基于生活习性、形态建成和分子特征研究黏菌四目代表类群的系统发育关系
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摘要
黏菌是一类广泛存在于陆地生态系统中的真核生物,它与生境的长期进化选择塑造了其特有的营养体和子实体形态特征。目前主要是基于子实体形态特征,将黏菌分成了鹅绒菌目、刺轴菌目、无丝菌目、团毛菌目、绒泡菌目和发网菌目六大类,其中鹅绒菌目因其孢子外生的特点明显与其它五个孢子内生的类群不同。有关刺轴菌目、无丝菌目、团毛菌目、绒泡菌目和发网菌目之间的系统发育关系一直吸引着许多黏菌学者的目光,但不同研究者基于不同的形态和分子特征构建的各类群系统发育树不同。本研究从无丝菌目、团毛菌目、绒泡菌目和发网菌目代表类群在自然界中的生活习性入手,结合形态建成过程,保守和不保守的分子特征,探讨了它们在黏菌系统发育中的进化位置,希望为黏菌的分类学和进化发育学发展补充新的理论依据。主要研究结果如下：
1.在吉林省、西藏自治区和四川省代表区域共获得78种黏菌,隶属于鹅绒菌目、无丝菌目、团毛菌、绒泡菌目和发网菌目7科22属,它们的基物类型为枯枝落叶、倒木和树皮三种,除枯枝落叶的pH受树种影响有明显的差异之外,倒木和树皮的pH之间无显著差异。不同分类阶元偏好的基物类型和pH不同。鹅绒菌目和无丝菌目黏菌的基物类型单一,都为倒木,团毛菌目、发网菌目和绒泡菌目黏菌的基物类型多样。其中团毛菌目黏菌的基物类型主要为倒木、发网菌目为倒木和枯枝落叶、绒泡菌目主要为枯枝落叶。另外,各目偏好的pH之间无显著差异；利用16S rDNA基因初探无丝菌目、团毛菌目、绒泡菌目和发网菌目14个样品内部的细菌类群,仅有9个样品内部检测到了细菌,它们分别为变形菌门(包括α、β和γ,三个纲)和放线菌门细菌,其中γ-变形菌纲细菌为广布种。另外,黏菌内部所含的细菌种类可能与它们的基物类型和pH有关,与分类地位无关,还需要进一步补充数据来求证；隶属于绒泡菌目的大孢钙皮菌、鳞钙皮菌、淡黄绒泡菌、细钙丝菌、煤绒菌和针箍菌6个显型原生质团在谷类、菇类和蔬菜类食物处理前48h的觅食过程具有物种特异性,各原生质团本身的营养状况与其生境有关,对营养物质的需求与它们的分类地位有关。
2.在实验室培养的团毛菌目、绒泡菌目和发网菌目共14种黏菌的形态建成过程基础上,发现团毛菌目、绒泡菌目和发网菌目黏菌在原生质团的形成过程和生长方式上存在共性,绒泡菌目和发网菌目黏菌在原生质团形成子实体阶段也存在许多共性,且发网菌目具有更高级可移动的珊瑚状结构。结合有关无丝菌目黏菌形态建成的文献资料,从四日对应的原生质团生活史策略及子实体形态结构的复杂程度来看,无丝菌目为较原始的类群,团毛菌目、发网菌目和绒泡菌目为较高级的有同源性的类群,其中发网菌目和绒泡菌目从团毛菌目进化而来。
3.新获得了鹅绒菌、大孢钙皮菌、鳞钙皮菌、辐射双皮菌、蛇形半网菌和长尖团毛菌6种黏菌的细胞色素氧化酶Ⅰ部分DNA序列,其中鹅绒菌目的序列明显比刺轴菌目、团毛菌目、发网菌目和绒泡菌目长,且后四个目的序列高度保守,无内含子区域。在DNA转录成mRNA时,绒泡菌目和发网菌目有较多的C碱基插入,而刺轴菌目和团毛菌目没有。构建的ML系统树也将绒泡菌目和发网菌目稳定的聚在了一个分支,它们为较进化的类群,亲缘关系较近；获得的大孢钙皮菌a-微管蛋白DNA序列全长1159bp,177-235bp区域为内含子,两端区域共1100bp碱基为外显子。外显子预测编码的氨基酸序列为366aa,与多头绒泡菌α-微管蛋白的相似性为100%,但核苷酸序列不同,存在同义突变现象；新获得了白头高杯菌、光果菌(内蒙和四川)、大孢钙皮菌、鳞钙皮菌、孔膜菌、异型团网菌、赭褐筛菌、圈绒泡菌、小绒泡菌、苔生双皮局、细钙丝菌、彩囊钙丝菌、煤绒菌、扁绒泡菌和针箍菌共18个ITS1,5.8S和ITS2序列,其中12种绒泡菌目黏菌的基因片段在800-2000bp之间,变异较大,特别是其中的ITS1区域。团毛菌目和无丝菌目变异较小,总长度和GC%都比绒泡菌目少。绒泡菌目比团毛菌目和无丝菌目进化速度快。
因此,基于黏菌四目代表类群的生活习性、形态建成和分子特征来看,无丝菌目为较原始的类群,团毛菌目、发网菌目和绒泡菌目为较高级的类群,其中发网菌目和绒泡菌目亲缘关系较近可能从团毛菌目进化而来。
Myxomycetes are a kind of eukaryotic organisms that exist widely in terrestrial ecosystem. Their specific morphological characteristics of vegetative and fruiting body are shaped by long-term evolution and selection between their habitat and themself. The classification of Myxomycetes depends mainly on morphological characteristics of fruiting body and includes six main groups (Ceratiomyxales, Echinosteliales, Liceales, Trichiales, Physarales and Stemonitales). Ceratiomyxales, a group of species with exospores, are distinctly different from