基于加权共变化网络分析水稻根系微生物群落间的差异

为了解水稻根系微生物群落间的差异,比较水稻根内、根表以及根际3个生态位微生物群落组成差异;探究水稻根系生态位之间、变化种群间的相互关系;以期为今后水稻根系微生物研究提供具有参考价值的依据.本研究利用WGCNA算法对水稻根系3个生态位的微生物群落数据分别构建共表达网络,找出根内、根表以及根际微生物群落间的差异网络,以网络为单位比较分析不同生态位间微生物群落的差异,并基于共变化网络分析进一步探究差异种群间的相互关系.通过WGCNA算法对水稻根系3个生态位的微生物群落进行共表达网络分析,结果发现:在水稻根内-根表-根际3个生态位间,微生物群落构成的共表达互作网络存在差异.进一步分析3个生态位间差异网络,发现根际-根表差异网络中的OTUs分布于6个门18个属中,优势菌门为变形菌门(Proteobacteria,72.97％);在根际-根内差异网络中的OTUs分布于9个门35个属,优势菌门为变形菌门(Proteobacteria,66.36％)、放线菌门(Actinobacteria,9.09％)、拟杆菌门(Bacteroidetes,10.9％);根表-根内差异网络中的OTUs分布于12个门36个属中,其中优势菌门为变形菌门(Proteobacteria,41.41％)、拟杆菌门(Bacteroidetes,10.10％)、厚壁菌门(Firmicutes,12.12％)、疣微菌门(Verrucomicrobia,10.10％).Rhodobacter、No-vosphingobium等3个核心菌属、Blvii28、Dechloromonas等6个核心菌属和Cellvibrio、Geobacter等5个核心菌属,分别在根际-根表差异种群微生物共变化网络、根际-根内差异种群微生物共变化网络和根表-根内差异种群微生物共变化网络中起重要的调控作用.     

广东省本地油茶和引种油茶根际土壤微生物群落特征

【背景】近年来,油茶低效林面积较大,根际土壤微生物影响林木抗性和生长,对林业可持续发展具有重要意义。【目的】了解广东省本地油茶和引种油茶根际土壤微生物群落特征。【方法】利用高通量测序分析油茶根际土壤微生物群落组成。【结果】油茶根际土壤细菌有26门77纲201目377科593属676种,真菌有14门50纲121目266科502属631种。油茶根际土壤中的优势细菌为酸杆菌门和变形菌门,优势真菌为子囊菌门和担子菌门。两种油茶根际土壤微生物组成差异显著,本地油茶根际土壤的细菌多样性显著高于引种油茶。在门水平上,脱硫杆菌门细菌和罗兹菌门、被孢霉门真菌的相对丰度在两种油茶间差异显著,Amorphotheca在本地油茶根际土壤中特异性富集。两种油茶根际土壤细菌碳代谢相对丰度差异显著,真菌以腐生营养型为主,其次为病理营养型和共生营养型。本地油茶根际土壤中显著富集土壤腐生菌,而共生营养型真菌(尤其是丛枝菌根真菌)相对丰度(6.43%)显著低于引种油茶中(21.83%)。此外,有机质和养分含量是影响油茶根际土壤微生物群落的关键因子。【结论】本地油茶和引种油茶根际土壤微生物群落组成和结构差异显著,Amorp...     

