Biolog方法在环境微生物群落研究中的应用

环境微生物群落研究具有非常重要的理论和应用价值。本文介绍了一种测定微生物代谢的Ｂｉｏｌｏｇ微平板法 ,以及这种新方法在环境微生物群落研究方面的应用成果。1　环境微生物群落研究的意义与手段1 .1　环境微生物群落的研究内容环境微生物是由多个种群 (ｐｏｐｕｌａｔｉｏｎ)组成的微生物群落 (ｃｏｍｍｕｎｉｔｙ) ,不同种群之间存在着共生、互利、共存、竞争等各种复杂的关系 ,在物质循环和能量转化过程中发挥着重要作用。对环境微生物群落的研究可以从微生物的量 ,代谢活性 ,群落结构及代谢功能等几个不同层面上进行。其中 ,微生物…     

基因芯片技术在环境微生物群落研究中的应用

基因芯片技术作为一种快速、敏感、高通量的检测技术,近几年来在环境微生物群落研究中的应用越来越广泛并且得到充分的发展.它不仅可以研究环境微生物群落的微生物分布、种类、功能、动力学变化,还能分析环境污染等环境因素改变对其微生物生态的影响.本文按照基因芯片探针的设计方法,将环境样品群落研究基因芯片分为系统寡核苷酸芯片、功能基因芯片、群落基因组芯片、宏基因组芯片,并简要综述了该技术在活性污泥、土壤、水等环境样品微生物群落研究上的应用,最后,本文展望了该技术的研究方向和在寻找不同环境微生物群落之间差异微生物、差异基因或差异表达基因研究中的应用前景.     

MAR-FISH技术及其在环境微生物群落与功能研究中的应用

对复杂环境中微生物群落结构和功能的研究是微生物生态学的重要任务。尽管现代分子生物学技术已经成功地用于解析环境中微生物的群落结构, 但是这些方法并不能提供微生物的原位生理学信息。而一种新的方法, 微观放射自显影和荧光原位杂交集成技术(MAR-FISH)则能够同时在单细胞水平上, 检测复杂环境中微生物的系统发育信息及其生理特性。本文总结了MAR-FISH方法的原理, 实验步骤及其在环境微生物群落与功能研究中的应用。     

长期施肥对农田黑土微生物群落功能多样性的影响

为了研究长期不同施肥对农田黑土微生物群落功能多样性的影响,采用Biolog ECO微平板培养法,对已经连续施肥35年的农业部哈尔滨黑土生态环境重点野外科学观测试验站4种处理(CK、NPK、M、MNPK)的两个土层(0～20、20～40 cm)微生物群落功能多样性进行研究.结果表明: 在0～20 cm土层,有机无机肥(MNPK)配施能够显著提高土壤微生物对碳源的利用能力以及群落代谢功能的丰富度、多样性和优势度,而在20～40 cm土层则低于单施化肥(NPK)处理,两个土层单施化肥均降低土壤微生物群落代谢均匀度.不同施肥处理土壤微生物对6种碳源的利用率在0～20和20～40 cm两个土层间存在差异,而在每个土层的处理间差异显著(P<0.05),但各处理间的变化规律在两个土层中不一致.典范对应分析(CCA)结果表明,各处理土壤微生物群落代谢功能在0～20和20～40 cm土层间存在差异,且在两个土层的处理间也存在差异,而土壤养分含量对各处理土壤微生物群落代谢功能的影响规律在两个土层中较为相似.长期不同施肥会对耕层及以下土壤微生物群落功能多样性产生影响,在20～40 cm土层中单施化肥对微生物群落功能多样性的影响较大.     

