农业土壤微生物基因与群落多样性研究进展

介绍了群落基因组多样性、结构多样性与功能多样性相互关系的研究方法 ,重点论述了近年来农业土壤微生物群落遗传、结构与功能多样性的研究进展。同时总结了耕作措施和养分管理对农业土壤微生物群落多样性的影响 ,提出微生物序列分析、比较基因组学和微生物芯片技术与传统研究技术结合将有助于对微生物群落结构与功能和生物与环境因素对土壤微生物群落影响的深刻理解     

PCR-RFLP法探讨三个人工湖微生物群落多样性

目的：探讨牡丹江市区三个人工湖（月牙湖、牛角湖、南湖）的微生物群落多样性。方法：从三个水样中分别提取微生物DNA,选取通用引物扩增16S rDNA片段,对扩增产物进行RFLP分析。结果：不同的样品由于其中的微生物多样性的差异,酶切产物在凝胶上显示的相对位置和条带数目都有一定差异。结论：牛角湖样品的条带数目最多,表明牛角湖的微生物群落多样性最为丰富。     

人体皮肤微生物群落研究进展

皮肤作为人体最大的器官,上面定居着各种各样的微生物,它们大部分是无害的,甚至对人体有益。皮肤表面的生态环境因不同的表面特征和外部因素而呈现不同的格局,使得分布于皮肤上的微生物群落出现差异。分子生物学技术的发展使研究皮肤表面微生物群落的高度多样性和多变性成为可能,而且可从生态系统角度去理解和认识皮肤微生物。本文就皮肤微生物群落的主要特点、微生物群落与疾病的联系及其具体应用等方面作一综述。     

种植体周围炎生物膜的微生物群落多样性研究进展

种植体周围炎是发生在骨性结合种植体周围组织的炎症,是由微生物引发的感染性疾病,可引起种植体周围支持组织丧失而导致种植失败。阐明种植体周围炎生物膜的微生物学基础,可为制定相应防治策略提供理论依据。随着测序技术的发展,基于16S rRNA基因的测序分析技术逐渐应用于与口腔种植体相关的微生物学研究,使人们对种植体周围炎生物膜的微生物群落多样性有了更全面的了解,也进一步认识到种植体周围炎和牙周炎菌斑生物膜的微生物结构存在显著差别。本文根据基于16S rRN基因A序列分析技术的最新研究成果,对种植体周围炎菌斑生物膜的微生物学研究进展作一综述。     

农药污染对土壤微生物群落功能多样性的影响

根据95种不同的单一联底物上的BIOLOGGN微平板系统的反应所构造的多样性指数，结果表明农药严重污染的土壤微生物群落的Shannon指数和均度、Simpson指数、Mclntosh指数和均度均显著低于无污染的对照。说明农药严重污染导致土壤微生物群落功能多样性的下降，减少了能利用有关碳底物的微生物的数量，降低微生物对单一碳底物的利用能力。     

青岛市秋季空气微生物群落多样性

采用KC-6120空气综合采样器采集空气微生物样品,通过构建16S/18SrDNA克隆文库方法分析青岛市市区街道秋季空气微生物群落结构特征.结果表明： 空气细菌分布在6大类,分别为变形菌门(78.8%)、厚壁菌门(14.6%)、放线菌门(4.0%)、浮霉菌门(1.3%)、蓝藻门(0.7%)和栖热菌门(0.6%),优势菌属为不动杆菌属(39.7%)、葡萄球菌属(11.3%)、鞘脂单胞菌属(8.6%)和副球菌属(6.0%).空气真菌分布在子囊菌门(97.5%)和担子菌门(2.5%),优势菌属为核腔菌属(76.5%)、炭角菌属(13.6%)和外瓶霉属(2.5%).空气微生物中存在不动杆菌属、鞘脂单胞菌、葡萄球菌等致病菌或条件致病菌,以及引发多种农作物枯萎死亡的麦类核腔菌、团炭角菌和角状平脐疣孢等真菌.     

