原核微生物之菌和微菌

本文明确了对于现行中文对原核微生物习惯命名中的虚字"菌"字,在定义希腊文名词bios和新拉丁文名词bius-um-a时可具有实际意义。与微(micro/mikros)组合时,表示有尺寸特征,但这种特征与其他原核微生物的尺寸区别不大,有待实践中进一步细化。本文总结80多属460多种和亚种的微生物,提出命名法能够表达的微生物特征层次,进一步明确这些种属的细菌属性,以促进国内外交流。     

原核微生物之竿菌

140多年前发表的竿菌和杆(小杆)菌同属最早发现和定名的细菌类之一,迄今已有成百上千的菌种得到鉴定、分类和命名。中文微生物学命名和整理滞后,引发了一些不必要的麻烦和困惑,不利于我国微生物学的普及发展和国际交流。本文试图对已经合格发表的近100属1 130多种竿菌进行系统的形态学(含芽孢和/或孢子)、生境、生物化学和细菌属性梳理和分类,理清和制定竿菌种属的中文-拉丁文互译规则,有利于推动中外交流和发展。     

原核微生物之杆菌和小杆菌

原核微生物的发现已有约340年,成千上万的原核微生物被发现和命名。近年来,随着分子生物学技术的发展,众多新的种属已经得到鉴定和命名,对这些微生物系统的总结并对中文命名系统适当调整已迫在眉睫。本文试图对人类发现最早、总量最多的350多属1 500多种杆菌和120多属1 200多种小杆菌进行总结和归纳,从生境、形态学(动静态、形状和尺寸)、生物化学、细菌和古菌属性等特征层次规范这类菌属的命名,期盼有助于推动国内外微生物分类学发展,有利于推动国际交流与合作。     

球类原核微生物

球类或类球(果菌、球菌、璆菌、卵菌、橄菌等)微生物是原核微生物最早发现、最重要和最常见的细胞生命形态之一,迄今已有果菌140余属800多种60多亚种,球菌30余属60多种,璆菌10余属20多种,八球菌7属40多种,橄菌9属10多种,卵菌10余属30多种,合计约210属1 000余种和亚种。国内外对这些微生物的总结分析较少,本文试图对此进行系统的总结和规范,明确其形态特征、生境、生化、多样性和域归属,以推动对此类微生物分类和功能的进一步研发,推动国际间的交流与合作。     

我国原核微生物分类学七十年北大核心

2022年和2023年分别是中国微生物学会成立70周年和《微生物学报》创刊70周年,我国原核微生物分类学研究从白手起家、跟踪模仿到逐步走上国际舞台,从跟跑、并跑到整体处于国际先进行列,部分领域领跑国际同行,并为国际同行提供微生物数据服务,也已走过了70个岁月。这些成绩的取得是我国原核微生物分类领域学者几代人努力的结果,是与国家发展、民族复兴同频共振的结果。特别是近30年,我国原核微生物分类无论从理论、方法创新还是新物种发现方面都取得了令人瞩目的成绩,在国际上的地位和影响力日益提高,已经逐渐成为国际原核系统分类领域的主导力量。本文本着尊重历史、客观求实的态度梳理了70年来我国在细菌和古菌分类学及相关领域的发展脉络和取得的成绩,并结合该领域最新发展方向进行了展望。     

基于分级过滤的自然水体原核微生物群落分析

自然水体中微生物种类丰富,采集了上海周边的湖水、河水、海(岸)水、井水四类水体各两处样品,设计了含0.1μm终端截留孔径的半自动分级过滤装置分离富集不同粒径的水体微生物,使用原核微生物通用引物对16S rRNA基因V3+V4区扩增,高通量测序获得序列,对四类水体中的微生物群落进行比较分析,关注了能穿透0.22μm常规除菌过滤孔径的超微小微生物。结果显示水体环境主导了微生物的群落差异,河水与湖水中的群落总体接近,不同于海(岸)水和井水;海(岸)水和井水的微生物群落差异较大。0.1μm上截留的优势超微小微生物在河水与湖水样品中均为Proteobacteria门SAR11 clade目的Clade Ⅲ和Actinobacteria门Sporichthyaceae科HgcI clade,海(岸)水中为Proteobacteria门SAR11 clade目的Clade Ia和Nanoarchaeota门Woesearchaeia古菌,井水中为Nanoarchaeota门Woesearchaeia属古菌以及未定域或未分类的微生物。其中未定域的微生物16S rRNA基因在系统发育树上单独成簇,可能是古菌的一个新类型。本研究所使用的分级过滤装置显示了在发掘超微小微生物上的潜力。     