衡阳紫色土丘陵坡地植被恢复对土壤微生物功能多样性的影响

以典型湖南省衡阳紫色土丘陵坡地不同植被恢复阶段为研究对象,采用空间代替时间序列的方法,选用立地条件基本相似的草本(狗尾草,GS)、灌草(紫薇-狗尾草,FG)、灌丛(牡荆+剌槐,FX)和乔灌(枫香+苦楝-牡荆,AF)群落阶段,运用Biolog-ECO微平板技术,对4个不同恢复阶段0～10和10～20 cm土层的土壤微生物功能多样性进行研究,探讨植被恢复对土壤微生物功能多样性的影响.结果表明: 植被恢复后土壤微生物群落代谢活性显著升高,同一土层不同恢复阶段AWCD值的大小顺序为乔灌群落＞灌丛群落＞灌草群落＞草本群落,相同恢复阶段不同土层的AWCD值的大小顺序为0～10 cm＞10～20 cm;主成分分析(PCA)表明,灌草群落与灌丛群落具有相似的土壤微生物C源利用方式及代谢功能,而草本群落、乔灌群落具有不同的C源利用方式及代谢功能,在主成分分离中起主要贡献作用的C源是糖类、氨基酸类以及代谢中间产物和次生代谢物;土壤微生物的Shannon物种丰富度指数(H)、Shannon均匀度指数(E)、Simpson优势度指数(D)和McIntosh指数(U)均以乔灌群落最高,灌草群落和灌丛群落次之,草本群落最低;相关分析表明,土壤含水量(SWC)、土壤总有机碳(STOC)、全氮(TN)、全磷(TP)和速效磷(AP)对土壤微生物代谢功能及功能多样性指数有重要影响,脲酶(URE)、磷酸酶(APE)、蔗糖酶(INV)和过氧化氢酶(CAT)活性与土壤微生物代谢功能及功能多样性指数存在显著相关关系.表明植被恢复可使土壤微生物代谢功能增强,土壤微生物繁殖加快、数量增大,从而促进土壤微生物对土壤C源的利用强度.     

生物冶金过程中的关键微生物及其碳循环代谢途径研究

【目的】深入研究极端酸性环境中微生物的碳循环过程。【方法】应用16S r RNA高通量测序和功能基因芯片技术对德兴铜矿中浸矿堆(LH)和积液池(LS)两个子系统中的微生物群落结构组成和功能基因组成进行分析;并运用PICRUSt功能基因预测的方法对群落功能进行预测。【结果】功能基因芯片和功能预测分析都表明碳循环基因在子系统间存在显著差异(P0.05),且碳固定相关的卡尔文循环、还原性三羧酸循环等基因以及碳降解相关的己聚糖和纤维素等基因在LS系统中都要明显高于LH系统。碳循环功能基因在子系统之间的差异与环境条件相关,其中TON、Ca、ES、Fe3+和P作用显著。【结论】在极端酸性环境中,环境条件的差异会对微生物群落碳循环功能基因产生筛选作用,参与碳循环的微生物的种类和相对丰度都发生变化,最终改变了群落碳循环模式。     

基因芯片及其在环境微生物研究中的应用

基因芯片因其具有高密度、高灵敏度、快速 (实时 )检测、经济、自动化和低背景水平等特点 ,而广泛应用于不同的研究领域。目前 ,应用于环境微生物研究的基因芯片主要有功能基因芯片 (FGAs)、系统发育的寡核苷酸芯片 (POAs)和群落基因组芯片 (CGAs)。综述了基因芯片在环境微生物研究中的应用 ,包括自然环境中微生物的基因表达分析、比较基因组分析和混合微生物群落的分析等。讨论了基因芯片面临的挑战和前景展望     

变性梯度凝胶电泳在环境微生物生态学中的应用

PCR-变性梯度凝胶电泳(PCR-DGGE)具有可靠性强、重复性好、方便快捷等优点,已被广泛应用于环境生态学中微生物群落多样性、动态性分析和功能细菌的跟踪。本文综述了PCR-DGGE技术的基本原理,不同DNA提取方法的比较,不同PCR方式的比较及其在环境生态学中研究微生物群落多样性、环境中微生物群落变化的动态监测、硝化菌-反硝化菌和硫酸还原菌(SRB)的动态分析和监测等领域中的应用,并对该技术自身存在的局限性和应用前景进行了评价。     

