微生物群落

null What is microbial community ecology? The ISME Journal (2009), 1–8 Allan Konopka Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA 吕毅 2009.11.7 What is microbial community ecology? The ISME Journal (2009), 1–8 Allan Konopka Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA 吕毅 2009.11.7nullIntroduction As microbial communities are of primary importance in biogeochemical transformations. Predicting future environmental conditions. There is great interest in applying modern technologies in genome-enabled biology and analytical chemistry to concurrently study both the identity and the function of complex microbial communities. nullWhat is a microbial community? Elements of microbial community analysis Additional directions for future research What is a microbial community?What is a microbial community?Communities are defined as multi-species assemblages, in which organisms live together in a contiguous environment and interact with each other. This discipline seeks to analyze how biological assemblages are structured, what are their functional interactions and how community structure changes in space and time.nullClements (1916) viewed the community as a ‘supra-organism’, which had a well-defined level of organization with tight interactions among organisms that comprise a causal system and gives rise to emergent properties. 群落的界限可能跟物理三维空间关系不大，而与物种的相互作用关系的强弱有关。nullThe alternative individualistic concept (Gleason, 1926) is that many species co-occur in a habitat because they tolerate similar physical and chemical conditions and do not necessarily interact with each other. 另一种观点是：可以忍受相似的物理和化学环境而聚集在一起的微生物群，不需要相互作用。Define microbial ecologyDefine microbial ecologyMicroorganisms-------Microns fungal hyphae-------millimeters water-saturated sediments-------meters As a result, the strength of interaction among organisms and the defined spatial scale may vary substantially for investigator-defined microbial communities.nullKonopka defined four ecosystems derived by considering the environment from the microbe’s local perspective (Table 1). Each has particular characteristics that define important selective forces in that habitat, but which also impact the spatial scale over which microbial interactions occur.nullnullElements of microbial community analysis Levin (1999) proposed that ‘the most important challenge for ecologists remains to understand the linkages between what is going on at the level of the physiology and behavior of individual organisms and emergent properties such as the productivity and resiliency of ecosystems.’ Important elements for analysis of microbial communities comprise fluxes, interactions and properties.（1）Analysis of community functional pathways（1）Analysis of community functional pathwaysMany reactions in chemoheterotrophs entail conversion of chemical elements from organic forms to inorganic forms that can be used by primary producers for new biomass synthesis. The analysis of material and energy flow through distributed metabolic networks of microbes could lead to a predictive understanding of ecosystems.Technically, it is possible to measure the rates of specific biogeochemical processes and to census the phylogenetic identities of the resident microbes. Increasingly sophisticated analytical methods such as NanoSIMS（高清晰二次离子质谱仪）and Raman spectroscopy can permit the use of stable isotopes to measure process rates, with subsequent analyses of labeled macromolecules to phylogenetically identify the microbial catalyst. SIPTechnically, it is possible to measure the rates of specific biogeochemical processes and to census the phylogenetic identities of the resident microbes. Increasingly sophisticated analytical methods such as NanoSIMS（高清晰二次离子质谱仪）and Raman spectroscopy can permit the use of stable isotopes to measure process rates, with subsequent analyses of labeled macromolecules to phylogenetically identify the microbial catalyst. SIP(2)Interactions among organisms(2)Interactions among organismsInterest in microbial community ecology is a consequence of the postulate that interactions between organisms (microbe–microbe and microbe–metazoan) are of essential importance for understanding ecosystem dynamics and the evolutionary ecology of individual organisms. nullnullThese include not only short-term (physiological) interactions, but also potentially deeper consequences that arise from horizontal gene transfer or co-evolution of traits between different microbes or a microbe and a multicellular organism. 不仅是短期相互作用的影响，还可能由水平基因转移或不同微生物和多细胞生物间的特征共演化导致更深入的结果。(3)Emergent properties应激特征(3)Emergent properties应激特征An analysis of these properties can lead to an understanding of how the system responds to both external and internal perturbations, and provides the capability to predict system dynamics in response to environmental change. 应激特征往往能反映出内外环境变化时生态系统做出的反应。还可预测系统的动态变化。（4）Taxonomic diversity（4）Taxonomic diversityAn inventory of diversity within a discrete sample has two important components— taxon richness and the relative abundance of different taxa in the community.类群的丰度（含量）和不同类的相对丰度（百分比） The analysis of 16S rRNA gene sequences directly from environmental samples has greatly enriched our understanding of global microbial diversity.nullAnalysis of relative abundance is conceptually very important to the other properties of communities, but a consequence of undersampling is that detection and quantitation of taxa present at low relative abundance is imprecise.一般会忽略掉丰度低的群落 New DNA sequencing technologies (pyrosequencing) can provide enough data ,and the application of theoretical constructs to community assembly can suggest methods of analysis that provide informative rank-abundance distributions for microbial communities.