水稻典型品种日本晴和IR24根系微生物组的解析

植物的各项生命活动与其根系微生物组密不可分,且根系微生物组的组成易受到植物生长环境和基因型的影响。为进一步探究中国北方地区种植的不同品种水稻根系微生物组的差异及其相互作用机制,本研究以种植于北京昌平和上庄农场的水稻典型品种日本晴(Nipponbare)和IR24为研究对象,基于16S rRNA基因扩增子测序技术获得根系微生物组序列,利用多样性分析、组成型分析、机器学习的随机森林和网络分析等方法,对旺盛生长期的两种不同品种的水稻根系微生物组进行详细比较。研究发现,种植地点和水稻基因型显著影响了水稻根系微生物组的群落结构,不同基因型导致了根系微生物组在物种分类组成上以及细菌间相互关系的差异,而且根系微生物组能作为生物标记跨地点区分宿主的基因型。本研究结果为深入理解我国北方种植的水稻根系微生物组的组成规律以及从根系微生物与植物互作的角度对品种进行改良提供了数据和理论基础。     

连作障碍与根际微生态研究 Ⅰ. 根系分泌物及其生态效应

作物、蔬菜、果树以及苗木长期连作后,皆出现生长衰退和产量降低。许多研究结果表明,连作条件下土壤生态环境对植物生长有很大的影响,尤以植物残体与病原微生物的分解产物,对植物有致毒作用,并影响植物根系分泌物正常代谢,以致于发生自毒作用。本文围绕根系分泌物与根际微生态的相互关系,系统地介绍连作障碍条件下,影响根系分泌物的环境因素(土壤空气、湿度、养分与微生物)、活性物质(自身毒素、残体分解物、微生物产生毒素)、土壤病原菌等的根际效应,为深入研究根系分泌物与连作障碍的相互作用机制提供启示。     

连作障碍与根际微生态研究Ⅰ.根系分泌物及其生态效应

作物、蔬菜、果树以及苗木长期连作后,皆出现生长衰退和产量降低．许多研究结果表明,连作条件下土壤生态环境对植物生长有很大的影响,尤以植物残体与病原微生物的分解产物,对植物有致毒作用,并影响植物根系分泌物正常代谢,以致于发生自毒作用．本文围绕根系分泌物与根际微生态的相互关系,系统地介绍连作障碍条件下,影响根系分泌物的环境因素（土壤空气、湿度、养分与微生物）、活性物质（自身毒素、残体分解物、微生物产生毒素）、土壤病原菌等的根际效应,为深入研究根系分泌物与连作障碍的相互作用机制提供启示．     

土壤微食物网生物和土壤微生物对小星穗薹草生长和土壤养分的影响差异

土壤微食物网生物是影响土壤养分循环的重要驱动因素,其对植物生长和土壤养分的影响大于广受关注的土壤微生物。通过土壤生物添加实验,对比分析了在土壤微食物网生物添加、土壤微生物添加和灭菌土壤三种处理条件下,湿生草本植物小星穗薹草的生物量、形态和生理性状以及土壤养分含量等指标,以探究土壤微食物网生物和土壤微生物对植物生长和土壤养分的差异性影响。结果表明,土壤微食物网生物对植物的促进作用显著大于土壤微生物的作用。土壤微食物网生物未改变植物的根系性状,而土壤微生物使植物的根系形态发生明显改变。不同土壤生物添加处理的土壤有效养分含量也存在显著差异。该研究证明了土壤微食物网生物更有利于植物生长。研究结果为深入认识土壤微食物网生物对植物生长和土壤养分周转的重要性、推动植物与土壤生物相互作用过程和影响机制研究提供了新视角和可靠数据。     

