Rhizosphere Microbial Community Composition Affects Cadmium and Zinc Uptake by the Metal-Hyperaccumulating Plant Arabidopsis halleri

The remediation of metal-contaminated soils by phytoextraction depends on plant growth and plant metal accessibility. Soil microorganisms can affect the accumulation of metals by plants either by directly or indirectly stimulating plant growth and activity or by (im)mobilizing and/or complexing metals. Understanding the intricate interplay of metal-accumulating plants with their rhizosphere microbiome is an important step toward the application and optimization of phytoremediation. We compared the effects of a “native” and a strongly disturbed (gamma-irradiated) soil microbial communities on cadmium and zinc accumulation by the plant Arabidopsis halleri in soil microcosm experiments. A. halleri accumulated 100% more cadmium and 15% more zinc when grown on the untreated than on the gamma-irradiated soil. Gamma irradiation affected neither plant growth nor the 1 M HCl-extractable metal content of the soil. However, it strongly altered the soil microbial community composition and overall cell numbers. Pyrosequencing of 16S rRNA gene amplicons of DNA extracted from rhizosphere samples of A. halleri identified microbial taxa (Lysobacter, Streptomyces, Agromyces, Nitrospira, “Candidatus Chloracidobacterium”) of higher relative sequence abundance in the rhizospheres of A. halleri plants grown on untreated than on gamma-irradiated soil, leading to hypotheses on their potential effect on plant metal uptake. However, further experimental evidence is required, and wherefore we discuss different mechanisms of interaction of A. halleri with its rhizosphere microbiome that might have directly or indirectly affected plant metal accumulation. Deciphering the complex interactions between A. halleri and individual microbial taxa will help to further develop soil metal phytoextraction as an efficient and sustainable remediation strategy.     

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.     

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。     

Host genotype controls ecological change in the leaf fungal microbiome

Leaf fungal microbiomes can be fundamental drivers of host plant success, as they contain pathogens that devastate crop plants and taxa that enhance nutrient uptake, discourage herbivory, and antagonize pathogens. We measured leaf fungal diversity with amplicon sequencing across an entire growing season in a diversity panel of switchgrass (Panicum virgatum). We also sampled a replicated subset of genotypes across 3 additional sites to compare the importance of time, space, ecology, and genetics. We found a strong successional pattern in the microbiome shaped both by host genetics and environmental factors. Further, we used genome-wide association (GWA) mapping and RNA sequencing to show that 3 cysteine-rich receptor-like kinases (crRLKs) were linked to a genetic locus associated with microbiome structure. We confirmed GWAS results in an independent set of genotypes for both the internal transcribed spacer (ITS) and large subunit (LSU) ribosomal DNA markers. Fungal pathogens were central to microbial covariance networks, and genotypes susceptible to pathogens differed in their expression of the 3 crRLKs, suggesting that host immune genes are a principal means of controlling the entire leaf microbiome.

Leaf fungal microbiomes can strongly influence host plant success. Monitoring the leaf fungal microbiome of switchgrass over time shows microbial ecological succession, and reveals the host plant genes that influence community-wide changes.     

Impact of a resistance gene against a fungal pathogen on the plant host residue microbiome: The case of the Leptosphaeria maculans–Brassica napus pathosystem

Oilseed rape residues are a crucial determinant of stem canker epidemiology as they support the sexual reproduction of the fungal pathogen Leptosphaeria maculans. The aim of this study was to characterize the impact of a resistance gene against L. maculans infection on residue microbial communities and to identify microorganisms interacting with this pathogen during residue degradation. We used near-isogenic lines to obtain healthy and infected host plants. The microbiome associated with the two types of plant residues was characterized by metabarcoding. A combination of linear discriminant analysis and ecological network analysis was used to compare the microbial communities and to identify microorganisms interacting with L. maculans. Fungal community structure differed between the two lines at harvest, but not subsequently, suggesting that the presence/absence of the resistance gene influences the microbiome at the base of the stem whilst the plant is alive, but that this does not necessarily lead to differential colonization of the residues by fungi. Direct interactions with other members of the community involved many fungal and bacterial amplicon sequence variants (ASVs). L. maculans appeared to play a minor role in networks, whereas one ASV affiliated to Plenodomus biglobosus (synonym Leptosphaeria biglobosa) from the Leptosphaeria species complex may be considered a keystone taxon in the networks at harvest. This approach could be used to identify and promote microorganisms with beneficial effects against residue-borne pathogens and, more broadly, to decipher the complex interactions between multispecies pathosystems and other microbial components in crop residues.     