丹参内生拮抗细菌DS-R5对丹参根际和根表土壤细菌群落结构的影响CSCD

目的 探究生防细菌DS-R5施入丹参植株后根际和根表土壤细菌群落组成及多样性变化。方法 向丹参植株根部施入生防细菌DS-R5,以未施用细菌为对照组,分别采集根际和根表土壤样品提取总DNA,扩增样品总DNA的V3-V4区,采用Illumina MiSeq测序平台对PCR扩增产物进行双端测序分析,利用生物信息学分析解析丹参植株根际土壤和根表土壤细菌群落结构组成及多样性。结果 菌株DS-R5处理后增加了根际土壤细菌群落的多样性和丰度,降低了根表土壤细菌群落的多样性和丰度;高通量测序得到的根际和根表土壤的有效序列数量和OTU数量相比对照组均有所下降,根际土壤处理样品中微生物种类最丰富,根表土壤处理样品中微生物种类最少,根际土壤处理样品与根际土壤对照物种种类更接近;在门水平上,根际土壤处理样品相比对照变形菌门丰度下降,酸杆菌门丰度升高,根表土壤处理样品相比对照变形菌门和酸杆菌门丰度均升高,放线菌门丰度降低;在属水平上,根际土壤处理样品中鞘氨醇单胞菌属、芽胞杆菌属、慢生根瘤菌属相比根际土壤对照占比均有升高,根表土壤处理样品相比对照黄杆菌属和伯克菌属丰度下降,而土壤中的优势菌属根瘤菌属和芽胞杆菌属丰度升高。结论 丹参植株施用生防细菌DS-R5后,改变了根际土壤和根表土壤中微生物群落结构和多样性。     

百里杜鹃保护区马缨杜鹃土壤真菌群落特征

近年来,贵州百里杜鹃保护区戛木管理区发现有部分马缨杜鹃感染根腐病,造成其大量死亡,致病机制尚不明确。为了研究马缨杜鹃根腐病发病区土壤真菌群落结构组成,探讨真菌微生物种类组成变化与根腐病发病的关联,以感病马缨杜鹃根部土壤和未感病马缨杜鹃根部土壤的土壤为对象,利用高通量测序技术进行测序,发现2份感病杜鹃根部土壤中分别有846和911个操作分类单元(operating taxonomic unit, OTUs),而未感病杜鹃根部土壤仅有439个OTUs。通过分析土壤真菌物种丰度和分类、α-多样性、β-多样性、主成分(principal component analysis, PCA)分析和聚类分析。结果表明:感病马缨杜鹃和未感病马缨杜鹃根部土壤真菌多样性和群落结构存在较大差异,未感病杜鹃根部土壤的真菌微生物种类明显少于感病杜鹃根部土壤。     

不同生境黑果枸杞根际与非根际土壤微生物群落多样性

研究典型生境黑果枸杞根际与非根际土壤微生物群落多样性及其与土壤理化性质间的关系,为进一步研究黑果枸杞抗逆性提供理论数据。采集新疆精河县艾比湖地区(EB)盐碱地、乌苏市(WS)路旁荒地、五家渠市(WQ)人工林带的黑果枸杞根际与非根际土壤,利用Illumina-MiSeq高通量测序技术分析细菌和真菌群落组成和多样性。结果表明:根际土壤细菌多样性高于非根际土壤(WQ除外),而根际真菌多样性低于非根际土壤。WQ非根际土壤细菌和真菌多样性均高于EB和WS;根际细菌多样性排序为EBWSWQ,根际真菌多样性排序为WSEBWQ。根际土壤优势细菌门依次是变形菌门、拟杆菌门、放线菌门、酸杆菌门,真菌优势门为子囊菌门、担子菌门。根际土壤细菌变形菌门、拟杆菌门、酸杆菌门的相对丰度高于非根际土壤,而厚壁菌在根际土壤中的丰度显著降低,真菌优势门丰度在根际土和非根际土中的变化趋势因地区而异; Haliea、Gp10、Pelagibius、Microbulbifer、假单胞菌属、Thioprofundum、Deferrisoma是根际土壤细菌优势属;多孢子菌属、支顶孢属、Corollospora、Cochlonema是根际真菌优势属。细菌、真菌优势类群(门、属)的组成以及丰富度存在地区间差异,厚壁菌门在EB地区的丰富度显著高于含盐量较低的WS、WQ;盐碱生境EB中根际土壤嗜盐细菌的丰度高于非盐碱生境(WQ、WS),如盐单胞菌属、动性球菌属、Geminicoccu、Pelagibius、Gracilimonas、Salinimicrobium等。小囊菌属是EB根际真菌的最优势属,Melanoleuca是WQ和WS的最优势属,地孔菌属、Xenobotrytis、Brachyconidiellopsis、多孢子菌属等在EB根际土壤中的丰度显著高于WQ和WS。非盐碱生境(WS和WQ)的微生物群落之间的相似性较高,并且高于与盐碱环境(EB)之间的相似性,表明土壤含盐量对微生物群落组成丰度具有重要的影响。     

