Mycology at the Institute of Microbiology, Russian Academy of Sciences: history and prospects for the future

This review deals with the historical development of mycology at the Winogradsky Institute of Microbiology (Russian Academy of Sciences). Starting from the works of Academician G.A. Nadson, the review considers from the historical perspective the main achievements of the researchers of the Institute in the field of mycology, including such important subfields as the cytology, genetics, physiology, and biochemistry of mycelial fungi and yeast. The review concerns itself with the major theoretical ideas generated by the team of the Laboratory of Experimental Mycology in the course of their studies of micro- and macromycetes. Special attention is also given to recent developments in biotechnology and medicine, including the development of new drug preparations from biologically active substances of fungi.     

Specialization and medical mycology in the US, Britain and Japan

This paper attempts to bring new insights to a long-standing historical debate over medical specialization by analyzing the formation of medical mycology, a somewhat marginal biomedical discipline that emerged in the mid-twentieth century around studies of fungal disease in humans. The study of fungi predates that of bacteria and viruses, but from the 1880s it became eclipsed by bacteriology. However, in the postwar period, there were moves to establish medical mycology as an independent speciality. I trace the processes that led to the launch of professional societies in the United States, Britain and Japan, three major players in medical mycology, and more broadly in biomedicine. The analysis of the three different national contexts illustrates how geographical, medico-technological, epidemiological, political and social conditions gave the specialty a distinctive character in each country; this was further complicated by the different and changing medical fields in which fungal diseases were studied and treated. The three case studies show medical specialization as a process that is not simply cumulative but responds to specific historical events and developments.     

Some highlights in the history of fungi in medicine – A personal journey

The history of the role of fungi in the development of medicine has largely been neglected. Here the early recognition of the germ theory will be discussed in relation to surface infections, the “cholera fungus theory” and recognition of the phenomenon of microbial antagonism. This leads to a short review of the history of those antibiotics produced by fungi, notably penicillin. Finally, the history of the recognition of the potential role fungi play as casual agents of cancer will be discussed; although currently neglected, this work may prove to be of future significance. This history of medical mycology is discussed from the standpoint of my own interest and research into this fascinating, and often overlooked area of medical history.     

中国菌物分类学和多样性研究的历史与现状概况

我国菌物分类学研究始于20世纪初,经过百余年的不断探索和发展,取得了丰硕的成果,并逐渐走进世界前列。本研究通过对世界菌物名称信息库Fungal Names进行数据统计,对发现自中国的菌物新物种和中国学者发表菌物新分类单元等数据开展分析,从中揭示中国菌物分类学的历史和发展趋势。过去,一共有2 214位中国学者参与发表了15 626个菌物新分类单元,包括 3个新纲、27个新目及亚目、117个新科及亚科、769个新属及亚属、11 100个新种、322个新种下单元和3 288个新组合。在全球已知的菌物物种中,自中国发现的新物种有10 233种,隶属于 3界13门44纲174目572科2 379属,占全球已知物种多样性的6.84%,居世界第二位。地理分布上,我国西南地区(云南、四川、贵州、西藏)和低纬度的热带、亚热带地区(中国台湾、广东)发现的新物种最多。根据每年发现的新分类单元数量趋势和命名作者的构成,可将中国菌物分类学的发展历史分为五个阶段：外人在华采菌及研究(1750s-1929)、中国菌物分类学起步(1930-1949)、新中国菌物分类学早期发展(1950-1977)、全国性菌物标本采集与研究(1978-2010)、走进世界前列(2011至今)。本研究对每个发展时期的分类学概况和重要历史事件进行了总结和回顾,通过上述综述性研究,有助于系统地了解中国菌物分类学不同阶段的发展趋势和研究概况,为学科当下和未来的发展提供参考。     

