珞珈山森林土壤原生动物生态学研究及土壤原生动物定量方法探讨

１９９３年１月至１２月,用直接计数法和培养计数法对武昌珞珈山森林土壤原生动物进行了周年定量研究,发现原生动物丰度的周年动态趋势为：春季（３—５月）达到高峰,低谷出现在冬季（１—２月）,夏秋季保持较平稳的变动。原生动物丰度与土壤环境因子间的相关性分析结果表明,原生动物丰度的周年动态与土壤含水量及土壤ｐＨ值的变化呈显著的正相关,与土壤温度的变化无明显相关关系。珞珈山森林土壤原生动物优势种为梨波豆虫（Ｂｏｄｏｅｄａｘ）、球波豆虫（Ｂｏｄｏｇｌｏｂｏｓｕｓ）、卵形隐滴虫（Ｃｒｙｐｔｏｍｏｎａｓｏｖａｔａ）、长尾尾滴虫（Ｃｅｒｃｏｍｏｎａｓｌｏｎｇｉｃａｕｄａ）、线条三足虫（Ｔｒｉｎｅｍａｌｉｎｅａｒｓ）、斜口三足虫（Ｔ．ｅｎｃｈｅｌｙｓ）、长匣壳虫（Ｃｅｎｔｒｏｐｙｘｉｓｅｌｏｎｇａｔａ）、宽口圆壳虫（Ｃｙｃｌｏｐｙｘｉｓｅｕｒｏｓｔｏｍａ）。常见种有梨波豆虫（Ｂｏｄｏｅｄａｘ）、球波豆虫（Ｂ．ｇｌｏｂｏｓｕｓ）、跳侧滴虫（Ｐｌｅｕｒｏｍｏｎａｓｊａｃｕｌａｎｓ）、长尾尾滴虫（Ｃｅｒｃｏｍｏｎａｓｌｏｎｇｉｃａｕｄａ）、小滴虫（Ｍｏｎａｓｍｉｎｉｍｕｍ）、斜口三足虫（Ｔｒｉｎｅｍａｅｎｃｈｅｌｙｓ）、线条三足虫（Ｔ     

基于宏基因组技术分析全球不同温度带土壤微生物多样性

【背景】温度在塑造大尺度的土壤微生物群落方面发挥了重要作用,但目前针对全球不同温度带大尺度土壤微生物多样性方面的研究十分缺乏。【目的】明确不同温度带大尺度土壤微生物组成和功能的差异变化。【方法】从宏观的角度运用宏基因组技术对不同温度带土壤微生物群落的组成和功能进行分析。【结果】细菌的物种多样性随着温度带纬度的升高而增多,真菌的物种多样性在温带最多,在寒带最小且假丝酵母属(Candida)占绝对优势。3个温度带间除物种多样性存在差异外,微生物群落中物种丰度差异也较大,优势属和特殊属各有不同。其中值得注意的是,假单胞菌属(Pseudomonas)和芽孢杆菌属(Bacillus)的丰度在不同温度带间存在显著差异,且随着温度带纬度的升高而增多,而链霉菌属(Streptomyces)、地嗜皮菌属(Geodermatophilus)、红色杆菌属(Rubrobacter)和小单孢菌属(Micromonospora)的丰度随温度带纬度的升高而降低。在功能方面,发现与翻译后修饰、蛋白质周转、伴侣(posttranslational modification, protein turnover, chap...     

454测序法在环境微生物生态研究中的应用

传统的Sanger测序技术虽已成熟,但其速度和成本的限制满足不了大规模测序的要求。第二代高通量测序技术结合了乳胶微粒和皮升级反应的454焦磷酸测序法,作为一种高通量测序技术,具有分析结果准确、高速、高灵敏度和高自动化的特点。对454测序法的技术原理和操作步骤进行了介绍,对近年来运用该方法在环境微生物生态研究领域的进展进行了综述。     

