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。     

Structure and ecological function of the soil microbiome affecting plant–soil feedbacks in the presence of a soil-borne pathogen

Interactions between plants and soil microbes are important for plant growth and resistance. Through plant–soil-feedbacks, growth of a plant is influenced by the previous plant that was growing in the same soil. We performed a plant–soil feedback study with 37 grass, forb and legume species, to condition the soil and then tested the effects of plant-induced changes in soil microbiomes on the growth of the commercially important cut-flower Chrysanthemum in presence and absence of a pathogen. We analysed the fungal and bacterial communities in these soils using next-generation sequencing and examined their relationship with plant growth in inoculated soils with or without the root pathogen, Pythium ultimum. We show that a large part of the soil microbiome is plant species-specific while a smaller part is conserved at the plant family level. We further identified clusters of plant species creating plant growth promoting microbiomes that suppress concomitantly plant pathogens. Especially soil inocula with higher relative abundances of arbuscular mycorrhizal fungi caused positive effects on the Chrysanthemum growth when exposed to the pathogen. We conclude that plants differ greatly in how they influence the soil microbiome and that plant growth and protection against pathogens is associated with a complex soil microbial community.     

Evolutionary ecology of plant-microbe interactions: soil microbial structure alters selection on plant traits

? Below-ground microbial communities influence plant diversity, plant productivity, and plant community composition. Given these strong ecological effects, are interactions with below-ground microbes also important for understanding natural selection on plant traits? ? Here, we manipulated below-ground microbial communities and the soil moisture environment on replicated populations of Brassica rapa to examine how microbial community structure influences selection on plant traits and mediates plant responses to abiotic environmental stress. ? In soils with experimentally simplified microbial communities, plants were smaller, had reduced chlorophyll content, produced fewer flowers, and were less fecund when compared with plant populations grown in association with more complex soil microbial communities. Selection on plant growth and phenological traits also was stronger when plants were grown in simplified, less diverse soil microbial communities, and these effects typically were consistent across soil moisture treatments. ? Our results suggest that microbial community structure affects patterns of natural selection on plant traits. Thus, the below-ground microbial community can influence evolutionary processes, just as recent studies have demonstrated that microbial diversity can influence plant community and ecosystem processes.     

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.     

Rhizobien in der Pflanzenmikrobiota

Rhizobia in the plant microbiota The plant microbiota is of critical importance for plant growth and survival in soil. To explore mechanisms underlying plant‐microbiota interactions, defined commensal communities can be composed from microbiota culture collections and co‐cultivated with germ‐free plants to determine their impact on plant growth and health. The order Rhizobiales belongs to the core microbiota and includes nitrogen‐fixing bacteria that are known to engage in symbiotic interactions with legumes. Compatible host‐symbiont pairs are needed for a functional symbiosis, which involves the activation of highly specialized and interdependent signaling pathways between the two partners. Comparative genome analysis of more than 1,300 legume symbionts and rhizobial root commensals from non‐leguminous plants revealed that the most recent common ancestor of rhizobia lacked the gene repertoire needed for symbiosis and was able to colonize roots of a wide variety of plants. During evolution, key symbiosis genes were acquired multiple independent times by commensals belonging to different families of the Rhizobiales order.     

Microbiome-mediated signal transduction within the plant holobiont

Microorganisms colonizing the plant rhizosphere and phyllosphere play crucial roles in plant growth and health. Recent studies provide new insights into long-distance communication from plant roots to shoots in association with their commensal microbiome. In brief, these recent advances suggest that specific plant-associated microbial taxa can contribute to systemic plant responses associated with the enhancement of plant health and performance in face of a variety of biotic and abiotic stresses. However, most of the mechanisms associated with microbiome-mediated signal transduction in plants remain poorly understood. In this review, we provide an overview of long-distance signaling mechanisms within plants mediated by the commensal plant-associated microbiomes. We advocate the view of plants and microbes as a holobiont and explore key molecules and mechanisms associated with plant–microbe interactions and changes in plant physiology activated by signal transduction.     

