天山一号冰川前沿生态系统真菌群落结构演替及分布格局

【目的】分析真菌群落结构和多样性随着一号冰川退缩前沿年代序列的变化,揭示真菌群落的演替轨迹及环境因子对群落组成的影响。【方法】采用宏基因组学研究方法,结合生物信息学和统计学分析技术,对取自一号冰川末端表面冰尘,底部和前沿14个样品进行总DNA的提取,ITS基因的扩增并使用Illumina Miseq平台测序,通过相关生物地理化学特性综合分析在不同年代序列下真菌群落结构及其演替规律。【结果】经测序,筛选和质控分析获得185103条rawreads,占78.3%的非单序列在97%的相似度聚类分析共得到300个操作分类单元(OTU),共划分为6个门:子囊菌门(Ascomycota,52.7%)、担子菌门(Basidiomycota,16.9%)、壶菌门(Chytridiomycota,15.1%)、接合菌门(Zygomycota,2.4%)和球囊菌门(Glomeromycota,1.2%)。从演替初期到后期阶段虽然子囊菌的序列数逐渐下降而担子菌出现缓慢上升趋势,但子囊菌随着土壤年代序列的增加始终为优势类群,壶菌在冰川底部和前沿基层普遍存在且丰度仅次于子囊菌和担子菌。我们在缺乏植被的最新退缩基层发现依靠自养型宿主存活的活体营养菌,如Taphrinomycetes、Urediniomycetes和Ustilaginomycetes。从冰川底部和前沿基层检测到丰度较高的酵母菌,而粪生真菌(coprophilous fungi)仅仅出现在冰川前沿基层,共23个操作分类单元。球囊菌仅在前沿部分样品中存在,有着十分狭小的生态位分布。【结论】一号冰川前沿随着年代序列的增加真菌群落存在明显的演替轨迹和多样性的显著变化,不同生态位真菌类群组成的相似性较低且都存在明显的指示性真菌类群。     

林木共生菌系统及其作用机制——以杨树为例

杨树（Populus）是重要造林树种,也是研究林木基础生物学性状的模式材料。不仅如此,杨树可与多种细菌（内生细菌、内生固氮菌和根际促生菌）和真菌（外生菌根真菌、丛枝菌根真菌和内生真菌）类群建立共生关系,为揭示树木和微生物之间的互惠共生机制提供了理想模型。这些共生菌能积极调控林木生长发育、营养吸收和生理生态过程。目前在杨树-双色蜡蘑（Laccaria bicolor）形成的外生菌根发育、提高杨树耐盐、耐重金属的生理与分子机制、叶片内生真菌群落结构与病害发生、菌根辅助细菌和菌丝内共生细菌-真菌-杨树形成的三重跨界共生等方面取得多项突破。近年来,一批模式草本植物微生物组（microbiome）计划相继实施,对共生菌群落结构和功能的认识有了革命性的进步。以美洲黑杨、毛果杨和胶杨为代表的林木微生物组研究也已启动,表明宿主基因型和环境因子可显著影响共生菌群落结构与物种组成;在根际（rhizosphere）和内生（endosphere）环境存在结构和功能迥异的菌群。另一方面,以根系为诱饵,通过宿主表型来推测菌群功能的反向\"钓鱼\"策略将推动林木根际微生物工程研究,为揭示杨树-微生物群落的相互关系、菌群进化搭建了研究模型。总之,深入认识多元微生物对林木表型和生理代谢的表观遗传学调控机制将为今后创制新型菌剂并用于高效育苗和抗性育种提供新的思路,具有重要的科学意义和应用价值。     

贡嘎山冰川退缩区植物-土壤反馈与植物间相互作用

植物-土壤反馈是揭示陆地生物群落动态变化的关键环节,为理解植物间相互作用及植被群落变化过程奠定基础。本研究以贡嘎山冰川退缩区原生演替早(5~10年)、中(30~40年)和晚期(80~100年)3个阶段典型土壤以及各阶段优势植物为对象,采用盆栽控制试验,比较优势植物在不同土壤条件下的生物量,并量化植物间相互作用以及植物-土壤反馈的方向与强度,为探究贡嘎山冰川退缩区植被群落演替规律提供依据。结果表明:(1)植物-土壤反馈作用显著影响植物在本土中的生物量,早期沙棘(Hippophae rhamnoides)在本土中生长最差,沙棘的植物-土壤反馈系数为负值;演替中期冬瓜杨(Populus purdomii)的反馈系数趋于零;晚期峨眉冷杉(Abies fabri)在本土中生长最好,峨眉冷杉的反馈系数为正值。(2)混种时,早期沙棘与演替中、晚期植物间相互作用指数为负值;中期冬瓜杨、川滇柳(Salix rehderiana)与演替早、晚期植物的相互作用指数接近于零,晚期植物峨眉冷杉、麦吊云杉(Picea brachytyla)与演替早、中期植物相互作用指数为正值。从植物-土壤反馈的方向来看,贡嘎山植被演替从早期负反馈,中期中性反馈,过渡到晚期正反馈。此外,演替早期沙棘促进演替中晚期植物生长,演替中期冬瓜杨、川滇柳对演替早晚期植物无显著影响,晚期峨眉冷杉、麦吊云杉更利于与演替早中期植物相互竞争。结果显示,植物-土壤反馈与植物间相互作用共同驱动了贡嘎山冰川退缩区植被快速演替,直至顶极群落。     

