毛竹的异质性空间点格局分析

毛竹是一种重要的经济用材,研究其空间分布格局有益于对其空间发生进行预测。选取了一块空间肥量分布不均的毛竹样地,使用异质性空间点格局分析方法对毛竹的空间分布进行了研究,结果发现毛竹在给定的距离尺度下呈现出显著的泊松分布,而并不是聚集分布。同时选用二元二次方程拟合观察的数据,发现对毛竹强度的拟合优度较高。研究揭示出异质性空间环境中毛竹的分布特点,潜在地表明土壤肥量的空间分布对毛竹空间分布的影响,对毛竹的集约化经营具有重要的指导意义;同时,鉴于国内生态研究中较少采用异质性空间点格局分析方法,研究对于推动这种方法在国内生态学研究中的普及还具有一定的参考价值。     

天目山保护区森林群落植物多样性对毛竹入侵的响应及动态变化

为探讨毛竹(Phyllostachys edulis)入侵对周围森林群落的影响,作者于2005-2011年在天目山自然保护区进行了7年长期定位观测实验,研究了毛竹入侵地森林群落的植物物种多样性变化.结果表明:毛竹入侵对周围森林群落植物物种多样性产生了不利影响:毛竹林乔木层和灌木层植物的Simpson指数小于针阔混交林和毛竹-针阔混交林,而草本层的Simpson指数则大于针阔混交林和毛竹-针阔混交林.植物物种丰富度、Simpson指数和Pielou均匀度指数随时间发生了较大变化:毛竹入侵的森林群落其乔木层和灌木层的物种丰富度、Simpson指数和Pielou均匀度指数显著降低(P＜0.05),草本层的物种丰富度显著提高(P＜0.05),Simpson指数和Pielou均匀度指数未表现出明显的变化.毛竹-针阔混交林去除毛竹后,乔木层和灌木层物种丰富度和Simpson指数增加,草本层物种丰富度、Simpson指数和Pielou均匀度指数明显下降.可见,毛竹入侵使森林群落植物多样性发生实质性的变化,对自然保护区植物群落造成了重大影响.由此可见,要使保护区物种多样性得到保护,除进行科学的管理外,还需要控制毛竹蔓延.     

Expression and functional analysis of two PsbS genes in bamboo (Phyllostachys edulis)

Higher plants have an array of photoprotection mechanisms alleviating the harmful effects of light. Non‐photochemical quenching (NPQ) is one of the photoprotective mechanisms, which dissipates the excess of light energy absorbed in the light‐harvesting complexes (LHCs) into thermal energy. The photosystem II subunit S (PsbS), a member of the LHC family thought to be present exclusively in higher plants, is supposed to activate NPQ through interactions with antenna proteins. However, the roles of PsbS in bamboo remain unclear. Here, two genes of bamboo (Phyllostachys edulis), PePsbS1 and PePsbS2, are investigated and functionally analyzed. PePsbS1 and PePsbS2 have a similar gene structure with three introns separated by two exons, which encode 269 and 268 amino acid residues, respectively. Tissue‐specific analysis showed that PePsbS1 and PePsbS2 are highly expressed in leaf blade. Besides, they are both upregulated in the leaf blade when plantlets are submitted to an increased and prolonged light intensity, suggesting that they are light‐induced. Western blot analysis indicated that the accumulation level of total PePsbSs is consistent with what obtained by quantitative real‐time polymerase chain reaction for PePsbS1 and PePsbS2. Transgenic Arabidopsis plants overexpressing PePsbS1 and PePsbS2 both displayed an enhanced photoprotection. Moreover, the expression of PePsbS1 and PePsbS2 could both rescue the NPQ of Arabidopsis npq4 mutant, indicating that the PsbSs are functionally conserved between monocots and dicots. These results indicated that both PePsbS1 and PePsbS2 could circumvent photoinhibition and enhance photoprotection, which are key factors for bamboo's adaptation to different light environment.     