昭苏县野生羊肚菌根际土壤细菌多样性研究

采集昭苏县野生羊肚菌(Morchella esculenta)根际水平直径10 cm、深度0～30 cm范围内的3层各10 cm土壤样品,利用Illumina miseq 2×300 bp高通量测序技术和生物信息学分析方法检测细菌类群的多样性。结果显示,细菌群落Chao和Shannon指数在0～30 cm土层中的平均值分别为152和3.68,且两种指数在10～20 cm土层均最高;细菌群落在各分类水平上的类群(最大类群丰度)分别为变形菌门(Proteobacteria,36.3%)、厚壁菌门(Firmicutes)和拟杆菌门(Bacteroidetes)等13门;黄杆菌科(Flavobacteriaceae,8.4%)、芽胞杆菌科(Bacillaceae)和葡萄球菌科(Staphylococcaceae)等43科;葡萄球菌属(Staphylococcus,7.1%)、杆状菌属(Bacillus)和Cloacibacterium等52属;不能培养的α-变形杆菌(uncultured α-proteobacterium,2.0%)、不能培养的嗜甲基菌科1种(uncultured Methylophilaceae bacterium)和路西法芽胞杆菌(Bacillus luciferensis)等44种。检测到固氮菌32属,包括15属自生固氮菌、9属共生固氮菌和8属联合固氮菌。结果表明,羊肚菌土壤根际微生物样品中细菌类群具有多样性,10～20 cm土层根际微生物多样性较高,但很多种类丰度较低;该土样含有丰富的固氮菌,这对栽培羊肚菌如何选地或覆土具有一定的指导意义。     

DNA指纹图谱技术在土壤微生物多样性研究中的应用

土壤中的微生物多样性是十分丰富的,传统培养方法对土壤微生物多样性的研究有很大局限性。近年来,各种基于16S rDNA基因的指纹图谱分析技术取得了长足的进步,并广泛应用于土壤微生物多样性的研究。这些技术主要有变性梯度凝胶电泳(DGGE)/温度梯度凝胶电泳(TGGE)、单链构象多态性(SSCP)、随机引物扩增多态性DNA(RAPD)、限制性片段长度多态性(RFLP)和扩增核糖体DNA限制性分析(ARDRA)等。对这些技术近年来在土壤微生物多样性研究领域的应用予以简短综述,并初步探讨未来几年土壤微生物分子生态学发展的方向。     

宏基因组技术在开发极端环境未培养微生物中的应用

人类对自然环境中约99％的微生物不能用传统的方法进行纯培养,对于极端环境中的微生物更是知之甚少.随着宏基因组技术的出现,人们可对选一庞大的未知世界进行多方面研究.目前研究者利用这一技术已经对地球上的多种极端生境进行了研究,并取得了很多新的成就.简要概述这一技术在极端环境未培养微生物研究中的应用.     

根施生物炭对设施连作土壤氮素转化及黄瓜幼苗根系氮代谢的影响

设施连作土壤普遍存在由于氮素过量积累导致的土壤障碍问题。本研究以不添加生物炭作为对照,以添加5%的生物炭(质量比)为处理,采用盆栽方式分析了生物炭对土壤微生物群落结构、氮循环功能基因丰度以及黄瓜幼苗根系生长和氮素代谢相关基因表达的影响,以期探明外源添加生物炭对设施连作土壤氮素转化的调控作用。结果表明：与对照相比,设施连作土壤添加生物炭处理后显著提高了黄瓜幼苗的株高、根系干重、总根长、根表面积和根体积;改善了根区环境,诱导黄瓜通过上调植物氮代谢相关基因的表达促进了黄瓜根系对氮素的吸收。施入生物炭显著提高了土壤微生物生物量氮、硝态氮和亚硝态氮含量,显著提高了土壤中变形菌门和蓝细菌门以及鞘脂单胞菌(土壤固氮菌)等氮代谢相关菌群丰度;增加了土壤硝化、氮同化还原功能基因丰度;增强了参与氮代谢的羟胺脱氢酶、硝基单加氧酶和碳酸酐酶活性。综上,根施生物炭改善了设施连作土壤理化性质和微生物生态系统,通过促进硝化作用和氮同化作用来调节土壤的氮循环过程,提高了植株对土壤氮素的吸收能力,最终促进了黄瓜植株生长。     

