High incidence of plant growth-stimulating bacteria associated with the rhizosphere of wheat grown on salinated soil in Uzbekistan

Soil salinization is increasing steadily in many parts of the world and causes major problems for plant productivity. Under these stress conditions, root-associated beneficial bacteria can help improve plant growth and nutrition. In this study, salt-tolerant bacteria from the rhizosphere of Uzbek wheat with potentially beneficial traits were isolated and characterized. Eight strains which initially positively affect the growth of wheat plants in vitro were investigated in detail. All eight strains are salt tolerant and have some of the following plant growth-beneficial properties: production of auxin, HCN, lipase or protease and wheat growth promotion. Using sequencing of part of the 16S rDNA, the eight new isolates were identified as Acinetobacter (two strains), Pseudomonas aeruginosa , Staphylococcus saprophyticus , Bacillus cereus , Enterobacter hormaechei , Pantoae agglomerans and Alcaligenes faecalis . All these strains are potential human pathogens. Possible reasons for why these bacteria present in the rhizosphere and establish there are discussed.     

Plants respond to pathogen infection by enhancing the antifungal gene expression of root-associated bacteria

Plant health and fitness widely depend on interactions with soil microorganisms. Some bacteria such as pseudomonads can inhibit pathogens by producing antibiotics, and controlling these bacteria could help improve plant fitness. In the present study, we tested whether plants induce changes in the antifungal activity of root-associated bacteria as a response to root pathogens. We grew barley plants in a split-root system with one side of the root system challenged by the pathogen Pythium ultimum and the other side inoculated with the biocontrol strain Pseudomonas fluorescens CHA0. We used reporter genes to follow the expression of ribosomal RNA indicative of the metabolic state and of the gene phlA, required for production of 2,4-diacetylphloroglucinol, a key component of antifungal activity. Infection increased the expression of the antifungal gene phlA. No contact with the pathogen was required, indicating that barley influenced gene expression by the bacteria in a systemic way. This effect relied on increased exudation of diffusible molecules increasing phlA expression, suggesting that communication with rhizosphere bacteria is part of the pathogen response of plants. Tripartite interactions among plants, pathogens, and bacteria appear as a novel determinant of plant response to root pathogens.     

The rhizosphere: a playground and battlefield for soilborne pathogens and beneficial microorganisms

The rhizosphere is a hot spot of microbial interactions as exudates released by plant roots are a main food source for microorganisms and a driving force of their population density and activities. The rhizosphere harbors many organisms that have a neutral effect on the plant, but also attracts organisms that exert deleterious or beneficial effects on the plant. Microorganisms that adversely affect plant growth and health are the pathogenic fungi, oomycetes, bacteria and nematodes. Most of the soilborne pathogens are adapted to grow and survive in the bulk soil, but the rhizosphere is the playground and infection court where the pathogen establishes a parasitic relationship with the plant. The rhizosphere is also a battlefield where the complex rhizosphere community, both microflora and microfauna, interact with pathogens and influence the outcome of pathogen infection. A wide range of microorganisms are beneficial to the plant and include nitrogen-fixing bacteria, endo- and ectomycorrhizal fungi, and plant growth-promoting bacteria and fungi. This review focuses on the population dynamics and activity of soilborne pathogens and beneficial microorganisms. Specific attention is given to mechanisms involved in the tripartite interactions between beneficial microorganisms, pathogens and the plant. We also discuss how agricultural practices affect pathogen and antagonist populations and how these practices can be adopted to promote plant growth and health.     

AM真菌在植物病虫害生物防治中的作用机制

丛枝菌根(Arbuscular Mycorrhizae,AM)真菌是一类广泛分布于土壤生态系统中的有益微生物,能与大约80%的陆生高等植物形成共生体。由土传病原物侵染引起的土传病害被植物病理学界认定为最难防治的病害之一。研究表明,AM真菌能够拮抗由真菌、线虫、细菌等病原体引起的土传性植物病害,诱导宿主植物增强对病虫害的耐/抗病性。当前,利用AM真菌开展病虫害的生物防治已经引起生态学家和植物病理学家的广泛关注。基于此,围绕AM真菌在植物病虫害生物防治中的最新研究进展,从AM真菌改变植物根系形态结构、调节次生代谢产物的合成、改善植物根际微环境、与病原微生物直接竞争入侵位点和营养分配、诱导植株体内抗病防御体系的形成等角度,探究AM真菌在植物病虫害防治中的作用机理,以期为利用AM真菌开展植物病虫害的生物防治提供理论依据,并对本领域未来的发展方向和应用前景进行展望。     