毛黄堇根腐病根际土壤微生物群落结构及多样性

目的：研究健康毛黄堇植株和患根腐病毛黄堇植株根际土壤微生物群落多样性和组成差异，探讨其与毛黄堇病害发生的关系，为针对性开展防治工作提供科学依据。方法：利用Illumina MiSeq技术，比较健康和患病根际土壤微生物群落结构特征及差异。结果：患病根际土细菌群落α多样性降低，真菌群落α多样性升高。健康和患病植株细菌、真菌门水平的组成结构及相对丰度差异均较小，细菌优势门为变形菌门和放线菌门，真菌为子囊菌门。属水平上组成结构复杂，优势细菌属为Subgroup＿6等，优势真菌属为曲霉属。患病植株差异标志物种主要为小单孢菌科细菌和核盘菌科真菌。结论：土壤微生物群落多样性和结构与毛黄堇健康状态密切相关，致病真菌相对丰度增加可能是导致病害发生的重要原因。     

自然林下与田间根腐三七根际微生物群落特征及比较分析

【背景】三七根际微生物群落特征与其土传根腐病害密切相关,而针对自然林下根腐三七的相关研究鲜见报道。【目的】比较分析自然林下与田间根腐三七根际土壤微生物群落的组成特征,结合土壤理化性质与酶活性分析,为三七根腐病害防治与仿野生栽培提供科学依据。【方法】采集自然林下与田间根腐三七根际土壤,利用高通量测序技术,分析土壤细菌与真菌群落的物种组成与多样性,并测定土壤理化性质和酶活性。【结果】自然林下与田间根腐三七根际土壤中细菌和真菌群落组成具有明显差异,自然林下根腐三七根际土壤中担子菌门(Basidiomycota)、酸杆菌门(Acidobacteria)和疣微菌门(Verrucomicrobia)的相对丰度较高,而田间根腐三七根际土壤中子囊菌门(Ascomycota)、变形菌门(Proteobacteria)和绿弯菌门(Chloroflexi)的相对丰度较高。在属分类水平,镰刀菌属(Fusarium)是自然林下根腐三七根际土壤中的优势菌群,相对丰度为17.30%,而癣囊腔菌属(Plectosphaerella)是田间根腐三七根际土壤中的优势菌群,相对丰度为22.55%;Candidatus Ba...     

竹叶兰根系共生真菌群落结构及生物学功能初探

为研究竹叶兰Arundina graminifolia根系共生真菌的群落结构及对寄主的营养作用,采用高通量测序技术对野生竹叶兰根围土壤、根表、根内3个生态位真菌的种类及生物学功能进行鉴定与预测。所测竹叶兰根系共生真菌的平均辛普森指数为根围0.972、根 表0.905、根内0.703,说明3个位点都具有丰富的共生真菌;根围土壤真菌香农指数7.393显著高于根表和根内香农指数4.728和2.872,根表真菌多样性显著高于根内（P<0.05）。根表、根内有子囊菌门、担子菌门、罗兹壶菌门、壶菌门、毛霉菌门和被孢霉门,较根围土壤缺少球囊菌门和梳霉菌门;分子方差分析（AMOVA）证实3个生态位的真菌群落结构差异极显著（P=0.004）。各生态位丰度最高的20个真菌仅属于子囊菌和担子菌的40个属,其中子囊菌有30个属,种类数量占优势,而担子菌的单个种类丰度高于子囊菌。根围土壤腐生型真菌占优势（44.07%）;根表主要有腐生、病原、共生型真菌;根内真菌营养类型差异大,样品M1的共生型真菌为优势类型（97.21%）,M2、M3以腐生型占优（90.96%）。优势共生型真菌有革菌属Threlephora、根须腹菌属Rhizopogon和Dentiscutata,腐生型真菌主要有长毛孔菌属Funalia和Vuilleminia,均为担子菌。研究结果为揭示竹叶兰与根系真菌的营养关系以及共生真菌的开发提供了依据。     