the other five orders, a group of species with endospores. The phylogenetic relationships of five orders with endospores have been attracting the attention of many researchers, but there are too many different contentions based on different morphological and molecular characteristics. In the paper, based on their living habits in nature, features of morphogenesis, and conservative and variational molecular characteristics, the positions of Liceales, Trichiales, Physarales and Stemonitales in the phylogeny evolution of Myxomycetes were studied. Hope to provide some new theoretical proofs for the development of taxonomy and evolutionary biology of Myxomycetes. Main results for this study are as follows:
1.78species, which were collected from some typical regions of Jilin Province, Sichuan Province and Tibet Autonomous Region, belonged to Ceratiomyxales, Liceales, Trichiales, Physarales and Stemonitales,7families,22genus. Their substratum types were litter, log and bark, whose pH was no significant difference except that of the litter. It was easily affected by species of tree. Each taxonomic category had preferential substratum type and pH. The substratum types of Ceratiomyxales and Liceales were stable and log, and those of Trichiales, Physarales and Stemonitales were diverse. Those of Trichiales were mainly log, those of Stemonitales were log and litter, and those of Physarales were mainly litter. In addition, there was no significant difference of pH among five groups; Diversity of internal bacterium of14samples in four orders was detected by16S rDNA gene. Bacteria were only detected from9samples and belonged to Proteobacteria (including Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria) and Actinobacteria. Gammaproteobacteria was the dominant population. In addition, there may be some difference of bacterium diversity in different habitats and pH range, not affected by taxonomic status and needed more data to prove that; The foraging process of six phaneroplasmodia (Didymium megalosporum, D. squamulosum, Physarum melleum, Badhamia gracilis, Fuligo septica and Physarella oblonga) to three treatments during 48hours was characteristic for themselves. The nutritional status of each phaneroplasmodium was related to its habitat and the nutritional requirement of each phneroplasmodium was related to its taxonomic status.