Small localized breeding populations in a widely distributed coastal shark species

Identifying the geographical scale at which natural populations structure themselves is essential for conservation. One way to gauge this structure is by estimating local effective population size (N_e) and the associated measure of effective number of breeders (N_b), as the smaller and more isolated natural populations are, the smaller N_e and N_b they will present. However, as N_e and N_b are greatly influenced by demographic events and by both species’ behavior and biology, assessing the effectiveness of sample design is necessary to ensure the reliability of said estimates. Here, we first test the sample size effect on yearly N_b and generational N_e estimates from a lemon shark Negaprion brevirostris nursery in Bimini (The Bahamas) and subsequently compare these parameters to estimates of the minimal number of breeders based on pedigree reconstruction. We found that yearly estimates of N_b are positively correlated to annual variations in number of breeders estimated via pedigree reconstructions. Moreover, we measured that 30 individuals from a single cohort were sufficient to obtain reliable yearly estimates of N_b in Bimini’s lemon sharks. We then estimated generational N_e in 10 lemon shark nurseries across the Western Atlantic. Almost every nursery sampled represents an independent population on a generational time scale, with N_e rarely higher than 100 individuals. Our study reveals strong local population structure in lemon sharks, and thus their exposure to localized depletion or extirpation, suggesting that studies of coastal shark nursery areas could routinely estimate N_e and N_b to obtain management-relevant information on adult populations.

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A new and widely distributed species of Pseudoarachniotus

Summary A new species ofPseudoarachniotus, P. hyalinosporus, is described and illustrated. A total of 54 isolates of this species was studied and their growth was compared on several media.Although certain differences appeared in colonial coloration and growth characteristics, all strains were similar in 2 fundamental characteristics, viz., type of ascospore and type of gametangial initials and their subsequent development. The initials in early stages are often so closely appressed one to another that they give the appearance of a single structure. Further development takes place by the elongation of the ascogonium which forms a loop around the male initial at right angles to the linear plane of that initial. The ascospores ofP. hyalinosporus are small, about 2.2 × 3.3µ, thin-walled, oval, hyaline to very pale yellow, and smooth, thereby differing fromPseudoarachniotus reticulatus which has globose, echinulate-reticulate ascospores, andP. roseus andP. citrinus which have large, thick-walled, oval to oblate ascospores. Furthermore, the colonies ofP. roseus are red, those ofP. citrinus are yellow, and inP. hyalinosporus colonies are white with pale yellow asciferous areas and usually with a great deal of green pigment both above and reverse. Of the 54 strains of this new species, 25 were isolated from rodent lungs, 9 from dung, 19 from soil and one from a tinea pedis condition.Pseudoarachniotus hyalinosporus was found in two collections from India and it appears to be widely distributed in California.Supported in part by Botany Department Research Grant # 1344, University of California, Los Angeles, California.A portion of this study was made possible through laboratory facilities provided by Dr.B. Samantarai, Ravenshaw College, Cuttuck, Orissa, India.     

基于物种分布模型评价土壤因子对我国毛竹潜在分布的影响

基于单类别支持向量机方法的物种分布模型, 利用政府间气候变化专门委员会(IPCC)气候情景模式和联合国粮食与农业组织(FAO)的全球土壤数据, 模拟1981-2099年我国毛竹(Phyllostachys edulis)的潜在空间分布及变化趋势, 比较考虑土壤因子前后模拟结果的差异, 旨在探究土壤因子对毛竹潜在空间分布模拟结果的影响。结果表明, 仅以气候因子为模拟变量和同时考虑气候与土壤因子为模拟变量的毛竹潜在空间分布模拟均具有较高精度, 毛竹潜在分布区表现为面积增加并向北扩张。模拟因子重要性分析表明表征温暖程度的气候因子在毛竹潜在分布模拟中起主导作用, 而表征土壤质地和酸碱性的土壤因子以限制性作用为主。同时考虑气候与土壤因子的模拟结果具有较高的模拟效率, 且在未来气候变化情景模式下毛竹潜在分布区面积增幅与向北迁移幅度均小于仅使用气候因子的模拟, 表明土壤要素对毛竹潜在分布具有明显的限制作用, 该结果对现在的毛竹潜在分布模拟研究具有重要的补充作用。     