植物微生物组生态功能与群落构建过程研究进展

植物各个器官表面及内部定殖着高度多样化的微生物群落,这些微生物与植物长期共进化,作为宿主植物的“共生功能体”(holobiont)在植物生长发育、养分吸收、病害抵御和环境胁迫适应性等方面发挥了重要作用。得益于近10年来多组学技术的发展和应用,有关植物微生物群落的多样性、组成和功能特征、群落构建的驱动因素和植物–微生物互作机制等方面研究取得了一系列重要进展。然而,与土壤微生物组相比,目前对植物微生物组的认识及其应用尚且不足。本文系统总结了植物微生物组的组成特征,植物微生物在调节植物生长发育、促进养分吸收、提高病害抵御能力及环境胁迫适应性等方面的功能及作用机制,从宿主选择、环境因子以及生物互作3个方面总结了驱动植物微生物群落构建的因素,并着重阐述了植物–微生物互作如何塑造植物微生物群落以及如何调节对植物的有益功能。此外,我们对未来植物微生物组研究和应用面临的挑战进行了展望,如核心微生物组挖掘和合成群落构建,植物–微生物互作的分子调控机制,植物微生物群落水平上的互作机制等。深入理解植物微生物群落特征、生态功能以及构建过程对于精准调控植物微生物组以提高植物适应性和生产力以及维持生态系统健康具有...     

环丙沙星对土壤微生物量碳和土壤微生物 群落碳代谢多样性的影响

采用氯仿熏蒸浸提法和Biolog法,分析环丙沙星作用下的土壤微生物量碳和微生物群落碳代谢多样性,以揭示环丙沙星在环境中残留对土壤微生物学性状的影响.结果表明,环丙沙星(wCIP≥0.1 μg/g)对土壤微生物量碳含量影响显著(P＜0.05),土壤中环丙沙星浓度愈高,微生物量碳含量愈低,100μg/g的环丙沙星处理使土壤微生物量碳含量下降58.69％.环丙沙星对土壤微生物群落碳代谢功能影响显著,环丙沙星降低了土壤微生物对碳水化合物、羧酸、氨基酸、聚合物、酚类和胺类的碳源利用率;环丙沙星(wCIP≥0.1 μg/g)显著影响了土壤微生物群落碳源代谢强度和代谢多样性,但不同浓度的环丙沙星对土壤微生物群落碳代谢功能的影响不同,0.1、1、10 μg/g的环丙沙星处理对土壤微生物群落碳代谢功能的影响主要表现在处理前期(用药第7天、21天),这种影响在处理后期(用药第35天)表现不明显,100μg/g的环丙沙星在用药的前期和后期均显著影响土壤微生物群落碳代谢功能,土壤中环丙沙星积累到该浓度可能对土壤微生物群落碳代谢功能产生难以逆转的长期影响.     

针茅草原放牧衰退演替阶段的模糊聚类分析

本文利用模糊聚类分析的系统聚类法和ISODATA分类法,对短花针茅草原因过度放牧而形成的衰退演替系列的各阶段进行了分类;比较成功地在群落分类上联合使用了PCA排序与ISODATA分类。结果表明:这两种方法都将衰退演替系列分成4个阶段,它们是短花针茅群落、扁穗冰草群落、冷蓠群落和亚氏旋花群落。这与前人用其他方法分类的结果相似。本文为群落分类提供了两种合理、可行的数学分类方法。     

Comparison of molecular fingerprinting methods for analysis of soil microbial community structure

Denaturing gradient gel electrophoresis (DGGE), terminal-restriction fragment length polymorphism (T-RFLP) analysis, and automated ribosomal intergenic spacer analysis (ARISA) have been widely used as molecular fingerprinting methods for analysis of microbial communities. To find suitable methods, we compared the three fingerprinting methods by analyzing soil fungal communities in four differing land-use types: bare ground, crop fields, grasslands, and forests. We also examined optimal primer pairs for DGGE analysis by comparing single and mixed DNA samples of cultured fungal populations. Principal coordinate analysis (PCO), nonmetric multidimensional scaling method (NMDS), and analysis of similarities (ANOSIM), which are major multivariate statistical analyses for quantifying fingerprint patterns, were compared. All three fingerprinting methods yielded clear discrimination of soil fungal communities among the four land-use types, irrespective of statistical methods. The advantages and disadvantages of the three fingerprinting methods were discussed.     

