植物有益伯克霍尔德氏菌的研究进展及其在农业中的应用

伯克霍尔德氏菌属是一类革兰氏阴性细菌,其具有广泛的地理及生态位分布。近年来,随着对植物相关的伯克霍尔德氏菌的研究增加,越来越多的证据表明,伯克霍尔德氏菌是一类重要的植物相关的有益微生物。伯克霍尔德氏菌能够通过生物固氮、解磷作用,促进植物对氮、磷的吸收;还能够产生吲哚乙酸等植物激素、分泌抗菌物质抑制病原菌的生长,因此,伯克霍尔德氏菌在促进植物生长和维持植物健康方面具有较大的应用潜力。本文对近些年来关于植物有益的伯克霍尔德氏菌的研究进展进行了综述,并讨论了其在农业上的应用前景。     

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.     

Arbuscular mycorrhizal fungi stimulate organic phosphate mobilization associated with changing bacterial community structure under field conditions

The extraradical hyphae of arbuscular mycorrhizal fungi (AMF) harbour and interact with a microbial community performing multiple functions. However, how the AMF‐microbiome interaction influences the phosphorus (P) acquisition efficiency of the mycorrhizal pathway is unclear. Here we investigated whether AMF and their hyphal microbiome play a role in promoting organic phosphorus (P) mineralizing under field conditions. We developed an AMF hyphae in‐growth core system for the field using PVC tubes sealed with membrane with different size of pores (30 or 0.45 μm) to allow or deny AMF hyphae access to a patch of organic P in root‐free soil. AMF and their hyphae associated microbiome played a role in enhancing soil organic P mineralization in situ in the field, which was shown to be a function of the change in bacteria community on the hyphae surface. The bacterial communities attached to the AMF hyphae surface were significantly different from those in the bulk soil. Importantly, AMF hyphae recruited bacteria that produced alkaline phosphatase and provided a function that was absent from the hyphae. These results demonstrate the importance of understanding trophic interactions to be able to gain insight into the functional controls of nutrient cycles in the rhizosphere.     

Comparative analysis of bacterial diversity in the rhizosphere of tomato by culture-dependent and -independent approaches

The microbiome in the rhizosphere–the region surrounding plant roots–plays a key role in plant growth and health, enhancing nutrient availability and protecting plants from biotic and abiotic stresses. To assess bacterial diversity in the tomato rhizosphere, we performed two contrasting approaches: culture-dependent and -independent. In the culture-dependent approach, two culture media (Reasoner’s 2A agar and soil extract agar) were supplemented with 12 antibiotics for isolating diverse bacteria from the tomato rhizosphere by inhibiting predominant bacteria. A total of 689 bacterial isolates were clustered into 164 operational taxonomic units (OTUs) at 97% sequence similarity, and these were found to belong to five bacterial phyla (Proteobacteria, Actinobacteria, Bacteroidetes, Acidobacteria, and Firmicutes). Of these, 122 OTUs were retrieved from the antibiotic-containing media, and 80 OTUs were recovered by one specific antibiotic-containing medium. In the culture-independent approach, we conducted Illumina MiSeq amplicon sequencing of the 16S rRNA gene and obtained 19,215 high-quality sequences, which clustered into 478 OTUs belonging to 16 phyla. Among the total OTUs from the MiSeq dataset, 22% were recovered in the culture collection, whereas 41% of OTUs in the culture collection were not captured by MiSeq sequencing. These results showed that antibiotics were effective in isolating various taxa that were not readily isolated on antibiotic-free media, and that both contrasting approaches provided complementary information to characterize bacterial diversity in the tomato rhizosphere.     

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.     

Plant Growth-Promoting Rhizobacteria Associated with Ancient Clones of Creosote Bush (Larrea tridentata)

Plant growth-promoting rhizobacteria (PGPR) are common components of the rhizosphere, but their role in adaptation of plants to extreme environments is not yet understood. Here, we examined rhizobacteria associated with ancient clones of Larrea tridentata in the Mohave desert, including the 11,700-year-old King Clone, which is oldest known specimen of this species. Analysis of unculturable and culturable bacterial community by PCR-DGGE revealed taxa that have previously been described on agricultural plants. These taxa included species of Proteobacteria, Bacteroidetes, and Firmicutes that commonly carry traits associated with plant growth promotion, including genes encoding aminocyclopropane carboxylate deaminase and β–propeller phytase. The PGPR activities of three representative isolates from L. tridentata were further confirmed using cucumber plants to screen for plant growth promotion. This study provides an intriguing first view of the mutualistic bacteria that are associated with some of the world’s oldest living plants and suggests that PGPR likely contribute to the adaptation of L. tridentata and other plant species to harsh environmental conditions in desert habitats.     