毛竹萜类合成酶基因家族序列鉴定与表达分析

通过生物信息学方法,对毛竹(Phyllostachys edulis(Carrière)J.Houzeau)TPS基因家族的成员进行鉴定,并对其编码蛋白的理化性质、基因结构、进化关系、蛋白结构、启动子元件及表达模式进行了分析。结果表明,毛竹全基因组含有14个TPS候选基因,大小为693~2439 bp。编码蛋白等电点为5.08~8.17。系统发育分析结果显示,毛竹含有TPS-a、TPS-b、TPS-e/f、和TPS-g 4个亚家族,成员数目分别为6、5、2、1个。TPS蛋白质二级结构中,α-螺旋和无规则卷曲所占比重较大;毛竹TPS基因家族各成员蛋白三维结构比较相似。基因启动子分析共获得50个调控元件,可分为6大类,其中光响应相关元件数量最多,共包含17个顺式调控元件。基于转录组测序数据构建的基因表达谱热图分析结果表明,Pe TPS在叶、花和笋等7个组织中的表达差异明显,表现出组织特异性,其中Pe TPS9仅在早花期花序中表达,Pe TPS8仅在叶中表达。     

不同类型毛竹林土壤活性有机碳

以江西省安福县毛竹纯林、竹阔混交林、竹杉混交林为研究对象,探讨不同类型毛竹林的土壤活性有机碳的变化.结果表明:(1)土壤总有机碳和易氧化态碳含量以毛竹纯林最高,分别为13.1和2.15 g·kg-1;微生物生物量碳和热水浸提有机碳以竹杉混交林最高,分别为123.3和349.0 mg· kg-1.(2)3种类型毛竹林土壤活性有机碳的含量均随土层深度的增加而呈现出先快后慢的下降趋势.(3)土壤总有机碳、微生物生物量碳、热水浸提有机碳和易氧化态碳之间的相关性均达到极显著水平(P＜0.01),后三者在一定程度上表征了土壤中活性较高部分的碳含量.     

毛竹SWEET基因家族的全基因组鉴定与分析

糖外排转运蛋白(Sugars will eventually be exported transporters, SWEETs)在植物生理活动和发育过程中起重要作用。为探究SWEET基因家族在毛竹(Phyllostachys edulis)的生长发育过程中起的作用,基于毛竹基因组数据,通过生物信息学方法对SWEET基因家族成员进行鉴定,并对其编码的蛋白质理化性质、系统进化及共线性关系、基因结构、启动子元件及表达模式、蛋白互作网路分析、GO注释等进行细致分析。研究结果表明:该家族基因结构、基序和结构域相对保守,所有成员均含有MtN3_slv结构域。上游启动子序列中含有多个同非生物胁迫以及生长发育相关元件,结合转录组表达量分析显示,多个家族成员在毛竹不同组织器官均有表达。共线性分析揭示毛竹SWEET家族在演化过程中存在全基因组多倍化事件。蛋白互作网路分析挖掘出2个重要核心家族成员,GO注释分析进一步证实毛竹SWEET主要负责体内糖类物质的转运。以上结果为毛竹SWEET基因功能鉴定提供了重要参考,对于毛竹快速生长分子机制研究打下了基础。     

毛竹GRF转录因子家族的全基因组鉴定与分析

利用生物信息学方法,于毛竹(Phyllostachys edulis (Carr.) Lehaie)全基因组中鉴定获得18个GRF转录因子,并对其理化特性、保守结构域、系统发育关系、mi R396靶位点以及基因表达模式进行了分析。结果表明,18个Pe GRF蛋白长度为170～551 aa,分子量为18.5～58.8 k D;这些Pe GRF蛋白均具有QLQ和WRC结构域,部分Pe GRF含有FFD和TQL保守结构域。对毛竹、拟南芥(Arabidopsis thaliana (L.) Heynh)和水稻(Oryza sativa L.)的系统进化分析结果显示,毛竹18个GRF可分为3个亚类,且单子叶植物毛竹和水稻的GRF转录因子亲缘关系更近。mi R396靶位点预测分析结果发现,在13个Pe GRF基因序列的编码区存在毛竹mi R396结合位点; Pe GRF基因表达模式分析结果显示,Pe GRF主要在毛竹的竹笋中表达。     