十字花科作物根肿病对根际土壤微生物群落的影响

为探究根肿病对十字花科作物根际土壤微生物多样性的影响,以罹病大白菜和健康株根际土壤为研究对象,采用高通量测序技术对2组样本的细菌16S rDNA和真菌ITS基因进行序列测定,分析了样本间的微生物群落结构和组成差异,同时测定根际土壤理化性质,探讨根肿病、土壤微生物群落、土壤环境因子三者的相关性。研究表明:1)患病植株根际土壤pH和总磷、总钾、碱解氮、速效钾含量显著低于正常植株根际土,而交换性钙含量明显增加。2)根肿病的发生降低了根际土壤中细菌种群的丰富度和多样性程度,但对根际土壤中的真菌α-多样性无明显影响。3)变形菌门、拟杆菌门、放线菌门等是所测土壤样本的主要优势细菌种群,其中患病植株根际土壤中拟杆菌门丰度显著高于健康植株根际土壤,放线菌门丰度则显著降低(P0.05)。优势细菌纲为γ-变形菌纲、拟杆菌纲、α-变形菌纲、放线菌纲、酸杆菌纲等,2组土壤样本间多种优势细菌纲相对丰度差异显著。4)根际土壤优势真菌类群为子囊菌门、被孢霉门、担子菌门和壶菌门,其相对丰度在患病和健康株根际土壤样本中均有明显差异。主要真菌纲为散囊菌纲、被孢霉纲、锤舌菌纲等,并且土壤样本间的多种优势真菌纲相对丰度存在显著性差异。5)主坐标分析结果表明病株根际土壤与健康株根际土壤细菌和真菌群落结构差异明显,冗余分析结果显示速效钾和交换性钙是根际土壤微生物群落变化的主要影响因素。研究结果为揭示根肿病发生的根际微生态机制以及研发根肿病综合防控技术提供理论支撑。     

两种盐生植物根际土壤细菌多样性和群落结构

应用高通量测序技术对西北干旱区两种盐生植物黑果枸杞和里海盐爪爪根际土壤细菌的多样性和群落结构进行研究,旨在揭示两种耐盐植物根际土壤细菌之间以及根际与非根际细菌群落结构间的差异,为深入研究盐生植物根际土壤微生物与耐盐性之间的关系提供理论基础。结果表明:黑果枸杞、里海盐爪爪根际细菌多样性丰度高于非根际土,黑果枸杞根际土壤细菌多样性丰度高于里海盐爪爪。根际和非根际土壤细菌群落的组成和丰度存在差异,从黑果枸杞和里海盐爪爪根际土壤中分别检测出细菌21门289属和22门304属,而从非根际土壤中分别检测出28门285属和24门336属;在两种盐生植物根际土壤中,变形菌门和厚壁菌门均为优势门;拟杆菌门、放线菌门、蓝细菌门及浮霉菌门在根际土壤中的丰度显著高于非根际土壤,而厚壁菌门在根际土壤中的丰度低于非根际土壤。两种植物根际土壤中的细菌优势门和优势属的数量均高于非根际土壤,在黑果枸杞和里海盐爪爪的根际土壤中的细菌优势属分别有10个和9个,而二者非根际土壤中的细菌优势属各有4个,其中假单胞菌属是根际和非根际土壤中的共有优势属。黑果枸杞和里海盐爪爪根系细菌群落组成和丰度存在差异,只有假单胞菌属和盐单胞菌属是两种植物根际土壤中的共有优势属。Unifrac分析和聚类分析表明,两种盐生植物根际土壤细菌之间的相似性大于根际和非根际细菌群落间的相似性。细菌多样性与土壤有机碳、有机质、总氮正相关,与pH、电导率负相关,电导率和pH,有机碳和总氮分别是非根际土,根际土壤细菌群落物种组成的主要影响因素。     

Systematic significance of mature embryo of bamboos

The mature embryo of seven species belonging to five genera of Indian bamboos is described. In all these the basic pattern of embryo organisation is same: the scutellar and coleoptilar bundles are not separated by an internode, the epiblast is absent, the lower portion of the scutellum and the coleorhiza are separated by a cleft and the margins of embryonic leaves overlap. The features unique to fleshy fruited bamboos are: presence of a massive scutellum, the juxtaposition of plumule and radicle and the occurrence of a bud in the axil of the coleoptile. The fleshy fruit bearing bamboos should be classified into one group, the tribeMelocanneae. Evidence is provided to recognise additional groups in the subfamilyBambusoideae.     

