真菌与植物共生机制研究进展

真菌与植物共生是一种非常普遍、复杂和重要的生物学现象。真菌与植物共生部位、共生类型和共生结构的多样性,以及参入共生的真菌和植物多样性奠定真菌与植物共生的生物学基础。真菌与植物首先通过分子"对话"的生化机制相互识别构建共生体,进而由真菌和植物双方生理机制调控共生体发育及其生理功能,以构建稳定有效的共生体。真菌与植物的空间、营养和功能生态位很多是相近的,双方均面临相同的生态选择压力,需要共同抵抗不良生境,以适应更多环境。因此,真菌和植物通过两者共生的生态学机制增强植物抗逆性,减轻有害生物危害,提高其竞争力和生境的适应能力。真菌和植物长期的协同演化过程中,种群间的基因交流及其差异导致不同的基因组合,奠定了共生体多样化的基础与资源。此遗传学机制形成的多种遗传组合的共生体不仅使真菌和植物在各环境压力下共存,还可以不断进化发展。真菌和植物共生研究方面已形成较为完善的体系,加强真菌与植物共生理论的研究,特别是该类共生体遗传背景、基因与环境互作效应及其机制的阐明,将有助于诠释真菌与植物共生的生物学机制。     

Symbiosis specificity in the legume: rhizobial mutualism

Legume plants are able to engage in root nodule symbiosis with nitrogen-fixing soil bacteria, collectively called rhizobia. This mutualistic association is highly specific, such that each rhizobial species/strain interacts with only a specific group of legumes, and vice versa. Symbiosis specificity can occur at multiple phases of the interaction, ranging from initial bacterial attachment and infection to late nodule development associated with nitrogen fixation. Genetic control of symbiosis specificity is complex, involving fine-tuned signal communication between the symbiotic partners. Here we review our current understanding of the mechanisms used by the host and bacteria to choose their symbiotic partners, with a special focus on the role that the host immunity plays in controlling the specificity of the legume - rhizobial symbiosis.     

Genome-Wide Functional Divergence after the Symbiosis of Proteobacteria with Insects Unraveled through a Novel Computational Approach

Symbiosis has been among the most important evolutionary steps to generate biological complexity. The establishment of symbiosis required an intimate metabolic link between biological systems with different complexity levels. The strict endo-cellular symbiotic bacteria of insects are beautiful examples of the metabolic coupling between organisms belonging to different kingdoms, a eukaryote and a prokaryote. The host (eukaryote) provides the endosymbiont (prokaryote) with a stable cellular environment while the endosymbiont supplements the host's diet with essential metabolites. For such communication to take place, endosymbionts' genomes have suffered dramatic modifications and reconfigurations of proteins' functions. Two of the main modifications, loss of genes redundant for endosymbiotic bacteria or the host and bacterial genome streamlining, have been extensively studied. However, no studies have accounted for possible functional shifts in the endosymbiotic proteomes. Here, we develop a simple method to screen genomes for evidence of functional divergence between two species clusters, and we apply it to identify functional shifts in the endosymbiotic proteomes. Despite the strong effects of genetic drift in the endosymbiotic systems, we unexpectedly identified genes to be under stronger selective constraints in endosymbionts of aphids and ants than in their free-living bacterial relatives. These genes are directly involved in supplementing the host's diet with essential metabolites. A test of functional divergence supports a strong relationship between the endosymbiosis and the functional shifts of proteins involved in the metabolic communication with the insect host. The correlation between functional divergence in the endosymbiotic bacterium and the ecological requirements of the host uncovers their intimate biochemical and metabolic communication and provides insights on the role of symbiosis in generating species diversity.     

