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。     

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。     

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。     

我国原核微生物分类学七十年

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...     

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。     

A New Generic Name for the Hoolock Gibbon (Hylobatidae)

Contrary to usual practice, the generic nomen Bunopithecus is not applicable to hoolock gibbons. We recount the history of its application and explain why it is spurious. We supply a new generic name, list the characters and content of the genus, and compare it to the other 3 genera of the Hylobatidae.     

Karyological and taxonomic studies of Dugesia japonica from the Southwest Islands of Japan-II

The karyotypes of Dugesia japonica from the southern part of the Southwest Islands of Japan (the Nansei Shotô) include diploidy, triploidy, mixoploidy, and mixoaneuploidy. Animals having karyotypes based on n = 8 were found on Okinawa Island, Ishigaki Island, Iriomote Island, and Yonaguni Island, while animals having karyotypes based on n = 7 were found on Okinawa Island, Miyako Island, and Ishigaki Island. Toward the northern end of this island chain, at Tanegashima Island, Yakushima Island, and Amami-Ôshima Island, karyotypes based on n = 8 occurred; and on one of these, Tanegashima Island, n = 7 also occurred. Our data provide further support of the karyotypical distinction between the two subspecies of D. japonica: D. j. japonica has karyotypes based on n = 8 and D. j. ryukyuensis has karyotypes based on n = 7. Taking into consideration the geological history of the Southwest Islands and the ties of their faunas to those of adjacent areas, we can explain the current geographical distribution of the two subspecies in these islands as the result of two separate invasions by D. japonica, one in the Miocene and one after the early Quaternary.     

Diversity and abundance of ammonia-oxidizing archaea and bacteria in polluted mangrove sediment

Ammonia oxidation by microorganisms is a critical process in the nitrogen cycle. Recent research results show that ammonia-oxidizing archaea (AOA) are both abundant and diverse in a range of ecosystems. In this study, we examined the abundance and diversity of AOA and ammonia-oxidizing beta-proteobacteria (AOB) in estuarine sediments in Hong Kong for two seasons using the ammonia monooxygenase A subunit gene (amoA) as molecular biomarker. Relationships between diversity and abundance of AOA and AOB and physicochemical parameters were also explored. AOB were more diverse but less abundant than AOA. A few phylogenetically distinct amoA gene clusters were evident for both AOA and AOB from the mangrove sediment. Pearson moment correlation analysis and canonical correspondence analysis (CCA) were used to explore physicochemical parameters potentially important to AOA and AOB. Metal concentrations were proposed to contribute potentially to the distributions of AOA while total phosphorus (TP) was correlated to the distributions of AOB. Quantitative PCR estimates indicated that AOA were more abundant than AOB in all samples, but the ratio of AOA/AOB (from 1.8 to 6.3) was smaller than most other studies by one to two orders. The abundance of AOA or AOB was correlated with pH and temperature while the AOA/AOB ratio was with the concentrations of ammonium. Several physicochemical factors, rather than any single one, affect the distribution patterns suggesting that a combination of factors is involved in shaping the dynamics of AOA and AOB in the mangrove ecosystem.     

一株高效解磷菌的筛选鉴定及溶磷性能

【背景】土壤中大部分磷元素是以难溶性磷酸盐的形式存在,不能被农作物有效利用,而传统化学肥料会带来环境污染等问题。【目的】解决土壤磷缺失现状,开发新型、安全、高效的微生物菌肥。【方法】取武汉科技大学图书馆后土壤为试验材料,筛选出一株高效解磷菌。通过个体形态鉴定、生理生化鉴定、16S rRNA基因序列分析鉴定菌株,以NBRIP为基础培养基进行条件优化,借助高效液相色谱进行细菌解磷机理探究。【结果】所筛选的高效解磷菌株为唐菖蒲伯克霍尔德氏菌(Burkholderia gladioli)。在20种氨基酸中,D-蛋氨酸对菌株的生长和溶磷促进作用最好,促进效果达到19.09%和16.16%,甲酸钠对菌株的生长和溶磷有抑制效果,抑制效果达到39.08%和10.66%。该菌株通过分泌葡萄糖醛酸、D-L-苹果酸等有机酸溶解环境中的磷酸盐,将菌株制作成菌肥对辣椒幼苗有明显的促生长作用。【结论】利用唐菖蒲伯克霍尔德氏菌(Burkholderia gladioli)分泌有机酸溶解土壤中的磷酸盐,可为生物肥料的制备和应用提供一定的理论参考。     

Unexpected and novel putative viruses in the sediments of a deep-dark permanently anoxic freshwater habitat

Morphological diversity, abundance and community structure of viruses were examined in the deep and anoxic sediments of the volcanic Lake Pavin (France). The sediment core, encompassing 130 years of sedimentation, was subsampled every centimeter. High viral abundances were recorded and correlated to prokaryotic densities. Abundances of viruses and prokaryotes decreased with the depth, contrasting the pattern of virus-to-prokaryote ratio. According to fingerprint analyses, the community structure of viruses, bacteria and archaea gradually changed, and communities of the surface (0–10 cm) could be discriminated from those of the intermediate (11–27 cm) and deep (28–40 cm) sediment layers. Viral morphotypes similar to virions of ubiquitous dsDNA viruses of bacteria were observed. Exceptional morphotypes, previously never reported in freshwater systems, were also detected. Some of these resembled dsDNA viruses of hyperthermophilic and hyperhalophilic archaea. Moreover, unusual types of spherical and cubic virus-like particles (VLPs) were observed. Infected prokaryotic cells were detected in the whole sediment core, and their vertical distribution correlated with both viral and prokaryotic abundances. Pleomorphic ellipsoid VLPs were visible in filamentous cells tentatively identified as representatives of the archaeal genus Methanosaeta, a major group of methane producers on earth.