竹叶兰根系共生真菌群落结构及生物学功能初探

为研究竹叶兰Arundina graminifolia根系共生真菌的群落结构及对寄主的营养作用,采用高通量测序技术对野生竹叶兰根围土壤、根表、根内3个生态位真菌的种类及生物学功能进行鉴定与预测。所测竹叶兰根系共生真菌的平均辛普森指数为根围0.972、根 表0.905、根内0.703,说明3个位点都具有丰富的共生真菌;根围土壤真菌香农指数7.393显著高于根表和根内香农指数4.728和2.872,根表真菌多样性显著高于根内（P<0.05）。根表、根内有子囊菌门、担子菌门、罗兹壶菌门、壶菌门、毛霉菌门和被孢霉门,较根围土壤缺少球囊菌门和梳霉菌门;分子方差分析（AMOVA）证实3个生态位的真菌群落结构差异极显著（P=0.004）。各生态位丰度最高的20个真菌仅属于子囊菌和担子菌的40个属,其中子囊菌有30个属,种类数量占优势,而担子菌的单个种类丰度高于子囊菌。根围土壤腐生型真菌占优势（44.07%）;根表主要有腐生、病原、共生型真菌;根内真菌营养类型差异大,样品M1的共生型真菌为优势类型（97.21%）,M2、M3以腐生型占优（90.96%）。优势共生型真菌有革菌属Threlephora、根须腹菌属Rhizopogon和Dentiscutata,腐生型真菌主要有长毛孔菌属Funalia和Vuilleminia,均为担子菌。研究结果为揭示竹叶兰与根系真菌的营养关系以及共生真菌的开发提供了依据。     

天山一号冰川前沿生态系统真菌群落结构演替及分布格局

【目的】分析真菌群落结构和多样性随着一号冰川退缩前沿年代序列的变化,揭示真菌群落的演替轨迹及环境因子对群落组成的影响。【方法】采用宏基因组学研究方法,结合生物信息学和统计学分析技术,对取自一号冰川末端表面冰尘,底部和前沿14个样品进行总DNA的提取,ITS基因的扩增并使用Illumina Miseq平台测序,通过相关生物地理化学特性综合分析在不同年代序列下真菌群落结构及其演替规律。【结果】经测序,筛选和质控分析获得185103条rawreads,占78.3%的非单序列在97%的相似度聚类分析共得到300个操作分类单元(OTU),共划分为6个门:子囊菌门(Ascomycota,52.7%)、担子菌门(Basidiomycota,16.9%)、壶菌门(Chytridiomycota,15.1%)、接合菌门(Zygomycota,2.4%)和球囊菌门(Glomeromycota,1.2%)。从演替初期到后期阶段虽然子囊菌的序列数逐渐下降而担子菌出现缓慢上升趋势,但子囊菌随着土壤年代序列的增加始终为优势类群,壶菌在冰川底部和前沿基层普遍存在且丰度仅次于子囊菌和担子菌。我们在缺乏植被的最新退缩基层发现依靠自养型宿主存活的活体营养菌,如Taphrinomycetes、Urediniomycetes和Ustilaginomycetes。从冰川底部和前沿基层检测到丰度较高的酵母菌,而粪生真菌(coprophilous fungi)仅仅出现在冰川前沿基层,共23个操作分类单元。球囊菌仅在前沿部分样品中存在,有着十分狭小的生态位分布。【结论】一号冰川前沿随着年代序列的增加真菌群落存在明显的演替轨迹和多样性的显著变化,不同生态位真菌类群组成的相似性较低且都存在明显的指示性真菌类群。     

不同植物群落下铜尾矿废弃地生物结皮中真菌群落结构的比较

分布于铜尾矿废弃地的裸地表面及维管植物群落中的生物土壤结皮在尾矿废弃地生态恢复过程中扮演重要角色。利用分子生物学技术探讨了不同维管植物下以及不同演替阶段的生物土壤结皮中真菌的多样性及其群落结构的变化。结果表明:生物土壤结皮中的真菌主要包括子囊菌门(Ascomycota)、担子菌门(Basidiomycota)和壶菌门(Chytridiomycota),其中子囊菌门占绝对优势,其相对丰度为55.12%—87.73%,其次为担子菌门相对丰度为12.27%—43.86%;不同样本真菌群落结构在门、纲、目以及属的水平存在显著差异;生物土壤结皮中真菌群落结构和多样性的差异与维管植物群落类型以及演替阶段不同的生物土壤结皮的类型有关,与基质化学性质之间无显著的相关性。     