丛枝菌根真菌对黄瓜枯萎病的影响

盆栽条件下播种黄瓜Cucumis sativus同时接种丛枝菌根真菌Glomus etunicatum,4周后对接种处理和对照黄瓜苗分别浇灌Fusairum oxysporum f.sp.cucumerinum分生孢子悬液,2周后测定幼苗生物量、根内丙二醛、可溶性糖与游离脯氨酸含量及根围真菌和细菌数量。结果表明:接种Glomus etunicatum根系干重增加了9.3%,提高了根内可溶性糖和游离脯氨酸含量,显著减少了根围真菌数量,降低了黄瓜枯萎病的发病率和病情指数。而不接种Glomus etunicatum的黄瓜苗根系干重减少了28.0%。研究认为AM真菌Glomus etunicatum对黄瓜枯萎病具有一定的生防价值。     

Microbial leaf degraders in boreal streams: bringing together stochastic and deterministic regulators of community composition

1. Leaves that fall into the water represent a new habitat for microorganisms to colonise in streams, providing an opportunity to study colonisation and the subsequent regulation of community structure. We explored community composition of bacteria and fungi on decomposing alder leaves in nine streams in central Sweden, and describe their relationship with environmental variables. Succession of the microbial community was studied in one of the streams for 118 days. Microbial community composition was examined by denaturing gradient gel electrophoresis on replicate samples of leaves from each stream. 2. During succession in one stream, maximum taxon richness was reached after 34 days for bacteria and 20 days for fungi respectively. Replicate samples within this stream differed between each other earlier in colonisation, while subsequently such variation among replicate communities was low and remained stable for several weeks. Replicate samples taken from all the nine streams after 34 days of succession showed striking similarities in microbial communities within‐streams, although communities differed more strongly between streams. 3. Canonical analysis of microbial communities and environmental variables revealed that water chemistry had a significant influence on community composition. This influence was superimposed on a statistical relationship between the properties of stream catchments and microbial community composition. 4. The catchment regulates microbial communities in two different ways. It harbours the species pool from which the in‐stream microbial community is drawn and it governs stream chemistry and the composition of organic substrates that further shape the communities. We suggest that there is a random element to colonisation early in succession, whereas other factors such as species interactions, stream chemistry and organic substrate properties, result in a more deterministic regulation of communities during later stages.     

Spatial distribution of discrete RAPD phenotypes of a root endophytic fungus, Phialocephala fortinii, at a primary successional site on a glacier forefront

Phialocephala fortinii is among the few identified hyphomycetes belonging to the Mycelium radicis atrovirens complex. This 'dark-septate endophyte' has a global distribution and colonizes a wide variety of host plants. In this study, the spatial distribution of discrete genets of P. fortinii on the forefront of a receding glacier was analysed using the randomly amplified polymorphic DNA (RAPD) technique to determine plants colonized and patterns of colonization. In two consecutive years of sampling, a total of 74 isolates of P. fortinii were obtained from nine plant species, typically ectomycorrhizal, ericoid mycorrhizal or non-mycorrhizal. The isolates showed substantial variation, sharing on average approx. half the RAPD markers. In the first year, three isolates belonging to a single genet were obtained from two plants separated by a distance of nearly 1.5 m. The continuity of this genet was assessed by a sampling the following year. No isolates similar to that, or any of the genets collected the year before were observed. Consequently, the identical isolates from the previous year were concluded to represent discontinuous ramets. Two additional large genets were observed during the second year of sampling, which inhabited roots of several plants representing three different species. These data suggest that the sharing of P. fortinii genets among plant species might play a fundamental role in adaptation and interaction within the whole plant community in a system undergoing primary succession.     

