微生物组学对植物病害微生物防治研究的启示

植物病害的微生物防治研究主要集中在植物、病原菌和生防菌三者的互作关系上,相对忽视了植物微生物组/群的作用。越来越多的研究表明,植物内生微生物、根围土壤微生物和叶围微生物均不同程度地参与了植物防病的机制。为了更好地了解相关进展,本文选择部分代表性研究,详述了植物微生物组/群的构成,并结合案例介绍了植物微生物组/群对寄主植物的防/致病作用、对植物病原菌致病性的影响,以及施用生防菌对植物微生物组/群的影响。微生物组学的发展为生防机制领域提出了新的研究思路,有利于发现更加科学的防治手段。     

植物内生菌研究进展

内生菌由于生长于植物体内且不引起植物病害所以不易被发现,它是一类具有高实用价值的植物内生微生物。经过人们的不断研究,越来越多的植物内生菌被发现,其活性代谢产物的优势也得到了更多研究者的认可。综述了国内外有关植物内生菌研究的主要成果和进展,并从植物内生菌的发现、研究历史、多样性、生理生化特性以及植物内生菌与宿主植物间的作用关系等多个层次进行了概述,以期为植物内生菌相关研究提供参考。     

根际微生物组组装与植物健康

土壤微生物拥有高度多样化的群落结构,其通过与植物发生复杂的相互作用影响植物健康,也被称为植物的第二基因组。最近研究表明植物能通过改变根际分泌物的组成影响根际微生物群落的组装,反之,根际微生物群落组成的改变能够通过影响植物营养吸收和抵御生物及非生物胁迫的能力影响植物健康。除此之外,农艺管理也是影响土壤微生物群落组装方式的重要因素。但到目前为止,根际微生物与宿主植物及土壤微生物之间互作机制的研究尚不清楚。本文将从农艺管理和宿主植物对微生物群落组装的影响及根际微生物组对植物健康的影响进行总结,为增加作物产量提供机会。     

根际微生物组中细菌趋化系统的生态功能

在根际微环境中,特定的土壤微生物能够利用自身独特的趋化系统感应根系分泌物,响应植物的选择性招募。细菌的趋化系统介导了植物-微生物以及微生物间相互作用,在植物对根际微生物组的选择中发挥着关键的生态学功能。综述了根际微生物组中细菌趋化系统的研究进展,从生态学的角度提出了未来针对根际细菌趋化系统的研究方向,旨在阐明根际细菌趋化系统的生态学功能,为增进理解作物根际微生物组的募集过程,以及未来农业中根际微生物组的重组构建奠定理论基础。     

Shifts in chemical and microbiological properties belowground of invader Ageratina adenophora along an altitudinal gradient

入侵植物紫茎泽兰根围土壤化学及微生物属性海拔变化格局 热带地区山地生态系统是外来植物入侵的重要区域,是研究外来植物扩散机制的“天然实验室”。本研究试图探明入侵植物紫茎泽兰(Ageratina adenophora)根围土壤化学(pH及土壤养分)和微生物(酶活性和细菌群落)特性沿海拔梯度的变化规律。本研究以哀牢山(1400–2400 m)不同海拔梯度分布的紫茎泽兰为研究对象,采集根围土,测定土壤有机碳及养分含量,以及植物根系碳和氮含量。分析与土壤有机碳、氮及磷循环的酶活性,通过计算土壤酶化学计量参数,探究微生物生长代谢利用碳、氮及磷的规律。借助高通量测序技术对16S rDNA的V4区测序,分析细菌群落结构。研究结果显示,海拔显著影响紫茎泽兰根系氮及及其根围土壤有机碳含量,且这些测量指标在海拔2000 m  出现拐点。处在低海拔,入侵植物快速生长耗竭土壤中相对缺乏的磷,磷素是限制微生物生长的重要养分元素;而在高海拔,微生物需要投入更多的能量降解有机质获取碳,导致微生物生长的碳限制。细菌群落β多样性及pH  是决定不同海拔酶化学计量参数差异的重要因子;变形菌门和酸杆菌门是决定微生物养分利用状况的主要细菌门类。这些结果阐明了不同海拔梯度上紫茎泽兰根围土壤微生物的养分利用规律,有助于认识入侵植物沿海拔扩散机制。     