The core microbiome bonds the Alpine bog vegetation to a transkingdom metacommunity

Bog ecosystems fulfil important functions in Earth's carbon and water turnover. While plant communities and their keystone species Sphagnum have been well studied, less is known about the microbial communities associated with them. To study our hypothesis that bog plants share an essential core of their microbiome despite their different phylogenetic origins, we analysed four plant community plots with 24 bryophytes, vascular plants and lichen species in two Alpine bogs in Austria by 16S rDNA amplicon sequencing followed by bioinformatic analyses. The overall bog microbiome was classified into 32 microbial phyla, while Proteobacteria (30.8%), Verrucomicrobia (20.3%) and Planctomycetes (15.1%) belonged to the most abundant groups. Interestingly, the archaeal phylum Euryarcheota represented 7.2% of total microbial abundance. However, a high portion of micro‐organisms remained unassigned at phylum and class level, respectively. The core microbiome of the bog vegetation contained 177 operational taxonomic units (OTUs) (150 526 seq.) and contributed to 49.5% of the total microbial abundance. Only a minor portion of associated core micro‐organisms was host specific for examined plant groups (5.9–11.6%). Using our new approach to analyse plant–microbial communities in an integral framework of ecosystem, vegetation and microbiome, we demonstrated that bog vegetation harboured a core microbiome that is shared between plants and lichens over the whole ecosystem and formed a transkingdom metacommunity. All micro‐ and macro‐organisms are connected to keystone Sphagnum mosses via set of microbial species, for example Burkholderia bryophila which was found associated with a wide spectrum of host plants and is known for a beneficial plant–microbe interaction.     

植物病害防治相关微生物组研究进展与展望

微生物是人类活动过程中重要的生物资源。植物及其根围土壤中生存着大量多种多样的微生物,这些微生物与植物健康之间存在着密不可分的关系。近年来,基因测序技术的快速发展为植物微生物组结构和功能的研究提供了极大的便利,多种植物相关的微生物组得到了解析。同时更多研究者聚焦于植物病害相关的微生物组研究,通过差异分析,发现了一些特定的有益于植物健康的微生物菌群。此外,植物根围或根内微生物塑造的内在原理也得到了进一步的揭示。一系列植物微生物组研究为植物病害防治和新的微生物资源的挖掘提供了更多思路。     

Small changes in rhizosphere microbiome composition predict disease outcomes earlier than pathogen density variations

Even in homogeneous conditions, plants facing a soilborne pathogen tend to show a binary outcome with individuals either remaining fully healthy or developing severe to lethal disease symptoms. As the rhizosphere microbiome is a major determinant of plant health, we postulated that such a binary outcome may result from an early divergence in the rhizosphere microbiome assembly that may further cascade into varying disease suppression abilities. We tested this hypothesis by setting up a longitudinal study of tomato plants growing in a natural but homogenized soil infested with the soilborne bacterial pathogen Ralstonia solanacearum. Starting from an originally identical species pool, individual rhizosphere microbiome compositions rapidly diverged into multiple configurations during the plant vegetative growth. This variation in community composition was strongly associated with later disease development during the later fruiting state. Most interestingly, these patterns also significantly predicted disease outcomes 2 weeks before any difference in pathogen density became apparent between the healthy and diseased groups. In this system, a total of 135 bacterial OTUs were associated with persistent healthy plants. Five of these enriched OTUs (Lysinibacillus, Pseudarthrobacter, Bordetella, Bacillus, and Chryseobacterium) were isolated and shown to reduce disease severity by 30.4–100% when co-introduced with the pathogen. Overall, our results demonstrated that an initially homogenized soil can rapidly diverge into rhizosphere microbiomes varying in their ability to promote plant protection. This suggests that early life interventions may have significant effects on later microbiome states, and highlights an exciting opportunity for microbiome diagnostics and plant disease prevention.Subject terms: Microbial ecology, Microbial ecology     