冰川前缘土壤微生物原生演替的生态特征——以乌鲁木齐河源1号冰川为例

为了解冰川前缘土壤微生物在原生演替过程中的生态特征及其影响因素,用空间距离代替时间序列,以乌鲁木齐河源1号冰川终碛堤为起点,沿6个不同演替时期(0,4,15,31,43a和对照)的样带采集土样,以冰川附近发育良好的土壤为对照,测定土壤酶活性、微生物氮矿化与脱氨作用以及微生物生物量。结果表明,土壤脲酶、蛋白酶、酸性磷酸酶、芳基硫酸酯酶、蔗糖酶活性、微生物氮矿化及脱氨作用随演替时间而增加,微生物生物量碳和氮变化呈波动状,趋势不明显。相关分析表明,土壤有机质与酶活、微生物生物量存在极显著正相关(P0.01)。1号冰川前缘微生物多样性指数随着演替时间持续增加,但目前仍未达稳定状态。     

丛枝菌根真菌对黄瓜枯萎病的影响

Pot experiment was conducted to explore whether nursery inoculation of cucumber with Glomus etunicatum could alleviate fusarium wilt caused by Fusarium oxysporum f. sp. cucumerinum. Four-week-old seedlings inoculated with Glomus etunicatum were infected with F. oxysporum f. sp. cucumerinum by pouring conidial suspension. Biomass, contents of malonaldehyde (MDA), soluble sugar and free proline in roots, as well as the quantity of bacteria and fungi in rhizosphere were determined. The results indicated that the root dry weight of seedlings preinoculated with Glomus etunicatum increased by 9.3%; contents of soluble sugar and free proline in roots increased, and the quantity of fungi in rhizosphere decreased significantly. The disease incidence and disease index of Fusarium wilt were reduced. On the contrary, root dry weight of seedlings without inoculation with Glomus etunicatum was reduced by 28.0%. It is concluded that Glomus etunicatum is beneficial to biocontrol of Fusarium wilt of cucumber seedlings.     

天山林区土壤真菌多样性及其群落结构

土壤真菌群落结构对森林生态系统功能的维持具有重要作用,目前对天山林区土壤微生物的种类和群落结构了解甚少。为了解天山不同植被类型下土壤真菌的群落动态及优势菌属,使用Illumina MiSeq高通量测序技术,研究天山林区根际土与非根际土中真菌群落组成及多样性。结果表明:(1)对有效序列进行OTU聚类(operational taxonomic unit)后共得到14121个OTUs,经注释划分为7个门、33个纲、109个目、255个科、444个属、677个种;(2)子囊菌门(Ascomycota)和担子囊菌门(Basidiomycota)是天山植物的优势菌门,灌丛中相对丰度较高的有帚枝霉属(Sarocladium)、鬼笔属(Lysurus)、Microidium;云杉林中相对丰度较高的属有镰刀属(Fusarium)、赤霉属(Gibberella)、丝盖伞属(Inocybe);(3)灌丛与云杉林土壤真菌的群落结构和丰富度有显著差异,灌丛土壤真菌的多样性和丰富度更高,云杉林中阴坡的土壤真菌丰富度较高而阳坡和林窗较低;(4)丝盖伞属(Inocybe)、被孢霉属(Mortierella)、赤霉属(Gibberella)、镰刀属(Fusarium)与云杉的生长可能具有密切的关系。本文推测,根际土壤真菌的多样性和丰富度较低可能是导致云杉幼苗成活率低等更新障碍的问题。     

桂林会仙喀斯特湿地芦苇群落土壤微生物数量动态分析

以广西桂林会仙喀斯特湿地典型芦苇植物群落为研究对象,于春、夏、秋、冬四个季节分别采集0~10cm,10~20 cm和20~30 cm不同层次的土壤样品,分析根际微生物与非根际微生物的数量特征及季节动态变化特点,探讨微生物数量对水热季节变化的响应规律。结果表明:不同季节的根际微生物与非根际微生物组成,均以细菌占绝对优势;微生物数量分布大小顺序为细菌放线菌真菌,细菌最高比例为96.62%,放线菌最高比例为35.38%,真菌的比例较低,最高仅为0.30%。细菌,真菌和放线菌的垂直变化明显,均随着土层的增加而呈现递减的趋势。不同土壤层次根际微生物与非根际微生物的季节变化一致,细菌数量表现为夏季秋季春季冬季,真菌数量表现为秋季夏季春季冬季,放线菌数量表现为秋季春季夏季冬季;细菌、放线菌、真菌的最大值分别为2.70×10~7、1.92×10~6、3.35×10~4cfu·g~-1,土壤微生物数量与土壤有机碳、全氮、全磷、全钾、速效氮、速效磷、速效钾等呈显著正相关。芦苇植物群落根际土壤微生物呈现出一定的根际效应,并与微生物数量、土壤深度、月平均降雨量和月平均气温变化等有关,而在冬季的根际效应则表现不显著。土壤养分含量是调节会仙喀斯特湿地土壤微生物数量变化的一个主要因素。     

