Phylogenetic position of Cryothecomonas inferred from nuclear-encoded small subunit ribosomal RNA

The systematic position of the genus Cryothecomonas has been determined from an analysis of the nuclear-encoded small subunit ribosomal RNA gene of Cryothecomonas longipes and two strains of Cryothecomonas aestivalis. Our phylogenetic trees inferred from maximum likelihood, distance and maximum parsimony methods robustly show that the genus Cryothecomonas clusters within the phylum Cercozoa, and is related to the sarcomonad flagellate Heteromita globosa. Morphological data supporting the taxonomic placement of Cryothecomonas near the sarcomonad flagellates has been compiled from the literature. The high number of nucleotide substitutions found between two morphologically indistinguishable strains of Cryothecomonas aestivalis suggests the possibility of cryptic species within Cryothecomonas aestivalis.     

西藏沙棘5种不同组织内生细菌多样性

西藏沙棘(Hippophae tibetana)是分布于高寒高海拔地区的一类特殊的放线菌结瘤植物, 弗兰克氏菌能够侵染其根部形成根瘤, 因共生固氮等作用而增强其生态适应性。在西藏沙棘的根瘤中, 除了弗兰克氏菌之外还有其他内生菌, 而弗兰克氏菌又不仅仅在根瘤中有分布。为了探究弗兰克氏菌在西藏沙棘不同组织中的定殖及可能的迁移规律, 分析不同组织中内生细菌的群落结构及多样性, 本研究以生长在甘肃省天祝藏族自治县抓喜秀龙金强河河滩地的西藏沙棘为材料, 应用16S rRNA扩增子高通量测序技术, 对西藏沙棘根瘤、茎、枝、叶和种子等不同组织的内生细菌多样性进行了分析。研究结果表明, 西藏沙棘根瘤内生细菌群落丰富度及多样性最高, 种子内生细菌群落丰富度最低, 茎内生细菌群落多样性最低。西藏沙棘5种不同组织中的弗兰克氏菌和其他内生细菌多样性都具有一定差异, 变形菌门均为优势门, 弗兰克氏菌属(Frankia)为根瘤内生细菌群落的优势属, 弗莱德门菌属(Friedmanniella)为茎内生细菌群落的优势属, 寡养单胞菌属(Stenotrophomonas)为枝、叶和种子内生细菌群落的优势属。研究结果还表明, 弗兰克氏菌属不仅仅存在于西藏沙棘的根瘤, 还能够分布于其他组织, 且在同一种组织中存在弗兰克氏菌属的不同“种”; 而在西藏沙棘不同组织中, 也分布有弗兰克氏菌属的相同“种”。此外, 对西藏沙棘5种不同组织内生细菌中的功能菌株的分析表明, 不同组织中均存在着具有固氮、促生和抑菌功能的内生细菌, 但具有固氮作用的内生细菌主要分布于根瘤, 具有促生作用以及抑菌功能的内生细菌主要分布于枝和叶。综上, 西藏沙棘5种不同组织内生细菌具有丰富的多样性, 但各组织内生细菌的群落结构和优势种群有所不同, 且不同组织也能够定殖具有多种功能的内生细菌。     

不同衰退等级蒙古沙冬青根内真菌多样性与群落结构

本研究根据沙冬青现有的生长状况,将内蒙古西鄂尔多斯保护区珍稀濒危植物蒙古沙冬青群落分为轻度衰退、中度衰退和重度衰退3个衰退等级,并选取一个未衰退的沙冬青群落作为对照,应用Illumina Hiseq测序平台,对这4个沙冬青群落的植株根内真菌进行高通量测序分析。测序共获得215个真菌的OTU,不同衰退等级沙冬青根内真菌群落结构在门、科、属水平上都有显著差异。Top 10属中的Agaricus、Tomentella、Tricholoma、Fusarium、Inocybe以及Tuber这6个属真菌在所有衰退等级的沙冬青都有分布。不同衰退等级的沙冬青根内都有腐生或寄生真菌和“共生”真菌分布,不同衰退等级两类群的真菌占比不同且呈现出动态变化,随着衰退等级的增加沙冬青根内腐生真菌或寄生真菌与“共生”真菌比例显著增高。土壤有机质与土壤容重具有协同作用,且对Agaricus、Inocybe、Fusarium、Penicillium、Amphinema具有正相关影响,对Tricholoma、Tomentella、Tuber具有负相关影响。     

