Soil microbial community analysis using denaturing gradient gel electrophoresis

The most biological diversity on this planet is probably harbored in soils. Understanding the diversity and function of the microbiological component of soil poses great challenges that are being overcome by the application of molecular biological approaches. This review covers one of many approaches being used: separation of polymerase chain reaction (PCR) amplicons using denaturing gradient gel electrophoresis (DGGE). Extraction of nucleic acids directly from soils allows the examination of a community without the limitation posed by cultivation. Polymerase chain reaction provides a means to increase the numbers of a target for its detection on gels. Using the rRNA genes as a target for PCR provides phylogenetic information on populations comprising communities. Fingerprints produced by this method have allowed spatial and temporal comparisons of soil communities within and between locations or among treatments. Numerous samples can be compared because of the rapid high throughput nature of this method. Scientists now have the means to begin addressing complex ecological questions about the spatial, temporal, and nutritional interactions faced by microbes in the soil environment.

Soil microbial community analysis using terminal restriction fragment length polymorphisms

Terminal restriction fragment length polymorphism (T-RFLP) analysis is a polymerase chain reaction (PCR)-fingerprinting method that is commonly used for comparative microbial community analysis. The method can be used to analyze communities of bacteria, archaea, fungi, other phylogenetic groups or subgroups, as well as functional genes. The method is rapid, highly reproducible, and often yields a higher number of operational taxonomic units than other, commonly used PCR-fingerprinting methods. Sizing of terminal restriction fragments (T-RFs) can now be done using capillary sequencing technology allowing samples contained in 96- or 384-well plates to be sized in an overnight run. Many multivariate statistical approaches have been used to interpret and compare T-RFLP fingerprints derived from different communities. Detrended correspondence analysis and the additive main effects with multiplicative interaction model are particularly useful for revealing trends in T-RFLP data. Due to biases inherent in the method, linking the size of T-RFs derived from complex communities to existing sequence databases to infer their taxonomic position is not very robust. This approach has been used successfully, however, to identify and follow the dynamics of members within very simple or model communities. The T-RFLP approach has been used successfully to analyze the composition of microbial communities in soil, water, marine, and lacustrine sediments, biofilms, feces, in and on plant tissues, and in the digestive tracts of insects and mammals. The T-RFLP method is a user-friendly molecular approach to microbial community analysis that is adding significant information to studies of microbial populations in many environments.

内蒙古高原成熟和退化羊草草原群落物种功能特性与土壤微生物量C、N、P对氮素添加响应

氮素是大多数陆地生态系统初级生产力的主要限制因子。由于人类的工业和农业生产活动不断加剧，导致全球性氮沉降增加，使大多数生态系统氮素的可获得性增强。从而降低或消除了氮素对生态系统的限制作用，加速了生态系统生物地球化学过程，对物种多样性和生态系统结构与功能产生了显著的影响。但由于成土母质、气候条件、地形地貌、植被组成等的差异，不同生态系统类型对氮素增加的响应也不尽相同。欧洲和北美一些发达国家地区对于草地生态系统对于全球性氮沉降增加响应进行了较全面的研究，对于分布广泛的欧亚大陆草原研究相对不足。 本文研究选择对于欧亚大陆草原较具代表性的成熟羊草草原群落及该群落的退化类型为研究对象，从1999年开始，在这两类群落中选取地形相对平缓均一，植被组成一致的地段设置了施肥小区并进行持续氮素添加实验。本文研究了成熟和退化羊草草原群落物种功能特性与土壤微生物量C、N、P对氮素添加响应。 羊草群落中6种主要植物的地上生物量、种群密度、比叶面积、叶氮和叶绿素含量对于氮素添加响应以及各指标之间相关关系的分析表明：比叶面积、基于质量的叶片含氮量和叶绿素含量、叶绿素a和叶绿素b的比值等叶片水平上物种功能特性间的相互作用，共同影响和决定了种群密度和地上生物量对氮素添加的响应。羊草通过提高比叶面积、叶片叶绿素含量和含氮量、种群密度及个体生物量等多重调节功能对氮素添加做出响应。西伯利亚羽茅主要通过提高比叶面积、单位质量叶片的叶绿素含量和含氮量，以及株丛生物量，使其在群落占据优势。大针茅和冰草在提高比叶面积、叶片叶绿素含量和含氮量的调节能力相对较低，种群密度沿氮素添加梯度显著降低。黄囊苔草只能通过提高叶片叶绿素含量和含氮量对氮素添加做出响应，其叶绿素a与叶绿素b的比值沿氮素添加梯度逐渐降低，种群密度和地上生物量也显著降低。糙隐子草的叶绿素a与叶绿素b比值沿氮素添加梯度显著降低，但由于糙隐子草具有较高的SLA，且对叶绿素、叶片含氮量的调节能力较强，氮素添加处理没有对其种群密度和地上生物量产生显著的影响。上述结果支持Tilman的光资源竞争假说和Knops等的物种替代假说。 成熟和退化羊草群落土壤微生物量、土壤有机碳、全氮、全磷、速效氮、pH以及凋落物碳、氮、磷含量的测定结果表明：（1）成熟羊草群落表层土壤微生物量碳、氮、磷含量均随氮素添加量的增加而降低;退化羊草群落表层土壤微生物量碳、氮、磷含量沿氮素梯度表现出先增加而后降低的趋势;相关分析的结果显示各群落土壤微生物量碳、氮、磷均与土壤pH呈显著的正相关。（2）微生物量碳、氮、磷含量均随土层深度的增加而下将;而对照的微生物量碳、氮、磷含量则与土壤有机质含量呈显著正相关。（3）年度间降水量差异对土壤微生物量碳、氮、磷具有较大影响。综合上述研究结果，我们认为成熟羊草群落土壤微生物生长不受氮素限制，但退化群落不同;氮素添加导致的土壤酸化作用可能是两类群落表层土壤微生物量下降的主要因素，且这种影响主要集中在0-10cm的表层土壤;表层土壤微生物量碳、氮、磷对氮素添加的响应可能还受到其它因子（如生长季降水量）的影响;深层土壤微生物量较低主要是由于土壤有机质含量较低的缘故。