热带珊瑚岛植物种植对土壤改良及其微生物群落形成的影响

植被及关联的土壤微生物对于维持热带珊瑚岛的生态系统功能和稳定性具有重要作用。采集了植物种植前的种植土和种植早期珊瑚砂土,以及栽植幼苗基质中的根际土和非根际土,利用扩增子测序的手段,分析其中的真菌和细菌的多样性、群落组成及变化。分析结果显示,种植土、幼苗基质中的非根际土和根际土可能是珊瑚砂土壤中微生物的重要来源,其中最主要的类群包括以担子菌门和接合菌门为代表的真菌,以及以变形菌门、酸杆菌门为代表的细菌。珊瑚砂土的真菌丰度（864.2±41.4,为每0.25 g土的物种数）显著低于来自苗基质的根际土（1086.1±64.3,P=0.014）和苗非根际土（1251.4±48.1,P < 0.001）;珊瑚砂土的细菌丰度与苗基质根际土和非根际土之间并没有显著性差异。通过对比种植土和植物种植后的珊瑚砂土的微生物群落β-多样性,也发现植物种植对真菌和细菌类群组成产生了影响;主要类群接合菌门真菌相对丰度从0.2%增加到17.4%,而伞菌纲真菌的相对丰度从20.8%下降到0.9%,β-变形菌纲细菌的相对丰度从17.7%下降到0.1%。研究结果启示,珊瑚砂土壤微生物的组成并非是对不同来源微生物进行简单的集合,其中生活史与植物关系密切的微生物类群,目前还未在珊瑚砂土壤中表现出优势分布;相反,一些在植物根际和非根际土中较少出现的微生物,在珊瑚砂土壤中则广为存在,从而说明土壤微生物群落恢复过程的复杂性。     

Commercial high-throughput sequencing and its applications in DNA analysis

DNA sequences can be used for the analysis of genetic variation and gene function. The high-throughput sequencing techniques that have been developed over the past three years can read as many as one billion bases per run, and are far less expensive than the traditional Sanger sequencing method. Therefore, the high-throughput sequencing has been applied extensively to genomic analyses, such as screening for mutations, construction of genomic methylation maps, and the study of DNA-protein interactions. Although they have only been available for a short period, high-throughput sequencing techniques are profoundly affecting many of the life sciences, and are opening out new potential avenues of research. With the highly-developed commercial high-throughput sequencing platforms, each laboratory has the opportunity to explore this research field. Therefore, in this paper, we have focused on commercially-popular high-throughput sequencing techniques and the ways in which they have been applied over the past three years.     

传统醋曲储存过程中的微生物多样性

【背景】醋曲是我国传统谷物醋酿造中的重要微生物来源,通常一次制备分批使用。【目的】解析传统醋曲储存过程中微生物群落结构变化规律。【方法】从山西晋南一家百年老醋坊分别采集大曲原料、新制醋曲、储存7个月和12个月的醋曲,利用高通量测序技术分析微生物多样性。【结果】从4组样品中共找到610个真菌可操作分类单元(operational taxonomic unit, OTU)和747个细菌OTU。子囊菌门(Ascomycota,占比95%)和厚壁菌门(Firmicutes,占比81%)分别为优势的真菌和细菌类群。醋曲成品中约1/3的真菌OTU和约95%的细菌OTU可在醋曲原料中找到,说明原料是醋曲的重要微生物来源。相较于新制醋曲,储存7个月和12个月醋曲中的真菌和细菌多样性均显著降低。醋曲贮存过程中微生物群落结构发生明显改变,并且相较于真菌群落结构,细菌群落结构更易波动。相较于醋曲原料,醋曲成品中显著富集扣囊复膜孢酵母(Saccharomycopsis fibuligera)、东方伊萨酵母(Issatchenkiaorientalis)等真菌,以及克罗彭斯特菌属(Kroppenstedtia)...     