土壤环境下的根际微生物和植物互作关系研究进展

植物根系、土壤、根际微生物以及根际范围内其他因子等组成了根际微生态系统,在根际微生态系统中的不同组分之间存在着广泛的相互作用,其中以根系-土壤-微生物之间的相互作用网络最为复杂,同时也对整个根际系统的稳定和发展有着至关重要的影响。综述了近年来国内外对于土壤环境中根际互作关系研究的进展,探讨了土壤环境对植物和根际微生物群落的影响,植物如何调控根际微生物群落的组装和稳定过程,以及根际微生物对植物生长发育、病原菌防卫和抗逆性的调控作用等,分别从土壤环境、宿主植物和根际微生物三个层面,分析了它们在根际互作关系中的角色和作用机制,以期为农业生产和环境保护提供一定指导意义和借鉴作用。     

拟南芥与叶际微生物组的互作遗传机制——基于网络作图理论

叶际微生物组对植物的生长发育至关重要，但植物与其定殖微生物组相互作用机制尚不明确。目前植物与微生物互作研究多集中于根际微生物组，对叶际微生物组的研究较少，且这些研究未能从微生物互作的角度探究植物与微生物的相互作用机理。基于网络作图理论，将拟南芥基因组SNP （Single Nucleotide Polymorphisms）分子标记数据与微生物组网络特征值相关联，挖掘影响叶际微生物组网络结构的枢纽基因，以探究拟南芥塑造叶际微生物组网络结构的遗传机制。通过对188株拟南芥及其叶际微生物组数据的分析，识别出四种关系下的中心节点微生物，筛选到622个显著SNP位点。进一步构建了贝叶斯遗传网络，获得26个枢纽基因，这些基因可能参与了植物抗病、激素分泌和生长发育相关的分子途径。本研究从全基因组角度探究植物调控自身微生物组的遗传机制，揭示植物与微生物组如何互作促进植物健康，将为精准分子育种提供理论基础和遗传资源，并为合成菌群用于创制新型菌剂提供数据支持，具有重要的科学意义和应用价值。     

根际微生物群落功能与调控的研究进展

根际微生物群落是随植物长期进化及地球生境变迁而形成的动态微生物系统。随着多组学技术的不断发展，人们对根际微生物群落结构与功能的研究日益深入。根际微生物群落中的功能微生物类群，如植物促生细菌、植物促生真菌等，通过与植物建立紧密的物质、能量与信息联系，参与植物激素合成、难溶营养物解离、生物固氮、微生物拮抗、生长因子供应等系列生物学过程，从而提高植物营养物质吸收与抗逆能力，为植物的健康和高效生长提供重要保障。这些微生物中的某些成员已被开发成微生物刺激剂，广泛应用于作物增产抗逆与农田地力提升。近年来，多学科的交叉融合为根际微生物群落结构-功能-调控策略的交互式研究提供新的机遇，推动了基于合成生物学与材料科学技术的合成微生物组的发展。尤其是在核心微生物互作方面，人工蛋白创制、磁性组装、生物炭强化等策略能够增强核心微生物与目标植物之间的物理连接作用，大幅提高合成微生物组的工作效率和稳定性，从而有效驱动作物增产增收，提高污染修复效率。因此，根际微生物群落结构、功能与调控的深入研究，必将为绿色农业发展提供不竭动力。     