布雷费尔德对真菌的进化观点在真菌分类中所起的影响

布雷费尔德(O. Brefeld)虽对真菌纯培养方法的改进和真菌发育与生理知识作出了不少贡献,但他的主要贡献还是对真菌系统发育的观点。按照他的这种观点,卵菌不是真正的真菌,它应与粘菌一起排除在真菌之外,而真正的真菌应从接合菌开始。他并将子囊菌和担子菌分别分为半子囊菌和真子囊菌,半担子菌和真担子菌。     

布雷费尔德对真菌的进化观点在真菌分类中所起的影响*

布雷费尔德(O. Brefeld)虽对真菌纯培养方法的改进和真菌发育与生理知识作出了不少贡献,但他的主要贡献还是对真菌系统发育的观点。按照他的这种观点,卵菌不是真正的真菌,它应与粘菌一起排除在真菌之外,而真正的真菌应从接合菌开始。他并将子囊菌和担子菌分别分为半子囊菌和真子囊菌,半担子菌和真担子菌。     

贝加尔针茅草原土壤真菌群落结构对氮素和水分添加的响应

研究氮沉降和降雨变化对土壤真菌群落结构的互作效应,对未来预测多个气候变化因子对草地生态系统的交互作用具有重要意义。以施氮和灌溉模拟氮沉降和降雨增加,采用裂区设计,应用高通量测序技术,研究8个氮添加水平(0、15、30、50、100、150、200、300 kg N hm~(-2)a~(-1))和2个水分添加水平(不灌溉、模拟夏季增雨100 mm灌溉)对土壤真菌群落结构的影响。结果表明,氮素和水分添加后,土壤真菌群落中占优势的门类分别为接合菌门Zygomycota(22.0%—48.9%)、担子菌门Basidiomycota(7.8%—18.5%)、子囊菌门Ascomycota(9.4%—20.1%)、球囊菌门Glomeromycota(0.7%—3.1%)、壶菌门Chytridiomycota(0.1%—1.3%)。常规降雨条件下,随着氮添加水平升高,接合菌门相对丰度呈现出先升高后降低的趋势,N50处理最高;子囊菌门相对丰度在高氮添加时(N100—N300)呈升高趋势。而在氮素和水分同时添加条件下,随着氮添加水平升高,接合菌门相对丰度呈降低趋势,子囊菌门相对丰度变化则不明显。在相同的氮添加水平下,水分添加使接合菌门相对丰度增加,而担子菌门、子囊菌门、球囊菌门和壶菌门的相对丰度降低。在不同氮素和水分添加条件下,有5个土壤真菌门类11个真菌纲相对丰度变化显著。接合菌门的Mortierella属,担子菌门的Entolomataceae科和Geastrum属相对丰度变化极显著,可作为土壤真菌群落结构变化的指示种。PCo A分析结果也表明氮素和水分添加改变了土壤真菌群落结构。植物-土壤-微生物系统的结构方程模型结果表明,植物群落组成及植物物种丰富度的变化是土壤真菌群落结构发生变化的主要影响因素,土壤无机氮及p H的变化主要通过影响植物群落间接影响真菌群落,其对真菌群落的直接影响则较小。综上,氮素和水分添加改变了土壤真菌群落结构,且两者存在明显的互作效应,水分添加可改变氮添加对土壤真菌群落的影响。     

中国菌生非地衣型子囊菌资源

菌生真菌是指以其他真菌为宿主的真菌,是重要的自然生物资源.它们不是系统学上的分类群,而是特殊生境真菌,包括子囊菌、担子菌和接合菌的种类.其中菌生子囊菌是动植物以及其他真菌的内生菌、寄生菌或腐生菌,少数种己用于植物病害的生物防治,对其进行研究具有重要的理论意义和应用潜力.作者汇总了我国丰富的非地衣型菌生子囊菌资源,目前己报道该类真菌132种,其中以担子菌为宿主的约63种,以子囊菌为宿主的38种,其余或对基物的选择性不强或宿主真菌的分类地位不详,部分种类表现出对基物真菌或者宿主真菌的选择性.同时,对菌生真菌与宿主真菌相互作用方式、菌生子囊菌在植物病害防控中的应用以及少数种类对食用菌栽培的为害进行了简要概述.     

