浅谈《墨尔本法规》中的“采集”、“新命名”和“命名人引证”等术语

正1采集在《国际藻类、菌物和植物命名法规》(International Code of Nomenclature for Algae,Fungi,and Plants)(Melbourne Code,以下简称《墨尔本法规》)(http://www.iapt-taxon.org/nomen/main.php)(Mc Neill et al,2012)中,名称的命名模式是与其永久关联的成分(element)(见规则7.2)。自从术语"采     

昆明盐矿古老岩盐沉积中的原核生物多样性

应用PCR-DGGE和rRNA分析法研究了昆明盐矿古老岩盐沉积中的原核生物多样性。样品的细菌DGGE分析得到27条带,古菌得到18条带。样品与纯培养得到的19个属菌株的DGGE图谱对比分析发现,细菌18个属菌株,只有1个属菌株与样品中的1条带迁移位置都不一致;古菌1个属的菌株不与样品中任何条带迁移位置一致。表明纯培养所得菌株并非该环境中的优势类群。同时,建立了样品细菌和古菌的16S rDNA克隆文库,从中分别挑取36个细菌克隆和20个古菌克隆进行ARDRA分析。细菌可分为10个OTUs,其中3个OTUs是优势类群,分别占38.9%,25.0%,16.7%,其余7个OTUs各含有1个克隆。古菌分为8个OTUs,没有明显的优势类群。每个OTU的代表克隆16S rDNA序列分析表明,细菌分属3大类群:α-Proteobacteria,γ-Proteobacteria和Actinobacteria,以Pseudomonas属菌为优势,含有其它岩盐沉积中没有发现的Actinobacteria。古菌主要是Halorubrum属、Haloterrigena属菌和未培养古菌。本研究表明,昆明盐矿古老岩盐沉积具有较丰富的原核生物多样性,含有大量未知的、未培养或不可培养的原核生物,但在原核生物物种组成和丰度上,免培养与此前的纯培养研究结果存在一定差异。因此,结合使用两类方法才能较全面地认识高盐极端环境微生物的多样性。     

生物谱系命名法规简评

基于林奈命名法和林奈分类系统的生物分类系统已经存在250多年并仍然为广大生物学工作者使用,由此产生的国际动物、植物、细菌的命名法规亦执行了100年(1905年,国际植物命名法规第1版产生),并在不断修订.随着分类方法的不断进步,林奈分类系统的一些缺陷逐渐显露,一种被称为生物谱系命名法规(PhyloCode)的新的命名法出现在人们眼前.这种基于系统发育系统学的命名法规一经问世就引起诸多争论,但是,作为一种新的命名法规,无论与传统的命名法规融合还是独立发展,对于已有的分类系统都是一个新的机遇和挑战.     

中国药用真菌名录及部分名称的修订

近年来,我国对药用真菌的研究和利用越来越重视,相关报道逐年增加。针对有些种类鉴定有误、拉丁学名使用没有严格遵守最新国际植物命名法规、命名人缩写不规范等问题,作者系统考证了我国药用真菌的名称,共收录473种,对每种名称按新近的研究成果和最新命名法规(维也纳法规)进行了订正,对过去的错误报道或不存在的名称进行了修正,将曾报道的、但应作为其他种的同物异名者列在其正名之后,所有名称定名人的缩写全部按国际植物命名法规的要求加以规范化。每种名称之后还列举了该种的主要药用功能或价值,并引证了主要参考文献。     

云南热带户用沼气池的原核生物群落结构研究

【目的】揭示云南热带农村户用沼气池中的原核生物(细菌和古菌)的群落结构特征。【方法】采用16S r RNA基因克隆文库技术对云南(北)热带代表性气候区的户用沼气池中的原核生物(细菌和古菌)多样性进行研究。【结果】得到细菌330条有效序列,划分为108个OTUs,文库覆盖度为81.5%;古菌有效序列185条,划分为17个OTUs,文库覆盖度为97.8%。通过Gen Bank数据库进行相似性比对与系统发育分析,结果表明:大部分细菌为未知细菌(Unclassified bacteria,占24.19%),优势细菌类群归属拟杆菌门(Bacteroidetes,占23.58%)、绿弯菌门(Chloroflexi,占21.46%)、厚壁菌门(Firmicutes,占13.91%)和变形菌门(Proteobacteria,占8.74%);古菌主要的优势类群为乙酸盐营养型的甲烷八叠球菌目(Methanosarcinales)的鬃毛甲烷菌属(Methanosaeta,占76.75%);此外还检测到少量未培养的泉古菌门细菌(Crenarchaeota,占9.19%)。【结论】云南(北)热带代表性气候区的农村户用沼气池中的微生物种类十分丰富,不同微生物种类的丰度存在明显差异,并存在明显优势种群,且细菌比古菌具有更丰富的多样性。     