中国灵芝学名之管见

灵芝是最重要的药用真菌之一,在我国已有2,000多年的记载和利用历史。虽然早在一百多年前法国真菌学家Patouillard就有给中国的灵芝冠上Ganoderma lucidum这一学名,并沿用至今,但随着分子生物学技术的不断发展,人们认识到过去外国人的定名并不正确。实际上,G.lucidum是1871年由William Curtis根据采自英国的标本描述的新物种。最近的研究表明,我国广泛分布和栽培的灵芝与产于欧洲的G.lucidum不同,是一个独立的种,其合法的拉丁学名应为G.lingzhi。鉴于"灵芝"这一名称在中国已使用2,000余年,故建议"G.lingzhi"的汉语学名为"灵芝"(俗称赤芝),而灵芝属的模式种G.lucidum的汉语学名改为"亮盖灵芝"(俗称白肉灵芝或白灵芝)。灵芝Ganoderma lingzhi广泛分布于东亚暖温带和亚热带,其主要形态特征是孔口表面新鲜时浅黄色至硫磺色、成熟时菌肉中有黑褐色区带、管口壁厚度为80–120μm。亮盖灵芝G.lucidum主要分布于欧洲和亚洲,在我国分布于东北、华北、华中和西南海拔较高地区,其孔口表面新鲜时白色至奶油色、成熟时菌肉中无黑褐色区带、管口壁厚度为40–80μm。四川灵芝G.sichuanense尽管其担孢子与灵芝G.lingzhi相似,但基于其模式标本ITS序列的系统发育研究表明,该种与灵芝不同,是个独立的种,且在广东也有发现。     

Ficus racemosa is pollinated by a single population of a single agaonid wasp species in continental South‐East Asia

High specificity in the Ficus‐agaonid wasp mutualism has lead to the assumption of a mostly ‘one‐to‐one’ relationship, albeit with some exceptions. This view has been challenged by new molecular data in recent years, but surprisingly little is known about local and spatial genetic structuring of agaonid wasp populations. Using microsatellite markers, we analysed genetic structuring of Ceratosolen fusciceps, the fig wasp pollinating Ficus racemosa, a fig tree species widely distributed from India to Australia. In sampling stretching from the south of China to the south of Thailand we found evidence for only a single pollinating wasp species in continental South‐East Asian mainland. We found no evidence for the co‐occurrence of cryptic species within our subcontinent sampling zone. We observed no spatial genetic structure within sites and only limited structuring over the whole sampling zone, suggesting that F. racemosa is pollinated by a single population of a single agaonid wasp species all over continental South‐East Asia. An additional sample of wasps collected on F. racemosa in Australia showed clear‐cut genetic differentiation from the Asian continent, suggesting allopatric divergence into subspecies or species. We propose that the frequent local co‐occurrence of sister species found in the literature mainly stems from contact zones between biogeographic regions, and that a single pollinator species over wide areas might be the more common situation everywhere else.     

Environmental stress leads to genome streamlining in a widely distributed species of soil bacteria