Effect of crop rotation and soil cover on alteration of the soil microflora generated by the culture of transgenic plants producing opines

The culture of transgenic Lotus corniculatus plants producing opines, which are bacterial growth substrates, leads to the selection of rhizospheric bacteria able to utilize these substrates. We have investigated the fate of the opine-utilizing community over time under different experimental conditions following elimination of selective pressure exerted by the transgenic plants. These plants were removed from the soil, which was either left unplanted or replanted with wild-type L. corniculatus or wheat plants. The density of opine-utilizing bacteria in the fallow soils remained essentially unchanged throughout the experiment, regardless of the soil of origin (soil planted with wild-type or transgenic plants). When wild-type Lotus plants were used to replace their transgenic counterparts, only the bacterial populations able to utilize the opines were affected. Long-term changes affecting the opine-utilizing bacterial community on Lotus roots was dependent upon the opine studied. The concentration of nopaline utilizers decreased, upon replacement of the transgenic plants, to a level similar to that of normal plants, while the concentration of mannopine utilizers decreased to levels intermediate between transgenic and normal plants. These data indicate that: (i) the opine-utilizing bacterial populations can be controlled in the rhizosphere via plant-exudate engineering; (ii) the interaction between the engineered plants and their root-associated micro-organisms is transgene specific; and (iii) alterations induced by the cultivation of transgenic plants may sometimes be persistent. Furthermore, opine-utilizing bacterial populations can be controlled by crop rotation. Therefore, favouring the growth of a rhizobacterium of agronomic interest via an opine-based strategy appears feasible.     

Mycorrhizosphere interactions to improve plant fitness and soil quality

Arbuscular mycorrhizal fungi are key components of soil microbiota and obviously interact with other microorganisms in the rhizosphere, i.e. the zone of influence of plant roots on microbial populations and other soil constituents. Mycorrhiza formation changes several aspects of plant physiology and some nutritional and physical properties of the rhizospheric soil. These effects modify the colonization patterns of the root or mycorrhizas (mycorrhizosphere) by soil microorganisms. The rhizosphere of mycorrhizal plants, in practice a mycorrhizosphere, harbors a great array of microbial activities responsible for several key ecosystem processes. This paper summarizes the main conceptual principles and accepted statements on the microbial interactions between mycorrhizal fungi and other members of rhizosphere microbiota and discusses current developments and future trends concerning the following topics: (i) effect of soil microorganisms on mycorrhiza formation; (ii) mycorrhizosphere establishment; (iii) interactions involved in nutrient cycling and plant growth; (iv) interactions involved in the biological control of plant pathogens; and (v) interactions to improve soil quality. The main conclusion is that microbial interactions in the rhizosphere of mycorrhizal plants improve plant fitness and soil quality, critical issues for a sustainable agricultural development and ecosystem functioning. This revised version was published online in August 2006 with corrections to the Cover Date.     

Plant growth-promoting bacteria as inoculants in agricultural soils

Plant-microbe interactions in the rhizosphere are the determinants of plant health, productivity and soil fertility. Plant growth-promoting bacteria (PGPB) are bacteria that can enhance plant growth and protect plants from disease and abiotic stresses through a wide variety of mechanisms; those that establish close associations with plants, such as the endophytes, could be more successful in plant growth promotion. Several important bacterial characteristics, such as biological nitrogen fixation, phosphate solubilization, ACC deaminase activity, and production of siderophores and phytohormones, can be assessed as plant growth promotion (PGP) traits. Bacterial inoculants can contribute to increase agronomic efficiency by reducing production costs and environmental pollution, once the use of chemical fertilizers can be reduced or eliminated if the inoculants are efficient. For bacterial inoculants to obtain success in improving plant growth and productivity, several processes involved can influence the efficiency of inoculation, as for example the exudation by plant roots, the bacterial colonization in the roots, and soil health. This review presents an overview of the importance of soil-plant-microbe interactions to the development of efficient inoculants, once PGPB are extensively studied microorganisms, representing a very diverse group of easily accessible beneficial bacteria.     