Genetic-evolutionary basis of symbiosis doctrine

The author presents the current notion of symbiosis as one of the main adaptation of an organism to changeable environment. Symbiosis is considered as a super organism genetic system within which there are different interactions (including mutualism and antagonism). Genetic integration of symbiotic partners can be realized as cross regulation of their genes, exchange of gene products (proteins, RNA), gene amplification and sometimes gene transfer between organisms. On the phenotypic level these processes result in signal interactions, integration of partner metabolic systems and development of symbiotic organs. Co-evolution is considered as an assemblage of micro- and macroevolution processes basing on pre-adaptations and proceeding under influence of different forms of natural selection (individual, frequency-depended and kin selection). Symbiosis can be compared with sexual process since both are the forms of organism integration characterized by different genetic mechanisms and evolutionary consequences. The genome evolution in symbiotic microorganisms can proceed by: 1) simplification of genome in obligate symbiosis (loss of genes that are necessary for independent existence, transfer of some genes to the host organism); 2) complication of genome in facultative symbiosis (increase in genome plasticity, structural and functional differentiation of genome into systems controlling free-living and symbiotic parts of life cycle). Most of symbiotic interactions are correlated to an increase in genetic plasticity of an organism that can lead to evolutionary saltations and origin of new forms of life.     

城市废弃物资源化共生网络:概念、特征及体系解析

挖掘城市废弃物中有价值的资源,已经成为世界各国开展废弃物开发与管理的共同选择。产业共生是推动经济绿色发展和提高资源效率的战略工具,已经成为探讨废弃物资源化利用问题的重要视角。将产业共生理论引入城市废弃物资源化利用领域,提出城市废弃物资源化共生网络的概念,并将其典型特征概括为"四个统一",即价值网络与责任网络的统一,集聚共生与虚拟共生的统一,稳健型与脆弱性的统一以及自组织性与主体建构性的统一。借鉴超网络理论构建城市废弃物资源化共生网络体系的结构模型,并从共生单元、共生模式、共生界面和共生环境4个层面对该模型进行详细解析。城市废弃物资源化共生网络可分为核心网络和外围网络,两者之间存在全方位、多层次的合作机制。在城市废弃物资源化共生网络中,共生单元具有多层次性和多样性特征,它们之间存在着不同类型、效率各异的共生关系,推动共生模式向对称互惠一体化共生进化是破解城市废弃物资源化利用难题的关键;共生界面具有物质交换、能量传递、信息共享、知识传播及利益协调等多样化功能,而共生关系的进化以及共生界面功能发挥又依赖于优越的共生环境。此外,城市废弃物资源化共生网络有依托型、平等型、嵌套型和虚拟型等4种运作模式,国内典型案例分析表明这4种运作模式将长期并存。     

从细胞内共生到多尺度共生：回顾与展望

基于共生概念的历史变化,目前人们普遍接受了广义共生概念。即共生是包含互利共生（mutualism）、偏利共生（commensalism）和拮抗/寄生（antagonism/parasitism）的共生连续体。本文简述了近20年间,全球9次国际共生学术大会取得的重要成果,对细胞内共生、时间、空间以及多种互作尺度共生关系的研究利用进展进行了评述。同时展望了一些活跃共生领域的研究概况,如共生失调 （dysbiosis）、植物-微生物-昆虫三角共生关系（plant-microbe-insect triangle）、细菌-真菌互作（bacterial- fungal interaction,BFI）、菌根菌-真菌内生细菌-植物多方共生联盟（multipartite symbiosis consortium）以及与共生相关微生物组的集合群落（metacommunity）研究及应用等。共生（symbiosis）正成为当代生物学的核心原则,正以一种与更宏大系统方法相一致的概念,从根本上改变了传统上的一些生物学概念,如孤立性的个体（individuality）概念。基因组测序和高通量RNA技术分析揭示,动、植物与共生微生物的重要互作,打破了迄今为止生物个体的特征边界,挑战了这些学科的定义;共生不仅是一对一的互利共生关系,共生实际是多种共生模式的连续共生体。此外,植物-昆虫-微生物互作的三角关系;菌根-真菌-真菌内生细菌-植物的多方联盟等新关系的发现,更把生命科学推向了快速发展的方向。这些科学进展不仅对生物科学的遗传学、免疫学、进化、发育、解剖学和生理学的研究至关重要,拓宽了新的视野,而且对农业中生物制剂研发,人类微生物组的管理及调控,以及对发酵食品及工业微生物生产的设计和管理将产生积极影响。     