The role of ABC transporters in kin recognition in Arabidopsis thaliana

The ability to sense and respond to the surrounding rhizosphere including communications with neighboring plants and microbes is essential for plant survival. Recently, it has been established that several plant species including Arabidopsis thaliana have the ability to recognize rhizospheric neighbors based or their genetic identity. This study investigated the role of ABC transporters in kin recognition in A. thaliana based on previous evidence that root secretions are involved in the kin recognition response and that ABC transporters are responsible for secretion of a number of compounds. Three genes, AtPGP1, AtATH1 and AtATH10, are all implicated to be partially involved in the complex kin recognition response in A. thaliana based on this report. These findings highlight the importance of ABC transporters in understanding root secretions and plant-plant community interactions.Key words: root biology, rhizosphere, kin recognition, root secretions, Arabidopsis     

Ancestry and adaptive radiation of Bacteroidetes as assessed by comparative genomics

To date, the phylum Bacteroidetes comprises more than 1,500 described species with diverse ecological roles. However, there is little understanding of archetypal Bacteroidetes traits at a genomic level. In this study, a representative set of 89 Bacteroidetes genomes was compiled, and pairwise reciprocal best-match gene comparisons and gene syntenies were used to identify common traits that allowed Bacteroidetes evolution and adaptive radiation to be traced. The type IX secretion system (T9SS) was highly conserved among all studied Bacteroidetes. Class-level comparisons furthermore suggested that the ACIII-caa₃COX super-complex evolved in the ancestral aerobic bacteroidetal lineage, and was secondarily lost in extant anaerobic Bacteroidetes. Another Bacteroidetes-specific respiratory chain adaptation was the sodium-pumping Nqr complex I that replaced the ancestral proton-pumping complex I in marine species. T9SS plays a role in gliding motility and the acquisition of complex macro-molecular organic compounds, and the ACIII-caa₃COX super-complex allows effective control of electron flux during respiration. This combination likely provided ancestral Bacteroidetes with a decisive competitive advantage to effectively scavenge, uptake and degrade complex organic molecules, and therefore has played a pivotal role in the successful adaptive radiation of the phylum.     

Diversity of rhizospheric and endophytic bacteria isolated from dried fruit of Ficus carica

There is currently an increasing demand for the characterization of endophytic bacteria isolated from different parts of plants (rhizosphere, roots, fruit, leaf) in order to improve the organic agriculture practices. The current research was performed to identify both rhizospheric bacteria isolated from the rhizosphere of Ficus carica in three different sites in the north of Tunisia and endophytic bacteria isolated from dried figs. We then characterized them for a diversity of plant growth-promoting (PGP) activities. A collection of 120 isolates from rhizospheric soil and 9 isolates from dried figs was obtained and purified. 16SrDNA gene amplification of rhizospheric bacteria revealed significant diversity and allowed for the assigning of the isolates to 6 phyla: Gammaproteobacteria, Alphaproteobacteria, Betaproteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. Representative strains of the collection (90 strains) were tested for numerous PGP activities and resistance to abiotic stresses. The most common PGP trait for all bacteria from the three regions was siderophore production (62%), followed by cellulase (38%), then protease activity (37%), then by lipases activity (17%) and lastly by solubilization of phosphates (9%). Twenty -three strains that showed most PGP traits were selected, 8 strains presented 12 or more, and 15 strains displayed between 7 and 11 of 17 PGP activities. The majority of the isolates manifested a possible adaptation to abiotic stress and unfavorable environments. PCR-DGGE analysis of soil rhizosphere of the three sites allowed also for the acquisition of a Cluster analysis of rhizospheric bacterial communities. Our current study identified and characterized for the first time in Tunisia rhizospheric and endophytic bacteria from dried fruit of Ficus carica.     

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.     