Indirect reduction of Ralstonia solanacearum via pathogen helper inhibition

The rhizosphere microbiome forms a first line of defense against soilborne pathogens. To date, most microbiome enhancement strategies have relied on bioaugmentation with antagonistic microorganisms that directly inhibit pathogens. Previous studies have shown that some root-associated bacteria are able to facilitate pathogen growth. We therefore hypothesized that inhibiting such pathogen helpers may help reduce pathogen densities. We examined tripartite interactions between a model pathogen, Ralstonia solanacearum, two model helper strains and a collection of 46 bacterial isolates recovered from the tomato rhizosphere. This system allowed us to examine the importance of direct (effects of rhizobacteria on pathogen growth) and indirect (effects of rhizobacteria on helper growth) pathways affecting pathogen growth. We found that the interaction between rhizosphere isolates and the helper strains was the major determinant of pathogen suppression both in vitro and in vivo. We therefore propose that controlling microbiome composition to prevent the growth of pathogen helpers may become part of sustainable strategies for pathogen control.Subject terms: Microbial ecology, Microbial ecology, Microbial ecology     

Impact of biochar application to soil on the root-associated bacterial community structure of fully developed greenhouse pepper plants

Adding biochar to soil has environmental and agricultural potential due to its long-term carbon sequestration capacity and its ability to improve crop productivity. Recent studies have demonstrated that soil-applied biochar promotes the systemic resistance of plants to several prominent foliar pathogens. One potential mechanism for this phenomenon is root-associated microbial elicitors whose presence is somehow augmented in the biochar-amended soils. The objective of this study was to assess the effect of biochar amendment on the root-associated bacterial community composition of mature sweet pepper (Capsicum annuum L.) plants. Molecular fingerprinting (denaturing gradient gel electrophoresis and terminal restriction fragment length polymorphism) of 16S rRNA gene fragments showed a clear differentiation between the root-associated bacterial community structures of biochar-amended and control plants. The pyrosequencing of 16S rRNA amplicons from the rhizoplane of both treatments generated a total of 20,142 sequences, 92 to 95% of which were affiliated with the Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes phyla. The relative abundance of members of the Bacteroidetes phylum increased from 12 to 30% as a result of biochar amendment, while that of the Proteobacteria decreased from 71 to 47%. The Bacteroidetes-affiliated Flavobacterium was the strongest biochar-induced genus. The relative abundance of this group increased from 4.2% of total root-associated operational taxonomic units (OTUs) in control samples to 19.6% in biochar-amended samples. Additional biochar-induced genera included chitin and cellulose degraders (Chitinophaga and Cellvibrio, respectively) and aromatic compound degraders (Hydrogenophaga and Dechloromonas). We hypothesize that these biochar-augmented genera may be at least partially responsible for the beneficial effect of biochar amendment on plant growth and viability.     

Mechanism of plant growth promotion by rhizobacteria

Plant growth results from interaction of roots and shoots with the environment. The environment for roots is the soil or planting medium which provide structural support as well as water and nutrients to the plant. Roots also support the growth and functions of a complex of microorganisms that can have a profound effect on the growth anti survival of plants. These microorganisms constitute rhizosphere microflora and can be categorized as deleterious, beneficial, or neutral with respect to root/plant health. Beneficial interactions between roots and microbes do occur in rhizosphere and can be enhanced. Increased plant growth and crop yield can be obtained upon inoculating seeds or roots with certain specific root-colonizing bacteria- 'plant growth promoting rhizobacteria'. In this review, we discuss the mechanisms by which plant growth promoting rhizobacteria may stimulate plant growth.     

Stimulated saprotrophic fungi in arable soil extend their activity to the rhizosphere and root microbiomes of crop seedlings

Saprotrophic fungi play an important role in ecosystem functioning and plant performance, but their abundance in intensively managed arable soils is low. Saprotrophic fungal biomass in arable soils can be enhanced with amendments of cellulose-rich materials. Here, we examined if sawdust-stimulated saprotrophic fungi extend their activity to the rhizosphere of crop seedlings and influence the composition and activity of other rhizosphere and root inhabitants. After growing carrot seedlings in sawdust-amended arable soil, we determined fungal and bacterial biomass and community structure in roots, rhizosphere and soil. Utilization of root exudates was assessed by stable isotope probing (SIP) following ¹³CO₂-pulse-labelling of seedlings. This was combined with analysis of lipid fatty acids (PLFA/NLFA-SIP) and nucleic acids (DNA-SIP). Sawdust-stimulated Sordariomycetes colonized the seedling's rhizosphere and roots and actively consumed root exudates. This did not reduce the abundance and activity of bacteria, yet higher proportions of α-Proteobacteria and Bacteroidia were seen. Biomass and activity of mycorrhizal fungi increased with sawdust amendments, whereas exudate consumption and root colonization by functional groups containing plant pathogens did not change. Sawdust amendment of arable soil enhanced abundance and exudate-consuming activity of saprotrophic fungi in the rhizosphere of crop seedlings and promoted potential beneficial microbial groups in root-associated microbiomes.     