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。     

Prokaryotic taxa play keystone roles in the soil microbiome associated with woody perennial plants in the genus Buxus

The microbiome associated with ornamental plants has largely been neglected, despite its potential for impacting plant health. This work characterized the composition, diversity, and microbial co‐associations in the soil microbiome associated with species and cultivars of plant in the genus Buxus (common name boxwood), a group of woody perennial shrubs commonly used in residential landscapes and found in native ecosystems. Soil was collected from 82 individual curated boxwood accessions at the U.S. National Arboretum National Boxwood Collection. Amplicon libraries targeting archaea, bacteria, and fungi were generated and sequenced using the Illumina MiSeq platform. Identification of individual sequence variants resulted in 275 archaeal, 15,580 bacterial, and 7,525 fungal taxa. Neither spatial distance among samples nor association with different types of boxwood were significant predictors of soil microbiome composition. However, archaeal and bacterial diversity was significantly different in soil from distinct types of boxwood. Co‐association networks indicated that archaea and bacteria show greater evidence of being keystone taxa than fungi. Overall, this work demonstrates the potential for targeting specific keystone taxa to shift the soil microbiome associated with these boxwood accessions and that planting different species or cultivars in the landscape may shift the diversity of prokaryotic microorganisms.     

Metaproteomics as a tool for studying the protein landscape of human-gut bacterial species

Host-microbiome interactions and the microbial community have broad impact in human health and diseases. Most microbiome based studies are performed at the genome level based on next-generation sequencing techniques, but metaproteomics is emerging as a powerful technique to study microbiome functional activity by characterizing the complex and dynamic composition of microbial proteins. We conducted a large-scale survey of human gut microbiome metaproteomic data to identify generalist species that are ubiquitously expressed across all samples and specialists that are highly expressed in a small subset of samples associated with a certain phenotype. We were able to utilize the metaproteomic mass spectrometry data to reveal the protein landscapes of these species, which enables the characterization of the expression levels of proteins of different functions and underlying regulatory mechanisms, such as operons. Finally, we were able to recover a large number of open reading frames (ORFs) with spectral support, which were missed by de novo protein-coding gene predictors. We showed that a majority of the rescued ORFs overlapped with de novo predicted protein-coding genes, but on opposite strands or in different frames. Together, these demonstrate applications of metaproteomics for the characterization of important gut bacterial species.     

The rice foot rot pathogen Dickeya zeae alters the in-field plant microbiome

Studies on bacterial plant diseases have thus far been focused on the single bacterial species causing the disease, with very little attention given to the many other microorganisms present in the microbiome. This study intends to use pathobiome analysis of the rice foot rot disease, caused by Dickeya zeae, as a case study to investigate the effects of this bacterial pathogen to the total resident microbiome and to highlight possible interactions between the pathogen and the members of the community involved in the disease process. The microbiome of asymptomatic and the pathobiome of foot-rot symptomatic field-grown rice plants over two growing periods and belonging to two rice cultivars were determined via 16S rRNA gene amplicon sequencing. Results showed that the presence of D. zeae is associated with an alteration of the resident bacterial community in terms of species composition, abundance and richness, leading to the formation of microbial consortia linked to the disease state. Several bacterial species were significantly co-presented with the pathogen in the two growing periods suggesting that they could be involved in the disease process. Besides, culture-dependent isolation and in planta inoculation studies of a bacterial member of the pathobiome, identified as positive correlated with the pathogen in our in silico analysis, indicated that it benefits from the presence of D. zeae. A similar microbiome/pathobiome experiment was also performed in a symptomatically different rice disease evidencing that not all plant diseases have the same consequence/relationship with the plant microbiome. This study moves away from a pathogen-focused stance and goes towards a more ecological perception considering the effect of the entire microbial community which could be involved in the pathogenesis, persistence, transmission and evolution of plant pathogens.     

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.     

Consistent associations with beneficial bacteria in the seed endosphere of barley (Hordeum vulgare L.)