2. Based on relevant literature and14species'features of morphogenesis in Trichiales, Physarales and Stemonitales, the forming process and growth method of plasmodia among Trichiales, Physarales and Stemonitales were similar. There were also many similarities in the morphological characteristics between Physarales and Stemonitales during the forming process of fruiting body. But Stemonitales had an advanced and mobile coralloidal mass. Based on reported morphogenesis features of Liceales, from the perspective of complexity of plasmodial life history strategy and fruiting body morphology, Liceales was more primitive group, and Trichiales, Physarales and Stemonitales were more advanced groups. In addition, there was a homology among Trichiales, Physarales and Stemonitale, and Physarales and Stemonitale may derive from Trichiales.
3. Partial cytochrome oxidase I genes of Ceratiomyxa fruticulosa, D. megalosporum, D. squamulosum, Diderma radiatum, Hemitrichia serpula and Trichia decipiens were first gained. That of Ceratiomyxales was longer than those of Echinosteliales, Trichiales, Physarales and Stemonitales, which were highly conservative and no intron area. When the DNA was transcribed into mRNA, those of Physarales and Stemonitales had more insertion of Cs, but those of Echinosteliales and Trichiales had not. The phylogenetic tree constructed by maximum likelihood method gathered Physarales and Stemonitales together, which were more advanced groups; Partial DNA sequence of a-tubulin of plasmodia in D. megalosporum was1159bp in length, whose region from177bp to235bp was intron area and remaining regions were exon area. The coded amino acid sequence was366aa in length and was fully identical with the same sequence of P. polycephalum. But the DNA sequences between them were different, and there were same sense mutation; Eighteen genes of ITS region and5.8S rDNA of ribosome were gained firstly from15species, including Craterium leucocephalum, P. compressum (fruiting body and plasmodium), P. gyrosum, P. pusillum, P. oblonga (fruiting body and plasmodium), B. gracilis, B. utricularis, F. septica, L. fragilis (Sichuan Province and Inner Mongolia Autonomous Region), D. megalosporum, D. squamulosum, D. chondrioderma, Arcyria occidentalis, Enteridium splendens, Cribraria argiliacea. Those of12species in Physarales were800-2000bp in length and had a large variation especially at the region of ITS1. Those of species in Liceales and Trichiales were less than in Physarales in the length and the value of GC%. So the speed of evolution of Physarales was faster than those of Trichiales and Liceales.
Therefore, based on living habits in nature, morphogenesis and molecular characteristics of Liceales, Trichiales, Physarales and Stemonitales, Liceales were more primitive groups, and Trichiales, Physarales and Stemonitales were more advanced groups. In addition, Physarales and Stemonitale had close gentic relationship and were derived from Trichiales.
1.在吉林省、西藏自治区和四川省代表区域共获得78种黏菌,隶属于鹅绒菌目、无丝菌目、团毛菌、绒泡菌目和发网菌目7科22属,它们的基物类型为枯枝落叶、倒木和树皮三种,除枯枝落叶的pH受树种影响有明显的差异之外,倒木和树皮的pH之间无显著差异。不同分类阶元偏好的基物类型和pH不同。鹅绒菌目和无丝菌目黏菌的基物类型单一,都为倒木,团毛菌目、发网菌目和绒泡菌目黏菌的基物类型多样。其中团毛菌目黏菌的基物类型主要为倒木、发网菌目为倒木和枯枝落叶、绒泡菌目主要为枯枝落叶。另外,各目偏好的pH之间无显著差异；利用16S rDNA基因初探无丝菌目、团毛菌目、绒泡菌目和发网菌目14个样品内部的细菌类群,仅有9个样品内部检测到了细菌,它们分别为变形菌门(包括α、β和γ,三个纲)和放线菌门细菌,其中γ-变形菌纲细菌为广布种。另外,黏菌内部所含的细菌种类可能与它们的基物类型和pH有关,与分类地位无关,还需要进一步补充数据来求证；隶属于绒泡菌目的大孢钙皮菌、鳞钙皮菌、淡黄绒泡菌、细钙丝菌、煤绒菌和针箍菌6个显型原生质团在谷类、菇类和蔬菜类食物处理前48h的觅食过程具有物种特异性,各原生质团本身的营养状况与其生境有关,对营养物质的需求与它们的分类地位有关。