Molecular phylogeny of Besnoitia and the genetic relationships among Besnoitia of cattle, wildebeest and goats

Knowledge on parasites of the genus Besnoitia is sparse, which are classified in the subfamily Toxoplasmatinae of the phylum Apicomplexa. This arrangement hypotheses that Besnoitia represents the sister group to species such as Toxoplasma gondii and Hammondia hammondi. In order to test this hypothesis, phylogenetic analyses of 18S ribosomal DNA (rDNA) from Besnoitia, Hammondia, Isospora, Frenkelia, Eimeria, Neospora, Sarcocystis and Toxoplasma were performed. The 18S rDNA of Besnoitia besnoiti, Besnoitia jellisoni and Eimeria alabamensis were amplified by PCR and sequenced. Phylogenetic analyses by parsimony and maximum-likelihood methods showed Besnoitia to be reproducibly the sister group to a clade containing Hammondia, Neospora and Toxoplasma. Furthermore, Besnoitia of cattle, wildebeest and goats had identical ITS1 rDNA sequences, which questions the use of the taxon Besnoitia caprae to describe the Besnoitia found in goats.     

海南岛不同林龄木麻黄凋落物内外细菌多样性及其化感潜力

凋落物在生态系统中具有重要作用。为了对比凋落物内外微生物的多样性和群落结构,选取海南省海口市桂林洋海滨区3个林龄木麻黄凋落物为研究对象,采用Illumina Miseq高通量测序,对凋落物内外微生物的多样性和组成进行分析。结果表明: 凋落物外生细菌的多样性高于内生细菌,中龄林凋落物内外细菌多样性和丰富度均最高,其次是幼龄林,成熟林最低。菌群群落组成分析表明: 在门分类水平上,变形菌门和放线菌门最为丰富(约占总数的80%);属水平上,短小杆菌属、Jatrophihabitans、分支杆菌属、放线孢菌属、Mucilaginibacter、假单孢菌属等在不同林龄间表现出显著差异。主坐标分析(PCoA)表明,凋落物内生细菌受林龄的影响较大,而外生细菌受环境因子的影响较大;解淀粉芽孢杆菌发酵液对木麻黄种子化感潜力最强,且其中含有2,2′-亚甲基双-(4-甲基-6-叔丁基苯酚)等化感物质,表明解淀粉芽孢杆菌参与了化感物质的合成。凋落物微生物群落多样性对木麻黄的化感作用有一定影响,这为探讨微生物在木麻黄凋落物降解过程中作用的研究奠定基础。     

小兴安岭大亮子河国家森林公园不同生境下土壤细菌多样性和群落结构

土壤细菌是森林生态系统的一个重要组成成分, 是生态系统中物质循环和能量流动的重要参与者, 细菌群落组成和生物多样性是反映土壤生态功能的重要指标。本文利用高通量测序技术分析了大亮子河国家森林公园内红松(Pinus koraiensis)林、落叶松(Larix gmelinii)林、蒙古栎(Quercus mongolica)林、枫桦(Betula costata)林、针阔混交林、灌木林和草甸等7种不同生境土壤细菌群落组成和多样性的差异性, 探讨该地区土壤细菌群落对不同生境的响应, 为地区森林生态系统的经营管理及生态系统稳定性的维护提供科学理论基础。在门的水平上, 各生境的细菌群落组成基本一致, 其中变形菌门(Proteobacteria)、放线菌门(Actinobacteria)、酸杆菌门(Acidobacteria)和疣微菌门(Verrucomicrobia)在7种生境土壤中相对丰度均大于10.0%, 是细菌中的优势菌门。在属的水平上, 共测得245个菌属, 各样地共有属118个, 占总属数的48.2%, 占总相对丰度的97.8%; 优势菌属分别为Spartobacteria_ genera_incertae_sedis、Gaiella、Gp16、Gp4, 占总相对丰度的47.0%, Spartobacteria_genera_incertae_sedis在7种生境土壤中丰度均最高。7种生境下的土壤细菌多样性和土壤理化因子存在着显著的差异, 红松林的土壤细菌群落多样性和丰富度均高于其他生境。土壤pH是大亮子河森林公园影响土壤细菌多样性的关键因子。     

