Edaphic and host plant factors are linked to the composition of arbuscular mycorrhizal fungal communities in the root zone of endangered Ulmus chenmoui Cheng in China

Despite the importance of arbuscular mycorrhizal fungi (AMF) within deciduous forest ecosystems, we know little about how natural AMF communities are structured in the root zone of the endangered elm species Ulmus chenmoui. In this study, three U. chenmoui sampling sites, differing with respect to plant health, age, and growth status, were selected in Anhui Province, China. AMF biodiversity in the root zones of individual U. chenmoui trees was investigated using high‐throughput sequencing. In total, 61 AMF operational taxonomic units were detected. Five genera, namely Glomus (62.82%), Paraglomus (17.82%), Rhizophagus (4.29%), Septoglomus (4.06%) and Funneliformis (2.35%), and 29 species of AMF were identified. Correlation analysis indicated that available soil phosphorus and potassium concentrations were the main edaphic factors influencing AMF community structure. There was a difference in AMF species richness among the three U. chenmoui stands. Our study showed that soil nutrient concentrations and plant health, age, and growth status can exert a selective effect on the composition of the AMF population in the soil in the root zones of U. chenmoui trees.     

Specificity and localised distribution of mycorrhizal fungi in the soil may contribute to co-existence of orchid species

Co-occurring orchid species tend to occupy different areas and associate with different mycorrhizal fungi, suggesting that orchid mycorrhizal (OrM) fungi may be unevenly distributed within the soil and, therefore, impact the aboveground spatial distribution of orchids. To test this hypothesis, we investigated spatial variations in the community of potential OrM associates within the roots of three co-habitating orchid species (Anacamptis morio, Gymnadenia conopsea, and Orchis mascula) and the surrounding soil in an orchid-rich calcareous grassland in Southern Belgium using 454 amplicon pyrosequencing. Putative OrM fungi were broadly distributed in the soil, although variations in community composition were strongly related to the proximal host plant. The diversity and frequency of sequences corresponding to OrM fungi in the soil declined with increasing distance from orchid plants, suggesting that the clustered distribution of orchid species may to some extent be explained by the localised distribution of species-specific mycorrhizal associates.     

丛枝菌根真菌物种多样性研究进展

丛枝菌根真菌(Arbuscular mycorrhizal fungi,AMF)在不同生态系统均发挥至关重要的作用,研究其多样性能够为AMF物种资源的保护和利用提供科学依据。AMF不能被离体纯培养以及自身的高变异性等因素严重阻碍了对其进行深入研究,随着研究方法的不断改进,尤其是新一代测序技术的运用,极大加速了人们对AMF物种多样性的认识。本文主要从AMF分类系统、不同宿主植物和不同生境中的AMF物种多样性及AMF物种多样性研究方法(包括形态鉴定、Sanger测序和高通量测序)方面介绍AMF物种多样性研究进展,并且探讨AMF物种多样性研究中存在的主要问题,认为在今后AMF物种多样性研究中不仅要注重运用新的研究手段,还应该着重解决AMF不能离体纯培养的问题。     

Elucidating cryptic dynamics of Theileria communities in African buffalo using a high‐throughput sequencing informatics approach

1. Increasing access to next‐generation sequencing (NGS) technologies is revolutionizing the life sciences. In disease ecology, NGS‐based methods have the potential to provide higher‐resolution data on communities of parasites found in individual hosts as well as host populations.
2. Here, we demonstrate how a novel analytical method, utilizing high‐throughput sequencing of PCR amplicons, can be used to explore variation in blood‐borne parasite (Theileria—Apicomplexa: Piroplasmida) communities of African buffalo at higher resolutions than has been obtained with conventional molecular tools.
3. Results reveal temporal patterns of synchronized and opposite fluctuations of prevalence and relative abundance of Theileria spp. within the host population, suggesting heterogeneous transmission across taxa. Furthermore, we show that the community composition of Theileria spp. and their subtypes varies considerably between buffalo, with differences in composition reflected in mean and variance of overall parasitemia, thereby showing potential to elucidate previously unexplained contrasts in infection outcomes for host individuals.
4. Importantly, our methods are generalizable as they can be utilized to describe blood‐borne parasite communities in any host species. Furthermore, our methodological framework can be adapted to any parasite system given the appropriate genetic marker.
5. The findings of this study demonstrate how a novel NGS‐based analytical approach can provide fine‐scale, quantitative data, unlocking opportunities for discovery in disease ecology.