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。     

Stochastic and deterministic processes shape bioenergy crop microbiomes along a vertical soil niche

Sustainable biofuel cropping systems aim to address climate change while meeting energy needs. Understanding how soil and plant-associated microbes respond to these different cropping systems is key to promoting agriculture sustainability and evaluating changes in ecosystem functions. Here, we leverage a long-term biofuel cropping system field experiment to dissect soil and root microbiome changes across a soil-depth gradient in poplar, restored prairie and switchgrass to understand their effects on the microbial communities. High throughput amplicon sequencing of the fungal internal transcribed spacer (ITS) and prokaryotic 16S DNA regions showed a common trend of root and soil microbial community richness decreasing and evenness increasing with depth. Ecological niche (root vs. soil) had the strongest effect on community structure, followed by depth, then crop. Stochastic processes dominated the structuring of fungal communities in deeper soil layers while operational taxonomic units (OTUs) in surface soil layers were more likely to co-occur and to be enriched by plant hosts. Prokaryotic communities were dispersal limited at deeper depths. Microbial networks showed a higher density, connectedness, average degree and module size in deeper soils. We observed a decrease in fungal-fungal links and an increase of bacteria–bacteria links with increasing depth in all crops, particularly in the root microbiome.     

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.     

Variable influences of soil and seed-associated bacterial communities on the assembly of seedling microbiomes

Plants grown in distinct soils typically harbor distinct microbial communities, but the degree of the soil microbiome influence on plant microbiome assembly remains largely undetermined. We also know that the microbes associated with seeds can contribute to the plant microbiome, but the magnitude of this contribution is likely variable. We quantified the influence of soil and seed microbiomes on the bacterial community composition of seedlings by independently inoculating seeds from a single cultivar of wheat (Triticum aestivum) with 219 unique soil slurries while holding other environmental factors constant, determining the composition of the seed, soil, and seedling bacterial communities via cultivation-independent methods. Soil bacterial communities exert a strong, but variable, influence on seedling bacterial community structure, with the extent of the soil bacterial contribution dependent on the soil in question. By testing a wide range of soils, we were able to show that the specific composition of the seedling microbiome is predictable from knowing which bacterial taxa are found in soil. Although the most ubiquitous taxa associated with the seedlings were seed derived, the contributions of the seed microbiome to the seedling microbiome were variable and dependent on soil bacterial community composition. Together this work improves our predictive understanding of how the plant microbiome assembles and how the seedling microbiome could be directly or indirectly manipulated to improve plant health.Subject terms: Microbial ecology, Next-generation sequencing, Microbial ecology     

Root microbiome assembly of As-hyperaccumulator Pteris vittata and its efficacy in arsenic requisition

The assemblage of root-associated microorganisms plays important roles in improving their capability to adapt to environmental stress. Metal(loid) hyperaccumulators exhibit disparate adaptive capability compared to that of non-hyperaccumulators when faced with elevated contents of metal(loid)s. However, knowledge of the assemblage of root microbes of hyperaccumulators and their ecological roles in plant growth is still scarce. The present study used Pteris vittata as a model plant to study the microbial assemblage and its beneficial role in plant growth. We demonstrated that the assemblage of microbes from the associated bulk soil to the root compartment was based on their lifestyles. We used metagenomic analysis and identified that the assembled microbes were primarily involved in root–microbe interactions in P. vittata root. Notably, we identified that the assembled root microbiome played an important role in As requisition, which promoted the fitness and growth of P. vittata. This study provides new insights into the root microbiome and potential valuable knowledge to understand how the root microbiome contributes to the fitness of its host.     

Intraspecific and intergenerational differences in plant–soil feedbacks

Interactions between plant and soil communities are known to play an integral role in shaping ecosystems. Plants influence the composition of soil communities and soil communities in turn influence plant performance. Such a plant–soil feedback may incur selection pressure on plants and the associating soil community. However, the evolutionary consequences of these above–belowground feedback interactions remain largely speculative. Here we assess whether plant–soil feedback effects differ between intraspecific plant populations and between generations within the same plant population. We used two populations of Trifolium pratense and assessed their performance when grown in association with their home versus away soil biota. Both populations were colonized by distinct microbial communities and performed better with their own home soil communities than with the soil community from the other intraspecific population, demonstrating intraspecific positive feedback effects of home soil. In one of the two populations, we found that plant performance and the root associated microbiota community differed between parental and progeny plants when inoculated with their own home soil. Differences in root associated community characteristics could explain more than 80% of the variation in performance among the progeny and parental plants. Our results highlight that intraspecific differences in both plant and associated soil communities shape plant–soil feedback effects, and consequently indicate that plant–soil feedback can influence the direction of selection between intraspecific plant populations.     