林木共生菌系统及其作用机制——以杨树为例

杨树（Populus）是重要造林树种,也是研究林木基础生物学性状的模式材料。不仅如此,杨树可与多种细菌（内生细菌、内生固氮菌和根际促生菌）和真菌（外生菌根真菌、丛枝菌根真菌和内生真菌）类群建立共生关系,为揭示树木和微生物之间的互惠共生机制提供了理想模型。这些共生菌能积极调控林木生长发育、营养吸收和生理生态过程。目前在杨树-双色蜡蘑（Laccaria bicolor）形成的外生菌根发育、提高杨树耐盐、耐重金属的生理与分子机制、叶片内生真菌群落结构与病害发生、菌根辅助细菌和菌丝内共生细菌-真菌-杨树形成的三重跨界共生等方面取得多项突破。近年来,一批模式草本植物微生物组（microbiome）计划相继实施,对共生菌群落结构和功能的认识有了革命性的进步。以美洲黑杨、毛果杨和胶杨为代表的林木微生物组研究也已启动,表明宿主基因型和环境因子可显著影响共生菌群落结构与物种组成;在根际（rhizosphere）和内生（endosphere）环境存在结构和功能迥异的菌群。另一方面,以根系为诱饵,通过宿主表型来推测菌群功能的反向"钓鱼"策略将推动林木根际微生物工程研究,为揭示杨树-微生物群落的相互关系、菌群进化搭建了研究模型。总之,深入认识多元微生物对林木表型和生理代谢的表观遗传学调控机制将为今后创制新型菌剂并用于高效育苗和抗性育种提供新的思路,具有重要的科学意义和应用价值。     

Alleviation of fungicide-induced phytotoxicity in greengram [Vigna radiata (L.) Wilczek] using fungicide-tolerant and plant growth promoting Pseudomonas strain

This study was designed to explore beneficial plant-associated rhizobacteria exhibiting substantial tolerance against fungicide tebuconazole vis-à-vis synthesizing plant growth regulators under fungicide stressed soils and to evaluate further these multifaceted rhizobacteria for protection and growth promotion of greengram [Vigna radiata (L.) Wilczek] plants against phytotoxicity of tebuconazole. Tebuconazole-tolerant and plant growth promoting bacterial strain PS1 was isolated from mustard (Brassica compestris) rhizosphere and identified as Pseudomonas aeruginosa following 16S rRNA gene sequencing. The P. aeruginosa strain PS1 solubilized phosphate significantly and produced indole acetic acid, siderophores, exo-polysaccharides, hydrogen cyanide and ammonia even under tebuconazole stress. Generally, tebuconazole at the recommended, two and three times the recommended field rate adversely affected the growth, symbiosis, grain yield and nutrient uptake in greengram in a concentration dependent manner. In contrast, the P. aeruginosa strain PS1 along with tebuconazole significantly, increased the growth parameters of the greengram plants. The inoculant strain PS1 increased appreciably root nitrogen, shoot nitrogen, root phosphorus, shoot phosphorus, and seed yield of greengram plants at all tested concentrations of tebuconazole when compared to the uninoculated plants treated with tebuconazole. The results suggested that the P. aeruginosa strain PS1, exhibiting novel plant growth regulating physiological features, can be applied as an eco-friendly and plant growth catalyzing bio-inoculant to ameliorate the performance of greengram in fungicide stressed soils.     

A Drought Resistance-Promoting Microbiome Is Selected by Root System under Desert Farming

Background

Traditional agro-systems in arid areas are a bulwark for preserving soil stability and fertility, in the sight of “reverse desertification”. Nevertheless, the impact of desert farming practices on the diversity and abundance of the plant associated microbiome is poorly characterized, including its functional role in supporting plant development under drought stress.

Methodology/Principal Findings

We assessed the structure of the microbiome associated to the drought-sensitive pepper plant (Capsicum annuum L.) cultivated in a traditional Egyptian farm, focusing on microbe contribution to a crucial ecosystem service, i.e. plant growth under water deficit. The root system was dissected by sampling root/soil with a different degree of association to the plant: the endosphere, the rhizosphere and the root surrounding soil that were compared to the uncultivated soil. Bacterial community structure and diversity, determined by using Denaturing Gradient Gel Electrophoresis, differed according to the microhabitat, indicating a selective pressure determined by the plant activity. Similarly, culturable bacteria genera showed different distribution in the three root system fractions. Bacillus spp. (68% of the isolates) were mainly recovered from the endosphere, while rhizosphere and the root surrounding soil fractions were dominated by Klebsiella spp. (61% and 44% respectively). Most of the isolates (95%) presented in vitro multiple plant growth promoting (PGP) activities and stress resistance capabilities, but their distribution was different among the root system fractions analyzed, with enhanced abilities for Bacillus and the rhizobacteria strains. We show that the C. annuum rhizosphere under desert farming enriched populations of PGP bacteria capable of enhancing plant photosynthetic activity and biomass synthesis (up to 40%) under drought stress.