Taxonomic status of the species of the green algal genusNeochloris

Komárek has recently reviewed the various species assigned to the green algal genusNeochloris Starr (Chlorococcales, Chlorococcaceae) and removed those with uninucleate vegetative cells to a new genus,Ettlia. Watanabe & Floyd, unaware ofKomárek's work, also reviewed the species ofNeochloris and distributed them among three genera—Neochloris, Chlorococcopsis gen. nov., andParietochloris gen. nov.—on the basis of details of the covering of the zoospore and the arrangement of the basal bodies of the flagellar apparatus. This paper reconciles these two treatments and makes additional recommendations at the ranks of genus, family, order, and class.     

Analysis of twin of eyeless regulation during early embryogenesis in Drosophila melanogaster

The Drosophila Pax6 homolog twin of eyeless (toy) is so far the first zygotically expressed gene involved in eye morphogenesis in Drosophila. The study of its expression during embryogenesis is therefore informative of the initial events of eye development in Drosophila. We have analyzed how the initial expression domain of toy at cellular blastoderm is regulated. We show that the three maternal patterning systems active in the cephalic region (the anterior, terminal and dorsal-ventral systems) cooperate with zygotically activated gap genes to shape the initial expression domain of toy. Whereas Bicoid, Dorsal and Torso signaling synergistically act as activators, Hunchback, Knirps and Decapentaplegic act as repressors.     

Phylogeny of cardinalfishes (Teleostei: Gobiiformes: Apogonidae) and the evolution of visceral bioluminescence

The cardinalfishes (Apogonidae) are a diverse clade of small, mostly reef-dwelling fishes, for which a variety of morphological data have not yielded a consistent phylogeny. We use DNA sequence to hypothesize phylogenetic relationships within Apogonidae and among apogonids and other acanthomorph families, to examine patterns of evolution including the distribution of a visceral bioluminescence system. In conformance with previous studies, Apogonidae is placed in a clade with Pempheridae, Kurtidae, Leiognathidae, and Gobioidei. The apogonid genus Pseudamia is recovered outside the remainder of the family, not as sister to the superficially similar genus Gymnapogon. Species sampled from the Caribbean and Western Atlantic (Phaeoptyx, Astrapogon, and some Apogon species) form a clade, as do the larger-bodied Glossamia and Cheilodipterus. Incidence of visceral bioluminescence is found scattered throughout the phylogeny, independently for each group in which it is present. Examination of the fine structure of the visceral bioluminescence system through histology shows that light organs exhibit a range of morphologies, with some composed of complex masses of tubules (Siphamia, Pempheris, Parapriacanthus) and others lacking tubules but containing chambers formed by folds of the visceral epithelium (Acropoma, Archamia, Jaydia, and Rhabdamia). Light organs in Siphamia, Acropoma, Pempheris and Parapriacanthus are distinct from but connected to the gut; those in Archamia, Jaydia, and Rhabdamia are simply portions of the intestinal tract, and are little differentiated from the surrounding tissues. The presence or absence of symbiotic luminescent bacteria does not correlate with light organ structure; the tubular light organs of Siphamia and chambered tubes of Acropoma house bacteria, those in Pempheridae and the other Apogonidae do not.     