Applying Industrial Symbiosis to Smallholder Farms

The study of industrial symbiosis (IS) has largely focused on the exchange of energy and materials among industrial processes in an effort to increase value and reduce environmental impact. Agricultural systems, particularly those located in developing countries, can benefit from the principles of IS. Relatively few studies have analyzed the potential benefits of integrated material and energy flows in smallholder farming, even though these systems are considered essential to the world's food supply and poverty reduction. Although the concepts can be applied to virtually any system, the study of industrial symbiosis has traditionally focused on industrialized systems in developed countries. The research presented here applies the principles of IS to smallholder farms using optimization techniques to maximize farm output while minimizing wastes. Our research links IS to the growing field of integrated farming research (IFR), which seeks to create new technologies that increase the production of farms by viewing the farm as a system. Bridging these fields enriches the potential for robust research outcomes in both areas and fills a current knowledge gap. IS benefits from exploring new applications and increasing its penetration into the developing world. IFR benefits from established IS tools to create alternate pathways for increased output based on symbiotic relationships. A small farming system in Liberia, West Africa, is used as a case study. System integration of individual unit processes shows increased productivity and decreased waste. The results of this analysis indicate that there are unrealized opportunities for IS in developing countries, and integration of IS techniques into smallholder farming operations has the potential for impacting sustainable development.     

Impediment to Symbiosis Establishment between Giant Clams and Symbiodinium Algae Due to Sterilization of Seawater

To survive the juvenile stage, giant clam juveniles need to establish a symbiotic relationship with the microalgae Symbiodinium occurring in the environment. The percentage of giant clam juveniles succeeding in symbiosis establishment (“symbiosis rate”) is often low, which is problematic for seed producers. We investigated how and why symbiosis rates vary, depending on whether giant clam seeds are continuously reared in UV treated or non treated seawater. Results repeatedly demonstrated that symbiosis rates were lower for UV treated seawater than for non treated seawater. Symbiosis rates were also lower for autoclaved seawater and 0.2-µm filtered seawater than for non treated seawater. The decreased symbiosis rates in various sterilized seawater suggest the possibility that some factors helping symbiosis establishment in natural seawater are weakened owing to sterilization. The possible factors include vitality of giant clam seeds, since additional experiments revealed that survival rates of seeds reared alone without Symbiodinium were lower in sterilized seawater than in non treated seawater. In conclusion, UV treatment of seawater was found to lead to decreased symbiosis rates, which is due possibly to some adverse effects common to the various sterilization techniques and relates to the vitality of the giant clam seeds.     

Symbiosis, lateral function transfer and the (many) saplings of life

One of intuitions driving the acceptance of a neat structured tree of life is the assumption that organisms and the lineages they form have somewhat stable spatial and temporal boundaries. The phenomenon of symbiosis shows us that such ‘fixist’ assumptions does not correspond to how the natural world actually works. The implications of lateral gene transfer (LGT) have been discussed elsewhere; I wish to stress a related point. I will focus on lateral function transfer (LFT) and will argue, using examples of what many would call ‘superorganisms’, that the emergence of symbiotic individuals revives the importance of functional and adaptationist thinking in how we conceptualize the lineages of biological individuals. The consequence of the argument is that, if we really want to hold onto tree of life thinking, we had better accept that new saplings appear and disappear all the time.     

肠道微生物与昆虫的共生关系

昆虫肠道栖息着大量的微生物。随着近年来研究肠道微生物的方法不断进步,尤其是基于16S rDNA的分子生物学方法的应用,人们对肠道微生物的了解逐渐加深。昆虫肠道对于微生物的拓殖存在一定的选择作用。肠道微生物对昆虫寄主的作用包括提供营养、利用拓殖抗性抵抗外来微生物侵袭、参与多重营养关系、引起昆虫免疫反应。长期进化过程中肠道微生物与昆虫发展出紧密的共生关系,微生物发展出一系列手段适应昆虫肠道环境。文章从以上几个方面对近年来的研究进展进行总结,并对昆虫肠道微生态学的实践意义和将来可能的研究热点进行展望。     

