 24 h. With few exceptions, in vitro NN exposure tended to decrease bacterial growth metrics. However, the magnitude of the decrease and the NN concentrations at which effects were observed varied substantially across bacteria. Yeasts showed no consistent in vitro response to NNs. In nectar, we saw no effects of NN treatment on NIM community metrics. Rather, NIM abundance and diversity responded to inherent plant qualities like nectar volume. In conclusion, we found no evidence that NIMs respond to field-relevant NN levels in nectar within 24 h, but our study suggests that context, specifically assay methods, time and plant traits, is important in assaying the effects of NNs on microbial communities.