454焦磷酸测序分析几种哺乳动物粪便细菌多样性

摘要:【目的】分析比较几种哺乳动物粪便细菌群落多样性,了解粪便细菌多样性与动物进化和食物的关系。【方法】采集6 种哺乳动物粪便样品;提取总DNA;PCR扩增,获得16S rDNA V3标签片段;用454焦磷酸测序技术进行高通量测序;主要基于QIIME平台分析比较粪便细菌多样性。【结果】分析发现,厚壁菌门和拟杆菌门广泛存在于各样品中,并且占绝对优势。α多样性分析发现,杂食性的长臂猿、黑猩猩和川金丝猴的多样性最高,其次是肉食性的东北虎,来自熊科杂食性的亚洲黑熊和大熊猫的多样性最低。β 多样性分析发现,白眉长臂猿、黑猩猩、川金丝猴几种灵长目动物粪便的菌群相似,而大熊猫菌、黑熊、孟加拉虎几种食肉目动物粪便细菌群相似但食肉动物孟加拉虎主要又因含梭杆菌门而区别于其他动物。【结论】动物粪便细菌优势类群明显;同种动物重复样本的相似性最高,各种动物多样性存在差异,但几种灵长类动物粪便细菌多样性更丰富;动物粪便细菌的组成和动物的进化及食物相关。本研究为哺乳动物粪便菌资源及后续研究提供了借鉴。     

Effects of transgenic potatoes with an altered starch composition on the diversity of soil and rhizosphere bacteria and fungi

The aim of this study was to investigate potential effects on the composition of the bacterial and fungal diversity in rhizosphere and soil of a transgenic potato line (SIBU S1) which was modified in its starch composition by RNA anisensing, compared to the non-transgenic parental cultivar (SIBU) at the flowering stage in 2000. Furthermore a second non-transgenic cultivar (SOLANA) was included in the study. To avoid artefacts derived from cultivation depending approaches, molecular techniques based on 16S-(bacteria) and 18S-(fungi) rDNA respectively were used to describe the microbial community structure. Comparing 16S- and 18S-rDNA DGGE fingerprints from the different bulk soil samples, it could be shown that no significant differences between the two cultivars and the transgenic line were found. Similar results were obtained for the rhizosphere samples using the eubacterial, α-and β-proteobacterial and fungal specific primers with the exception of, the eubacterial DGGE patterns obtained for the rhizosphere of SOLANA. These patterns revealed that the relative abundance of one band was enhanced compared with the patterns of SIBU and SIBU S1 and the sequence of the differentiating band showed the highest similarity with Enterobacter amnigenus. When Pseudomonas specific primers were used, relevant differences were found between the rhizosphere patterns of the transgenic potato line (SIBU S1) and the parental cultivar (SIBU). However, clear effects of the cultivar SOLANA on the structure of the Pseudomonas community compared to SIBU were also detected.     

No support for occurrence of free-living Cladonia mycobionts in dead wood

Lichenised fungi are traditionally assumed to form obligate symbioses with algae or cyanobacteria and to be confined to the surface of their growing substratum. However, in a recent 454 pyrosequencing study of fungal communities in Picea abies logs, lichen-forming fungi were detected at a depth of more than 6 cm in dead wood, implying the existence of free-living lichen mycobionts. To determine whether this was the case, we investigated whether Cladonia spp., the most frequently encountered mycobionts, occurred in wood without their photobionts. We detected green algae in all samples with records of Cladonia spp. Hence, we found no evidence for free-living Cladonia mycobionts in wood. We suggest that the detected Cladonia DNA in these logs originates from vegetative propagules or thallus fragments dispersed into the logs by animals or water. However, the occurrence of free-living stages of other lichen-forming fungal taxa in dead wood cannot be excluded.     

Habitat selection and ecology of Xanthoria elegans (Link) Th. Fr. in glacier forefields: implications for lichenometry

Habitats occupied by the largest Xanthoria elegans (Link) Th. Fr. thalli at seven glacier forefields in the Canadian Rockies were studied to investigate the lichenometric assumption that large thalli occupy ideal sites for growth. The largest thalli were found on steep or overhanging facets at the base of grey limestone clasts that were embedded in moraines. These thalli were unfragmented, had nearly circular outlines, were bordered by barren rock and had SSE to S orientations. This is consistent with the general expectation that south-facing sites offer high solar input and a long snow-free season. Orientations other than south could result by chance or may reflect the importance of microscale factors (e.g. reflected rather than direct solar input). Closure of X. elegans communities and coalescence of thalli was only found at sites that were naturally fertilized with dung. It is concluded that all clasts do not afford homogeneous or ideal environments for lichen growth and do not have an equal chance of being colonized. This raises doubts concerning the validity of statistical normality assumptions in lichenometry and the use of grids to assess closure in lichen communities.