Phylogenetic analyses of the dinoflagellate Noctiluca scintillans based on beta-tubulin and Hsp90 genes

The noctilucid dinoflagellate Noctiluca scintillans is an unarmed heterotrophic protist that inhabits the world's oceans and is sometimes responsible for harmful red tides. The phylogenetic position of the noctilucids has been widely disputed because of two alternative views based on morphological characters and phylogenetic analyses using SSU rDNA. Specifically, noctilucids are either placed in a basal position within the dinoflagellates or they are seen as evolutionarily recent derivations descended from unarmored dinoflagellates in the order Gymnodiniales. Thus, the precise relationship of noctilucids to other dinoflagellates is still uncertain. In this study, we isolated β-tubulin and heat shock protein 90 genes from N. scintillans to examine this relationship further. The deduced amino acid sequences share commonly substituted amino acids and a deletion with other dinoflagellates, but not with Perkinsus marinus or other alveolates. Although Hsp90 analysis did not give robust support, β-tubulin analysis including an AU test, as well as combined analysis of these two amino acid sequences showed that N. scintillans is the next earliest branch after Oxyrrhis marina, within the dinoflagellates. Given the phylogenetic position of N. scintillans, its extremely specialized diploid trophont, and the primitive dinoflagellate-like characteristics of its haploid zoospore, we propose that noctilucids are a possible evolutionary link between ancestral diploid dinoflagellates and haploid core dinoflagellates. This implies that the transition from diploidy to haploidy in trophonts probably occurred via neoteny of a noctilucid-like zoospore.     

中国杭子梢属植物的研究

本文叙述了杭子梢属(gen.Campylotropis)植物的研究历史,说明在中国一共记录过59种杭子梢属植物,经过著者的研究整理,确定并提出了14种新的异名名称,经过详细考订,本属植物在中国已确知为29种、6变种、6变型。其中包括经发现和研究整理的新种4、新变种3、新变型3、新组合变种2、新组合变型3。此外尚有2个存疑种有待今后采集调查解决。本文历述了关于本属是否应该并入胡枝子属(gen.Lespedeza)这一问题所存在的长期争议之后,详细论述了本属与胡枝子属在特征上的异同诸点、进行了比较和分析,据此,明确地肯定本属与胡枝子属亲缘关系极为相近,但特征的分化已经必须确认本属应是与胡枝子属有明确区别的独立的属。此外,从特征分析中也可得出本属应是由胡枝子属大胡枝子组(sect.Macrolespedeza)演化发展而来的。本文在讨论了属内主要特征的演化趋势与种群关系之后,论述了本属在世界主要分布地区的种数和分布概况,同时将此与胡枝子属大胡枝子组的分布概况作了比较和分析,明确地认定我国机子梢属植物的大部分种类是本国西南地区发生的(中国有20个特有种),我国的西南地区是本属植物的分布中心,也是本属植物从较原始特征开始分化的一个特征分化多样化中心,并且此地区正是胡枝子属大胡枝子组与本属多数种类包括较原始种类分布相交叉的地区,因而我国的西南地区有可能即是本属植物的起源中心,并且这一起源应是与胡枝子属大胡枝子组植物分布到中国西南地区以后的分化发展想联系的。     

Unique organization of the 16S-23S intergenic spacer regions of strains of Acinetobacter baylyi provides a means for its identification from other Acinetobacter species

This paper extends an earlier report on rrn operon characteristics in members of the genus Acinetobacter. It describes a systematic approach towards developing and validating a protocol for elucidating how the intergenic spacer regions (ISR) in Acinetobacter baylyi strains are organized and allows the numbers of long and short ISRs to be determined. Experimental data confirmed the in silico predictions based on available A. baylyi rrn sequence data. All were shown to possess three long ISRs and 4 short ISRs, differing in most cases in length by about 90nt. However, the ISR arrangement in A. baylyi strain 93A2 was different. Although it also possessed 4 SISRs and three LISRs, their length difference was less (39nt) which was confirmed from its ISR sequence data. Primer sets for PCR identification of A. baylyi could then be determined. Applying the same approach to other species of Acinetobacter showed none shared the same ISR organization as A. baylyi. Its value in typing members of this genus is discussed.     