从IJSEM发表的论文看我国的微生物分类

介绍了各国 2 0 0 3年在IJSEM杂志发表论文的情况 ,我国学者在微生物分类学领域所做的工作 ,并对几个值得重视的问题进行了述评。     

基于不同通用引物比较分析肠道微生物群落变化

肠道微生物对于人体健康的重要作用已经得到广泛证实,目前,对肠道微生物的研究大多采用基于扩增细菌16S rRNA基因V3-V4区的高通量测序分析,对古菌的关注较少。本研究选择了一对可以同时扩增细菌和古菌16S rRNA基因的引物,通过比较人为干扰肠道微生物前后的群落变化,说明这对引物适宜分析人类肠道细菌和古菌群落变化并具有一定优越性。采集志愿者粪便样品,同时用仅能扩增细菌引物(B引物)和细菌古菌通用引物(AB引物)进行扩增和高通量测序;使用几个常用的rRNA数据库判断引物对细菌的覆盖度和对古菌的扩增能力。结果表明,AB引物在可以展示B引物扩增出的细菌群落的基础上,可以得到肠道中常见的产甲烷古菌的序列,同时也展示出人为干扰肠道微生物前后的群落结构变化。AB引物可以仅通过一次扩增和测序同时分析肠道中的细菌和古菌群落,更加全面展示肠道微生物群落结构,适用于肠道微生物相关研究。     

原核微生物铁超氧化物歧化酶的分子进化

超氧化物歧化酶（superoxide dismutase,SOD）在维持生物体内超氧阴离子自由基产生与消除的动态平衡中起着重要的作用。铁超氧化物歧化酶（ge—SOD）是原核生物和真核生物细胞器中专一的SOD酶,通过GenBank中搜集的原核生物Fe—SOD进行比对分析发现,Fe-SOD是相对保守的蛋白质,其中包含2个保守区域和1个可变区域,金属结合位点固定,Fe．SOD序列的比对可以反映物种间的进化关系,是研究原核生物分子进化的理想素材。     

基于高通量测序研究青藏高原茶卡盐湖微生物多样性

【目的】茶卡盐湖(Chaka Salt Lake,CSL)是青藏高原有名的天然结晶盐湖,具有独特的石盐盐湖矿床,盛产青盐。盐湖卤水环境中存在丰富的嗜盐菌资源和潜在的新种,细菌和古菌的群落结构特征和物种多样性尚不明确。【方法】采用Illumina高通量测序平台对茶卡盐湖水样和底泥混合物中的细菌和古菌群落进行16S r RNA基因(V3-V5区)高通量测序,检测4个样本的群落结构差异和微生物多样性。【结果】获得细菌和古菌总有效序列分别为117 192和110 571条。结果分析表明细菌和古菌的物种注释(Operational taxonomic unit,OTU)数目分别为421和317,获得分类地位明确的细菌种类为14门28纲170属,古菌为5门4纲34属。细菌的优势类群是厚壁菌门(Firmicutes),所占比例为68.37%,其次为变形菌门Proteobacteria(20.49%);优势种属依次为芽孢杆菌属Bacillus(41.94%)、海洋芽孢杆菌属Oceanobacillus(8.03%)、假单胞菌属Pseudomonas(7.67%)、盐厌氧菌属Halanaerobium(7.42%)和乳球菌属Lactococcus(7.38%);古菌的优势类群以广古菌门(Euryarchaeota)盐杆菌纲(Halobacteria)为主,优势菌是Halonotius(17.21%)和盐红菌属Halorubrum(16.23%)。【结论】揭示了茶卡盐湖中细菌和古菌的群落结构及物种多样性,为嗜盐菌的开发及后续微生物资源的挖掘提供了理论依据。     

Distinction of species in Aureobasidium and related genera by PCR-ribotyping

Taxonomic markers for differentiation of the anamorph genera Aureobasidium, Hormonema and Kabatiella were developed using PCR-ribotyping with the primers 5.8S-R and LR7 for amplification and the restriction enzymes Alul, DdeI, Hhal, MspI and RsaI for digestion. Aureobasidium and Hormonema are optimally differentiated with MspI; DdeI is particularly useful to distinguish aureobasidium, Kabatiella and Selenophoma. Relationships of the anamorph genera Aureobasidium, Hormoneng and Kabatiella with the teleomorph genera Pringsheimia and Dothiora are discussed.     