国内外菌物学研究热点和研究趋势分析——指导科研选题,助力科技创新

为了梳理和分析近些年国内外菌物学研究的整体状况、研究热点、发展脉络及研究趋势,本文分别以Web of Science核心数据集中20本菌物学SCI期刊的1 762篇文献、《菌物学报》近10年发表的1 347篇文章以及中国知网中2 128篇食用菌文献为研究对象,采用Citespace 5.0R7为数据分析工具,以关键词共现分析和文献共被引分析为主要研究方法,形成文献间引证与被引证的可视化知识网络。通过对可视化网络图谱的分析,揭示了近些年菌物学国内外的研究概况。分析结果表明,现今国际菌物学研究热点以医学真菌为主,并向生物合成、生物防治、内生真菌领域发展,国内菌物学研究以分类学、食用菌、内生真菌、次级代谢产物和漆酶为主要内容和研究热点。我们希望通过对菌物学文献的数据分析,帮助科学家及时掌握菌物学研究演变进程中具有重要作用的文献,捕捉研究热点,探测研究趋势,从而对学科研究动向做出合理判断,指导科学家未来科研选题。     

对菌物学进展的前瞻

本文简要地讨论了菌物学发展的前景,特别是在中国的前景。讨论的问题涉及到现代菌物分类新技术的概念以及和它密切相关的学科例如植物病原菌物学,菌物病理学,菌物生理学,菌物生态学,菌物地理学,生物工程在菌物中的应用,野生食用菌和药用菌的驯化栽培,菌根和菌毒。     

对菌物学进展的前瞻*

本文简要地讨论了菌物学发展的前景,特别是在中国的前景。讨论的问题涉及到现代菌物分类新技术的概念以及和它密切相关的学科例如植物病原菌物学,菌物病理学,菌物生理学,菌物生态学,菌物地理学,生物工程在菌物中的应用,野生食用菌和药用菌的驯化栽培,菌根和菌毒。     

The role of the amateur in mycology—what would we do without them!

The amateur's role in the history of mycology will be traced from its early roots deeply based in the collection of fungi for food to the amateur's present day activities. Attention will be drawn to the most important key amateur figures studying fungi solely or as a wider part of natural history in the eighteenth and nineteenth centuries, and the early part of the present century. How their work influenced the development of mycology will be demonstrated. It is often forgotten that the authorities attached to fungal names, including those we use in mycology on a daily basis, often belong to amateurs. The true professions of these amateurs, the net-work of correspondents they developed, etc. will be revealed and discussed in the context of an overall understanding of fungi as organisms. In addition the formation of mycological societies, and how they have become a focus of amateur activity and a source of accurate and disciplined information valuable to professional scientists will be plotted. The kind of work undertaken by amateurs I refer to will be demonstrated by documenting the activities of the British Mycological Society which celebrated its centenary in 1996. The continuing work of this band of workers and their counterparts throughout the world in the closing years of the millennium will be described. It is argued that they are nationally important and necessary resources, despite many governments or their advisers, especially the most influential ones, being under the delusion that systematics is not cutting edge science. It is also emphasized that amateurs will have an even more important role to play in the future as custodians of knowledge—until hopefully opinions change. The essential points of this paper were addressed to the 42nd Annual Meeting of the Mycological Society of Japan held at Kyoto University, Kyoto, on 16–17, May 1998.     

甲癣的病原学研究进展

甲真菌病是由皮肤癣菌、酵母菌及霉菌引起的甲板和甲下组织感染,皮肤癣菌是主要致病菌,其所致的甲真菌病称为甲癣.皮肤癣菌分为3个属:毛癣菌属、小孢子菌属和表皮癣菌属.随着医学真菌学基础知识的普及和真菌学诊疗水平的提高,越来越多的皮肤癣菌在甲中分离,临床上对甲癣致病真菌的正确鉴定对于制定治疗方案、评价预后以及流行病学监测等都有重要的指导意义.该文对国内外现有文献报道的甲癣的致病菌进行综述.     

