Divergence of evolutionary ways among common sym genes: CASTOR and CCaMK show functional conservation between two symbiosis systems and constitute the root of a common signaling pathway

In recent years a number of legume genes involved in root nodule (RN) symbiosis have been identified in the model legumes, Lotus japonicus (Lotus) and Medicago truncatula. Among them, a distinct set of genes has been categorized as a common symbiosis pathway (CSP), because they are also essential for another mutual interaction, the arbuscular mycorrhiza (AM) symbiosis, which is evolutionarily older than the RN symbiosis and is widely distributed in the plant kingdom. Based on the concept that the legume RN symbiosis has evolved from the ancient AM symbiosis, one issue is whether the CSP is functionally conserved between non-nodulating plants, such as rice, and nodulating legumes. We identified three rice CSP gene orthologs, OsCASTOR, OsPOLLUX and OsCCaMK, and demonstrated the indispensable roles of OsPOLLUX and OsCCaMK in rice AM symbiosis. Interestingly, molecular transfection of either OsCASTOR or OsCCaMK could fully complement symbiosis defects in the corresponding Lotus mutant lines for both the AM and RN symbioses. Our results not only provide a conserved genetic basis for the AM symbiosis between rice and Lotus, but also indicate that the core of the CSP has been well conserved during the evolution of RN symbiosis. Through evolution, CASTOR and CCaMK have remained as the molecular basis for the maintenance of CSP functions in the two symbiosis systems.     

Comparative genomics reveals high rates of horizontal transfer and strong purifying selection on rhizobial symbiosis genes

Horizontal transfer (HT) alters the repertoire of symbiosis genes in rhizobial genomes and may play an important role in the on-going evolution of the rhizobia–legume symbiosis. To gain insight into the extent of HT of symbiosis genes with different functional roles (nodulation, N-fixation, host benefit and rhizobial fitness), we conducted comparative genomic and selection analyses of the full-genome sequences from 27 rhizobial genomes. We find that symbiosis genes experience high rates of HT among rhizobial lineages but also bear signatures of purifying selection (low Ka : Ks). HT and purifying selection appear to be particularly strong in genes involved in initiating the symbiosis (e.g. nodulation) and in genome-wide association candidates for mediating benefits provided to the host. These patterns are consistent with rhizobia adapting to the host environment through the loss and gain of symbiosis genes, but not with host-imposed positive selection driving divergence of symbiosis genes through recurring bouts of positive selection.     

Plant hormones as signals in arbuscular mycorrhizal symbiosis

Abstract

Arbuscular mycorrhizal (AM) fungi are non-specific symbionts developing mutual and beneficial symbiosis with most terrestrial plants. Because of the obligatory nature of the symbiosis, the presence of the host plant during the onset and proceeding of symbiosis is necessary. However, AM fungal spores are able to germinate in the absence of the host plant. The fungi detect the presence of the host plant through some signal communications. Among the signal molecules, which can affect mycorrhizal symbiosis are plant hormones, which may positively or adversely affect the symbiosis. In this review article, some of the most recent findings regarding the signaling effects of plant hormones, on mycorrhizal fungal symbiosis are reviewed. This may be useful for the production of plants, which are more responsive to mycorrhizal symbiosis under stress.     

Symbiosis research at the end of the millenium

The development of symbiosis research over the closing 50 years of the last millenium is reviewed. At the beginning of this period, there had been very little previous research into aquatic microbial symbiosis. The advent of new experimental techniques, combined with the developing acceptance of the symbiotic origin of eukaryotic cell structure (and especially that chloroplasts evolved from a symbiosis involving photosynthetic aquatic microbes) brought symbiosis research into much greater prominence for a time in the 1970s and 1980s. Nevertheless, at the end of the millenuim, symbiosis as a subject still lacks a clear and strong identity amongst biologists in general. Three reasons are identified for this: continuing absence of a generally accepted definition of the term; little or no representation in the academic structure of biology; and the current adverse climate of research funding in many countries. However, the growing importance of symbiosis in biotechnology and in conserving biodiversity makes future prospects much brighter.     

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。     

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.     