臧穆先生发表的论著及新物种

<正>臧穆先生一生勤奋、刻苦,在真菌分类与系统学研究领域,对担子菌门和子囊菌门的许多类群进行了研究,特别是对我国牛肝菌目、蘑菇目、腹菌类和部分子囊菌都有深入研究;对苔藓中的一些类群也曾开展过分类研究,并有所建树。在牛肝菌目的研究中,先生倾注了毕生精力。该目是担子菌中最为复杂、争议最多和分类难度最大的     

医学真菌分类学最新进展

近年分子生物学、遗传学和生物信息学进步迅速,真菌分子系统学研究日新月异,真菌命名及分类已发生划时代的改变。诸多真菌存在种属拆分与合并,甚至菌名的改变,亟需更新相关信息。该文总结了子囊菌门(Ascomycota)、担子菌门(Basidiomycota)及接合菌门(Zygomycota)等分类学新进展,涵盖了主要医学真菌致病菌,如毛霉菌、皮肤癣菌、念珠菌、隐球菌、马拉色菌及暗色真菌等。     

中国森林大型真菌重要类群多样性和系统学研究

大型真菌主要为担子菌门的真菌和少数为子囊菌门的真菌,该类真菌具有重要的经济价值和生态功能,主要生长在森林生态系统中。30年来作者对我国几乎所有类型森林生态中的大型真菌进行了系统调查和采集,共采集标本11.2万号。基于对这些材料的形态学及分子系统学研究,并结合生态学和生物地理学特征,共鉴定出中国森林大型真菌4 250种,隶属于担子菌门和子囊菌门的21个目,发现和发表2个新科、4个新亚科、69个新属和885个新种。云南省是我国森林大型真菌最丰富的省份,描述于该省的新种有314种,占作者发表的全部中国新种的35%。这些研究为深入认识全球大型真菌物种多样性提供了中国的贡献,更新了我国重要食药用菌名称,揭示了我国毒蘑菇多样性基本特征,系统论述了我国森林病原菌的物种多样性,为资源利用、森林健康和保护提供了科学依据;论述了森林大型真菌代表性类群在种和属级水平的起源和演化,为今后开展重要类群科级、目级甚至纲级的系统进化关系提供了重要数据。     

Loss of the flagellum happened only once in the fungal lineage: phylogenetic structure of Kingdom Fungi inferred from RNA polymerase II subunit genes

Background  

At present, there is not a widely accepted consensus view regarding the phylogenetic structure of kingdom Fungi although two major phyla, Ascomycota and Basidiomycota, are clearly delineated. Regarding the lower fungi, Zygomycota and Chytridiomycota, a variety of proposals have been advanced. Microsporidia may or may not be fungi; the Glomales (vesicular-arbuscular mycorrhizal fungi) may or may not constitute a fifth fungal phylum, and the loss of the flagellum may have occurred either once or multiple times during fungal evolution. All of these issues are capable of being resolved by a molecular phylogenetic analysis which achieves strong statistical support for major branches. To date, no fungal phylogeny based upon molecular characters has satisfied this criterion.     

Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits

Based on an overview of progress in molecular systematics of the true fungi (Fungi/Eumycota) since 1990, little overlap was found among single-locus data matrices, which explains why no large-scale multilocus phylogenetic analysis had been undertaken to reveal deep relationships among fungi. As part of the project "Assembling the Fungal Tree of Life" (AFTOL), results of four Bayesian analyses are reported with complementary bootstrap assessment of phylogenetic confidence based on (1) a combined two-locus data set (nucSSU and nucLSU rDNA) with 558 species representing all traditionally recognized fungal phyla (Ascomycota, Basidiomycota, Chytridiomycota, Zygomycota) and the Glomeromycota, (2) a combined three-locus data set (nucSSU, nucLSU, and mitSSU rDNA) with 236 species, (3) a combined three-locus data set (nucSSU, nucLSU rDNA, and RPB2) with 157 species, and (4) a combined four-locus data set (nucSSU, nucLSU, mitSSU rDNA, and RPB2) with 103 species. Because of the lack of complementarity among single-locus data sets, the last three analyses included only members of the Ascomycota and Basidiomycota. The four-locus analysis resolved multiple deep relationships within the Ascomycota and Basidiomycota that were not revealed previously or that received only weak support in previous studies. The impact of this newly discovered phylogenetic structure on supraordinal classifications is discussed. Based on these results and reanalysis of subcellular data, current knowledge of the evolution of septal features of fungal hyphae is synthesized, and a preliminary reassessment of ascomal evolution is presented. Based on previously unpublished data and sequences from GenBank, this study provides a phylogenetic synthesis for the Fungi and a framework for future phylogenetic studies on fungi.     

Distinct seasonality of chytrid-dominated benthic fungal communities in the neritic oceans (Bohai Sea and North Yellow Sea)

Benthic fungal diversities in Bohai Sea and North Yellow Sea were investigated using pyrosequencing of 18S rDNA. Overall, Chytridiomycota dominated, followed by Basidiomycota, Ascomycota and Cryptomycota, in terms of alpha diversities and relative abundance. The beta diversity of benthic fungi showed a significant seasonality but no regional differences, accounted for by contrasting relative abundances of Chytridiomycota and Basidiomycota. Significantly seasonal changes in Chytridiomycota and Basidiomycota assemblage structure were also observed, but not for Ascomycota and Cryptomycota. Environmental filtering was more important than water depth and geographic distance in shaping the distribution of benthic fungi in the neritic oceans. The overall fungal beta diversity co-varied with concentration of chlorophyll a, pH, and salinity, distance from land, and water depth. The assemblage structure of benthic Chytridiomycota, Basidiomycota, Ascomycota and Cryptomycota co-varied with different sets of environmental parameters, suggesting their niche differentiations in the coastal sediments.     

Microbial Pathogens in the Fungal Kingdom

The fungal kingdom is vast, spanning ~1.5 to as many as 5 million species diverse as unicellular yeasts, filamentous fungi, mushrooms, lichens, and both plant and animal pathogens. The fungi are closely aligned with animals in one of the six to eight supergroups of eukaryotes, the opisthokonts. The animal and fungal kingdoms last shared a common ancestor ~1 billion years ago, more recently than other groups of eukaryotes. As a consequence of their close evolutionary history and shared cellular machinery with metazoans, fungi are exceptional models for mammalian biology, but prove more difficult to treat in infected animals. The last common ancestor to the fungal/metazoan lineages is thought to have been unicellular, aquatic, and motile with a posterior flagellum, and certain extant species closely resemble this hypothesized ancestor. Species within the fungal kingdom were traditionally assigned to four phyla, including the basal fungi (Chytridiomycota, Zygomycota) and the more recently derived monophyletic lineage, the dikarya (Ascomycota, Basidiomycota). The fungal tree of life project has revealed that the basal lineages are polyphyletic, and thus there are as many as eight to ten fungal phyla. Fungi that infect vertebrates are found in all of the major lineages, and virulence arose multiple times independently. A sobering recent development involves the species Batrachochytrium dendrobatidis from the basal fungal phylum, the Chytridiomycota, which has emerged to cause global amphibian declines and extinctions. Genomics is revolutionizing our view of the fungal kingdom, and genome sequences for zygomycete pathogens (Rhizopus, Mucor), skin-associated fungi (dermatophytes, Malassezia), and the Candida pathogenic species clade promise to provide insights into the origins of virulence. Here we survey the diversity of fungal pathogens and illustrate key principles revealed by genomics involving sexual reproduction and sex determination, loss of conserved pathways in derived fungal lineages that are retained in basal fungi, and shared and divergent virulence strategies of successful human pathogens, including dimorphic and trimorphic transitions in form. The overarching conclusion is that fungal pathogens of animals have arisen repeatedly and independently throughout the fungal tree of life, and while they share general properties, there are also unique features to the virulence strategies of each successful microbial pathogen.     