菌根学对生物类学科发展的意义

菌根（mycorrhiza）是真菌与植物之间形成的最广泛的共生体。菌根真菌（rnycorrhizal fungi）具有丰富遗传多样性、形态多样性、物种多样性、生态系统多样性和功能多样性。菌根真菌与植物协同进化,发挥生理生态功能,对促进农林牧业生产、保持生态系统的稳定及其可持续生产力具有重大而不可替代的作用。经过一个多世纪的研究发展,菌根学（mycorrhizology）——菌物学与植物学的杂交学科终于在21世纪诞生了。随着研究的深入,人们发现菌根学不仅与菌物学和植物学关系极为密切,而且还与生态学、土壤学、保护生物学、植物保护学、微生物学、食用菌学、园林园艺学、作物栽培与耕作学、昆虫学等密切相关。作为一门新兴学科,菌根学自身发展的同时,也大大促进了相关学科的进展。本文系统总结了菌根学对其他学科发展所作的贡献,旨在进一步加强菌根学与其他学科的交叉渗透,为菌根学与其他学科协同进化奠定理论基础、促进多学科合作研究,为21世纪生物学的更大发展注入新的活力。     

世界菌物新命名发表概况(2021年)

21世纪以来, 菌物新物种的发现速度逐渐加快。每个新发表的菌物新名称都蕴含着大量的分类学和多样性信息, 通过对这些信息进行统计和分析, 可以揭示菌物分类学的发展趋势和存在的问题。2021年全球共发表了3,734个菌物新名称, 包括288个新高阶分类单元(1个新门、2个新纲及新亚纲、16个新目及新亚目、36个新科、233个新属及次级属下单元)、2,551个新种及种下单元、782个新组合、113个其他新名称。这些新名称隶属于3界13门40纲159目425科1,165属, 伞菌和小型子囊菌是本年度最受关注的类群。全球有2,060位学者参与了菌物新名称的研究与发表工作, 为历史上命名作者数量最多的一年。中国学者在本年度的菌物新命名工作中做出了突出贡献, 约30%的新名称(1,124个)由中国学者参与发表。来自中国的命名作者共有380位, 是我国命名作者数量最多的一年。本年度发现的2,533个菌物新物种来自于世界7个大洲的101个国家和地区, 新物种丰富度最多的地区是亚洲东部和南部, 而中国发现了756个菌物新物种, 是发现新物种最多的国家, 占全球的近30%。我国南方地区的新物种数量远多于北方地区, 发现新物种最多的省份是云南省, 共发现248种, 占全国的33%。总体来看, 全球菌物新物种发现的速度与近年持平, 处于波动上升的趋势, 而中国的菌物分类学发展速度和贡献度仍在快速提升。建议未来的分类学研究工作中, 继续扩大研究地域和类群, 将新物种发现与完善高阶分类系统并重, 逐步揭示全球菌物多样性本底。     

新版国际植物命名法规(维也纳法规)中的主要变化

出版于2006年9月的最新版的《国际植物命名法规》,即维也纳法规（Vienna Code）,取代了圣路易斯法规（Saint Louis Code）而成为管理植物学（包括藻类学和真菌学）科学命名的唯一有效法规。本文报道了维也纳法规和圣路易斯法规之间的主要区别。这些区别包括两版法规在起始日期、有效发表、合格发表、化石植物、多型真菌、拼写和附录诸方面的不同。     

对晚清《植物学》一书中真菌学知识的考察

作为我国首部介绍西方近代植物学的书籍,晚清李善兰等人翻译的《植物学》一书也包含一小部分真菌学知识,这对我国近代真菌学的发展具有启蒙作用.通过对这部分内容的考察,发现在该书的分类体系中,真菌被视作一类植物,统称为“蕈类”,隶属于“通长类”（低等植物）.然而和植物学专有名词的创译相比,《植物学》的译者在翻译真菌学内容时,用词随意性较大,没有形成固定的译法,文中甚至还有错误.现代真菌学中常见的“真菌”“孢子”“子囊”等词汇,书中虽简单提及相应的概念,但并未创造出这些中文词汇.造成这种情况的原因,除了译者和时代的问题外,也与当时真菌学尚不发达、真菌学内容在植物学专著中篇幅较小、地位次要等因素有密切联系.     

