Metal accumulation and arbuscular mycorrhizal status in metallicolous and nonmetallicolous populations of <Emphasis Type="Italic">Pteris vittata</Emphasis> L. and <Emphasis Type="Italic">Sedum alfredii</Emphasis> Hance

Although Pteris vittata L. and Sedum alfredii Hance have been identified as an As hyperaccumulator and a Zn/Cd hyperaccumulator, respectively, for a few years, variations in metal accumulation among populations and their arbuscular mycorrhizal (AM) status have not been fully explored. Six populations of P. vittata and four populations of S. alfredii from southeast China were investigated. Up to 1,373 As, 680 Pb, 376 Zn, 4.8 Cd, 169 Cu mg kg⁻¹ in fronds of P. vittata and 358 As, 2,290 Pb, 23,403 Zn, 708 Cd, 342 Cu mg kg⁻¹ in shoots of S. alfredii were detected. Constitutive properties of As and Zn hyperaccumulation in metallicolous populations of P. vittata and S. alfredii, respectively, were confirmed. However, Cd hyperaccumulation in S. alfredii varied among populations. The two hyperaccumulators varied in efficiency in taking up other heavy metals. Different metal tolerance strategies adopted by the two hyperaccumulators varied among plant species and metal species. Low to moderate levels of AM colonization in P. vittata (4.2–12.8%) and S. alfredii (8.5–45.8%) were observed at uncontaminated and metal-contaminated sites. The relationship between metal concentrations and AM colonization in the two hyperacumulators was also examined. The abundance of AM fungal spores ranged from 16 to 190 spores per 25 g soil. Glomus microaggregatum, Glomus mosseae, Glomus brohultii and Glomus geosporum were the most common species associated with both P. vittata and S. alfredii. To our knowledge, this is the first report of AM fungal status in rhizosphere of P. vittata and S. alfredii.     

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.     

Effect of long-term organic and mineral fertilization strategies on rhizosphere microbiota assemblage and performance of lettuce

Long-term agricultural fertilization strategies gradually change soil properties including the associated microbial communities. Cultivated crops recruit beneficial microbes from the surrounding soil environment via root exudates. In this study, we aimed to investigate the effects of long-term fertilization strategies across field sites on the rhizosphere prokaryotic (Bacteria and Archaea) community composition and plant performance. We conducted growth chamber experiments with lettuce (Lactuca sativa L.) cultivated in soils from two long-term field experiments, each of which compared organic versus mineral fertilization strategies. 16S rRNA gene amplicon sequencing revealed the assemblage of a rhizosphere core microbiota shared in all lettuce plants across soils, going beyond differences in community composition depending on field site and fertilization strategies. The enhanced expression of several plant genes with roles in oxidative and biotic stress signalling pathways in lettuce grown in soils with organic indicates an induced physiological status in plants. Lettuce plants grown in soils with different fertilization histories were visibly free of stress symptoms and achieved comparable biomass. This suggests a positive aboveground plant response to belowground plant–microbe interactions in the rhizosphere. Besides effects of fertilization strategy and field site, our results demonstrate the crucial role of the plant in driving rhizosphere microbiota assemblage.     

Effects of inoculation of a plant growth promoting rhizobacterium <Emphasis Type="Italic">Burkholderia</Emphasis> sp. D54 on plant growth and metal uptake by a hyperaccumulator <Emphasis Type="Italic">Sedum alfredii</Emphasis> Hance grown on multiple metal contaminated soil

Batch experiments were designed to characterize a multiple metal resistant bacterium Burkholderia sp. D54 isolated from metal contaminated soils in the Dabaoshan Mine in South China, and a follow-up experiment was conducted to investigate the effects of inoculating the isolate on plant growth and metal uptake by Sedum alfredii Hance grown on soils collected from a heavily contaminated paddy field in Daxing County, Guangxi Zhuang Automounous Region, Southwest China. Our experiments showed that strain D54 produced indole acetic acid (IAA), siderophores, 1-aminocyclopropane-1-carboxylate (ACC) deaminase, and solubilizing inorganic phosphate and solubilized insoluble metal bearing minerals. Bacterial inoculation significantly enhanced S. alfredii biomass production, and increased both shoot and root Cd concentration, but induced little variation in root/shoot Pb concentration and shoot Zn concentration. Despite this, the total shoot and root uptake of Cd, Pb and Zn in S. alfredii inoculated with D54 increased greatly compared to the non-inoculated controls. It was concluded that inoculation with strain D54 could help S. alfredii grow better on metal contaminated soils, produce more biomass, and remove more metals from soil, which implies improved efficiency of phytoextraction from metal contaminated soil. The knowledge gained from the present experiments constitutes an important advancement in understanding of the interaction between plant growth-promoting bacteria and hyperaccumulators with regard to plant ability to grow and remove the multiple heavy metals from soils.     