     

樟根生产法培育的苗与常规苗的丛枝菌根真菌多样性

以湖南省林业科学院龙伏实验基地的3年生樟根生产（root production method,RPM）苗和同龄常规技术培育的苗木（以下简称常规苗）为研究对象,采集两种苗木的根系和根际土,观察根系上菌根形态,并对其苗木样品进行高通量测序研究,探索二者根系菌根特征及根系、根际土丛枝菌根真菌（arbuscular mycorrhizal fungi,AMF）群落结构及土壤微生境差异,旨在为进行接种有效性菌根苗木来改善常规苗木的土壤微生境,进而培育高质量苗木提供理论依据。结果显示：2种樟苗木根系均显示AM菌根特征,未见外生菌根结构。测序得到属于AMF群落的有效序列共25 738条,隶属1门,2纲,3目,5科,5属,按有效序列占比从高到低依次为Acaulospora、Glomus、Diversispora、Rhizophagus和Paraglomus。根生产法（RPM）苗和常规苗的优势属均为Acaulospora和Glomus,只是RPM苗中Glomus占比高（在根、根际土内占比分别为28.04%、57.36%）而常规苗中Acaulospora占比高（在根、根际土内占比分别为99.58%、42.2%）。2种苗木均是根际土内的丰富度指数（Ace和Chao）远高于根系,并且RPM苗根际土的丰富度指数高于常规苗,但二者根系内的丰富度指数无显著差异（P<0.05）。冗余分析结果显示,土壤pH和有效磷是决定AMF群落结构的主要影响因子。不同理化因子对AMF群落的菌属影响程度也不同。     

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.     

Arbuscular mycorrhizal fungal communities are phylogenetically clustered at small scales

Next-generation sequencing technologies with markers covering the full Glomeromycota phylum were used to uncover phylogenetic community structure of arbuscular mycorrhizal fungi (AMF) associated with Festuca brevipila. The study system was a semi-arid grassland with high plant diversity and a steep environmental gradient in pH, C, N, P and soil water content. The AMF community in roots and rhizosphere soil were analyzed separately and consisted of 74 distinct operational taxonomic units (OTUs) in total. Community-level variance partitioning showed that the role of environmental factors in determining AM species composition was marginal when controlling for spatial autocorrelation at multiple scales. Instead, phylogenetic distance and spatial distance were major correlates of AMF communities: OTUs that were more closely related (and which therefore may have similar traits) were more likely to co-occur. This pattern was insensitive to phylogenetic sampling breadth. Given the minor effects of the environment, we propose that at small scales closely related AMF positively associate through biotic factors such as plant-AMF filtering and interactions within the soil biota.     

丛枝菌根真菌群落对白三叶草生长的影响

不同施肥处理影响AMF(Arbuscular mycorrhizal fungi)群体结构,然而不同AMF群体结构对植物的生长以及养分吸收的影响尚未见报道,试验利用盆栽实验研究了7种不同来源的丛枝菌根真菌(AMF)群落对白三叶草生长和N、P、K以及微量元素Cu、Zn、Mn的吸收的影响。7种AMF群落分离自长期定位施肥试验地,分别为NPK、OM、CK、1/2OM、NP、NK和PK。每年施肥量是300kg N/hm2,135kg P2O5/hm2,300kg K2O/hm2。有机肥处理的N、P、K养分量与试验地NPK处理含量相同,原料以粉碎的麦秆为主,加上适量的大豆饼和棉仁饼,有机肥经堆制发酵后施用。试验土壤采用封丘试验地土壤,经灭菌处理。试验结果表明,接种不同AMF群落均能促进三叶草的生长,对养分吸收则表现不同。分离自CK试验地的AMF群落对三叶草侵染率显著低于其它6种AMF群落。分离自1/2OM和OM试验地的AMF群落较分离自NPK、CK、NP和NK的AMF群落显著促进了三叶草对P的吸收;各种AMF群落都促进了对N和K的吸收;分离自OM、CK、1/2OM、NP、NK试验地的降低了三叶草植株N含量;分离自NPK试验地的AMF群落提高了三叶草植物K含量;对于Cu、Zn、Mn元素的吸收,不同处理存在较大的差异。AMF群落对三叶草生长以及养分吸收贡献不同,这与不同施肥管理下不同AMF群落的优势种属的侵染率、养分转化以及菌丝发育及分布有关。     

来源对丛枝菌根真菌功能的影响

丛枝菌根真菌(arbuscular mycorrhizal fungi,AMF)是一种具有重要生态功能的根际微生物。影响AMF功能的因素主要包括AMF、宿主,以及其它生物与非生物环境。近年来,大量研究表明不同来源的AMF功能存在显著差异。结合该领域的最新研究成果,从基因变异和表型可塑性两方面分析了来源影响AMF功能的原因和维持机制,并对其生态学意义进行了探讨。认为应从群落水平上研究不同来源的AMF在生态系统中的功能,重视宿主的作用,保持研究对象的对等性,并区分AMF群落结构和来源对功能的不同影响。对未来的研究重点和方向进行了讨论和展望,试图为更加清晰、全面地认识AMF在生态系统中的功能,以及AMF适应特定土壤环境与宿主的机制提供参考。     