广西青藓科分类学修订

通过对采自广西24个县(市)的1 147份青藓科植物标本的逐一鉴定及相关文献的查阅,确认有广西青藓科植物11属、44种,其中包括广西青藓科植物新记录属1属,即拟异叶藓属(Pseudokindbergia),新记录种7种,分别为匐枝青藓(Brachythecium procumbens)、阔叶尖喙藓(Oxyrrhynchium latifolium)、泛生尖喙藓(O. vagans)、拟异叶藓(Pseudokindbergia dumosa)、华东细喙藓(Rhynchostegiella sinensis)、长肋拟青藓(Sciurohypnum populeum)和弯叶拟青藓(S. reflexum)。该文提供了修订后的广西青藓科植物名录,并对其中的新记录属、种的主要形态学识别特征、生境和地理分布等进行了详细描述。     

Host plants of someRhinanthoideae (Scrophulariaceae) of eastern North America

Twenty three species in 11 genera were examined in the field to determine hosts. OnlyStriga asiatica andSeymeria cassioides have a narrow host range being restricted to grasses and pines, respectively. These are the only species which cause pronounced and sometimes serious host damage. The other species attach to a great diversity of hosts.     

The effect of cyanobacteria and azolla on the performance of rice under different levels of fertilizer nitrogen

Cyanobacteria and/or azolla were inoculated, with urea at 0, 72 or 144 kg N/ha, in plots in which azolla-free Indica rice var. IR 28 was grown. Productive tillers, yield and nitrogen contents of grain and straw positively responded to inoculation with cyanobacteria or azolla, even with fertilizer-N up to 144 kg N/ha. Inoculation improved colonization by cyanobacteria. Azolla were superior to the asymbiotic cyanobacteria in enhancing rice performance. Urea at a rate of 72 kg N/ha was found to support the best colonizations when applied with cyanobacteria or azolla or, to give maximum rice yields, both inoculants.     

Evaluation of antiprotozoal and antimycobacterial activities of the resin glycosides and the other metabolites of Scrophularia cryptophila

Resin glycosides are secondary metabolites exclusive to the convolvulaceous plants. In this study, crypthophilic acids A–C (1–3), the first resin glycosides occurring in another family (Scrophulariaceae), and the other constituents of Scrophularia cryptophila were examined for in vitro antiprotozoal and antimycobacterial potentials. Except for crypthophilic acid B (2), all tested compounds exhibited growth-inhibitory effect against Trypanosoma brucei rhodesiense, with l-tryptophan (6) and buddlejasaponin III (7) being the most potent ones (IC₅₀'s 4.1 and 9.7 μg/ml). In contrast, the activity towards Trypanosoma cruzi was poor, and only crypthophilic acid C (3), 6 and 7 were trypanocidal at concentrations above 40 μg/ml. With the exception of 2 and 6, all compounds were active against Leishmania donovani. Harpagide (4) and 3 emerged as the best leishmanicidal agents (IC₅₀'s 2.0 and 5.8 μg/ml). Only compounds 3, 6 and 7 showed antimalarial activity against Plasmodium falciparum with IC₅₀ values of 4.2, 16.6 and 22.4 μg/ml. Overall the best and broadest spectrum activity was presented by compounds 3 and 7, as they inhibited all four parasitic protozoa. None of the isolates had significant activity against Mycobacterium tuberculosis (MICs >100 μg/ml) or were toxic towards mammalian (L6) cells. This is the first report of antiprotozoal activity for natural resin glycosides, as well as for harpagide (4), acetylharpagide (5), tryptophan (6) and buddlejasaponin III (7).     

Apoptotic Regulation of Caspase Activity

Intracellular cysteine aspartate-specific proteases (caspases) play both signaling and effector roles in realizing the program of cell death. Caspases function as proteolytic cascades unique for each cell type and signal triggering apoptosis. All parts of the proteolytic cascades are duplicated and controlled by feedback signals. Amplification cycles between pairs of caspases (the third and the sixth, the ninth and the third, the twelfth and the sixth, and others) help multiply the initial apoptotic signal. The presence of physiological inhibitors of apoptosis that directly interact with caspases creates a multilevel regulatory network of apoptosis in cell. The caspase proteolytic cascades are also regulated by sphingolipid secondary messengers, among them ceramide, sphingosine, and their phosphates. Moreover, an association of the caspase signaling with ubiquitin-dependent proteolysis is shown in cells. In particular, the use of extracellular activators and inhibitors of caspases allows irreversible activation of apoptosis in tumor cells or the prevention of apoptosis in cortical neurons under neurodegenerative diseases.