南极菲尔德斯半岛地区土壤原生动物生态学研究

作者于1994年12月至1995年2月设置13个采样站,对南极菲尔德斯半岛地区土壤原生动物进行了研究。共观察到原生动物37种,其中:鞭毛虫11种,肉足虫9种,纤毛虫17种;优势种为梨波豆虫,球波豆虫,小滴虫,聚滴虫,跳侧滴虫,磷壳虫和钩刺斜管虫;原生动物密度在采样站间的变化范围在33-577个/g干土之间,格鲁玻科湖岸边土壤站最低,而阿德雷岛苔藓下土壤站最高,回归分析表明:土壤原生动物密度与土壤含水量呈显着性直线相关。       

基于功能基因的微生物碳循环分子生态学研究进展

碳循环是生态系统中重要的生物地球化学元素循环之一。微生物参与碳固定、甲烷代谢、碳降解等多个重要的碳循环过程,深入了解微生物群落在碳循环过程中的功能和作用,有助于获悉微生物对全球气候变化的响应、适应和反馈机制,这也是微生物生态学研究的关键问题之一。传统的研究多集中于微生物分离培养技术,无法覆盖绝大部分未培养微生物,并且无法深入解析碳循环过程中微生物群落的结构和功能,宏基因组学技术的出现克服了这些缺陷,成为研究微生物群落结构和功能的有效手段。本文对目前宏基因组学的主要技术——定量PCR、DNA分子指纹图谱、基因芯片、克隆文库和高通量测序等技术进行了简要介绍,着重介绍了参与碳固定、甲烷生成和氧化、碳降解等主要碳循环过程的关键功能基因的研究现状,最后对碳循环过程中微生物宏基因组学研究的未来发展进行了总结与展望。     

环境微生物研究中机器学习算法及应用

微生物在环境中无处不在，它们不仅是生物地球化学循环和环境演化的关键参与者，也在环境监测、生态治理和保护中发挥着重要作用。随着高通量技术的发展，大量微生物数据产生，运用机器学习对环境微生物大数据进行建模和分析，在微生物标志物识别、污染物预测和环境质量预测等领域的科学研究和社会应用方面均具有重要意义。机器学习可分为监督学习和无监督学习2大类。在微生物组学研究当中，无监督学习通过聚类、降维等方法高效地学习输入数据的特征，进而对微生物数据进行整合和归类。监督学习运用有特征和标记的微生物数据集训练模型，在面对只有特征没有标记的数据时可以判断出标记，从而实现对新数据的分类、识别和预测。然而，复杂的机器学习算法通常以牺牲可解释性为代价来重点关注模型预测的准确性。机器学习模型通常可以看作预测特定结果的“黑匣子”，即对模型如何得出预测所知甚少。为了将机器学习更多地运用于微生物组学研究、提高我们提取有价值的微生物信息的能力，深入了解机器学习算法、提高模型的可解释性尤为重要。本文主要介绍在环境微生物领域常用的机器学习算法和基于微生物组数据的机器学习模型的构建步骤，包括特征选择、算法选择、模型构建和评估等，并对各种机器学习模型在环境微生物领域的应用进行综述，深入探究微生物组与周围环境之间的关联，探讨提高模型可解释性的方法，并为未来环境监测、环境健康预测提供科学参考。     

Fungal soil communities in a young transgenic poplar plantation form a rich reservoir for fungal root communities