深圳植物学大会有关菌物命名法的重要决定（英文）

2017年7月在深圳召开的第十九届国际植物学大会是该国际会议第一次在亚洲举行的大会。在大会正式日程之前一整周的命名法分会上,代表们专门就有关藻类、菌物与植物的命名法规问题进行了大量的讨论并做出了相关的决定。本文总结了有关菌物命名的相关讨论和决议。(1)菌物命名法管理:会议讨论了菌物命名法管理特别小组委员会的报告(2016),主要涉及菌物命名法分会要在国际菌物学大会上进行(其程序与国际植物学大会上的命名法分会并行,但提案表决不设机构投票权),有关菌物命名法规的提案要在《IMI Fungus》上发表、指导性电子邮件投票的参加人员、菌物命名法分会的官员为主席和秘书以及菌物命名法委员会要在国际菌物学大会选举等问题。这个一揽子的提案获得65.8%的赞成票通过,带来了具有里程碑意义的变化,决定了此后在国际命名法规中如何引入、修改或删除与菌物命名相关的规则。(2)保护名:这是在深圳会议上通过的关于菌物保护名的非常重要的议题,凡列入这些名单上的菌物名称可得到保护,不受未列入名单的其他名称的影响。(3)多型性菌物:有关废除以形态类型命名的多型性菌物名称在上一届国际植物学大会(2011)上就已通过,但保留了有关有性型名称对无性型具有优先权的规则。在这次深圳会议上,这个规则(57.2)也被彻底清除。现在确定菌物名称的使用不再以其为无性型或有性型模式所标定的名称来决定,而完全遵循发表日期的优先律。(4)地衣型真菌:地衣型真菌从来不受多型性真菌名称的影响,但由于上届大会上保留了有性型对无性型的优先权(规则57.2),有几位地衣学家为了避免在地衣方面引起争论,当时在会上提出地衣的名称不受这一规则管辖。随着深圳大会清除了规则57.2,任何有关地衣的特殊规定都一起消失。(5)模式标定:包括有模式注册、培养物作为模式、DNA序列作为模式、解释模式、图片后选模式等问题。从2019年1月1日起,指定菌物名称的后选模式、新模式或解释模式必须在3个认可的菌物名称注册网站(即Fungal Names,Index Fungorum或Myco Bank)上注册,获得注册号。从2019年1月1日开始,任何被指定为模式的培养物都必须指明是保留在代谢不活跃的状态,如果没有这个说明,该模式标定将被作为不合格发表。有关DNA序列作为模式的提案没有得到通过,但成立了一个专门委员会对这个问题进行研究。指定解释模式必须是因为现有的模式明显模糊不清才有必要进行。在没有实物标本情况下是否必须指定图片作为后选模式,而不管图片能否显示鉴别特征的问题没有得到解决,但由新成立的模式标定专门委员会进一步研究。(6)作者引证:关于删除名称作者引证中冒号":"的提案没有得到通过,但同意推荐可以"nom.sanct."作为替代使用,以表明其认可名称的地位。(7)同名:从2019年1月1日起,新发表的菌物名称如果与已有的细菌或原生动物名称相同将被判定为不合格的名称。(8)注册:此次大会除了规定后标定的模式必须注册外,没有其他注册问题的变化。(9)特型(special forms):有关接受那些以特型发表、符合基原名要求的名称的提案在会上获得通过。     

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。     

生命的三界学说以及生命的第三形式

1997年,Woese等人用比较16SrRNA序列的方法将生物分成三大类群,即真核类群,细菌类群和古生物类群。古细菌是既不同于原核生物也不同于真核生物的第三类生物。对生物三界学说的由来和发展、古细菌的分类、研究现状以及展望作一概述。     

中国食用菌名录

作者系统地考证了我国食用菌的名称,排除了过去报道中的187个名称,同时新增了82个名称,本文共收录中国食用菌966个分类单元,包括936种、23变种、3亚种和4变型。对每个名称按新近的研究成果和最新命名法规(维也纳法规)进行了订正,将曾报道的、但应作为其他种的同物异名者列在其正名之后,所有名称定名人的缩写全部按国际植物命名法规的要求加以规范化。     

我国古植物命名中若干值得重视的问题——兼述维也纳法规中有关的规定

根据2006年发表的新版国际植物命名法规(维也纳法规)的有关规则和条款,讨论我国古植物命名中一些值得重视的和存在的问题,着重在分类单元名称的合格发表、模式指定以及拉丁属、种名称构成和性别等几个方面.文中也介绍了新法规中对古植物形态分类单元(morphotaxa)定义的改变和相关规则的更动情况,以及有关在学位论文和电子版文档中发表分类单元名称等新规则.文后附有古植物命名的一些重要规则生效的日期和相关说明.     