Symbiosis of cornulitids with the cystoporate bryozoan Fistulipora in the Pridoli of Saaremaa,Estonia

Cornulites sp. and Fistulipora przhidolensis formed a symbiotic association in the Pridoli (latest Silurian) of Saaremaa Island, Estonia. This Cornulites sp.–F. przhidolensis association is the youngest example of cornulitid–bryozoan symbiosis. Symbiosis is indicated by intergrowth of both organisms. The cornulitids are completely embedded within the cystoporate bryozoan colony, leaving only their apertures free on the growth surface of bryozoan. In terms of food competition, this association could have been slightly harmful to F. przhidolensis as Cornulites sp. may have been a kleptoparasite. There may have been a small escalation in the evolution of the endobiotic life mode of cornulitids as the number of such associations increased from the Ordovician to Silurian. It is likely that Palaeozoic bryozoan symbiosis reached its maximum in the Late Ordovician. Most of the symbiotic bryozoans in the Palaeozoic are trepostomes, and the diversity of symbiotic associations was also greatest among trepostomes.     

‘The importance of symbiosis in philosophy of biology: an analysis of the current debate on biological individuality and its historical roots’

Symbiosis plays a fundamental role in contemporary biology, as well as in recent thinking in philosophy of biology. The discovery of the importance and universality of symbiotic associations has brought new light to old debates in the field, including issues about the concept of biological individuality. An important aspect of these debates has been the formulation of the hologenome concept of evolution, the notion that holobionts are units of natural selection in evolution. This review examines the philosophical assumptions that underlie recent proposal of the hologenome concept of evolution, and traces those debates back in time to their historical origins, to the moment when the connection between the topics of symbiosis and biological individuality first caught the attention of biologists. The review is divided in two parts. The first part explores the historical origins of the connection between the notion of symbiosis and the concept of biological individuality, and emphasizes the role of A. de Bary, R. Pound, A. Schneider and C. Merezhkowsky in framing the debate. The second part examines the hologenome concept of evolution and explores four parallelisms between contemporary debates and the debates presented in the first part of the essay, arguing that the different debates raised by the hologenome concept were already present in the literature. I suggest that the novelty of the hologenome concept of evolution lies in the wider appreciation of the importance of symbiosis for maintaining life on Earth as we know it. Finally, I conclude by suggesting the importance of exploring the connections among contemporary biology, philosophy of biology and history of biology in order to gain a better understanding of contemporary biology.     

根瘤菌共生固氮能力的进化模式

根瘤菌-豆科植物共生固氮体系对农业的可持续性发展至关重要,也是研究原核与真核生物互利共生的模式体系之一。长期以来,根瘤菌共生固氮相关研究主要集中在结瘤因子与固氮酶合成及调控等少数关键基因,但仅获得这些关键基因却不能保证细菌获得结瘤固氮能力。随着比较和功能基因组学的快速发展和应用,越来越多的研究发现根瘤菌使用了很多系统发育分支特异的遗传机制与豆科植物建立有效的共生关系,进一步揭示了双方互利共生的复杂性。本综述总结了近年来比较基因组学、遗传学以及实验进化等方面的相关研究进展,在此基础上讨论根瘤菌共生固氮能力的进化模式。     

Symbiosis instruction: considerations from the education workshop at the 6th ISS Congress

Herein, we summarize presentations on “Symbiosis” instruction given at the Education Workshop held at the 6th International Symbiosis Society Meeting in Madison WI. We convey our teaching experiences and methods in a variety of venues. Information on target audiences, course syllabi, and laboratory skills, utilizing various symbiotic systems are also presented. We hope this review will contribute to further adoption of symbiotic interactions in the classroom as well as the growth of currently developed courses in this field—a specific mission of this and previous International Symbiosis Society meetings.     