青岛市秋季空气微生物群落多样性

采用KC-6120空气综合采样器采集空气微生物样品,通过构建16S/18SrDNA克隆文库方法分析青岛市市区街道秋季空气微生物群落结构特征.结果表明： 空气细菌分布在6大类,分别为变形菌门(78.8%)、厚壁菌门(14.6%)、放线菌门(4.0%)、浮霉菌门(1.3%)、蓝藻门(0.7%)和栖热菌门(0.6%),优势菌属为不动杆菌属(39.7%)、葡萄球菌属(11.3%)、鞘脂单胞菌属(8.6%)和副球菌属(6.0%).空气真菌分布在子囊菌门(97.5%)和担子菌门(2.5%),优势菌属为核腔菌属(76.5%)、炭角菌属(13.6%)和外瓶霉属(2.5%).空气微生物中存在不动杆菌属、鞘脂单胞菌、葡萄球菌等致病菌或条件致病菌,以及引发多种农作物枯萎死亡的麦类核腔菌、团炭角菌和角状平脐疣孢等真菌.     

土地整理对土壤微生物群落多样性的影响

土地整理保证了我国耕地总量的动态平衡和占补平衡,已成为实现国土资源集约利用的主要手段,但整治过程中的强度扰动会对土壤质量产生一定的影响.为了解土地整理对土壤微生物多样性的影响,采用PLFA法研究了土地整理1年(Z1a)、4年(Z4a)后土壤微生物群落多样性的变化.结果表明: 与未整理(Z0)相比,土地整理1年后,土壤pH值提高了14.6%,土壤有机碳质量分数降低了65.4%;各菌群磷脂脂肪酸PLFAs含量和相对丰度均显著下降(P<0.05),下降幅度达43.4%～63.7%和25.2%～53.9%;真菌/细菌(F/B)显著下降(P<0.05),降低了35.9%,而革兰氏阳性菌/革兰氏阴性菌(G⁺/G^-)升高明显,增加了56.1%,均与有机碳的降低和pH值的升高有显著相关关系;土壤微生物多样性Shannon指数和均匀度指数(E)均显著下降,Z0与Z1a、Z4a之间的差异达显著水平;土地整理4年后,表征土壤微生物群落多样性的各指标相比整理1年的样地有所提升,但与未整理样地仍有显著差异.综上,土地整理显著影响着土壤微生物群落的组成,降低了土壤生态系统的稳定性.     

环境异质性影响土壤微生物群落的研究进展

环境异质性是影响微生物群落结构和多样性的重要因素,其涉及内容广泛,各异质性因素之间彼此关联。基于生物和非生物特征,可将环境异质性分为土地覆盖、植物、气候、土壤和地形等5种异质性因素。文章综述了上述五种环境异质性因素的概念和区别,并针对不同类型环境异质性因素对微生物群落的影响进行了较为全面的汇总和分析。通过梳理微生物生态学、生物信息学等相关研究方法和技术的发展,阐述了现阶段研究环境异质性与微生物互作关系的不足,并进行了展望。     

灌溉方式对稻田土壤微生物群落功能多样性的影响

为了探讨3种不同灌溉模式对土壤微生物群落功能多样性的影响。本研究采用Biolog-ECO板研究了双季稻田连续五年不同灌溉处理(长期灌溉,湿润灌溉,间歇灌溉)下的土壤微生物群落功能多样性。结果表明,不同灌溉方式处理的土壤微生物代谢活性强度为间歇灌溉湿润灌溉长期淹水灌溉。在不同的处理中,α-环式糊精和D-葡萄胺酸解释了主要的差异。氨基酸和糖类碳源是间歇灌溉和湿润灌溉灌溉模式下主要被利用的碳源,而酯类在长期淹水灌溉模式被利用的最多。通过评价3种灌溉方式下稻田土壤的代谢特征,证实了间歇灌溉方式有利于提高稻田土壤微生物的功能多样性,为稻田水分科学管理提供了理论依据。     

Dilution/extinction of community phenotypic characters to estimate relative structural diversity in mixed communities