Development of the SeqCode: A proposed nomenclatural code for uncultivated prokaryotes with DNA sequences as type

Over the last fifteen years, genomics has become fully integrated into prokaryotic systematics. The genomes of most type strains have been sequenced, genome sequence similarity is widely used for delineation of species, and phylogenomic methods are commonly used for classification of higher taxonomic ranks. Additionally, environmental genomics has revealed a vast diversity of as-yet-uncultivated taxa. In response to these developments, a new code of nomenclature, the Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode), has been developed over the last two years to allow naming of Archaea and Bacteria using DNA sequences as the nomenclatural types. The SeqCode also allows naming of cultured organisms, including fastidious prokaryotes that cannot be deposited into culture collections. Several simplifications relative to the International Code of Nomenclature of Prokaryotes (ICNP) are implemented to make nomenclature more accessible, easier to apply and more readily communicated. By simplifying nomenclature with the goal of a unified classification, inclusive of both cultured and uncultured taxa, the SeqCode will facilitate the naming of taxa in every biome on Earth, encourage the isolation and characterization of as-yet-uncultivated taxa, and promote synergies between the ecological, environmental, physiological, biochemical, and molecular biological disciplines to more fully describe prokaryotes.     

Relevance of phenotypic information for the taxonomy of not-yet-cultured microorganisms

To date, far less than 1% of the estimated global species of Bacteria and Archaea have been described and their names validly published. Aside from these quantitative limitations, our understanding of phenotypic and functional diversity of prokaryotes is also highly biased as not a single species has been described for 85 of the 118 phyla that are currently recognized. Due to recent advances in sequencing technology and capacity, metagenomic datasets accumulate at an increasing speed and new bacterial and archaeal genome sequences become available at a faster rate than newly described species. The growing gap between the diversity of Bacteria and Archaea held in pure culture and that detected by molecular methods has led to the proposal to establish a formal nomenclature for not-yet-cultured taxa primarily based on sequence information. According to this proposal, the concept of Candidatus species would be extended to groups of closely related genome sequences and their names validly published following established rules of bacterial nomenclature. The corresponding sequences would be deposited in public databases as the type. The suggested alterations of the International Code of Nomenclature of Prokaryotes raise concerns regarding (1) the reliability and stability of nomenclature, (2) the technological and conceptual limitations as well as availability of reference genomes, (3) the information content of in silico functional predictions, and (4) the recognition of evolutionary units of microbial diversity. These challenges need to be overcome to arrive at a meaningful taxonomy of not-yet-cultured prokaryotes with so far poorly understood phenotypes.     

Amendment of Articles 8, 9, 10, 21 and 78 of the International Code of Zoological Nomenclature to expand and refine methods of publication

The International Commission on Zoological Nomenclature has voted in favour of a revised version of the amendment to the International Code of Zoological Nomenclature that was proposed in 2008. The purpose of the amendment is to expand and refine the methods of publication allowed by the Code, particularly in relation to electronic publication. The amendment establishes an Official Register of Zoological Nomenclature (with ZooBank as its online version), allows electronic publication after 2011 under certain conditions, and disallows publication on optical discs after 2012. The requirements for electronic publications are that the work be registered in ZooBank before it is published, that the work itself state the date of publication and contain evidence that registration has occurred, and that the ZooBank registration state both the name of an electronic archive intended to preserve the work and the ISSN or ISBN associated with the work. Registration of new scientific names and nomenclatural acts is not required. The Commission has confirmed that ZooBank is ready to handle the requirements of the amendment.     

The importance of designating type material for uncultured taxa

Naming of uncultured Bacteria and Archaea is often inconsistent with the International Code of Nomenclature of Prokaryotes. The recent practice of proposing names for higher taxa without designation of lower ranks and nomenclature types is one of the most important inconsistencies that needs to be addressed to avoid nomenclatural instability. The Code requires names of higher taxa up to the rank of class to be derived from the type genus name, with a proposal pending to formalise this requirement for the rank of phylum. Designation of nomenclature types is crucial for providing priority to names and ensures their uniqueness and stability. However, only legitimate names proposed for axenic cultures can be used for this purpose. Candidatus names reserved for taxa lacking cultured representatives may be granted this right if recent proposals to use genome sequences as type material are endorsed, thereby allowing the Code to be fully applied to lineages represented by metagenome-assembled genomes (MAGs) or single amplified genomes (SAGs). Genome quality standards need to be considered to ensure unambiguous assignment of type material. Here, we illustrate the recommended practice by proposing nomenclature type material for four major uncultured prokaryotic lineages based on high-quality MAGs in accordance with the Code.     