Identification of Sinorhizobium meliloti early symbiotic genes by use of a positive functional screen

The soil bacterium Sinorhizobium meliloti establishes nitrogen-fixing symbiosis with its leguminous host plant, alfalfa, following a series of continuous signal exchanges. The complexity of the changes of alfalfa root structures during symbiosis and the amount of S. meliloti genes with unknown functions raised the possibility that more S. meliloti genes may be required for early stages of the symbiosis. A positive functional screen of the entire S. meliloti genome for symbiotic genes was carried out using a modified in vivo expression technology. A group of genes and putative genes were found to be expressed in early stages of the symbiosis, and 23 of them were alfalfa root exudate inducible. These 23 genes were further separated into two groups based on their responses to apigenin, a known nodulation (nod) gene inducer. The group of six genes not inducible by apigenin included the lsrA gene, which is essential for the symbiosis, and the dgkA gene, which is involved in the synthesis of cyclic beta-1,2-glucan required for the S. meliloti-alfalfa symbiosis. In the group of 17 apigenin-inducible genes, most have not been previously characterized in S. meliloti, and none of them belongs to the nod gene family. The identification of this large group of alfalfa root exudate-inducible S. meliloti genes suggests that the interactions in the early stages of the S. meliloti and alfalfa symbiosis could be complex and that further characterization of these genes will lead to a better understanding of the symbiosis.     

Genomic islands in Photorhabdus

Genomic islands are responsible for unique aspects of bacterial behavior such as symbiosis and pathogenicity. Photorhabdus luminescens is a pathogen of insects that spends part of its lifecycle in symbiosis with a nematode. Here, we describe novel genomic islands from Photorhabdus that are involved in symbiosis and pathogenicity, and discuss the inter-relationship between virulence factors used against invertebrates and vertebrates.     

国内外产业共生网络研究比较述评

产业共生网络是指基于物质及能量交换以及知识及基础设施共享而形成的在不同产业主体之间的合作共赢网络,是产业转型升级的重要保障。作为产业共生的运作方式,产业共生网络的研究国外从20世纪90年代开始从概念到实例就展开了一系列探讨,国内自2002年也开始在网络结构等方面开展相关研究。尤其在2008年以后,产业共生网络的研究方向不断拓宽,研究成果丰富多样。为明晰国内外产业共生网络研究的发展态势,促进产业共生网络理论体系的发展并使其得到有效应用。本文从共生网络内涵、结构、功能及评价、演化、管理调控等方面比较分析了国内外产业共生网络的研究进展,并对产业共生网络的发展前景做了展望。未来产业共生网络研究在不同尺度的比较及推演、数据信息平台的搭建以及产业共生网络演化模拟及管理调控的耦合等方面需重点关注。     

‘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.     

Phosphate import at the arbuscule: just a nutrient?

Central to the mutualistic arbuscular mycorrhizal symbiosis is the arbuscule, the site where symbiotic phosphate is delivered. Initial investigations in legumes have led to the exciting observation that symbiotic phosphate uptake not only enhances plant growth but also regulates arbuscule dynamics and is, furthermore, required for maintenance of the symbiosis. This review evaluates the possible role of the phosphate ion, not only as a nutrient but also as a signal that is necessary for reprogramming the host cortex cell for symbiosis.     

Sucrose synthase levels do not limit or regulate carbon transfer in the arbuscular mycorrhizal symbiosis

Abstract

Sucrose synthase (SuSy) is the main sucrose breakdown enzyme in plant sink tissues, including nodules, and is a possible candidate for the diversion of plant carbon to arbuscular mycorrhizal (AM) fungi in roots. We tested the involvement of SuSy in AM symbiosis of Glomus intraradices and Pisum sativum (pea). We observed that peas deficient in the predominant root isoform of SuSy were colonized successfully by AM fungi similar to wild-type roots. SuSy protein levels did not increase in roots as AM symbiosis developed, although SuSy protein levels did increase in nodules as the rhizobium symbiosis developed. Our results lead us to conclude that, unlike nodule symbiosis, SuSy protein does not limit or regulate carbon transfer in the AM symbiosis.     