“根际微生物”专刊征稿函

自1904年德国科学家Lorenz Hiltner提出根际概念以来,其研究内容不断得以丰富和发展。根际是植物吸收的关键门户,是实现农业绿色发展的关键调控区域。根际微生物对植物的生长和健康发挥重要作用,被看作是植物的第二基因组,类似于肠道微生物对人体的功能。根际微生物中的益生菌具有活化根区养分、促进植物生长、增强植物抗逆、抑制土传病害等功能,是微生物肥料和微生物农药的主要菌种来源。随着国内外微生物组研究的开展,根际微生物组的整体功能更受关注,充分挖掘根际微生物组的功能促进作物增产是农业微生物的主要研究前沿之一。     

病原效应蛋白HopB1抑制植物的天然免疫反应

植物在完成整个生活史的过程中无时无刻不受到环境中各种病原微生物(如细菌,真菌和病毒等)的侵染。这些病原微生物的侵染会引发严重的植物病害,造成世界范围内许多重要经济和粮食作物的大量减产,导致大量的经济损失并严重威胁人类的粮食安全。长期以来,农业育种人员经过不断的尝试和持续的改良大大提高了作物品种的抗病性,但由于病原微生物与植物互作的复杂性,目前人们依然需要面对各种严重的植物病害。因此研究病原微生物的致病机理和植物抗性机制显得尤为重要,通过对病原物和植物互作的研究能够为解决农业生产中农作物病虫害提供强有力的理论支持。     

Beneficial microbes going underground of root immunity

Plant roots interact with an enormous diversity of commensal, mutualistic, and pathogenic microbes, which poses a big challenge to roots to distinguish beneficial microbes from harmful ones. Plants can effectively ward off pathogens following immune recognition of conserved microbe‐associated molecular patterns (MAMPs). However, such immune elicitors are essentially not different from those of neutral and beneficial microbes that are abundantly present in the root microbiome. Recent studies indicate that the plant immune system plays an active role in influencing rhizosphere microbiome composition. Moreover, it has become increasingly clear that root‐invading beneficial microbes, including rhizobia and arbuscular mycorrhiza, evade or suppress host immunity to establish a mutualistic relationship with their host. Evidence is accumulating that many free‐living rhizosphere microbiota members can suppress root immune responses, highlighting root immune suppression as an important function of the root microbiome. Thus, the gate keeping functions of the plant immune system are not restricted to warding off root‐invading pathogens but also extend to rhizosphere microbiota, likely to promote colonization by beneficial microbes and prevent growth‐defense tradeoffs triggered by the MAMP‐rich rhizosphere environment.     

Rhizosphere microbiome functional diversity and pathogen invasion resistance build up during plant development

The rhizosphere microbiome is essential for plant growth and health, and numerous studies have attempted to link microbiome functionality to species and trait composition. However, to date little is known about the actual ecological processes shaping community composition, complicating attempts to steer microbiome functionality. Here, we assess the development of microbial life history and community-level species interaction patterns that emerge during plant development. We use microbial phenotyping to experimentally test the development of niche complementarity and life history traits linked to microbiome performance. We show that the rhizosphere microbiome assembles from pioneer assemblages of species with random resource overlap into high-density, functionally complementary climax communities at later stages. During plant growth, fast-growing species were further replaced by antagonistic and stress-tolerant ones. Using synthetic consortia isolated from different plant growth stages, we demonstrate that the high functional diversity of ‘climax’ microbiomes leads to a better resistance to bacterial pathogen invasion. By demonstrating that different life-history strategies prevail at different plant growth stages and that community-level processes may supersede the importance of single species, we provide a new toolbox to understand microbiome assembly and steer its functionality at a community level.     

The rhizosphere microbiome and plant health

The diversity of microbes associated with plant roots is enormous, in the order of tens of thousands of species. This complex plant-associated microbial community, also referred to as the second genome of the plant, is crucial for plant health. Recent advances in plant-microbe interactions research revealed that plants are able to shape their rhizosphere microbiome, as evidenced by the fact that different plant species host specific microbial communities when grown on the same soil. In this review, we discuss evidence that upon pathogen or insect attack, plants are able to recruit protective microorganisms, and enhance microbial activity to suppress pathogens in the rhizosphere. A comprehensive understanding of the mechanisms that govern selection and activity of microbial communities by plant roots will provide new opportunities to increase crop production.     