The impact of wildfire on vesicular-arbuscular mycorrhizal fungi and their potential to influence the re-establishment of post-fire plant communities

Wildfires are a typical event in many Australian plant communities. Vesicular-arbuscular mycorrhizal (VAM) fungi are important for plant growth in many communities, especially on infertile soils, yet few studies have examined the impact of wildfire on the infectivity of VAM fungi. This study took the opportunity offered by a wildfire to compare the infectivity and abundance of spores of VAM fungi from: (i) pre-fire and post-fire sites, and (ii) post-fire burned and unburned sites. Pre-fire samples had been taken in May 1990 and mid-December 1990 as part of another study. A wildfire of moderate intensity burned the site in late December 1990. Post-fire samples were taken from burned and unburned areas immediately after the fire and 6 months after the fire. A bioassay was used to examine the infectivity of VAM fungi. The post-fire soil produced significantly less VAM infection than the pre-fire soil. However, no difference was observed between colonization of plant roots by VAM fungi in soil taken from post-fire burned and adjacent unburned plots. Soil samples taken 6 months after the fire produced significantly more VAM than corresponding soil samples taken one year earlier. Spore numbers were quantified be wet-sieving and decanting of 100-g, air-dried soil subsamples and microscopic examination. For the most abundant spore type, spore numbers were significantly lower immediately post-fire. However, no significant difference in spore numbers was observed between post-fire burned and unburned plots. Six months after the fire, spore numbers were the same as the corresponding samples taken 1 year earlier. All plants appearing in the burned site resprouted from underground organs. All post-fire plant species recorded to have mycorrhizal associations before the fire had the same associations after the fire, except for species of Conospermum (Proteaceae), which lacked internal vesicles in cortical cells in the post-fire samples.     

不同海拔的三种杓兰属植物与菌根真菌群落组成相关性

本研究采集了四川黄龙沟沿海拔梯度3 170-3 400m上4个不同杓兰居群中3种杓兰植物根,利用克隆文库方法获得菌根真菌ITS序列,研究同一栖息地（黄龙沟）不同海拔梯度和不同杓兰对菌根真菌多样性和群落结构的影响。共得到18个可操作分类单元（OTU）,其中14个OTU隶属胶膜菌科Tulasnellaceae,为优势类群（99.6%）;2个OTU隶属腊壳菌科Sebacinaceae,2个OTU隶属亡革菌科Thelephoraceae。随着海拔升高,西藏杓兰菌根真菌多样性减少,而黄花杓兰和无苞杓兰没有明显变化;海拔对3种杓兰菌根真菌群落结构均无显著影响。3种杓兰之间菌根真菌群落结构差异显著且指示物种互不相同,说明在同一栖息地,杓兰对菌根真菌的偏好性显著影响其菌根真菌群落结构。这些研究结果利于了解环境变化对杓兰属植物菌根真菌区系组成的影响,为进一步探索菌根真菌与杓兰属植物的互作机制奠定基础。     

454测序技术在微生物生态学研究中的应用

以Sanger法(双脱氧核苷酸末端终止法)为代表的第1代测序技术由于其成本高、速度慢、通量低等不足,满足不了大规模测序的要求.进入21世纪后,以Roche 454为代表的第2代测序技术诞生了,454测序法作为一种高通量的测序方法,近年来已被广泛应用于微生物生态学研究中.介绍了该测序技术的原理和操作步骤,结合本实验室的研...     

Improving the genetic representation of rare taxa within complex microbial communities using DNA normalization methods

Complex microbial communities typically contain a large number of low abundance species, which collectively, comprise a considerable proportion of the community. This ‘rare biosphere’ has been speculated to contain keystone species and act as a repository of genomic diversity to facilitate community adaptation. Many environmental microbes are currently resistant to cultivation, and can only be accessed via culture‐independent approaches. To enhance our understanding of the role of the rare biosphere, we aimed to improve their metagenomic representation using DNA normalization methods, and assess normalization success via shotgun DNA sequencing. A synthetic metagenome was constructed from the genomic DNA of five bacterial species, pooled in a defined ratio spanning three orders of magnitude. The synthetic metagenome was fractionated and thermally renatured, allowing the most abundant sequences to hybridize. Double‐stranded DNA was removed either by hydroxyapatite chromatography, or by a duplex‐specific nuclease (DSN). The chromatographic method failed to enrich for the genomes present in low starting abundance, whereas the DSN method resulted in all genomes reaching near equimolar abundance. The representation of the rarest member was increased by approximately 450‐fold. De novo assembly of the normalized metagenome enabled up to 18.0% of genes from the rarest organism to be assembled, in contrast to the un‐normalized sample, where genes were not able to be assembled at the same sequencing depth. This study has demonstrated that the application of normalization methods to metagenomic samples is a powerful tool to enrich for sequences from rare taxa, which will shed further light on their ecological niches.     