Identification of Sinorhizobium meliloti Early Symbiotic Genes by Use of a Positive Functional Screen

The soil bacterium Sinorhizobium meliloti establishes nitrogen-fixing symbiosis with its leguminous host plant, alfalfa, following a series of continuous signal exchanges. The complexity of the changes of alfalfa root structures during symbiosis and the amount of S. meliloti genes with unknown functions raised the possibility that more S. meliloti genes may be required for early stages of the symbiosis. A positive functional screen of the entire S. meliloti genome for symbiotic genes was carried out using a modified in vivo expression technology. A group of genes and putative genes were found to be expressed in early stages of the symbiosis, and 23 of them were alfalfa root exudate inducible. These 23 genes were further separated into two groups based on their responses to apigenin, a known nodulation (nod) gene inducer. The group of six genes not inducible by apigenin included the lsrA gene, which is essential for the symbiosis, and the dgkA gene, which is involved in the synthesis of cyclic β-1,2-glucan required for the S. meliloti-alfalfa symbiosis. In the group of 17 apigenin-inducible genes, most have not been previously characterized in S. meliloti, and none of them belongs to the nod gene family. The identification of this large group of alfalfa root exudate-inducible S. meliloti genes suggests that the interactions in the early stages of the S. meliloti and alfalfa symbiosis could be complex and that further characterization of these genes will lead to a better understanding of the symbiosis.     

植物菌根共生磷酸盐转运蛋白

大多数植物能和丛枝菌根（arbuscular mycorrhiza, AM）真菌形成菌根共生体。AM能够促进植物对土壤中矿质营养的吸收,尤其是磷的吸收。磷的吸收和转运由磷酸盐转运蛋白介导。总结了植物AM磷酸盐转运蛋白及其结构特征,分析其分类及系统进化,并综述了AM磷酸盐转运蛋白介导的磷的吸收和转运过程及其基因的表达调控。植物AM磷酸盐转运蛋白属于Pht1家族成员,它不仅对磷的吸收和转运是必需的,而且对AM共生也至关重要,为进一步了解菌根形成的分子机理及信号转导途径提供了理论基础。     

丛枝菌根共生建成的信号识别机制

丛枝菌根(Arbuscular mycorrhiza,AM)共生是自然界中普遍存在的一种互惠共生现象,对促进土壤生态系统物质循环及维持生态系统稳定具有重要的意义。AM共生体的建立需要AM真菌和宿主植物间一系列复杂的信号识别、交换和传导。本文总结近年来相关文献,从AM共生体形成前期及AM共生体形成期两个阶段,分别综述了信号物质的生物合成过程、调控过程及其作用机制,希望有助于进一步认识AM共生体建成过程,同时通过分析当前研究工作的不足及未来研究动向,期望推动相关研究工作。     

Plant–Microbe Symbiosis: What Has Proteomics Taught Us?

Beneficial microbes have a positive impact on the productivity and fitness of the host plant. A better understanding of the biological impacts and underlying mechanisms by which the host derives these benefits will help to address concerns around global food production and security. The recent development of omics‐based technologies has broadened our understanding of the molecular aspects of beneficial plant–microbe symbiosis. Specifically, proteomics has led to the identification and characterization of several novel symbiosis‐specific and symbiosis‐related proteins and post‐translational modifications that play a critical role in mediating symbiotic plant–microbe interactions and have helped assess the underlying molecular aspects of the symbiotic relationship. Integration of proteomic data with other “omics” data can provide valuable information to assess hypotheses regarding the underlying mechanism of symbiosis and help define the factors affecting the outcome of symbiosis. Herein, an update is provided on the current and potential applications of symbiosis‐based “omic” approaches to dissect different aspects of symbiotic plant interactions. The application of proteomics, metaproteomics, and secretomics as enabling approaches for the functional analysis of plant‐associated microbial communities is also discussed.     

Genomic islands in Photorhabdus

Genomic islands are responsible for unique aspects of bacterial behavior such as symbiosis and pathogenicity. Photorhabdus luminescens is a pathogen of insects that spends part of its lifecycle in symbiosis with a nematode. Here, we describe novel genomic islands from Photorhabdus that are involved in symbiosis and pathogenicity, and discuss the inter-relationship between virulence factors used against invertebrates and vertebrates.