Recent interest in microbial diversity has led to increased emphasis on the development of appropriate techniques. Structural diversity encompasses the number and distribution of separate or interacting biological entities responsible for a given function within the overall set of functions of a community. This study evaluated an approach for estimating the relative degree of structural diversity in heterotrophic microbial communities by dilution to extinction of community phenotypic traits. Serial dilutions of environmental samples (rhizosphere, stream) were tested for community phenotypic traits (i.e. carbon source respiration). The non-linear relationship between the number of positive responses (i.e. functional richness or R) and inoculum density in each sample dilution (I) fit the simple rectangular hyperbola model, allowing estimation of the maximal richness (R(max)) and the inoculum density at half-maximal richness (K(I)). The later term appears to be useful in assessing relative structural diversity as evidenced by significantly higher values for communities with higher predicted species diversity. The examination of community functional characteristics across a series of dilutions, particularly in conjunction with other techniques, may be a useful approach for the study of microbial diversity and related ecological parameters such as niche width and metabolic redundancy.     

微生物群落多样性数学表征方法及其在污水处理系统研究中的应用

微生物群落在调节全球气候、人类健康和工业生物技术应用中扮演着重要角色。定量表征微生物群落多样性是认识微生物群落基本特征、动态变化和功能的前提。本文介绍了常用的α多样性指数,包括物种数目、Shannon-Weaver指数、Simpson多样性指数和Hill多样性指数;并介绍了其他多样性评估方法及其原理,包括能够评价样本对微生物群落各物种覆盖程度的稀释性曲线和Good’s coverage指数,以及能估算群落多样性的Chao1、ACE指数和基于物种丰度分布曲线的模型方法;并以最大规模的生物技术应用——污水处理厂为例,介绍了这些方法在认识微生物群落多样性中的应用。现有研究表明:所检测到的城市污水处理厂中微生物群落的物种数目和Shannon-Weaver指数随检测方法解析通量(样本大小)的增加而增大;但现有方法仍无法反映城市污水处理厂微生物群落的真实多样性。基于特定的物种丰度分布曲线对DNA样本数据进行模拟和重建,结果表明对群落物种数目的评估存在较大的不确定性;Shannon-Weaver指数,特别是Simpson多样性指数等受低丰度物种影响较小,可以准确计算,是评价和比较微生物群落分类学多样性的好手段。改进模型拟合方法和加大取样深度能提高微生物群落物种数目的评估精度。此外,认识微生物群落其他方面的多样性如系统发育多样性和功能多样性,也对认识微生物生态特征具有重要意义。     

Long-term cathode performance and the microbial communities that develop in microbial fuel cells fed different fermentation endproducts

To better understand how cathode performance and substrates affected communities that evolved in these reactors over long periods of time, microbial fuel cells were operated for more than 1 year with individual endproducts of lignocellulose fermentation (acetic acid, formic acid, lactic acid, succinic acid, or ethanol). Large variations in reactor performance were primarily due to the specific substrates, with power densities ranging from 835 ± 21 to 62 ± 1 mW/m³. Cathodes performance degraded over time, as shown by an increase in power of up to 26% when the cathode biofilm was removed, and 118% using new cathodes. Communities that developed on the anodes included exoelectrogenic families, such as Rhodobacteraceae, Geobacteraceae, and Peptococcaceae, with the Deltaproteobacteria dominating most reactors. Pelobacter propionicus was the predominant member in reactors fed acetic acid, and it was abundant in several other MFCs. These results provide valuable insights into the effects of long-term MFC operation on reactor performance.     