Description of two cultivated and two uncultivated new Salinibacter species,one named following the rules of the bacteriological code: Salinibacter grassmerensis sp. nov.; and three named following the rules of the SeqCode: Salinibacter pepae sp. nov., Salinibacter abyssi sp. nov., and Salinibacter pampae sp. nov.

Current -omics methods allow the collection of a large amount of information that helps in describing the microbial diversity in nature. Here, and as a result of a culturomic approach that rendered the collection of thousands of isolates from 5 different hypersaline sites (in Spain, USA and New Zealand), we obtained 21 strains that represent two new Salinibacter species. For these species we propose the names Salinibacter pepae sp. nov. and Salinibacter grassmerensis sp. nov. (showing average nucleotide identity (ANI) values < 95.09% and 87.08% with Sal. ruber M31^T, respectively). Metabolomics revealed species-specific discriminative profiles. Sal. ruber strains were distinguished by a higher percentage of polyunsaturated fatty acids and specific N-functionalized fatty acids; and Sal. altiplanensis was distinguished by an increased number of glycosylated molecules. Based on sequence characteristics and inferred phenotype of metagenome-assembled genomes (MAGs), we describe two new members of the genus Salinibacter. These species dominated in different sites and always coexisted with Sal. ruber and Sal. pepae. Based on the MAGs from three Argentinian lakes in the Pampa region of Argentina and the MAG of the Romanian lake Fără Fund, we describe the species Salinibacter pampae sp. nov. and Salinibacter abyssi sp. nov. respectively (showing ANI values 90.94% and 91.48% with Sal. ruber M31^T, respectively). Sal. grassmerensis sp. nov. name was formed according to the rules of the International Code for Nomenclature of Prokaryotes (ICNP), and Sal. pepae, Sal. pampae sp. nov. and Sal. abyssi sp. nov. are proposed following the rules of the newly published Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). This work constitutes an example on how classification under ICNP and SeqCode can coexist, and how the official naming a cultivated organism for which the deposit in public repositories is difficult finds an intermediate solution.     

在墨尔本召开的第18届国际植物学大会做出的有关名称发表要求的变化——电子出版物对你意味着什么？

《国际植物命名法规》的修订由每六年一次的国际植物学大会（IBC）命名分会来决定。第18届国际植物学大会在澳大利亚墨尔本举行;命名分会于2011年7月18日至22日召开,其决议获得7月30日的全体会议通过。“墨尔本法规”有几个重要的变化,将影响新名称的发表。这些变化中的两个将在“墨尔本法规”出版前的几个月,即于2012年1月1日起生效。通过以移动文档格式（Portable Document Format;pdf）在线发表的具有国际标准连续出版物号（ISSN）或国际标准图书编号（ISBN）的电子出版物,将构成有效发表。新分类群名称的合格发表所必须的拉丁文描述或特征集要将更改为拉丁文或英文描述或特征集要。此外,自2013年1月1日起,被处理为真菌的生物的新名称必须在原始资料（某一名称合格发表时与之有关的所有资料）中引证一个由一家公认的存储库（例如MycoBank）签发的标识码,才构成合格发表。本文提供了有关电子出版物的新规则的草案文本,并概述了相应的最佳做法。     

苦苣苔科植物学名种加词的问题

苦苣苔科植物是个研究活跃的类群,近年来随着新类群的报道和分类系统的变动,在该科的分类学研究中,出现了不少学名的种加词的性和属名不一致或出现拼写错误的情况,虽然这些错误不影响该名称的合格发表,但还是有必要根据《国际藻类、菌物和植物命名法规》进行改正。该文就苦苣苔科植物中属名以-stigma结尾的学名、属名以-cheilos结尾的学名、根据属名词尾不容易判断出性别的学名、拼写错误的名称等问题进行了分析,并对13个不符合法规的名称予以改正。此外,还就苦苣苔科植物学名的合格发表和规范使用进行了讨论。     

The importance of type species and their correct identification: A key example from tintinnid ciliates (Alveolata,Ciliophora, Spirotricha)

Types and the corresponding rules in the International Code of Zoological Nomenclature are crucial for taxonomy and are meant to provide nomenclatural stability. In the case of neotypification, especially diligent taxonomic work is required to retain continuity. In the present communication, we first outline the main principles of typification and neotypification. We then discuss a critical case, using a current example from the marine planktonic tintinnid genus Tintinnopsis Stein, 1867 (Alveolata, Ciliophora). This diverse and ubiquitous genus is nonmonophyletic, but its revision and the erection of new related genera is currently prevented by the uncertain affiliation of its type species.