Approaches to trophic analysis of paleocommunities

Trophic analysis of communities consists of three methods: (1) measuring energy flow, (2) reconstructing food chains. and (3) describing feeding habit - substrate niche patterns. The latter two methods are useful in interpreting evolutionary patterns and depositional environments of paleocommunities. Because the preserved trophic structure may differ significantly from the actual structure. each study must test the hypothesis that preserved trophic structure is related to the environment. Analysis of several modem marine communities shows that their 'preserved' structure would not differ greatly from the actual structure. A comparison of some Holocene communities with Tertiary and Cretaceous communities shows that some communities from comparable environments have distinct feeding habit-substrate niche patterns. Differences can be explained by the evolutionary stage of the biosphere. Trophic structure seems to be partly related to over-all environmental stability, to food resources, and to substrate type.     

Phylogenetic Composition of Rocky Mountain Endolithic Microbial Ecosystems

The endolithic environment, the pore space in rocks, is a ubiquitous microbial habitat. Photosynthesis-based endolithic communities inhabit the outer few millimeters to centimeters of rocks exposed to the surface. Such endolithic ecosystems have been proposed as simple, tractable models for understanding basic principles in microbial ecology. In order to test previously conceived hypotheses about endolithic ecosystems, we studied selected endolithic communities in the Rocky Mountain region of the United States with culture-independent molecular methods. Community compositions were determined by determining rRNA gene sequence contents, and communities were compared using statistical phylogenetic methods. The results indicate that endolithic ecosystems are seeded from a select, global metacommunity and form true ecological communities that are among the simplest microbial ecosystems known. Statistical analysis showed that biogeographical characteristics that control community composition, such as rock type, are more complex than predicted. Collectively, results of this study support the idea that patterns of microbial diversity found in endolithic communities are governed by principles similar to those observed in macroecological systems.     

Are we close enough? Comparing prairie reconstruction chronosequences to remnants following two site preparation methods in Missouri,U.S.A.

Prairie reconstruction has become a common method for reestablishing tallgrass prairie communities in the central United States. With the objective of creating plant communities that approximate remnant (reference) prairies, managers are interested in identifying: (1) best methods for reconstructing reference community conditions; (2) the rate of change in plant communities through time following reconstruction; and (3) species present in remnant communities but missing from reconstructed communities. This information is important in the development of adaptive management strategies during active reconstruction. We used a chronosequence approach to assess the success of two reconstruction methods in emulating local, reference remnant prairie plant communities. We compared broadcast dormant seeding following two types of site preparation, agricultural cropping (Crop) or herbicide control in existing grass assemblages (Grass), and remnant communities. The Crop site preparation method resulted in a rapid increase in richness shortly following seeding. Although more similar to remnant assemblages initially, the Grass method took longer for mean coefficient of conservatism and floristic quality index to approach conditions of the reference communities. However, neither method resulted in plant community compositions that converged with the reference through time. Further, indicator species analysis identified a diverse assemblage of species lacking from the reconstructed prairies. These results suggest the need to develop management strategies for establishing the “missing” species during reconstruction and provide further support for protection and conservation of existing remnant prairies.     

生物群落多样性的测度方法 V.生物群落物种数目的估计方法

群落的物种数目,即物种丰富度,是最古老、同时也是最基本的一个多样性概念,从对它的估计中可以得到关于物种灭绝速率方面的信息,这对生物多样性保护是非常重要的。已经提出了很多方法来估计群落中的物种数目,这些方法可以分为两大类,即基于理论抽样的方法和基于数据分析的方法。前者包括经典估计方法和贝叶斯估计方法;后者包括对数正态分布的积分方法、再抽样方法和种－面积曲线的外推方法。发现：（１）有些方法适用于动物群落,如大多数基于理论抽样的方法;有些方法则适用于植物群落,如大多数基于数据分析的方法;（２）这些方法还没有经过全面而系统地比较;（３）还没有一个普遍认为比较好的方法。因此,建议采用野外调查与模拟研究相结合的方法对各种估计方法进行系统地评价。     