Is there a plastid in Perkinsus atlanticus (Phylum Perkinsozoa)?

Perkinsus atlanticus is a pathogenic protist that infects the clam Ruditapes decussatus. The recent proposal for the inclusion of the genus Perkinsus in a new phylum, Perkinsozoa, in the infra-kingdom Alveolata, gave rise to controversies whether this genus should form a phylum on its own. Molecular analysis of some conserved nuclear genes shows a closer proximity of the genus Perkinsus to the dinoflagellates than to the apicomplexans. Studies on extranuclear genomes, however, could also be very helpful for a more precise definition of those phyla. In Perkinsozoa, there have been until now no reports about the isolation of mitochondria as well as no conclusive results about the presence of any plastids, therefore a comparison with the data already obtained in Apicomplexa and Dinoflagellata has not yet been possible. In this work, we identify a plastid in Perkinsus atlanticus, using ultrastructural techniques and inhibition growth tests. It will be important to analyze the plastid genome at a molecular level, in order to confirm if the plastid in Perkinsus is more similar to those of Dinoflagellata or Apicomplexa. Such information will doubtless contribute to a more precise determination of the phylogenetic position of the genus Perkinsus.     

中国桂樱属植物的分类研究

桂樱属(Laurocerasus Tourn.ex Duh.)是蔷薇科李亚科的一个属。它是De Tournefort(Institutiones rei Herbariae 627.t.403.1700)以Prunus laurocerasus L.和P.lusitanica L.两种奠定基础,而至1755年由Duhmal代为正式发表而建立。自该属建立以后的二百多年来,各国植物学家对其分类位置各持不同观点。     

篮状菌属分类概述及三个中国新记录种

篮状菌属真菌在空气、土壤中分布广泛,有些种类是重要的工业酶及色素生产菌,有些则可以引起食品的污染变质,还有些种是引起浅层或散播性感染的条件致病菌,如马尔尼菲篮状菌.篮状菌属在传统分类学上是一个有性型属,随着多相分类以及"一种真菌一个名称"概念的广泛普及,该属的概念已经发生了较大的变化,目前全世界已报道177个种.本文基...     

中国杜鹃花属的修订(一)

杜鹃花属Rhododendron Linn.植物是世界上的著名花卉, 在园艺上有较高的观赏价值, 近年来又发现有部分种类可供药用, 食用更是引起了广大科学工作者的浓厚兴趣, 并且全属植物种类繁多, 分布比较集中, 特有种也多, 而我国的西南地区又是其分布的中心地带, 我们在完成了"中国植物志"的编著之后, 现将有关的新等级, 新组合一并发表, 以便进行讨论。     

中国龙胆属植物研究(四)

龙胆属Gentiana (Tourn) L.是Tourneferot (1700)为纪念传说中的Illyria国王Gentius而建立的,对它作了描述,绘有墨线图。林奈在"植物属志"(1737),"植物种志"(1753)承认了该属,并重新进行了描述,记载23种。     

河南浓香型酒醅的真菌微生物菌群多样性及共变性

通过高通量测序研究河南三个不同酒厂的浓香型酒醅的真菌微生物菌群,逐次在门、纲、目、科和属5个水平上分析入窖酒醅和出窖酒醅的菌群多样性,探究酒醅发酵后菌群的共性变化规律.结果表明:出窖酒醅的真菌微生物多样性高于入窖酒醅的真菌微生物多样性,出窖酒醅的真菌主要有镰刀菌属Fusarium(相对丰度17％ ～32％),Plect...     