Fungal communities play a key role in ecosystem functioning. However, only little is known about their composition in plant roots and the soil of biomass plantations. The goal of this study was to analyze fungal biodiversity in their belowground habitats and to gain information on the strategies by which ectomycorrhizal (ECM) fungi form colonies. In a 2-year-old plantation, fungal communities in the soil and roots of three different poplar genotypes (Populus × canescens, wildtype and two transgenic lines with suppressed cinnamyl alcohol dehydrogenase activity) were analyzed by 454 pyrosequencing targeting the rDNA internal transcribed spacer 1 (ITS) region. The results were compared with the dynamics of the root-associated ECM community studied by morphotyping/Sanger sequencing in two subsequent years. Fungal species and family richness in the soil were surprisingly high in this simple plantation ecosystem, with 5944 operational taxonomic units (OTUs) and 186 described fungal families. These findings indicate the importance that fungal species are already available for colonization of plant roots (2399 OTUs and 115 families). The transgenic modification of poplar plants had no influence on fungal root or soil communities. Fungal families and OTUs were more evenly distributed in the soil than in roots, probably as a result of soil plowing before the establishment of the plantation. Saprophytic, pathogenic, and endophytic fungi were the dominating groups in soil, whereas ECMs were dominant in roots (87%). Arbuscular mycorrhizal diversity was higher in soil than in roots. Species richness of the root-associated ECM community, which was low compared with ECM fungi detected by 454 analyses, increased after 1 year. This increase was mainly caused by ECM fungal species already traced in the preceding year in roots. This result supports the priority concept that ECMs present on roots have a competitive advantage over soil-localized ECM fungi.     

Biofilm transplantation in the deep sea

A gold rush is currently going on in microbial ecology, which is powered by the possibility to determine the full complexity of microbial communities through next‐generation sequencing. Accordingly, enormous efforts are underway to describe microbiomes worldwide, in humans, animals, plants, soil, air and the ocean. While much can be learned from these studies, only experiments will finally unravel mechanisms. One of the key questions is how a microbial community is assembled from a pool of bacteria in the environment, and how it responds to change – be it the increase in CO₂ concentration in the ocean, or antibiotic treatment of the gut microbiome. The study by Zhang et al. ( 2016 ) in this issue is one of the very few that approaches this problem experimentally in the natural environment. The authors selected a habitat which is both extremely interesting and difficult to access. They studied the Thuwal Seep in the Red Sea at 850 m depth and used a remotely operated vehicle (ROV) to place a steel frame carrying substrata for biofilm growth into the brine pool and into the adjacent normal bottom water (NBW). Biofilms were allowed to develop for 3 days, and then those that had been growing in the brine pool were transported to normal bottom water and stayed there for another 3 days, and vice versa. The ‘switched’ biofilms were then compared with their source communities by metagenome sequencing. Strikingly, both ‘switched’ biofilms were now dominated by the same two species. These species were able to cope with conditions in both source ecosystems, as shown by assembly of their genomes and detection of expression of key genes. The biofilms had adapted to environmental change, rather than to brine pools or NBW. The study shows both the resilience and adaptability of biofilm communities and has implications for microbial ecology in general and even for therapeutic approaches such as transplantation of faecal microbiomes.     

Toward molecular trait‐based ecology through integration of biogeochemical,geographical and metagenomic data

Using metagenomic ‘parts lists’ to infer global patterns on microbial ecology remains a significant challenge. To deduce important ecological indicators such as environmental adaptation, molecular trait dispersal, diversity variation and primary production from the gene pool of an ecosystem, we integrated 25 ocean metagenomes with geographical, meteorological and geophysicochemical data. We find that climatic factors (temperature, sunlight) are the major determinants of the biomolecular repertoire of each sample and the main limiting factor on functional trait dispersal (absence of biogeographic provincialism). Molecular functional richness and diversity show a distinct latitudinal gradient peaking at 20°N and correlate with primary production. The latter can also be predicted from the molecular functional composition of an environmental sample. Together, our results show that the functional community composition derived from metagenomes is an important quantitative readout for molecular trait‐based biogeography and ecology.     