Plant–microbe networks in soil are weakened by century-long use of inorganic fertilizers

Understanding the changes in plant–microbe interactions is critically important for predicting ecosystem functioning in response to human-induced environmental changes such as nitrogen (N) addition. In this study, the effects of a century-long fertilization treatment (> 150 years) on the networks between plants and soil microbial functional communities, detected by GeoChip, in grassland were determined in the Park Grass Experiment at Rothamsted Research, UK. Our results showed that plants and soil microbes have a consistent response to long-term fertilization—both richness and diversity of plants and soil microbes are significantly decreased, as well as microbial functional genes involved in soil carbon (C), nitrogen (N) and phosphorus (P) cycling. The network-based analyses showed that long-term fertilization decreased the complexity of networks between plant and microbial functional communities in terms of node numbers, connectivity, network density and the clustering coefficient. Similarly, within the soil microbial community, the strength of microbial associations was also weakened in response to long-term fertilization. Mantel path analysis showed that soil C and N contents were the main factors affecting the network between plants and microbes. Our results indicate that century-long fertilization weakens the plant–microbe networks, which is important in improving our understanding of grassland ecosystem functions and stability under long-term agriculture management.     

Interactions among plants,bacteria, and fungi reduce extracellular enzyme activities under long‐term N fertilization

Atmospheric nitrogen (N) deposition has enhanced soil carbon (C) stocks in temperate forests. Most research has posited that these soil C gains are driven primarily by shifts in fungal community composition with elevated N leading to declines in lignin degrading Basidiomycetes. Recent research, however, suggests that plants and soil microbes are dynamically intertwined, whereby plants send C subsidies to rhizosphere microbes to enhance enzyme production and the mobilization of N. Thus, under elevated N, trees may reduce belowground C allocation leading to cascading impacts on the ability of microbes to degrade soil organic matter through a shift in microbial species and/or a change in plant–microbe interactions. The objective of this study was to determine the extent to which couplings among plant, fungal, and bacterial responses to N fertilization alter the activity of enzymes that are the primary agents of soil decomposition. We measured fungal and bacterial community composition, root–microbial interactions, and extracellular enzyme activity in the rhizosphere, bulk, and organic horizon of soils sampled from a long‐term (>25 years), whole‐watershed, N fertilization experiment at the Fernow Experimental Forest in West Virginia, USA. We observed significant declines in plant C investment to fine root biomass (24.7%), root morphology, and arbuscular mycorrhizal (AM) colonization (55.9%). Moreover, we found that declines in extracellular enzyme activity were significantly correlated with a shift in bacterial community composition, but not fungal community composition. This bacterial community shift was also correlated with reduced AM fungal colonization indicating that declines in plant investment belowground drive the response of bacterial community structure and function to N fertilization. Collectively, we find that enzyme activity responses to N fertilization are not solely driven by fungi, but instead reflect a whole ecosystem response, whereby declines in the strength of belowground C investment to gain N cascade through the soil environment.     

Seed mucilage interacts with soil microbial community and physiochemical processes to affect seedling emergence on desert sand dunes

Seedling emergence is a critical stage in the establishment of desert plants. Soil microbes participate in plant growth and development, but information is lacking with regard to the role of microbes on seedling emergence. We applied the biocides (captan and streptomycin) to assess how seed mucilage interacts with soil microbial community and physiochemical processes to affect seedling emergence of Artemisia sphaerocephala on the desert sand dune. Fungal and bacterial community composition and diversity and fungal–bacterial interactions were changed by both captan and streptomycin. Mucilage increased soil enzyme activities and fungal–bacterial interactions. Highest seedling emergence occurred under streptomycin and mucilage treatment. Members of the phyla Firmicutes and Glomeromycota were the keystone species that improved A. sphaerocephala seedling emergence, by increasing resistance of young seedlings to drought and pathogen. Seed mucilage directly improved seedling emergence and indirectly interacted with the soil microbial community through strengthening fungal–bacterial interactions and providing favourable environment for soil enzymes to affect seedling emergence. Our study provides a comprehensive understanding of the regulatory mechanisms by which soil microbial community and seed mucilage interactively promote successful establishment of populations of desert plants on the barren and stressful sand dune.     