楸树实生苗和嫁接苗根相关真菌群落结构和多样性

以1、2、3年生的楸树实生苗和嫁接苗（梓树砧木）根系为研究对象,通过对ITS rDNA区域标记扩增子的Illumina MiSeq测序,分析不同苗龄楸树实生苗和嫁接苗根相关真菌的结构组成和多样性。获得根相关真菌OTU共842个,分属4门、24纲、70目、134科、233属、347种;丛枝菌根真菌（arbuscular mycorrhizal fungi）AMF-OTU共42个,分属1门、1纲、3目、3科、3属、13种。根相关真菌和AMF的OTU数量、丰度和多样性在实生苗中均随苗龄的增加而降低,而在嫁接苗中则随着苗龄的增加而增加。门水平上,实生苗与嫁接苗根相关真菌的优势菌都是子囊菌门Ascomycota、担子菌门Basidiomycota和接合菌门Zygomycota,但它们的相对丰度有所差异;属水平上,实生苗和嫁接苗根相关真菌的优势菌种在组成和数量上都具有一定的差异性。楸树根相关真菌拥有3种营养模式和12个生态功能群,其中实生苗根系中病理营养型真菌的比例大于嫁接苗,腐生营养型则差异不大,而共生营养型则小于嫁接苗。生态功能群分析显示大多数楸树根系真菌表现出多种生存策略,部分真菌可以在植物-真菌-动物中跨界侵染。该研究可为楸树根相关真菌的利用提供一定的理论依据和基础。     

Rapid and reliable identification of Staphylococcus equorum by a species-specific PCR assay targeting the sodA gene

Rapid and reliable identification of Staphylococcus (S.) equorum was achieved by species-specific PCR assays. A set of primers targeting the manganese-dependent superoxide dismutase (sodA) gene of S.equorum was designed. Species-specificity of the primer set was evaluated by using a total of 112 strains (including 27 reference strains of the DSM collection), representing 26 different species of the genus Staphylococcus, 3 species of the genus Kocuria, and different strains of Macrococcus caseolyticus. By using primers SdAEqF and SdAEqR the expected PCR fragment was obtained only when DNA from S. equorum strains was used as template. The rapidity (about 4 h from DNA isolation to results) and reliability of the PCR procedures established suggests that the method may be profitably applied for specific detection and identification of S. equorum strains.     

Evolutionary history of Calosomina ground beetles (Coleoptera, Carabidae, Carabinae) of the world as deduced from sequence comparisons of the mitochondrial ND 5 gene

We deduced the phylogenetic relationships of 54 individuals representing 27 species of the Calosomina (Coleoptera, Carabidae) from various regions of the world from the mitochondrial NADH dehydrogenase subunit 5 (ND5) gene sequences. The results suggest that these Calosomina radiated into 17 lineages within a short time about 30 million years ago (Mya). Most of the lineages are composed of a single genus containing only one or a few species. In some cases, several species classified into the same genus (e.g., Calosoma maximowiczi, Calos. inquisitor and Calos. frigidum) appear separately in independent lineages, while in others a series of species classified into different genera fall into one lineage (e.g., Chrysostigma calidum, Blaptosoma chihuahua, Microcallisthenes wilkesi and Callisthenes spp.). Based on this molecular phylogeny and morphological data, the probable evolutionary history and mode of morphological differentiation of the Calosomina are discussed.     

The chemiluminescence response of bivalve haemocytes: utility in screening for immunomodulators and as a biomarker

Resistance to infectious diseases in bivalves depends primarily on the vigour and efficacy of haemocyte-dependent antimicrobial defence mechanisms. Like other phagocytes, haemocytes seem to rely on oxygen-independent (lysosomal hydrolases, lysozyme) and oxygen-dependent (reactive oxygen species) mechanisms to destroy ingested microorganisms. The generation of cytotoxic oxyradicals by haemocytes can be precisely quantified by means of a simple chemiluminescence (CL) assay using luminol or other CL probes. Tributyltin (TBT), and other environmental contaminants, at sublethal levels, will produce dose-dependent suppression of CL activity in haemocytes exposed in short-term, in vitro assays. Presumably, this suppression would find expression as impaired host defence capability. In fact, TBT has been shown to exacerbate progression and lethality of Perkinsus marinus infections in the oyster, Crassostrea virginica. This suggests that CL assays on haemocytes exposed in vitro to single agents or complex mixtures might be useful in screening for aquatic immunomodulators. Statistically significant alterations in CL responses of haemocytes withdrawn from bivalves exposed to xenobiotics in the laboratory or field are more difficult to identify because of high inter-animal variation; however, the use of haemocyte CL as a biomarker of effect merits further investigation.