The importance of the plant microbiome for host fitness has led to the concept of the “plant holobiont”. Seeds are reservoirs and vectors for beneficial microbes, which are very intimate partners of higher plants with the potential to connect plant generations. In this study, the endophytic seed microbiota of numerous barley samples, representing different cultivars, geographical sites and harvest years, was investigated. Cultivation-dependent and -independent analyses, microscopy, functional plate assays, greenhouse assays and functional prediction were used, with the aim of assessing the composition, stability and function of the barley seed endophytic bacterial microbiota. Associations were consistently detected in the seed endosphere with Paenibacillus, Pantoea and Pseudomonas spp., which were able to colonize the root with a notable rhizocompetence after seed germination. In greenhouse assays, enrichment with these bacteria promoted barley growth, improved mineral nutrition and induced resistance against the fungal pathogen Blumeria graminis. We demonstrated here that barley, an important crop plant, was consistently associated with beneficial bacteria inside the seeds. The results have relevant implications for plant microbiome ecology and for the holobiont concept, as well as opening up new possibilities for research and application of seed endophytes as bioinoculants in sustainable agriculture.     

Emerging Molecular Tools for Engineering Phytomicrobiome

Microbial plant interaction plays a major role in the sustainability of plants. The understanding of phytomicrobiome interactions enables the gene-editing tools for the construction of the microbial consortia. In this interaction, microbes share several common secondary metabolites and terpenoid metabolic pathways with their host plants that ensure a direct connection between the microbiome and associated plant metabolome. In this way, the CRISPR-mediated gene-editing tool provides an attractive approach to accomplish the creation of microbial consortia. On the other hand, the genetic manipulation of the host plant with the help of CRISPR-Cas9 can facilitate the characterization and identification of the genetic determinants. It leads to the enhancement of microbial capacity for more trait improvement. Many plant characteristics like phytovolatilization, phytoextraction, phytodesalination and phytodegradation are targeted by these approaches. Alternatively, chemical communications by PGPB are accomplished by the exchange of different signal molecules. For example, quorum-sensing is the way of the cell to cell communication in bacteria that lead to the detection of metabolites produced by pathogens during adverse conditions and also helpful in devising some tactics towards understanding plant immunity. Along with quorum-sensing, different volatile organic compounds and N-acyl homoserine lactones play a significant role in cell to cell communication by microbe to plant and among the plants respectively. Therefore, it is necessary to get details of all the significant approaches that are useful in exploring cell to cell communications. In this review, we have described gene-editing tools and the cell to cell communication process by quorum-sensing based signaling. These signaling processes via CRISPR- Cas9 mediated gene editing can improve the microbe-plant community in adverse climatic conditions.     

核心微生物组的研究及利用现状

随着分子生物学和生物信息学的飞速发展,新一代测序技术可以轻松地检测不同样本中复杂的微生物分类单元。面对这些复杂而大量的微生物组数据带来的分析挑战,利用核心微生物组的方法来描述和分析样本中的核心微生物组和关键种是近年来新的研究热点,这些结果将揭示与宿主健康、生长和生产等密切相关的微生物种类,有助于深入认识微生物与宿主间的相互关系,深刻理解微生物对宿主的影响作用,更好地理解微生物组在自然生态系统中的功能。本文阐述了核心微生物组的定义、研究方法、与动植物的关系等方面的研究及利用现状,为更好地利用核心微生物组解决环境、人类健康和农业生产问题提供思路。     

Hormones as go-betweens in plant microbiome assembly

The interaction of plants with complex microbial communities is the result of co-evolution over millions of years and contributed to plant transition and adaptation to land. The ability of plants to be an essential part of complex and highly dynamic ecosystems is dependent on their interaction with diverse microbial communities. Plant microbiota can support, and even enable, the diverse functions of plants and are crucial in sustaining plant fitness under often rapidly changing environments. The composition and diversity of microbiota differs between plant and soil compartments. It indicates that microbial communities in these compartments are not static but are adjusted by the environment as well as inter-microbial and plant–microbe communication. Hormones take a crucial role in contributing to the assembly of plant microbiomes, and plants and microbes often employ the same hormones with completely different intentions. Here, the function of hormones as go-betweens between plants and microbes to influence the shape of plant microbial communities is discussed. The versatility of plant and microbe-derived hormones essentially contributes to the creation of habitats that are the origin of diversity and, thus, multifunctionality of plants, their microbiota and ultimately ecosystems.     

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.