大港孔店油田水驱油藏微生物群落的分子分析

通过多聚酶链式反应温度梯度凝胶电泳（PCRTGGE）和构建16S rRNA基因克隆文库两种方法对比研究了大港油田孔二北断块注水井和采油井的微生物群落结构。16S rDNA V3区PCR扩增产物的TGGE图谱分析表明,这两个油井的微生物群落结构差异很大。注水井样品的TGGE图谱中有6条主要条带,而采油井样品中只有一个条带占绝对优势。同时,建立了两个样品的16S rRNA基因克隆文库,从中分别挑选了108和50个克隆进行限制性酶切片段长度多样性分析（ARDRA）。注水井样品有33个操作分类单元（OUT）,其中6个OUT是优势类型;而采油井样品只有8个OUT,有1个OUT在文库中占绝对优势。克隆文库和TGGE的研究结果一致,均表明注水井样品的微生物多样性比采油井丰富很多。每个OUT的代表克隆序列分析结果表明,注水井样品中的细菌主要属于α、β、γ变形菌纲和放线菌纲,尤其是红细菌亚纲（47%）。采油井样品的细菌主要属于α、β、γ变形菌纲,尤其是假单胞菌属（62%）。油藏微生物多样性的分子分析可为开展微生物采油技术研究奠定基础。     

Analysis of diurnal and vertical microbial diversity of a hypersaline microbial mat

Microbial mats are prokaryotic communities that provide model systems to analyze microbial diversity and ecophysiological interactions. Community diversity of microbial mat samples was assessed at 8:00 a.m. and 3:00 p.m. in a combined analysis consisting of 16S rRNA-denaturing gradient gel electrophoresis (DGGE) and phospholipid fatty acid (PLFA) profiles. The divergence index determined from PLFA and DGGE data showed that depth-related differences have a greater influence on diversity than temporal variations. Shannon and Simpson indices yielded similar values in all samples, which suggested the stable maintenance of a structurally diverse microbial community. The increased diversity observed at 3:00 p.m. between 2.5 and 4 mm can be explained mainly by diversification of anaerobic microorganisms, especially sulfate-reducing bacteria. In the afternoon sampling, the diversity index reflected a higher diversity between 4 and 5.5 mm depth, which suggested an increase in the diversity of strict anaerobes and fermenters. The results are consistent with the conclusion that hypersaline microbial mats are characterized by high degree of diversity that shifts in response to the photobiological adaptations and metabolic status of the microbial community. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Dedicated to the memory of David C. White.     

Change in microbial communities in acetate- and glucose-fed microbial fuel cells in the presence of light

Power densities produced by microbial fuel cells (MFCs) in natural systems are changed by exposure to light through the enrichment of photosynthetic microorganisms. When MFCs with brush anodes were exposed to light (4000 lx), power densities increased by 8–10% for glucose-fed reactors, and 34% for acetate-fed reactors. Denaturing gradient gel electrophoresis (DGGE) profiles based on the 16S rRNA gene showed that exposure to high light levels changed the microbial communities on the anodes. Based on 16S rRNA gene clone libraries of light-exposed systems the anode communities using glucose were also significantly different than those fed acetate. Dominant bacteria that are known exoelectrogens were identified in the anode biofilm, including a purple nonsulfur (PNS) photosynthetic bacterium, Rhodopseudomonas palustris, and a dissimilatory iron-reducing bacterium, Geobacter sulfurreducens. Pure culture tests confirmed that PNS photosynthetic bacteria increased power production when exposed to high light intensities (4000 lx). These results demonstrate that power production and community composition are affected by light conditions as well as electron donors in single-chamber air-cathode MFCs.     

海洋微生物多样性及其分子生态学研究进展

海洋微生物多样性的深入研究将有助于微生物资源更好的开发和利用,海洋微生物多样性有很大的研究价值和研究空间。海洋中大多数微生物处于未可培养状态,在分子生态学基础上对海洋未可培养微生物进行研究是当今微生物多样性研究的主要方向。近年来相关研究进展迅速,研究方法不断更新。主要从分子生态学角度对微生物多样性研究现状进行概述并详细分析探讨了相关的研究方法,而且从分子生态学与海洋微生物多样性研究相结合的层面,对本领域的研究进行展望。旨在为海洋微生物多样性的研究及海洋资源的可持续开发与利用提供参考。     

陆地植物群落物种多样性研究进展

生物多样性是当前生态学研究的热点之一,物种多样性层次是最直接、最易观察和最适合研究生物多样性的层次。总结了与群落动态、生境因子、取样尺度及生态系统相关的陆地植物物种多样性研究。同时,根据目前的趋势提出了多样性动态研究的发展动向。