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.     

Manipulating exudate composition from root apices shapes the microbiome throughout the root system

Certain soil microorganisms can improve plant growth, and practices that encourage their proliferation around the roots can boost production and reduce reliance on agrochemicals. The beneficial effects of the microbial inoculants currently used in agriculture are inconsistent or short-lived because their persistence in soil and on roots is often poor. A complementary approach could use root exudates to recruit beneficial microbes directly from the soil and encourage inoculant proliferation. However, it is unclear whether the release of common organic metabolites can alter the root microbiome in a consistent manner and if so, how those changes vary throughout the whole root system. In this study, we altered the expression of transporters from the ALUMINUM-ACTIVATED MALATE TRANSPORTER and the MULTIDRUG AND TOXIC COMPOUND EXTRUSION families in rice (Oryza sativa L.) and wheat (Triticum aestivum L.) and tested how the subsequent release of their substrates (simple organic anions, including malate, citrate, and γ-amino butyric acid) from root apices affected the root microbiomes. We demonstrate that these exudate compounds, separately and in combination, significantly altered microbiome composition throughout the root system. However, the root type (seminal or nodal), position along the roots (apex or base), and soil type had a greater influence on microbiome structure than the exudates. These results reveal that the root microbiomes of important cereal species can be manipulated by altering the composition of root exudates, and support ongoing attempts to improve plant production by manipulating the root microbiome.

One-sentence summary: The root microbiome of rice and wheat can be manipulated by altering the activity of root transporters and exudates.     

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。     

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.     

The effect of rhizosphere microbes outweighs host plant genetics in reducing insect herbivory

Rhizosphere microbes affect plant performance, including plant resistance against insect herbivores; yet, a direct comparison of the relative influence of rhizosphere microbes versus plant genetics on herbivory levels and on metabolites related to defence is lacking. In the crucifer Boechera stricta, we tested the effects of rhizosphere microbes and plant population on herbivore resistance, the primary metabolome, and select secondary metabolites. Plant populations differed significantly in the concentrations of six glucosinolates (GLS), secondary metabolites known to provide herbivore resistance in the Brassicaceae. The population with lower GLS levels experienced ~60% higher levels of aphid (Myzus persicae) attack; no association was observed between GLS and damage by a second herbivore, flea beetles (Phyllotreta cruciferae). Rhizosphere microbiome (disrupted vs. intact native microbiome) had no effect on plant GLS concentrations. However, aphid number and flea beetle damage were respectively about three‐ and seven‐fold higher among plants grown in the disrupted versus intact native microbiome treatment. These differences may be attributable to shifts in primary metabolic pathways previously implicated in host defence against herbivores, including increases in pentose and glucoronate interconversion among plants grown with an intact microbiome. Furthermore, native microbiomes with distinct community composition (as estimated from 16s rRNA amplicon sequencing) differed two‐fold in their effect on host plant susceptibility to aphids. The findings suggest that rhizosphere microbes, including distinct native microbiomes, can play a greater role than population in defence against insect herbivores, and act through metabolic mechanisms independent of population.     

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.     

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.     

Higher plants as bioindicators of metal contamination from Shangdong abandoned karst bauxite,southwestern China

• Bauxite mining on karst generates numerous ecological and environmental problems, including metal pollution, water and soil erosion and destruction of vegetation. Among these, the most important environmental problem is soil metal pollution. Higher plants have a great ability to adsorb metals and can be used as biological indicators. However, the study of bioindicators for soil contamination in karst bauxite is not clear.
• Plants and their soil were collected from an abandoned karst bauxite area at Shangdong, Guizhou Province, southwestern China. Plants were collected and identified as Pteris vittata, Pinus massoniana, Miscanthus floridulus, Coriaria nepalensis, Artemisia argyi and Senecio scandens.
• The content of metals in plant roots were in the order: P. vittata > M. floridulus > C. nepalensis, other plants roots had no consistent pattern. Concentrations of metal in plants (P. vittata and M. floridulus) and soil were: soil > root > leaf > stem. Levels of metals in soil samples easily exceeded background values, indicating that soil had been contaminated. Al and Fe were highest in soil samples of P. vittata, with a good correlation.
• Results show that the metal content determined in plants is relatively high, particularly in P. vittata. Data also suggest that P. vittata colonies were able to tolerate and accumulate high levels of metal elements, which evidences their suitability for use as bioindicatord of soil metal contamination caused by mining activities.