丛枝菌根真菌影响作物非生物胁迫耐受性的研究进展

土壤中存在着大量不同种类的微生物资源,土壤微生物能够与自然界中的大多数植物密切合作,其中丛枝菌根真菌(arbuscular mycorrhizal fungi,AMF)起着十分重要的作用。近年来,对于AMF的研究越来越多。AMF是存在于土壤中的重要真菌之一,是土壤中的菌根真菌菌丝与高等植物营养根系形成的一种联合体。AMF可以与陆地上90%左右的植物根系形成共生体,通过在植物根系形成重要的“丛枝菌根”结构而为植物提供更多的养分。为了了解接种AMF对作物生长过程中耐受一些非生物胁迫(如干旱、极端温度、重金属污染、盐分、不利的土壤pH变化等)性能方面的影响,基于之前接种AMF对养分胁迫下玉米生长影响的研究,在扩大作物品种的基础上,通过查阅大量文献,结合试验研究及对前人和近年来关于AMF的一些最新研究进展,获得了具有实践性意义的新发现：AMF与植物共生有助于植物生长,可以改善植物的营养状况,并且可以保护植物免受各种非生物环境胁迫的影响。由此可以得出结论：AMF通过各种机制改善植物生长状况,提高作物抗逆性,为作物增产、农民增收创造了福利,并且避免了由于肥料过量施用导致的一些污染环境问题。本文主要综述了接种AMF在各种非生物环境胁迫(干旱、极端温度、重金属污染、盐分、不利的土壤pH变化等)条件下对植株生长和发育的有利影响,并对目前存在的不足和今后研究的重点提出几点建议。     

根系间的相互作用——竞争与互利

植物根系间的相互作用分为竞争和互利两种形式 ,它是决定植物群落动态变化和群落结构的重要因素。根系间的竞争包括植株个体自身根系的竞争以及个体与个体根系间 (同种或异种 )的竞争两方面 ,前者的发生在农林系统中是不可避免的并且很难调控 ,后者可以分为种间植物根系的竞争和种内植物根系的竞争。还阐述了根系的竞争能力和与其密切相关的根系生长率、根组织的新陈代谢、植物的生长形式和根系的空间结构等植物特性 ,同时介绍了根系对水和养分的竞争机理、形式、影响以及竞争强度计算方法。接着具体分析包括根系错位在内的各种根系互利现象和相关机理。影响根系间相互作用的限制性因子有土壤营养的异质性、大气 CO2 浓度、地下草食生物、根系生产力和生物量、根系结构、形态和生理调节、土壤养分的扩散性以及植物间距等。随着科技的进步和各门学科的发展 ,未来根系的研究方向主要体现在结合实践优化农林系统中不同物种间的作用关系、预测根系竞争在全球气候变化下的发展规律、更新实验研究方法及手段研究作用机理等 3个方面。     

根系分泌物介导下植物-土壤-微生物互作关系研究进展与展望

根系分泌物是植物与土壤进行物质交换和信息传递的重要载体物质, 是植物响应外界胁迫的重要途径, 是构成植物不同根际微生态特征的关键因素, 也是根际对话的主要调控者。根系分泌物对于生物地球化学循环、根际生态过程调控、植物生长发育等均具有重要功能, 尤其是在调控根际微生态系统结构与功能方面发挥着重要作用, 调节着植物-植物、植物-微生物、微生物-微生物间复杂的互作过程。植物化感作用、作物间套作、生物修复、生物入侵等都是现代农业生态学的研究热点, 它们都涉及十分复杂的根际生物学过程。越来越多的研究表明, 不论是同种植物还是不同种植物之间相互作用的正效应或是负效应, 都是由根系分泌物介导下的植物与特异微生物共同作用的结果。近年来, 随着现代生物技术的不断完善, 有关土壤这一“黑箱”的研究方法与技术取得了长足的进步, 尤其是各种宏组学技术(meta-omics technology), 如环境宏基因组学、宏转录组学、宏蛋白组学、宏代谢组学等的问世, 极大地推进了人们对土壤生物世界的认知, 尤其是对植物地下部生物多样性和功能多样性的深层次剖析, 根际生物学特性的研究成果被广泛运用于指导生产实践。深入系统地研究根系分泌物介导下的植物-土壤-微生物的相互作用方式与机理, 对揭示土壤微生态系统功能、定向调控植物根际生物学过程、促进农业生产可持续发展等具有重要的指导意义。该文综述了根系分泌物的概念、组成及功能, 论述了根系分泌物介导下植物与细菌、真菌、土壤动物群之间的密切关系, 总结了探索根际生物学特性的各种研究技术及其优缺点, 并对该领域未来的研究方向进行了展望。     