Bacteria have highly flexible pangenomes, which are thought to facilitate evolutionary responses to environmental change, but the impacts of environmental stress on pangenome evolution remain unclear. Using a landscape pangenomics approach, I demonstrate that environmental stress leads to consistent, continuous reduction in genome content along four environmental stress gradients (acidity, aridity, heat, salinity) in naturally occurring populations of Bradyrhizobium diazoefficiens (widespread soil-dwelling plant mutualists). Using gene-level network and duplication functional traits to predict accessory gene distributions across environments, genes predicted to be superfluous are more likely lost in high stress, while genes with multi-functional roles are more likely retained. Genes with higher probabilities of being lost with stress contain significantly higher proportions of codons under strong purifying and positive selection. Gene loss is widespread across the entire genome, with high gene-retention hotspots in close spatial proximity to core genes, suggesting Bradyrhizobium has evolved to cluster essential-function genes (accessory genes with multifunctional roles and core genes) in discrete genomic regions, which may stabilise viability during genomic decay. In conclusion, pangenome evolution through genome streamlining are important evolutionary responses to environmental change. This raises questions about impacts of genome streamlining on the adaptive capacity of bacterial populations facing rapid environmental change.Subject terms: Population genetics, Microbial ecology, Bacterial genetics     

毛竹扩张对常绿阔叶林土壤微生物群落的影响

毛竹具有独特的生理生态学特征,会不断地向邻近的生态系统扩张。这一现象会造成生态系统退化、土壤理化性质和微生物群落结构改变等问题,引起了人们的高度关注。然而,目前关于毛竹扩张对微生物群落结构的影响研究甚少。以安吉灵峰寺林场的长期定位试验为平台,在4条毛竹扩张样带上依次设置常绿阔叶林(BLF)、竹-阔混交林(MEF)和毛竹林(PEF)样地,测定不同林型的土壤理化性质以及微生物群落特征。结果表明: 随着毛竹的扩张,土壤pH值显著上升,毛竹林土壤pH值分别比竹-阔混交林和常绿阔叶林高0.37和0.32,而有机碳、铵态氮、硝态氮含量显著降低;除丛枝菌根真菌外,其他主要微生物类群都有下降的趋势,且微生物多样性和丰富度显著降低。毛竹扩张对土壤碳输入及养分的改变是影响地下微生物群落生物量及结构的重要因素,其中土壤有机碳、铵态氮含量是影响土壤微生物群落变化的主要因子。     

Molecular characterization and primary functional analysis of PeVDE, a violaxanthin de-epoxidase gene from bamboo (Phyllostachys edulis)

Key message

PeVDE was expressed primarily in bamboo leaves, which was up-regulated under high light. The protein encoded by PeVDE had enzyme activity of catalyzing violaxanthin (V) to zeaxanthin (Z) through antheraxanthin (A) as assay shown in vitro.

Abstract

Violaxanthin de-epoxidase (VDE), a key enzyme of xanthophyll cycle, catalyzes conversion from violaxanthin (V) to zeaxanthin (Z) through antheraxanthin (A) to protect photosynthesis apparatus. A cDNA, PeVDE, encoding a VDE was isolated from bamboo (Phyllostachys edulis) by RT-PCR and RACE methods. PeVDE is 1,723 bp and contains an ORF encoding 451 amino acids, with a transit peptide of 103 amino acids. The mature protein is deduced to have 348 amino acids with a calculated molecular weight of 39.6 kDa and a theoretic isoelectric point of 4.5. Semi-quantitative RT-PCR assay indicated that the highest expression level of PeVDE was in leaf, which agreed with the accumulation pattern of PeVDE protein. Real time PCR results showed that PeVDE was up-regulated and reached the highest level after the treatment (1,200 μmo1 m^?2 s^?1) for 2 h, then decreased and kept at the level similar to that of 0.5 h after treatment for 8 h. To investigate the function of PeVDE, mature protein was heterologously expressed in Escherichia coli and the enzymatic activity assay was carried out using V as substrate. The pigments that formed in the reaction mixture were extracted and analyzed by HPLC method. Besides V, A and Z were detected in the reaction mixture, which indicated that the recombinant protein exhibited enzymatic activity of catalyzing V into Z through A. This study indicates that PeVDE functions through regulating the components of xanthophyll cycle, which might be one of the critical factors that contribute to the growth of bamboo under naturally varying light conditions.     