2.在实验室培养的团毛菌目、绒泡菌目和发网菌目共14种黏菌的形态建成过程基础上,发现团毛菌目、绒泡菌目和发网菌目黏菌在原生质团的形成过程和生长方式上存在共性,绒泡菌目和发网菌目黏菌在原生质团形成子实体阶段也存在许多共性,且发网菌目具有更高级可移动的珊瑚状结构。结合有关无丝菌目黏菌形态建成的文献资料,从四日对应的原生质团生活史策略及子实体形态结构的复杂程度来看,无丝菌目为较原始的类群,团毛菌目、发网菌目和绒泡菌目为较高级的有同源性的类群,其中发网菌目和绒泡菌目从团毛菌目进化而来。
3.新获得了鹅绒菌、大孢钙皮菌、鳞钙皮菌、辐射双皮菌、蛇形半网菌和长尖团毛菌6种黏菌的细胞色素氧化酶Ⅰ部分DNA序列,其中鹅绒菌目的序列明显比刺轴菌目、团毛菌目、发网菌目和绒泡菌目长,且后四个目的序列高度保守,无内含子区域。在DNA转录成mRNA时,绒泡菌目和发网菌目有较多的C碱基插入,而刺轴菌目和团毛菌目没有。构建的ML系统树也将绒泡菌目和发网菌目稳定的聚在了一个分支,它们为较进化的类群,亲缘关系较近；获得的大孢钙皮菌a-微管蛋白DNA序列全长1159bp,177-235bp区域为内含子,两端区域共1100bp碱基为外显子。外显子预测编码的氨基酸序列为366aa,与多头绒泡菌α-微管蛋白的相似性为100%,但核苷酸序列不同,存在同义突变现象；新获得了白头高杯菌、光果菌(内蒙和四川)、大孢钙皮菌、鳞钙皮菌、孔膜菌、异型团网菌、赭褐筛菌、圈绒泡菌、小绒泡菌、苔生双皮局、细钙丝菌、彩囊钙丝菌、煤绒菌、扁绒泡菌和针箍菌共18个ITS1,5.8S和ITS2序列,其中12种绒泡菌目黏菌的基因片段在800-2000bp之间,变异较大,特别是其中的ITS1区域。团毛菌目和无丝菌目变异较小,总长度和GC%都比绒泡菌目少。绒泡菌目比团毛菌目和无丝菌目进化速度快。
因此,基于黏菌四目代表类群的生活习性、形态建成和分子特征来看,无丝菌目为较原始的类群,团毛菌目、发网菌目和绒泡菌目为较高级的类群,其中发网菌目和绒泡菌目亲缘关系较近可能从团毛菌目进化而来。
Myxomycetes are a kind of eukaryotic organisms that exist widely in terrestrial ecosystem. Their specific morphological characteristics of vegetative and fruiting body are shaped by long-term evolution and selection between their habitat and themself. The classification of Myxomycetes depends mainly on morphological characteristics of fruiting body and includes six main groups (Ceratiomyxales, Echinosteliales, Liceales, Trichiales, Physarales and Stemonitales). Ceratiomyxales, a group of species with exospores, are distinctly different from the other five orders, a group of species with endospores. The phylogenetic relationships of five orders with endospores have been attracting the attention of many researchers, but there are too many different contentions based on different morphological and molecular characteristics. In the paper, based on their living habits in nature, features of morphogenesis, and conservative and variational molecular characteristics, the positions of Liceales, Trichiales, Physarales and Stemonitales in the phylogeny evolution of Myxomycetes were studied. Hope to provide some new theoretical proofs for the development of taxonomy and evolutionary biology of Myxomycetes. Main results for this study are as follows:
1.78species, which were collected from some typical regions of Jilin Province, Sichuan Province and Tibet Autonomous Region, belonged to Ceratiomyxales, Liceales, Trichiales, Physarales and Stemonitales,7families,22genus. Their substratum types were litter, log and bark, whose pH was no significant difference except that of the litter. It was easily affected by species of tree. Each taxonomic category had preferential substratum type and pH. The substratum types of Ceratiomyxales and Liceales were stable and log, and those of Trichiales, Physarales and Stemonitales were diverse. Those of Trichiales were mainly log, those of Stemonitales were log and litter, and those of Physarales were mainly litter. In addition, there was no significant difference of pH among five groups; Diversity of internal bacterium of14samples in four orders was detected by16S rDNA gene. Bacteria were only detected from9samples and belonged to Proteobacteria (including Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria) and Actinobacteria. Gammaproteobacteria was the dominant population. In addition, there may be some difference of bacterium diversity in different habitats and pH range, not affected by taxonomic status and needed more data to prove that; The foraging process of six phaneroplasmodia (Didymium megalosporum, D. squamulosum, Physarum melleum, Badhamia gracilis, Fuligo septica and Physarella oblonga) to three treatments during 48hours was characteristic for themselves. The nutritional status of each phaneroplasmodium was related to its habitat and the nutritional requirement of each phneroplasmodium was related to its taxonomic status.