Advances and perspective in research on plant-soil-microbe interactions mediated by root exudates

根系分泌物是植物与土壤进行物质交换和信息传递的重要载体物质, 是植物响应外界胁迫的重要途径, 是构成植物不同根际微生态特征的关键因素, 也是根际对话的主要调控者。根系分泌物对于生物地球化学循环、根际生态过程调控、植物生长发育等均具有重要功能, 尤其是在调控根际微生态系统结构与功能方面发挥着重要作用, 调节着植物-植物、植物-微生物、微生物-微生物间复杂的互作过程。植物化感作用、作物间套作、生物修复、生物入侵等都是现代农业生态学的研究热点, 它们都涉及十分复杂的根际生物学过程。越来越多的研究表明, 不论是同种植物还是不同种植物之间相互作用的正效应或是负效应, 都是由根系分泌物介导下的植物与特异微生物共同作用的结果。近年来, 随着现代生物技术的不断完善, 有关土壤这一“黑箱”的研究方法与技术取得了长足的进步, 尤其是各种宏组学技术(meta-omics technology), 如环境宏基因组学、宏转录组学、宏蛋白组学、宏代谢组学等的问世, 极大地推进了人们对土壤生物世界的认知, 尤其是对植物地下部生物多样性和功能多样性的深层次剖析, 根际生物学特性的研究成果被广泛运用于指导生产实践。深入系统地研究根系分泌物介导下的植物-土壤-微生物的相互作用方式与机理, 对揭示土壤微生态系统功能、定向调控植物根际生物学过程、促进农业生产可持续发展等具有重要的指导意义。该文综述了根系分泌物的概念、组成及功能, 论述了根系分泌物介导下植物与细菌、真菌、土壤动物群之间的密切关系, 总结了探索根际生物学特性的各种研究技术及其优缺点, 并对该领域未来的研究方向进行了展望。     

植物根系分泌物的生态效应

根系分泌物是在一定的生长条件下 ,活的且未被扰动的根系释放到根际环境中的有机物质的总称 ,在植物主动适应和抵御不良环境中具有重要作用 :(1)通过化感作用影响根际微生物和周围其它植物的生长 ,并进一步改善植物的生态环境 (生物因素 ) ;(2 )通过对土壤中矿质元素的溶解、螯合作用、迁移和活化等作用 ,不仅在营养缺乏的情况下提高矿质营养元素的有效性 ,而且在面临重金属胁迫时能降低根际中金属污染物的活性 ,减少植物对金属的吸收。根系分泌物在植物与环境的相互作用中起着传递信息的作用     

干旱下植物激素影响作物根系发育的研究进展

植物激素是指在植物体内某些部位合成、可被运输到其他部位调控植物生长发育的微量有机物质,在植物生命活动中发挥重要作用。根系是作物吸收水分和养分的重要器官,其形态决定了作物获得养分和水分的能力。作物发达的根系与其抵抗干旱环境胁迫息息相关,而植物激素在作物根系发育中发挥关键作用,因此深入了解干旱胁迫下植物激素对作物根系发育的影响对农业的安全生产是至关重要的。本文就干旱胁迫下植物激素如何调控及不同激素协同调控作物根系生长发育的研究进行了概述,并讨论了激素在作物抗旱上应用的意义及将来可能开展的研究方向。     

The root microbiome: Community assembly and its contributions to plant fitness

The root microbiome refers to the community of microbes living in association with a plant's roots, and includes mutualists, pathogens, and commensals. Here we focus on recent advances in the study of root commensal community which is the major research object of microbiome-related researches. With the rapid development of new technologies, plant–commensal interactions can be explored with unprecedented breadth and depth. Both the soil environment and the host plant drive commensal community assembly. The bulk soil is the seed bank of potential commensals, and plants use root exudates and immune responses to build healthy microbial communities from the available microbes. The plant microbiome extends the functional system of plants by participating in a variety of processes, including nutrient absorption, growth promotion, and resistance to biotic and abiotic stresses. Plants and their microbiomes have evolved adaptation strategies over time. However, there is still a huge gap in our understanding of the regulatory mechanisms of plant–commensal interactions. In this review, we summarize recent research on the assembly of root microbial communities and the effects of these communities on plant growth and development, and look at the prospects for promoting sustainable agricultural development through the study of the root microbiome.     