Conclusions/Significance

Crop cultivation provides critical ecosystem services in arid lands with the plant root system acting as a “resource island” able to attract and select microbial communities endowed with multiple PGP traits that sustain plant development under water limiting conditions.     

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.     

Unseen fungal biodiversity and complex inter-organismal interactions in Protea flower heads

A unique microbiome occurs within the flower heads of various Protea species endemic to Africa. These include two lineages of ophiostomatoid fungi, Knoxdaviesia (Microascales) and Sporothrix (Ophiostomatales), that have members occurring exclusively in this environment and that rely on mites as their primary mode of spore dissemination. The mites, in turn, attach to the bodies of Protea-pollinating beetles and the beaks and bodies of birds for long-distance movement, establishing a hierarchical dispersal network for the ophiostomatoid fungi. This inter-organismal network is highly successful, achieving fungal dispersal over vast distances. Multiple species of fungi, mites and bacteria have been described from this unique niche over the past four decades. The intricacies of their symbiotic interactions continue to be unravelled. This review covers all current knowledge of the “distinctly African” Protea-ophiostomatoid fungus environment and illustrates the depth of a fascinating unseen fungal biodiversity niche.     

Characterization of rhizosphere and endophytic bacterial communities from leaves,stems and roots of medicinal Stellera chamaejasme L.

A diverse array of bacteria that inhabit the rhizosphere and different plant organs play a crucial role in plant health and growth. Therefore, a general understanding of these bacterial communities and their diversity is necessary. Using the 16S rRNA gene clone library technique, the bacterial community structure and diversity of the rhizosphere and endophytic bacteria in Stellera chamaejasme compartments were compared and clarified for the first time. Grouping of the sequences obtained showed that members of the Proteobacteria (43.2%), Firmicutes (36.5%) and Actinobacteria (14.1%) were dominant in both samples. Other groups that were consistently found, albeit at lower abundance, were Bacteroidetes (2.1%), Chloroflexi (1.9%), and Cyanobacteria (1.7%). The habitats (rhizosphere vs endophytes) and organs (leaf, stem and root) structured the community, since the Wilcoxon signed rank test indicated that more varied bacteria inhabited the rhizosphere compared to the organs of the plant. In addition, correspondence analysis also showed that differences were apparent in the bacterial communities associated with these distinct habitats. Moreover, principal component analysis revealed that the profiles obtained from the rhizosphere and roots were similar, whereas leaf and stem samples clustered together on the opposite side of the plot from the rhizosphere and roots. Taken together, these results suggested that, although the communities associated with the rhizosphere and organs shared some bacterial species, the associated communities differed in structure and diversity.     

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.     

Rhizosphere acid and alkaline phosphatase activity as a marker of P nutrition in nodulated Cyclopia and Aspalathus species in the Cape fynbos of South Africa

Cyclopia and Aspalathus species are important economic legumes in the Cape fynbos of South Africa, as they are used for making Honeybush and Rooibos tea, and for trade in the cut wild flower industry. The aim of this study was to assess acid and alkaline phosphatase activity in the rhizosphere of Cyclopia genistoides, Cyclopia subternata, Aspalathus caledonensis and Aspalathus aspalathoides as an indicator of P supply and P nutrition in the nutrient-poor soils of the Cape fynbos. Whether at Kokrivier or Kanetberg, the P enzyme activities were much higher in the rhizospheres of the legumes C. genistoides, C. subternata, A. caledonensis, and A. aspalathoides compared to those of the non-legumes Leucadendron strictum, Elegia thyrsoidea and Mimetes cucullatus, or bulk soil. As a result, plant-available P concentration in the rhizosphere, as well as shoot P levels closely mirrored acid and alkaline phosphatase activity in the rhizosphere of each plant species. Relative to younger plants, older Cyclopia species exhibited, much greater acid and alkaline phosphatase activity in the rhizosphere and this again resulted in much higher plant-available rhizosphere P. C. subternata plants developed from cuttings at Kanetberg showed greater rhizosphere acid and alkaline phosphatase activity than seedlings and bulk soil. As a result, the concentration of plant available-P and organic P were much higher in the rhizosphere of cuttings than seedlings, leading to greater shoot P in cuttings than seedlings. Taken together, these data suggest that rhizosphere P enzyme activity can be used as a good indicator of P supply and P nutrition in Cyclopia cuttings and seedlings, but less so in Aspalathus species in the Cape fynbos. The enhanced P nutrition in plants from cuttings probably accounts for the higher tea yields obtained by farmers when they use cuttings instead of seedlings in their plantations.