     

Effects of two types of herbivores on the population dynamics of a perennial herb

The joint effects of multiple herbivores on their shared host plant have received increasing interest recently. The influence of herbivores on population dynamics of their host plants, especially the relative roles of different types of damage, is, however, still poorly understood. Here, we present a modelling approach, including both deterministic and stochastic matrix modelling, to be used in estimating fitness effects of multiple herbivores on perennial plants. We examined the effects and relative roles of two specialist herbivores, a pre-dispersal seed predator, Euphranta connexa, and a leaf-feeding moth, Abrostola asclepiadis, on the population dynamics and long-term fitness of their shared host plant, a long-lived perennial herb Vincetoxicum hirundinaria (Asclepiadaceae). We collected demographic data during 3 years and combined these data with the effects of natural levels of herbivory measured from the same individuals. We found that both seed predation and leaf herbivory reduced population growth of V. hirundinaria, but only very high damage levels changed the growth trend of the vigorously growing study populations from positive to negative. Demographic modelling indicated that seed predation had a greater impact on plant population growth than leaf herbivory. The effect of leaf herbivory was weaker and diminished with increasing level of seed predation. Evaluation of individual fitness components, however, suggested that leaf herbivory contributed more strongly to host plant fitness than seed predation. Our results emphasize that understanding the effects of a particular herbivore on plant population dynamics requires also knowledge on other herbivores present in the system, because the effect of a particular type of herbivory on plant population dynamics is likely to vary according to the intensity of other types of herbivory. Furthermore, evaluating herbivore impact from using individual fitness components does not necessarily reflect the long-term effects on total plant fitness.     

Dual inoculation of dark septate endophytes and Trichoderma viride drives plant performance and rhizosphere microbiome adaptations of Astragalus mongholicus to drought

Rhizosphere microbiome adapts their structural compositions to water scarcity and have the potential to mitigate drought stress of plants. To unlock this potential, it is crucial to understand community responses to drought in the interplay between soil properties, water management and exogenous microbes interference. Inoculation with dark septate endophytes (DSE) (Acrocalymma vagum, Paraboeremia putaminum) and Trichoderma viride on Astragalus mongholicus grown in the non-sterile soil was exposed to drought. Rhizosphere microbiome were assessed by Illumina MiSeq sequencing of the 16S and ITS2 rRNA genes. Inoculation positively affected plant growth depending on DSE species and water regime. Ascomycota, Proteobacteria, Actinobacteria, Chloroflexi and Firmicutes were the dominant phyla. The effects of dual inoculation on bacterial community were greater than those on fungal community, and combination of P. putaminum and T. viride exerted a stronger impact on the microbiome under drought stress. The observed changes in soil factors caused by inoculation could be explained by the variations in microbiome composition. Rhizosphere microbiome mediated by inoculation exhibited distinct preferences for various growth parameters. These findings suggest that dual inoculation of DSE and T. viride enriched beneficial microbiota, altered soil nutrient status and might contribute to enhance the cultivation of medicinal plants in dryland agriculture.     

Highly diverse endophytes in roots of <Emphasis Type="Italic">Cycas bifida</Emphasis> (Cycadaceae), an ancient but endangered gymnosperm

As an ancient seed plant, cycads are one of the few gymnosperms that develop a root symbiosis with cyanobacteria, which has allowed cycads to cope with harsh geologic and climatic conditions during the evolutionary process. However, the endophytic microbes in cycad roots remain poorly identified. In this study, using next-generation sequencing techniques, we investigated the microbial diversity and composition of both the coralloid and regular roots of Cycas bifida (Dyer) K.D. Hill. Highly diverse endophytic communities were observed in both the coralloid and regular roots. Of the associated bacteria, the top five families were the Nostocaceae, Sinobacteraceae, Bradyrhizobiaceae, Bacillaceae, and Hyphomicrobiaceae. The Nectriaceae, Trichocomaceae, and Incertae sedis were the predominant fungal families in all root samples. A significant difference in the endophytic bacterial community was detected between coralloid roots and regular roots, but no difference was observed between the fungal communities in the two root types. Cyanobacteria were more dominant in coralloid roots than in regular roots. The divergence of cycad root structures and the modified physiological processes may have contributed to the abundance of cyanobionts in coralloid roots. Consequently, the colonization of cyanobacteria inhibits the assemblage of other endophytes. Our results contribute to an understanding of the species diversity and composition of the cycad-endophyte microbiome and provide an abbreviated list of potential ecological roles of the core microbes present.     