Colliding and interacting microbiomes and microbial communities - consequences for human health

Living ‘things’ coexist with microorganisms, known as the microbiota/microbiome that provides essential physiological functions to its host. Despite this reliance, the microbiome is malleable and can be altered by several factors including birth-mode, age, antibiotics, nutrition, and disease. In this minireview, we consider how other microbiomes and microbial communities impact the host microbiome and the host through the concept of microbiome collisions (initial exposures) and interactions. Interactions include changes in host microbiome composition and functionality and/or host responses. Understanding the impact of other microbiomes and microbial communities on the microbiome and host are important considering the decline in human microbiota diversity in the developed world – paralleled by the surge of non-communicable, inflammatory-based diseases. Thus, surrounding ourselves with rich and diverse beneficial microbiomes and microbial communities to collide and interact with should help to diminish the loss in microbial diversity and protect from certain diseases. In the same vein, our microbiomes not only influence our health but potentially the health of those close to us. We also consider strategies for enhanced host microbiome collisions and interactions through the surrounding environment that ensure increased microbiome diversity and functionality contributing to enhanced symbiotic return to the host in terms of health benefit.     

The rhizosphere microbiome: Plant–microbial interactions for resource acquisition

While horticulture tools and methods have been extensively developed to improve the management of crops, systems to harness the rhizosphere microbiome to benefit plant crops are still in development. Plants and microbes have been coevolving for several millennia, conferring fitness advantages that expand the plant’s own genetic potential. These beneficial associations allow the plants to cope with abiotic stresses such as nutrient deficiency across a wide range of soils and growing conditions. Plants achieve these benefits by selectively recruiting microbes using root exudates, positively impacting their nutrition, health and overall productivity. Advanced knowledge of the interplay between root exudates and microbiome alteration in response to plant nutrient status, and the underlying mechanisms there of, will allow the development of technologies to increase crop yield. This review summarizes current knowledge and perspectives on plant–microbial interactions for resource acquisition and discusses promising advances for manipulating rhizosphere microbiomes and root exudation.     

Biodiversity, evolution and adaptation of cultivated crops

The human diet depends on very few crops. Current diversity in these crops is the result of a long interaction between farmers and cultivated plants, and their environment. Man largely shaped crop biodiversity from the domestication period 12,000 B.P. to the development of improved varieties during the last century. We illustrate this process through a detailed analysis of the domestication and early diffusion of maize. In smallholder agricultural systems, farmers still have a major impact on crop diversity today. We review several examples of the major impact of man on current diversity. Finally, biodiversity is considered to be an asset for adaptation to current environmental changes. We describe the evolution of pearl millet in West Africa, where average rainfall has decreased over the last forty years. Diversity in cultivated varieties has certainly helped this crop to adapt to climate variation.     

Effect of long-term application of agrotechnical techniques and crops on soil microbial communities

Effects of long-term application of various fertilizers and crops on soil microbiomes in a long-term field experiment were investigated using the library of the 16S rRNA gene sequences obtained by highthroughput sequencing of the total DNA. The communities exhibited high diversity, with 655 microbial genera belonging to 34 phyla detected (31 bacterial and 3 archaeal ones). For analysis of the effect of the studied factors on community structure, a linear model was developed in order to simplify interpretation of the data of high-throughput sequencing and to obtain biologically important information. Liming was shown to modulate the effect of mineral fertilizers on the structure of microbial populations. The differences in the structure and alpha-diversity of microbial communities were shown to depend more on the crops and liming than on the fertilizers applied. Interaction between the crop factor and liming expressed as an ambiguous effect of liming on the microbiome in the presence of different plants was reliably demonstrated. Thus, in the case of barley and clover, liming resulted in increased taxonomic diversity of the community, while in the case of potato and flax it had an opposite effect.     