Phylogenetic composition of Rocky Mountain endolithic microbial ecosystems

The endolithic environment, the pore space in rocks, is a ubiquitous microbial habitat. Photosynthesis-based endolithic communities inhabit the outer few millimeters to centimeters of rocks exposed to the surface. Such endolithic ecosystems have been proposed as simple, tractable models for understanding basic principles in microbial ecology. In order to test previously conceived hypotheses about endolithic ecosystems, we studied selected endolithic communities in the Rocky Mountain region of the United States with culture-independent molecular methods. Community compositions were determined by determining rRNA gene sequence contents, and communities were compared using statistical phylogenetic methods. The results indicate that endolithic ecosystems are seeded from a select, global metacommunity and form true ecological communities that are among the simplest microbial ecosystems known. Statistical analysis showed that biogeographical characteristics that control community composition, such as rock type, are more complex than predicted. Collectively, results of this study support the idea that patterns of microbial diversity found in endolithic communities are governed by principles similar to those observed in macroecological systems.     

Importance of subaerial biofilms and airborne microflora in the deterioration of stonework: a molecular study

The study characterized the sessile microbial communities on mortar and stone in Milan University's Richini's Courtyard and investigated the relationship between airborne and surface-associated microbial communities. Active colonization was found in three locations: green and black patinas were present on mortar and black spots on stone. Confocal laser scanning microscopy, scanning electron microscopy and culture-independent molecular methods revealed that the biofilm causing deterioration was dominated by green algae and black fungi. The mortar used for restoration contained acrylic and siloxane resins that could be used by microorganisms as carbon and energy sources thereby causing proliferation of the biofilm. Epifluorescence microscopy and culture-based methods highlighted a variety of airborne microflora. Bacterial and fungal counts were quantitatively similar to those reported in other investigations of urban areas, the exception being fungi during summer (1–2 orders of magnitude higher). For the first time in the cultural heritage field, culture-independent molecular methods were used to resolve the structure of airborne communities near discoloured surfaces, and to investigate the relationship between such communities and surface-associated biofilms.     

Comparison of different methods for diversity ordering

Abstract. The measurement of diversity, one of the most important concepts in present-day ecology, can be improved by methods of diversity ordering which have recently been developed. This ordering is achieved by a D(α) diversity index family. Indices of this family show varying sensitivities to the rare and abundant species as the scale parameter, α, changes. The aim of this paper is to review and assess 12 methods of diversity ordering and discuss their relationships in detail. Two of the methods are new to the ecological literature. The diversity ordering methods are compared as to their effectiveness in graphically displaying the differences of community structure and demonstrating the (non-)comparability of communities. Small, medium and large data sets were used to evaluate the methods. A small artificial data set (five to seven species) and a large semi-artificial data set (31 — 141 species) are used in this paper. The results suggest that Rényi's diversity index family and Logarithmic dominance ordering are the most useful methods for diversity ordering of communities of all sizes. Right-tailsum diversity ordering performs well for small communities.     

Optimal extraction methods for the simultaneous analysis of DNA from diverse organisms and sample types

Using environmental DNA (eDNA) to assess the distribution of micro‐ and macroorganisms is becoming increasingly popular. However, the comparability and reliability of these studies is not well understood as we lack evidence on how different DNA extraction methods affect the detection of different organisms, and how this varies among sample types. Our aim was to quantify biases associated with six DNA extraction methods and identify one which is optimal for eDNA research targeting multiple organisms and sample types. We assessed each methods’ ability to simultaneously extract bacterial, fungal, plant, animal and fish DNA from soil, leaf litter, stream water, stream sediment, stream biofilm and kick‐net samples, as well as from mock communities. Method choice affected alpha‐diversity for several combinations of taxon and sample type, with the majority of the differences occurring in the bacterial communities. While a single method performed optimally for the extraction of DNA from bacterial, fungal and plant mock communities, different methods performed best for invertebrate and fish mock communities. The consistency of methods, as measured by the similarity of community compositions resulting from replicate extractions, varied and was lowest for the animal communities. Collectively, these data provide the first comprehensive assessment of the biases associated with DNA extraction for both different sample types and taxa types, allowing us to identify DNeasy PowerSoil as a universal DNA extraction method. The adoption of standardized approaches for eDNA extraction will ensure that results can be more reliably compared, and biases quantified, thereby advancing eDNA as an ecological research tool.