Addition and reexamination of Japanese species belonging to the genus Cercospora and allied genera. IX. Newly recorded species from Japan (4)

Pseudocercospora cyatheae C. Nakash. & S. Inaba on Cyathea sp. as a new species is described. Three species belonging to the genus Cercospora and allied genera are newly added to the mycoflora of Japan. They are Cercospora armoraciae on Armoracia rusticana, Passalora passaloroides on Amorpha fruticosa, and Pseudocercospora nogalesii on Cytisus scoparius.     

Atkinsiella dubia and its related species

Atkinsiella dubia, isolated from the mantle of abalone (Haliotis sieboldii), is described and illustrated as a new record from Japan. The fungus was also obtained from the gills of swimming crab (Portunus trituberculatus). Six other species of the genusAtkinsiella have hitherto been reported from various aquatic animals. The fungus is distinguished from the other six species by the morphology of its mycelia and the process of zoospore production. The most distinctive feature is that zoospores in the first motile stage ofA. dubia encyst in zoosporangia, unlike the other species. We therefore proposeHalocrusticida gen. nov. (Lagenidiales, Haliphthoraceae) for the other six species ofAtkinsiella. A key to species of the genusHalocrusticida is provided.     

Addition and reexamination of Japanese species belonging to the genus <Emphasis Type="Italic">Cercospora</Emphasis> and allied genera. VIII. Newly recorded species from Japan (3)

Four species belonging to the genus Cercospora and allied genera were newly added to the Japanese mycoflora. They are Cercospora plantaginis on Plantago asiatica, Pseudocercospora asystasiae on Asystasia gengetica, P. cassiae-fistulae on Cassia fistula, and Pseudocercosporella ranunculacearum on Clematis grata var. ryukyuensis.     

Addition and reexamination of Japanese species belonging to the genus <Emphasis Type="Italic">Cercospora</Emphasis> and allied genera. VII. Newly recorded species from Japan (2)

In the seventh report of the present series, four species of the genus Pseudocercospora were added to the Japanese mycoflora. They are Pseudocercospora catappae, P. mali, P. polysciatis-pinnatae, and P. puderi.     

Karyology of four land-planarian species of the genus Bipalium from Japan

We have employed a new scale for characterizing chromosomal forms in the karyotypes of four species of Bipalium from five localities in Japan. Specimens of Bipalium nobile Kawakatsu et Makino, 1982, from Yokohama had a diploid chromosome number of 2x = 10 (2m + 2sm + 2sm + st & sm + 2sm); specimens of the same species from Toyonaka had this number as well but with slightly different chromosomal form (2m + 2sm + sm & st + 2st + m & sm). An undescribed species from Sanjô, Bipalium sp. 2, with two dorsal stripes and a yellow head crescent, had 2x = 10 (2m + 2sm + 2sm + 2sm + 2m); and another undescribed species from Chichijima Island, Bipalium sp. 3, with five dorsal stripes, had 2x = 10 (2m + 2sm + 2sm + 2sm + 2m). A non-sexual bipaliid tentatively identified as Bipalium kewense Moseley, 1878, from Chichijima Island had 2x = 18 (2m + 2m + 2m + 2sm + 2st + 2sm + 2sm + 2sm + 2sm).     

Pollen morphology ofSonchus and related genera,and a general discussion

The pollen morphology of the taxa belonging to the generaAetheorhiza Cass.,Launaea Cass.,Reichardia Roth andSonchus L. in the Iberian Peninsula has been studied with light and electron microscopy. The pollen is 3(-4)-zonocolporate and echinolophate (without polar lacunae, but in general with prelacunae), with equatorial ridges and 15–20 lacunae: 3–4 poral, 6–8 abporal and 6–8 paraporal. Small to medium size, P × E = 19–36 × 23–42 µm; sometimes two different sizes have been found. Exine 3–9 µm thick and ornamentation microreticulate and echinate. The results clearly show the relationships between genera. Moreno-Socías, E., Mejías, J. A., Díez, M. J., 1994: Morfología polínica deLactuceae (Asteraceae) en la Península Ibérica, I.Lactuca y géneros relacionados. — Acta Bot. Malacitana.19: 103–113.