Current state and perspectives of fungal DNA barcoding and rapid identification procedures

Fungal research is experiencing a new wave of methodological improvements that most probably will boost mycology as profoundly as molecular phylogeny has done during the last 15 years. Especially the next generation sequencing technologies can be expected to have a tremendous effect on fungal biodiversity and ecology research. In order to realise the full potential of these exciting techniques by accelerating biodiversity assessments, identification procedures of fungi need to be adapted to the emerging demands of modern large-scale ecological studies. But how should fungal species be identified in the near future? While the answer might seem trivial to most microbiologists, taxonomists working with fungi may have other views. In the present review, we will analyse the state of the art of the so-called barcoding initiatives in the light of fungi, and we will seek to evaluate emerging trends in the field. We will furthermore demonstrate that the usability of DNA barcoding as a major tool for identification of fungi largely depends on the development of high-quality sequence databases that are thoroughly curated by taxonomists and systematists.     

基于科技计量学的全球真菌学研究态势分析

目的 对全球真菌学研究态势进行分析.方法 检索SCI-Expanded数据库2004～2013年全球真菌学研究研究相关文献,采用Web of Science自带软件及Excel 2007等软件进行定量分析,指标包括文献量、被引频次、h指数等.结果 全球真菌学研究近年来呈上升趋势,美国具有绝对领先,中国、德国、日本也是主要的贡献国家.中国真菌学研究排名第2,但论文整体被引频次偏低;主要贡献来自于2007年以后（98.79％）,中国高校是主要的研究机构,国家自然科学基金是最主要的资助来源.结论 2007年以来中国真菌学研究正处于较好的发展时机,但研究水平仍有待提高.     

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。     

New fungal classification and their applications in medicine

Fungi are gaining importance with the increased incidence of invasive, often fatal mycoses, in immunocompromised patients. In addition, the increased number of emerging opportunistic pathogens has prompted interest in studies pertaining to fungal classification. The traditional methods of identification and classification of these microorganisms are based on the morphology of the sexual and asexual reproductive structures. Recently, this system of classification has been shown incongruent with approaches that better establish phylogenetic relationships among these organisms. Novel aspects of fungal reclassification are described as follows: 1) the position of fungi in the historical classification systems, 2) the recognition of their polyphyly, based on comparative studies of nucleic acid sequences and on analysis of descent lines and, 3) the contribution of molecular phylogeny to medical mycology, including identification of mycotic agents, their molecular epidemiology, prevention of infection and methods of diagnosis.     

植物病原真菌的菌核研究进展

真菌菌核是相关真菌在特殊环境下由营养体菌丝交织和聚集形成的具有抵御恶劣环境能力的休眠结构,在真菌生活史及病原真菌的病害循环中具有重要的生物学和生态学意义。许多引起严重植物病害的病原真菌能够形成菌核,这类真菌通过菌核度过逆境。菌核在适宜条件下萌发形成子囊盘和孢子或菌丝,造成植物的侵染。本文从形成菌核的真菌种类、生物学特性、黑色素及分子生物学等方面进行综述,旨在为深入研究真菌菌核及其在真菌学、植物病理学及药用真菌学等领域应用提供研究思路和参考依据。     

关于进化真菌学教学内容的讨论

核酸序列的比较研究使进化真菌学的面貌发生了革命性的变化,分子系统发育揭示的关系反映出真菌进化的复杂性和多样性,真菌系统学反映真菌进化关系的自然系统还有很大的距离,有赖于新物种的不断发现和分子系统发育证据的不断丰富。