太湖浮游纤毛虫群落结构及其与环境因子的关系

用定量蛋白银染色法,对太湖浮游纤毛虫进行定性和定量研究,同时用多元统计方法分析生物和非生物因子对其影响。在全湖设置32个点位进行季度采样,共检出117种纤毛虫,隶属于3纲、15目、78属,其中95种鉴定到种的水平。纤毛虫平均丰度27 170个/L(1 500—139 150个/L),平均生物量600.6μg/L(16.7—8736.0μg/L),以寡毛目、前口目、盾纤目、缘毛目和钩刺目为主。优势种包括:浮游藤壶虫、趣尾毛虫、顶口睥睨虫、银灰膜袋虫、水生钟虫复合种、钟形钟虫、杯铃壳虫、双叉弹跳虫、大弹跳虫、短列裂隙虫、小裂隙虫、圆筒状似铃壳虫。纤毛虫群落结构空间异质性较高,丰度上呈现从南向北、从敞水区向沿岸河口区逐渐增加的趋势;北部湖区以小个体的寡毛目、盾纤目、前口目为主,而南部主要以大个体的寡毛目为主;从功能摄食类群上看,北部各点以食菌种类为主,而南部以食藻种类居多。该类群季节变化明显,于夏季出现丰度峰值,生物量是冬、夏季显著高于春、秋季。通过CCA多元分析发现,太湖纤毛虫群落结构差异主要与水体营养水平、桡足类数量和pH值等有关,且在不同季节由不同的环境因子调控。     

VIROME: a standard operating procedure for analysis of viral metagenome sequences

One consistent finding among studies using shotgun metagenomics to analyze whole viral communities is that most viral sequences show no significant homology to known sequences. Thus, bioinformatic analyses based on sequence collections such as GenBank nr, which are largely comprised of sequences from known organisms, tend to ignore a majority of sequences within most shotgun viral metagenome libraries. Here we describe a bioinformatic pipeline, the Viral Informatics Resource for Metagenome Exploration (VIROME), that emphasizes the classification of viral metagenome sequences (predicted open-reading frames) based on homology search results against both known and environmental sequences. Functional and taxonomic information is derived from five annotated sequence databases which are linked to the UniRef 100 database. Environmental classifications are obtained from hits against a custom database, MetaGenomes On-Line, which contains 49 million predicted environmental peptides. Each predicted viral metagenomic ORF run through the VIROME pipeline is placed into one of seven ORF classes, thus, every sequence receives a meaningful annotation. Additionally, the pipeline includes quality control measures to remove contaminating and poor quality sequence and assesses the potential amount of cellular DNA contamination in a viral metagenome library by screening for rRNA genes. Access to the VIROME pipeline and analysis results are provided through a web-application interface that is dynamically linked to a relational back-end database. The VIROME web-application interface is designed to allow users flexibility in retrieving sequences (reads, ORFs, predicted peptides) and search results for focused secondary analyses.     

几种主要分子生物学技术在真菌生态学研究中的应用

真菌在自然界的物质循环与降解等生态过程中发挥着重要的作用,是生态系统的重要组成部分。然而约90%的真菌种类仍然未知,且大部分难于分离和培养。因此核酸杂交;核酸序列分析;DNA指纹分析等分子生物学技术被用于真菌分类、鉴定、种群结构、群落多样性研究。本文综述了这几种主要分子生物学技术的基本原理及其在真菌生态学研究中的应用现状。     

Recent advances in soil seed bank research

Soil seed bank is an important component of ecosystem resilience and represents a stock of regeneration potential in many plant assemblages. Soil seed banks can be used to predict the composition of new plant recruitment. Species overcome periods of unfavorable weather conditions by building up a large seed bank. With this strategy, the species diversity is preserved and information on their dynamics and structure is retained. The research on soil seed bank has received wide interest because of its important role in plantation renovation and restoration, biological diversity preservation, vegetation succession and diffusion processes and other aspects. This paper reviews the relationship between soil seed bank and disturbance, geographic factor, vegetation and seed size and is aimed at providing some useful reference for future research.     

白蚁菌圃真菌多样性研究进展

白蚁菌圃存在于白蚁巢中,具有硬而脆的多孔结构,是特殊的真菌生存环境。当有白蚁在白蚁巢内活动时,蚁巢伞Termitomyces是菌圃上的优势菌;当白蚁巢被废弃,炭角菌Xylaria成为菌圃上的优势真菌。菌圃中还存在其他微生物如无性型真菌（anamorphic fungi）和酵母等。菌圃中的真菌很多具有潜在药用价值或其他经济价值。从蚁巢伞、炭角菌等主要真菌类群出发,结合分子生态学研究菌圃真菌多样性的方法,综述了白蚁菌圃真菌多样性的研究进展,揭示了目前的研究热点及存在的问题,并针对这些问题提出可能的发展方向。