(5)Functional diversity and functional redundancy(5)Functional diversity and functional redundancyHigher levels of redundancy for ecological functions should be related to the reliability with which an ecosystem will continue to deliver services in the face of environmental changes. 高水平的冗余可以是生态系统对环境的变化有较高的稳定性。（Figure 1）nullConceptual model of relationship between functional redundancy and ecosystem stability. 生态系统的稳定性和功能冗余的关系nullThe central question is how to assay and quantify functional diversity. In some cases, there are conserved regions of functional genes that can be used to assess the abundance of these genes in natural samples. Analysis of sequence differences among amplicons by fingerprinting techniques will permit an analysis of functional diversity, at least for abundant community members.（T-RFLP）nullThe other limitation to this molecular approach for analysis of functional diversity is that novel genes and enzymes will not be recognized.分子方法分析得到的一些基因和蛋白质不被公认。 A weakness of most current applications of community metagenomics or metaproteomics to complex communities is that gene sequences and proteins are disassociated from the intact organism that possessed them. As a result, the analyses cannot place a specific function in the context of the other functional properties of the organism. 群落宏基因组和蛋白质组的缺点就是脱离完整生物。所以，这种分析就不能在生物其他功能特征中显示特异性。nullA measure of functional redundancy could be derived from cataloging genes or proteins with annotated functions and correlated to ecosystem resiliency to experimentally imposed perturbations. 功能冗余的一种检测方法是直接来源于已有功能的基因或蛋白的数据库，另外一种方法是在实验性的干扰下，看基因表达情况与生态系统恢复性得相关。 For complex microbial communities, we may have to wait for the advent of technologies, whereby several hundred bacterial cells could be individually plucked from a habitat, and their genomes amplified and sequenced in a high-throughput and inexpensive manner. 新技术：复杂微生物群落的几百个细菌细胞分开分别得到一个菌落然后扩增，将他们的基因组进行高通量测序。单细胞的基因组扩增(6)Stability/resistance/resilience.(6)Stability/resistance/resilience.Resistance is related to the degree that a system does not exhibit an acute loss of function after imposition of a stress, whereas resilience connotes the rate at which functionality returns after an acute stress effect. ‘Stability’ could represent either the resistance of a system to acute, toxic effects or resilience, taking into account a longer-term perspective,in which stress imposes selection for resistant taxa present at low relative abundance.nullTheoretical and empirical work in ecology has investigated the idea that higher diversity within a community will lead to increased ecosystem stability. 多样性高，稳定性就高。（7）Community genetic potential.（7）Community genetic potential.Microbes (particularly Bacteria and Archaea) have mechanisms for gene transfer across broad phylogenetic barriers that do not occur at ecologically significant rates in other organisms. Thus, the resilience of microbial communities over a period of a few years to environmental perturbations may rest in part on the frequency of horizontal gene transfer within microbial communities. 微生物群落的恢复性可能部分决定于水平转移的频率。nullAnalysis of microbial community functionality requires not only the identification of a protein family, but also an understanding of the range of substrate usage. 微生物群落功能的分析需要蛋白质家族的鉴定和对底物的利用范围内的理解。 A larger problem is the substantial fraction (approximately 30%) of genes in sequenced bacterial genomes, for which no function is assignable at all. Perhaps their functions are unknown because they are unimportant under laboratory culture, which may mean that they are very significant for some ecological function in nature, but this would require significant experimentation to uncover. 我们无法发现基因在自然界中用到而实验条件下用不到的功能。Additional directions for future research that would aid in going beyond a descriptive to a predictive science of microbial community ecology might include several other experimental, computational and technical approaches:Additional directions for future research that would aid in going beyond a descriptive to a predictive science of microbial community ecology might include several other experimental, computational and technical approaches:null(1) Expansion of experimental approaches beyond those most commonly used in microbial ecology: 应用微生物生态的实验方法的扩展 a common experimental regime is manipulation of environmental factors in the field or in confined samples to analyze effects of abiotic factors on ecosystem processes. However, it is difficult to assess how microbial community structure impacts ecosystem functioning from these experiments. Application of experimental approaches such as common garden experiments （Ecological transplant studies in which organisms are reared under identical conditons.在相同条件下生长培养的生态移植）and reciprocal transplants（互惠移植） can provide community-level insights.(2) Predictive models at the community scale (2) Predictive models at the community scale this is a daunting task, and current models of aquatic or terrestrial ecosystems neither attempt to include microbiological diversity nor spatial heterogeneities. A path forward would include scaling at the fundamental microbial ecosystem level。 (3) Microbial model systems to test ecological theory (3) Microbial model systems to test ecological theory microcosm experiments have been criticized as unrepresentative surrogates of natural ecosystems.(4) Explicitly directing research efforts to the three specific elements of microbial community analysis identified above (4) Explicitly directing research efforts to the three specific elements of microbial community analysis identified above This can be accomplished through data mining of metagenomes or targeted approaches such as PCR amplification of known functional genes or development of activity-based proteomic approaches. 宏蛋白质组和宏基因组在微生物生态方面的作用还是很大。nullThank you