Friends and foes: streptomycetes as modulators of plant disease and symbiosis

The ecological role of soil streptomycetes within the plant root environment is currently gaining increased attention. This review describes our recent advances in elucidating the complex interactions between streptomycetes, plants, pathogenic and symbiotic microorganisms. Streptomycetes play diverse roles in plant-associated microbial communities. Some act as biocontrol agents, inhibiting plant interactions with pathogenic organisms. Owing to the antagonistic properties of streptomycetes, they exert a selective pressure on soil microbes, which may not always be for plant benefit. Others promote the formation of symbioses between plant roots and microbes, and this is in part due to their direct positive influence on the symbiotic partner, expressed as, e.g., promotion of hyphal elongation of symbiotic fungi. Recently, streptomycetes have been identified as modulators of plant defence. By repressing plant responses to pathogens they facilitate root colonisation with pathogenic fungi. In contrast, other strains induce local and systemic resistance against pathogens or enhance plant growth. In conclusion, while streptomycetes have a clear potential of acting as biocontrol agents, care has to be taken to avoid strains that select for virulent pathogens or enhance disease development. We argue towards the use of an integrated screening approach in the search for efficient biocontrol agents, including assays on in vitro antagonism, plant growth, and disease suppression.     

Two cultivated legume plants reveal the enrichment process of the microbiome in the rhizocompartments

The microbiomes of rhizocompartments (nodule endophytes, root endophytes, rhizosphere and root zone) in soya bean and alfalfa were analysed using high‐throughput sequencing to investigate the interactions among legume species, microorganisms and soil types. A clear hierarchical filtration of microbiota by plants was observed in the four rhizocompartments – the nodule endosphere, root endosphere, rhizosphere and root zone – as demonstrated by significant variations in the composition of the microbial community in the different compartments. The rhizosphere and root zone microbial communities were largely influenced by soil type, and the nodule and root endophytes were primarily determined by plant species. Diverse microbes inhabited the root nodule endosphere, and the corresponding dominant symbiotic rhizobia belonged to Ensifer for alfalfa and Ensifer–Bradyrhizobium for soya bean. The nonsymbiotic nodule endophytes were mainly Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes. The variation in root microbial communities was also affected by the plant growth stage. In summary, this study demonstrated that the enrichment process of nodule endophytes follows a hierarchical filtration and that the bacterial communities in nodule endophytes vary according to the plant species.     

Rhizosphere shapes the associations between protistan predators and bacteria within microbiomes through the deterministic selection on bacterial communities

The assembly of bacterial communities in the rhizosphere is well-documented and plays a crucial role in supporting plant performance. However, we have limited knowledge of how plant rhizosphere determines the assembly of protistan predators and whether the potential associations between protistan predators and bacterial communities shift due to rhizosphere selection. To address this, we examined bacterial and protistan taxa from 443 agricultural soil samples including bulk and rhizosphere soils. Our results presented distinct patterns of bacteria and protistan predators in rhizosphere microbiome assembly. Community assembly of protistan predators was determined by a stochastic process in the rhizosphere and the diversity of protistan predators was reduced in the rhizosphere compared to bulk soils, these may be attributed to the indirect impacts from the altered bacterial communities that showed deterministic process assembly in the rhizosphere. Interestingly, we observed that the plant rhizosphere facilitates more close interrelationships between protistan predators and bacterial communities, which might promote a healthy rhizosphere microbial community for plant growth. Overall, our findings indicate that the potential predator–prey relationships within the microbiome, mediated by plant rhizosphere, might contribute to plant performance in agricultural ecosystems.     

Are you what you eat? A highly transient and prey‐influenced gut microbiome in the grey house spider Badumna longinqua

Stable core microbial communities have been described in numerous animal species and are commonly associated with fitness benefits for their hosts. Recent research, however, highlights examples of species whose microbiota are transient and environmentally derived. Here, we test the effect of diet on gut microbial community assembly in the spider Badumna longinqua. Using 16S rRNA gene amplicon sequencing combined with quantitative PCR, we analyzed diversity and abundance of the spider's gut microbes, and simultaneously characterized its prey communities using nuclear rRNA markers. We found a clear correlation between community similarity of the spider's insect prey and gut microbial DNA, suggesting that microbiome assembly is primarily diet‐driven. This assumption is supported by a feeding experiment, in which two types of prey—crickets and fruit flies—both substantially altered microbial diversity and community similarity between spiders, but did so in different ways. After cricket consumption, numerous cricket‐derived microbes appeared in the spider's gut, resulting in a rapid homogenization of microbial communities among spiders. In contrast, few prey‐associated bacteria were detected after consumption of fruit flies; instead, the microbial community was remodelled by environmentally sourced microbes, or abundance shifts of rare taxa in the spider's gut. The reshaping of the microbiota by both prey taxa mimicked a stable core microbiome in the spiders for several weeks post feeding. Our results suggest that the spider's gut microbiome undergoes pronounced temporal fluctuations, that its assembly is dictated by the consumed prey, and that different prey taxa may remodel the microbiota in drastically different ways.