Genetic divergence in the small Indian mongoose (Herpestes auropunctatus), a widely distributed invasive species

The combination of founder events, random drift and new selective forces experienced by introduced species typically lowers genetic variation and induces differentiation from the ancestral population. Here, we investigate microsatellite differentiation between introduced and native populations of the small Indian mongoose (Herpestes auropunctatus). Many expectations based on introduction history, such as loss of alleles and relationships among populations, are confirmed. Nevertheless, when applying population assignment methods to our data, we observe a few specimens that are incorrectly assigned and/or appear to have a mixed ancestry, despite estimates of substantial population differentiation. Thus, we suggest that population assignments of individuals should be viewed as tentative and that there should be agreement among different algorithms before assignments are applied in conservation or management. Further, we find no congruence between previously reported morphological differentiation and the sorting of microsatellite variation. Some introduced populations have retained much genetic variation while others have not, irrespective of morphology. Finally, we find alleles from the sympatric grey mongoose (Herpestes edwardsii) in one small Indian mongoose within the native range, suggesting an alternative explanation for morphological differentiation involving a shift in female preferences in allopatry.     

Genome sequencing of a single cell of the widely distributed marine subsurface Dehalococcoidia,phylum Chloroflexi

Bacteria of the class Dehalococcoidia (DEH), phylum Chloroflexi, are widely distributed in the marine subsurface, yet metabolic properties of the many uncultivated lineages are completely unknown. This study therefore analysed genomic content from a single DEH cell designated ‘DEH-J10'' obtained from the sediments of Aarhus Bay, Denmark. Real-time PCR showed the DEH-J10 phylotype was abundant in upper sediments but was absent below 160 cm below sea floor. A 1.44 Mbp assembly was obtained and was estimated to represent up to 60.8% of the full genome. The predicted genome is much larger than genomes of cultivated DEH and appears to confer metabolic versatility. Numerous genes encoding enzymes of core and auxiliary beta-oxidation pathways were identified, suggesting that this organism is capable of oxidising various fatty acids and/or structurally related substrates. Additional substrate versatility was indicated by genes, which may enable the bacterium to oxidise aromatic compounds. Genes encoding enzymes of the reductive acetyl-CoA pathway were identified, which may also enable the fixation of CO₂ or oxidation of organics completely to CO₂. Genes encoding a putative dimethylsulphoxide reductase were the only evidence for a respiratory terminal reductase. No evidence for reductive dehalogenase genes was found. Genetic evidence also suggests that the organism could synthesise ATP by converting acetyl-CoA to acetate by substrate-level phosphorylation. Other encoded enzymes putatively conferring marine adaptations such as salt tolerance and organo-sulphate sulfohydrolysis were identified. Together, these analyses provide the first insights into the potential metabolic traits that may enable members of the DEH to occupy an ecological niche in marine sediments.     

Drivers of growth variability of Hymenaea stigonocarpa,a widely distributed tree species in the Brazilian Cerrado

Dendrochronology is a valuable tool to understanding climate-growth and growth-age relationships of native tree species from tropical forests. The information obtained from growth rings can elucidate climate responses of tree-growth under the ongoing environmental changes and support the development of sustainable forest management strategies based on species and site conditions. The Cerrado, which is a vast tropical savannah ecoregion of Brazil, has precipitation seasonality capable of inducing the formation of annual tree rings in moisture sensitive woody species. Hymenaea stigonocarpa is the typical tree species in the Cerrado with proven annual tree rings. It is an important commercial species that has been massively exploited for timber causing the considerable reduction of its natural populations. This study provides information about tree age and growth trajectories as well as climatic-growth signals of H. stigonocarpa in southeastern Brazil. We sampled 13 trees for tree-ring analysis. Tree-ring measurement and analysis were conducted using standard dendrochronological techniques. Sampled trees revealed the young successional stage of the stand, with ages varying from 20 to 35 years old. Nine out of 13 trees were used to build the standard chronology (1981 to 2013) that was positively correlated with precipitation at the end of the growing season (March-April). The chronology was able to capture SST anomalies patterns related to the South American Monsoon System. Growth modeling indicated that minimum logging diameter of 10.4cm is achieved at 24 years of age. The results reported here add valuable contribution to the discussion of sustainable management strategies for Cerrado ecoregion species.