An overview of major metagenomic studies on human microbiomes in health and disease

Many microbes are important symbiotes of human. They form specific microbiota communities, participate in various kinds of biological processes of their host and thus deeply affect human health status. Metagenomic sequencing has been widely used in human microbiota study due to its capacity of studying all genetic materials in an environment as a whole without any extra need of isolation or cultivation of microorganisms. Many efforts have been made by researchers in this area trying to dig out interesting knowledge from various metagenome data. In this review, we go through some prominent studies in the metagenomic area. We summarize them into three categories, constructing taxonomy and gene reference, characterization of microbiome distribution patterns, and detection of microbiome alternations associated with specific human phenotypes or diseases. Some available data resources are also provided. This review can serve as an entrance to this exciting and rapidly developing field for researchers interested in human microbiomes.     

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.     

Impacts of maize hybrids with different nitrogen use efficiency on root-associated microbiota based on distinct rhizosphere soil metabolites

Plant genotypes shape root-associated microbiota that affect plant nutrient acquisition and productivity. It is unclear how maize hybrids modify root-associated microbiota and their functions and relationship with nitrogen use efficiency (NUE) by regulating rhizosphere soil metabolites. Here, two N-efficient (NE) (ZD958, DMY3) and two N-inefficient (NIE) maize hybrids (YD9953, LY99) were used to investigate this issue under low N (60 kg N ha⁻¹, LN) and high N (180 kg N ha⁻¹, HN) field conditions. NE hybrids had higher yield than NIE hybrids under LN but not HN. NE and NIE hybrids recruited only distinct root-associated bacterial microbiota in LN. The bacterial network stability was stronger in NE than NIE hybrids. Compared with NIE hybrids, NE hybrids recruited more bacterial taxa that have been described as plant growth-promoting rhizobacteria (PGPR), and less related to denitrification and N competition; this resulted in low N₂O emission and high rhizosphere NO₃⁻-N accumulation. NE and NIE hybrids had distinct rhizosphere soil metabolite patterns, and their specific metabolites were closely related to microbiota and specific genera under LN. Our findings reveal the relationships among plant NUE, rhizosphere soil metabolites, root-associated microbiota, and soil nutrient cycling, and this information is informative for breeding NE crops.     

Comparison of different methods for determining lignin concentration and quality in herbaceous and woody plant residues

Background

The development and dispersal of seeds as well as their transition to seedlings represent perhaps the most critical stages of a plant’s life cycle. The endophytic and epiphytic microbial interactions that take place in, on, and around seeds during these stages of the plant’s life cycle may have profound impacts on plant ecology, health, and productivity. While our understanding of the seed microbiota has lagged far behind that of the rhizosphere and phyllosphere, many advances are now being made.

Scope

This review explores the microbial associations with seeds through various stages of the plant life cycle, beginning with the earliest stages of seed development on the parent plant and continuing through the development and establishment of seedlings in soil. This review represents a broad synthesis of the ecological and agricultural literature focused on seed-microbe interactions as a means of better understanding how these interactions may ultimately influence plant ecology, health, and productivity in both natural and agricultural systems. Our current understanding of seed-microbe associations will be discussed, with an emphasis on recent findings that specifically highlight the emerging contemporary understanding of how seed-microbe associations may ultimately impact plant health and productivity.

Conclusions

The diversity and dynamics of seed microbiomes represent the culmination of complex interactions with microbes throughout the plant life cycle. The richness and dynamics of seed microbiomes is revealing exciting new opportunities for research into plant-microbe interactions. Often neglected in plant microbiome studies, the renaissance of inquiry into seed microbiomes is offering exciting new insights into how the diversity and dynamics of the seed microbiome with plant and soil microbiomes as well as the microbiomes of dispersers and pollinators. It is clear that the interactions taking place in and around seeds indeed have significant impacts on plant health and productivity in both agricultural and natural ecosystems.