Application of ecological and evolutionary theory to microbiome community dynamics across systems

A fundamental aim of microbiome research is to understand the factors that influence the assembly and stability of host-associated microbiomes, and their impact on host phenotype, ecology and evolution. However, ecological and evolutionary theories applied to predict microbiome community dynamics are largely based on macroorganisms and lack microbiome-centric hypotheses that account for unique features of the microbiome. This special feature sets out to drive advancements in the application of eco-evolutionary theory to microbiome community dynamics through the development of microbiome-specific theoretical and conceptual frameworks across plant, human and non-human animal systems. The feature comprises 11 research and review articles that address: (i) the effects of the microbiome on host phenotype, ecology and evolution; (ii) the application and development of ecological and evolutionary theories to investigate microbiome assembly, diversity and stability across broad taxonomic scales; and (iii) general principles that underlie microbiome diversity and dynamics. This cross-disciplinary synthesis of theoretical, conceptual, methodological and analytical approaches to characterizing host–microbiome ecology and evolution across systems addresses key research gaps in the field of microbiome research and highlights future research priorities.     

Experimental temperatures shape host microbiome diversity and composition

Global climate change has led to more extreme thermal events. Plants and animals harbour diverse microbial communities, which may be vital for their physiological performance and help them survive stressful climatic conditions. The extent to which microbiome communities change in response to warming or cooling may be important for predicting host performance under global change. Using a meta-analysis of 1377 microbiomes from 43 terrestrial and aquatic species, we found a decrease in the amplicon sequence variant-level microbiome phylogenetic diversity and alteration of microbiome composition under both experimental warming and cooling. Microbiome beta dispersion was not affected by temperature changes. We showed that the host habitat and experimental factors affected microbiome diversity and composition more than host biological traits. In particular, aquatic organisms—especially in marine habitats—experienced a greater depletion in microbiome diversity under cold conditions, compared to terrestrial hosts. Exposure involving a sudden long and static temperature shift was associated with microbiome diversity loss, but this reduction was attenuated by prior-experimental lab acclimation or when a ramped regime (i.e., warming) was used. Microbial differential abundance and co-occurrence network analyses revealed several potential indicator bacterial classes for hosts in heated environments and on different biome levels. Overall, our findings improve our understanding on the impact of global temperature changes on animal and plant microbiome structures across a diverse range of habitats. The next step is to link these changes to measures of host fitness, as well as microbial community functions, to determine whether microbiomes can buffer some species against a more thermally variable and extreme world.     

New challenges in the study of the evolution of wild animals and their gut microbiome

In this viewpoint, by reviewing the recent findings on wild animals and their gut microbiomes, we found some potential new insights and challenges in the study of the evolution of wild animals and their gut microbiome. We suggested that wild animal gut microbiomes may come from microbiomes in the animals'' living habitats along with animals'' special behavior, and that the study of long‐term changes in gut microbiomes should consider both habitat and special behaviors. Also, host behavior would facilitate the gut microbiome transmission between individuals. We suggested that research should integrate the evolutionary history and physiological systems of wild animals to understand the evolution of animals and their gut microbiomes. Finally, we proposed the Noncultured‐Cultured‐Fermentation‐Model Animal pipeline to determine the function (diet digestion, physiology, and behavior) of these target strains in the wild animal gut.     

Neutral Models of Microbiome Evolution

There has been an explosion of research on host-associated microbial communities (i.e.,microbiomes). Much of this research has focused on surveys of microbial diversities across a variety of host species, including humans, with a view to understanding how these microbiomes are distributed across space and time, and how they correlate with host health, disease, phenotype, physiology and ecology. Fewer studies have focused on how these microbiomes may have evolved. In this paper, we develop an agent-based framework to study the dynamics of microbiome evolution. Our framework incorporates neutral models of how hosts acquire their microbiomes, and how the environmental microbial community that is available to the hosts is assembled. Most importantly, our framework also incorporates a Wright-Fisher genealogical model of hosts, so that the dynamics of microbiome evolution is studied on an evolutionary timescale. Our results indicate that the extent of parental contribution to microbial availability from one generation to the next significantly impacts the diversity of microbiomes: the greater the parental contribution, the less diverse the microbiomes. In contrast, even when there is only a very small contribution from a constant environmental pool, microbial communities can remain highly diverse. Finally, we show that our models may be used to construct hypotheses about the types of processes that operate to assemble microbiomes over evolutionary time.