Successional dynamics of the cultivated kelp microbiome

Kelp are important primary producers that are colonized by diverse microbes that can have both positive and negative effects on their hosts. The kelp microbiome could support the burgeoning kelp cultivation sector by improving host growth, stress tolerance, and resistance to disease. Fundamental questions about the cultivated kelp microbiome still need to be addressed before microbiome-based approaches can be developed. A critical knowledge gap is how cultivated kelp microbiomes change as hosts grow, particularly following outplanting to sites that vary in abiotic conditions and microbial source pools. In this study we assessed if microbes that colonize kelp in the nursery stage persist after outplanting. We characterized microbiome succession over time on two species of kelp, Alaria marginata and Saccharina latissima, outplanted to open ocean cultivation sites in multiple geographic locations. We tested for host-species specificity of the microbiome and the effect of different abiotic conditions and microbial source pools on kelp microbiome stability during the cultivation process. We found the microbiome of kelp in the nursery is distinct from that of outplanted kelp. Few bacteria persisted on kelp following outplanting. Instead, we identified significant microbiome differences correlated with host species and microbial source pools at each cultivation site. Microbiome variation related to sampling month also indicates that seasonality in host and/or abiotic factors may influence temporal succession and microbiome turnover in cultivated kelps. This study provides a baseline understanding of microbiome dynamics during kelp cultivation and highlights research needs for applying microbiome manipulation to kelp cultivation.     

The impact of the endophytic bacterial community on mulberry tree growth in the Three Gorges Reservoir ecosystem,China

Plant-associated microbes influence plant performance and may also impact biotic and abiotic stress tolerance. The microbiome of mulberry trees planted for ecological restoration in the hydro-fluctuation belt of the Three Gorges Reservoir Region, China, exhibited distinct patterns of localization. The endosphere exhibited lower α-diversity relative to the rhizosphere, but was more closely related to host growth status, especially in stem tissues. Pantoea was the predominant bacterial genus inhabiting the stems of two well-growing plants, while sequences identified as Pseudomonas and Pantoea were abundant in poorly growing plants. The complexity of the endophytic community was more connected to growth status in well-growing plants than it was in poorly growing plants. Among 151 endophytes cultured from collected samples of mulberry, 64 exhibited plant growth-promoting (PGP) potential in vitro and the majority of beneficial taxa were harvested from well-growing plants. Collectively, the present study indicates that the recruitment of beneficial endophytes may contribute to mulberry fitness under abiotic stress, and it provides a foundation for the development of a new strategy in vegetation restoration.     

Species-specific effects of live roots and shoot litter on soil decomposer abundances do not forecast plant litter-nitrogen uptake

Plant species produce litter of varying quality and differ in the quality and quantity of compounds they release from live roots, which both can induce different decomposer growth in the soil. To test whether differences in decomposer growth can forecast the amount of N species acquire from plant litter, as suggested by theory, we grew individuals of three grassland plants—Holcus lanatus, Plantago lanceolata and Lotus corniculatus—in soils into which ¹⁵N-labelled litter of either Holcus, Plantago or Lotus was added. We measured the effects of live roots and litter of each species on soil microbes and their protozoan and nematode feeders, and to link decomposer growth and plant nutrient uptake, we measured the amount of N taken up by plants from the added litter. We hypothesised that those species that induce the highest growth of microbes, and especially that of microbial feeders, will also take up the highest amount of N from the litter. We found, however, that although numbers of bacterial-feeding Protozoa and nematodes were on average lower after addition of Holcus than Plantago or Lotus litter, N uptake was higher from Holcus litter. Further, although the effects on Protozoa and bacterial- and fungal-feeding nematodes did not differ between the live plants, litter-N uptake differed, with Holcus being the most efficient compared to Plantago and Lotus. Hence, although microbes and their feeders unquestionably control N mineralization in the soil, and their growth differs among plant species, these differences cannot predict differences in litter-N uptake among plant species. A likely reason is that for nutrient uptake, other species-specific plant traits, such as litter chemistry, root proliferation ability and competitiveness for soil N, override in significance the species-specific ability of plants to induce decomposer growth.