2. Based on relevant literature and14species'features of morphogenesis in Trichiales, Physarales and Stemonitales, the forming process and growth method of plasmodia among Trichiales, Physarales and Stemonitales were similar. There were also many similarities in the morphological characteristics between Physarales and Stemonitales during the forming process of fruiting body. But Stemonitales had an advanced and mobile coralloidal mass. Based on reported morphogenesis features of Liceales, from the perspective of complexity of plasmodial life history strategy and fruiting body morphology, Liceales was more primitive group, and Trichiales, Physarales and Stemonitales were more advanced groups. In addition, there was a homology among Trichiales, Physarales and Stemonitale, and Physarales and Stemonitale may derive from Trichiales.
3. Partial cytochrome oxidase I genes of Ceratiomyxa fruticulosa, D. megalosporum, D. squamulosum, Diderma radiatum, Hemitrichia serpula and Trichia decipiens were first gained. That of Ceratiomyxales was longer than those of Echinosteliales, Trichiales, Physarales and Stemonitales, which were highly conservative and no intron area. When the DNA was transcribed into mRNA, those of Physarales and Stemonitales had more insertion of Cs, but those of Echinosteliales and Trichiales had not. The phylogenetic tree constructed by maximum likelihood method gathered Physarales and Stemonitales together, which were more advanced groups; Partial DNA sequence of a-tubulin of plasmodia in D. megalosporum was1159bp in length, whose region from177bp to235bp was intron area and remaining regions were exon area. The coded amino acid sequence was366aa in length and was fully identical with the same sequence of P. polycephalum. But the DNA sequences between them were different, and there were same sense mutation; Eighteen genes of ITS region and5.8S rDNA of ribosome were gained firstly from15species, including Craterium leucocephalum, P. compressum (fruiting body and plasmodium), P. gyrosum, P. pusillum, P. oblonga (fruiting body and plasmodium), B. gracilis, B. utricularis, F. septica, L. fragilis (Sichuan Province and Inner Mongolia Autonomous Region), D. megalosporum, D. squamulosum, D. chondrioderma, Arcyria occidentalis, Enteridium splendens, Cribraria argiliacea. Those of12species in Physarales were800-2000bp in length and had a large variation especially at the region of ITS1. Those of species in Liceales and Trichiales were less than in Physarales in the length and the value of GC%. So the speed of evolution of Physarales was faster than those of Trichiales and Liceales.
Therefore, based on living habits in nature, morphogenesis and molecular characteristics of Liceales, Trichiales, Physarales and Stemonitales, Liceales were more primitive groups, and Trichiales, Physarales and Stemonitales were more advanced groups. In addition, Physarales and Stemonitale had close gentic relationship and were derived from Trichiales.
引文
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