Symbiosis catalyses niche expansion and diversification

Interactions between species are important catalysts of the evolutionary processes that generate the remarkable diversity of life. Symbioses, conspicuous and inherently interesting forms of species interaction, are pervasive throughout the tree of life. However, nearly all studies of the impact of species interactions on diversification have concentrated on competition and predation leaving unclear the importance of symbiotic interaction. Here, I show that, as predicted by evolutionary theories of symbiosis and diversification, multiple origins of a key innovation, symbiosis between gall-inducing insects and fungi, catalysed both expansion in resource use (niche expansion) and diversification. Symbiotic lineages have undergone a more than sevenfold expansion in the range of host-plant taxa they use relative to lineages without such fungal symbionts, as defined by the genetic distance between host plants. Furthermore, symbiotic gall-inducing insects are more than 17 times as diverse as their non-symbiotic relatives. These results demonstrate that the evolution of symbiotic interaction leads to niche expansion, which in turn catalyses diversification.     

‘Habitat’ Suitability Index Mapping for Industrial Symbiosis Planning

By ‘working with the willing’, the National Industrial Symbiosis Programme (NISP) has successfully facilitated industrial symbiosis throughout the United Kingdom and, in the process, delivered significant economic and environmental benefits for both Programme members and the country as a whole. One of the keys to NISP's success is that, unlike failed attempts to plan and construct eco‐industrial systems from scratch, the Programme works largely with existing companies who have already settled in, developed, and successfully operate within a given locale. This article argues that existing and mature industrial systems provide the best prospects for identifying opportunities for, and ultimately facilitating, industrial symbiosis. Due to levels of diversification and operational fundamental niches that, in the fullness of time, develop within all industrial systems, industrially mature areas are deemed to be industrial symbiosis ‘conducive environments’. Building on the conservation biology concept of a habitat suitability index, the article presents a methodology for comparing a potential site for eco‐industrial development to a known baseline industrial ‘habitat’ already identified as being highly conducive to industrial symbiosis. The suitability index methodology is further developed and applied to a multi‐criteria evaluation geographic information system to produce a ‘habitat’ suitability map that allows practitioners to quickly identify potential industrial symbiosis hotspots (the methodology is illustrated for England). The article concludes by providing options for the development of symbiosis suitability indices and how they can be used to support the facilitation of industrial symbiosis and regional resource efficiency.     

Symbiotic status alters fungal eco-evolutionary offspring trajectories

Despite host-fungal symbiotic interactions being ubiquitous in all ecosystems, understanding how symbiosis has shaped the ecology and evolution of fungal spores that are involved in dispersal and colonization of their hosts has been ignored in life-history studies. We assembled a spore morphology database covering over 26,000 species of free-living to symbiotic fungi of plants, insects and humans and found more than eight orders of variation in spore size. Evolutionary transitions in symbiotic status correlated with shifts in spore size, but the strength of this effect varied widely among phyla. Symbiotic status explained more variation than climatic variables in the current distribution of spore sizes of plant-associated fungi at a global scale while the dispersal potential of their spores is more restricted compared to free-living fungi. Our work advances life-history theory by highlighting how the interaction between symbiosis and offspring morphology shapes the reproductive and dispersal strategies among living forms.     

Immunity and symbiosis

The invertebrate immune system, which has become a major research focus, shares basic features of innate immunity with vertebrates and men. A special feature apparently found only in invertebrates is their close association with vertically heritable symbiotic microorganisms. The validity of the simple view of symbiosis as a mutually beneficial interaction between two uneven partners mainly improving the nutritional state of the two companions has been challenged, however, as symbiotic interactions might involve more partners, and symbiotic functions of the microorganisms are much more diverse than previously assumed. Likewise, microorganisms considered to be mostly harmful to their hosts have been shown to enhance host fitness under some circumstances. The role of a symbiont itself might change between environments or life stages of the host and symbionts might have features previously thought to be specific for pathogens. Understanding symbiotic interactions requires the comprehension of the cross-talk between the symbiotic companions, and the dissection of how long-lasting infections are established without eliminating the symbiont by host immune responses. Fascinating new findings in this field revealed that symbiosis might contribute to defence against pathogens or natural enemies. New symbiont-based approaches to defeat agricultural pests or pathogen transmission by arthropod vectors are becoming conceivable.