Molecular and morphological diversity of fungi and the associated functions in three European nearby lakes

This study presents an original rDNA PCR and microscopic survey of pelagic freshwater fungal communities, and was designed to unveil the diversity of true Fungi (i.e. the kingdom Eumycota) in three contrasting lake ecosystems (Lakes Pavin, Aydat and Vassivière) located in the French Massif Central. Three clone libraries were constructed from samples collected in the euphotic layers of the lakes during spring 2007. Phylogenetic analysis of the combined data from the three lakes clustered our sequences into thee divisions: Chytridiomycota (50% of total sequences), Ascomycota (40%) and Basidiomycota (10% in Pavin and Aydat only). Several sequences were assigned to a novel Chytridiomycota clade first recovered in Lake Pavin in 2005. Most of the sequences retrieved in the investigated lakes were affiliated with known fungal species, most of which were apparently well adapted to thrive in the pelagic realm. Their main functions (i.e. parasitism and saprophytism), putatively inferred from the closest relatives of the retrieved molecular sequences, were confirmed by microscopic approaches and by enrichment experiments with pollen grains. The occurrence of three fungal forms (zoosporic, yeast and mycelial) was associated with different trophic modes, establishing fungi as strong potential competitors for various niches in pelagic ecosystems, primarily in relation to the processing of particulate organic matter and the production of propagule food sources for grazers. For the first time, this study provides insight into the diversity and the associated functions of all members of the Kingdom Eumycota investigated in the whole plankton fraction of aquatic ecosystems.     

Pathogenic fungi of marine animals: A taxonomic perspective

Fungi cause diseases in a variety of marine animal hosts. After a thorough review of published literature, we identified 225 fungal species causing infections of 193 animal species, for a total of 357 combinations of pathogenic fungi and marine animal hosts. Among the 193 animal host species, Chordata (100 species, 51.8 %) and Arthropoda (68 species, 35.2 %) were discovered to be the most frequently reported hosts of fungal pathogens. Microsporidia (111 species, 49.3 %) constitutes over half of the described pathogenic fungal species of marine animals, followed by Ascomycota (85 species, 37.8 %), Mucoromycota (22 species, 9.8 %), Basidiomycota (6 species, 2.7 %) and Chytridiomycota (1 species, 0.4 %). Microsporidia primarily parasitize marine arthropods and Teleostei fish, while Basidiomycota are primarily known to cause respiratory diseases of marine mammals. Ascomycota has a diverse host range, from mammals, fish, crustaceans, soft corals and sea turtle. Few Mucoromycota and Chytridiomycota were reported to infect marine animals. Fungal diseases documented in this review likely represent a fraction of fungal diseases in the ocean, where it was estimated to be inhabited by 2.15 million animal species. Intensification of aquaculture practices, global warming and marine pollution may increase fungal disease outbreak of marine animals. All the topics mentioned above will be discussed in greater details in this review.     

Fungal evolution: diversity,taxonomy and phylogeny of the Fungi

The fungal kingdom comprises a hyperdiverse clade of heterotrophic eukaryotes characterized by the presence of a chitinous cell wall, the loss of phagotrophic capabilities and cell organizations that range from completely unicellular monopolar organisms to highly complex syncitial filaments that may form macroscopic structures. Fungi emerged as a ‘Third Kingdom’, embracing organisms that were outside the classical dichotomy of animals versus vegetals. The taxonomy of this group has a turbulent history that is only now starting to be settled with the advent of genomics and phylogenomics. We here review the current status of the phylogeny and taxonomy of fungi, providing an overview of the main defined groups. Based on current knowledge, nine phylum‐level clades can be defined: Opisthosporidia, Chytridiomycota, Neocallimastigomycota, Blastocladiomycota, Zoopagomycota, Mucoromycota, Glomeromycota, Basidiomycota and Ascomycota. For each group, we discuss their main traits and their diversity, focusing on the evolutionary relationships among the main fungal clades. We also explore the diversity and phylogeny of several groups of uncertain affinities and the main phylogenetic and taxonomical controversies and hypotheses in the field.