新疆3种甘草根际土壤丛枝菌根真菌群落的多样性分析

为探究新疆地区药用甘草根际土壤丛枝菌根真菌的群落结构受宿主植物种类、土壤深度和土壤理化性质的影响,该实验采集了新疆地区乌拉尔甘草、胀果甘草、光果甘草根际0～20 cm、20～40 cm、40～60 cm 3个土层的土壤样品,基于Illumina Miseq高通量测序平台测定AM真菌群落结构和多样性,结合土壤理化性质,分...     

Dissimilar responses of fungal and bacterial communities to soil transplantation simulating abrupt climate changes

Both fungi and bacteria play essential roles in regulating soil carbon cycling. To predict future carbon stability, it is imperative to understand their responses to environmental changes, which is subject to large uncertainty. As current global warming is causing range shifts toward higher latitudes, we conducted three reciprocal soil transplantation experiments over large transects in 2005 to simulate abrupt climate changes. Six years after soil transplantation, fungal biomass of transplanted soils showed a general pattern of changes from donor sites to destination, which were more obvious in bare fallow soils than in maize cropped soils. Strikingly, fungal community compositions were clustered by sites, demonstrating that fungi of transplanted soils acclimatized to the destination environment. Several fungal taxa displayed sharp changes in relative abundance, including Podospora, Chaetomium, Mortierella and Phialemonium. In contrast, bacterial communities remained largely unchanged. Consistent with the important role of fungi in affecting soil carbon cycling, 8.1%–10.0% of fungal genes encoding carbon‐decomposing enzymes were significantly (p < 0.01) increased as compared with those from bacteria (5.7%–8.4%). To explain these observations, we found that fungal occupancy across samples was mainly determined by annual average air temperature and rainfall, whereas bacterial occupancy was more closely related to soil conditions, which remained stable 6 years after soil transplantation. Together, these results demonstrate dissimilar response patterns and resource partitioning between fungi and bacteria, which may have considerable consequences for ecosystem‐scale carbon cycling.     

菌根真菌与兰科植物氮营养关系的研究进展

兰科植物是典型的菌根植物。兰菌根是兰科植物根与真菌形成的菌根共生体。兰菌根真菌的营养来源影响宿主植物的生活方式和营养水平。氮是植物生长的主要限制因子。兰科植物具有富集氮的特征, 其组织和器官的氮含量通常高于同生境中的其他植物。该文综述了兰菌根真菌类别、兰科植物氮营养特征和兰菌根的氮转移机制等的研究进展, 以期为兰科植物资源的保护、再生及可持续利用的相关研究提供参考和借鉴。     

Divergence of mycorrhizal fungal communities in crop production systems

Mycorrhizal fungi are present in all arable soils and colonize nearly all crops and weed pests of crops. They may be involved as mutualists or pathogens of crops in well known but poorly understood phenomena such as crop rotation and green manure effects on soil productivity. Crop change effects on mycorrhizal fungal community parameters were evaluated in three field experiments. In Experiment 1, soybean (Glycine max (L.) Merr. cv. Douglas) was grown continuously or rotated with corn (Zea mays L.), milo (Sorghum bicolor (L.) Moench), or fescue (Festuca arundinacea Schreb cv. Johnstone) for two years, then soybean was grown on all plots. Continuous soybean plots were dominated byGigaspora spp., while rotated crops were dominated byGlomus spp. Differences in communities and community indices of continuous soybean and rotated plots were reduced after growing soybeans on rotated plots. In Experiment 2, a fescue sod was plowed and pearl millet (Pennisetum americanum Leeke) or crabgrass (Digitaria sanguinalis (L.) Scop.) grown. Both hosts resulted in great changes in populations of individual species, decreases in community dominance, and increases in community diversity and equitability. Crabgrass also resulted in reduced species richness. In Experiment 3, tobacco (Nicotiana tabacum L.) or fescue was planted on adjacent tracts of land with a long-term history of either fescue (30 yr) or sorghum-sudangrass (Sorghum bicolor (L.) Moench. ×S. sudanense (Piper) Staph.) (3 yr). The long-term cropping history had major effects on the mycorrhizal fungal communities which were related to the expression of mycorrhizal stunt disease of tobacco. Changes occurred in these communities in response to either current-season crop. These experiments suggest that crop rotation causes large changes in mycorrhizal fungal communities, that these changes may be involved in the rotation effect on soil productivity, and that design of cropping systems should take mycorrhizal fungal communities into consideration.