Isolation and characterization of bacteria associated with two sand dune plant species, Calystegia soldanella and Elymus mollis

Little is known about the bacterial communities associated with the plants inhabiting sand dune ecosystems. In this study, the bacterial populations associated with two major sand dune plant species, Calystegia soldanella (beach morning glory) and Elymus mollis (wild rye), growing along the costal areas in Tae-An, Chungnam Province, were analyzed using a culture-dependent approach. A total of 212 bacteria were isolated from the root and rhizosphere samples of the two plants, and subjected to further analysis. Based on the analysis of the 16S rDNA sequences, all the bacterial isolates were classified into six major phyla of the domain Bacteria. Significant differences were observed between the two plant species, and also between the rhizospheric and root endophytic communities. The isolates from the rhizosphere of the two plant species were assigned to 27 different established genera, and the root endophytic bacteria were assigned to 21. Members of the phylum Gammaproteobacteria, notably the Pseudomonas species, comprised the majority of both the rhizospheric and endophytic bacteria, followed by members of Bacteroidetes and Firmicutes in the rhizosphere and Alphaproteobacteria and Bacteroidetes in the root. A number of isolates were recognized as potentially novel bacterial taxa. Fifteen out of 27 bacterial genera were commonly found in the rhizosphere of both plants, which was comparable to 3 out of 21 common genera in the root, implying the host specificity for endophytic populations. This study of the diversity of culturable rhizospheric and endophytic bacteria has provided the basis for further investigation aimed at the selection of microbes for the facilitation of plant growth.     

Organic fertilizers alter the composition of pathogens and arbuscular mycorrhizal fungi in maize roots

Roots of agricultural crops, including maize, are hosts of different microorganisms, many beneficial, like plant growth and health‐promoting arbuscular mycorrhizal fungi (AMF), as well as pathogens including Pythium, Polymyxa and Microdochium. To improve crop nutrition and health, profound knowledge is required regarding how agricultural practices affect field populations of root‐associated microorganisms. Hence, the objective of this work was to evaluate the effect of crop genotype and organic fertilizers on the plant growth performance of maize and their root‐associated microorganisms. The experiment was conducted as a fully factorial greenhouse pot experiment with maize cultivars (two land races and two hybrids) and organic fertilizers (green manure, cow manure and compost) as the two main factors. Plants were harvested 8 weeks after sowing. In general, the different maize cultivars responded similarly to the applications of the organic fertilizers. Cow manure and compost increased plant growth, whereas green manure had limited effect on plant growth. Root colonization with AMF was reduced by green manure with rape. Infection with the root pathogens Pythium and Polymyxa was reduced by all organic fertilizers, whereas in contrast, infection with Microdochium increased with the majority of the organic fertilizers applied. In conclusion, both maize genotype and organic fertilizers affect the abundance of AMF and root pathogens in maize, which should be considered when developing management strategies of these root‐inhabiting microorganisms.     

Root Colonization by Inoculated Plant Growth-Promoting Rhizobacteria

Certain rhizobacteria referred to as 'plant growth-promoting rhizobacteria' (PGPR) can contribute to the biological control of plant pathogens and improve plant growth. They enhance root development either directly by producing phytohormones, or indirectly by inhibiting pathogens through the synthesis of different compounds. PGPR are likely to be of great interest in sustainable crop protection and have drawn much attention in recent years. However, the use of these bacteria to protect crops sometimes fails because rhizobacteria are unable to recolonize the rhizosphere of inoculated plants. The colonization of roots by inoculated bacteria is an important step in the interaction between beneficial bacteria and the host plant. However, it is a complex phenomenon influenced by many biotic and abiotic parameters, some of which are now apparent. This paper summarises knowledge on rhizosphere colonization by PGPR.     

Perturbation of maize rhizosphere microflora following seed bacterization with Burkholderia cepacia MCI 7

Introduction of a large quantity of exogenous microorganisms may disrupt a local ecosystem and affect the natural microflora. In this work we investigated the effects of the introduction of a plant growth promoting strain of Burkholderia cepacia into the rhizosphere of maize on both indigenous B. cepacia populations and microbial community structure of total culturable bacteria using the concept of r/K strategy. Moreover we studied the distribution of bacterial populations in the root system at various soil depths. Seed bacterization was used as application method. Root colonization of the introduced strain occurred mainly on roots close to the plant stem, whereas indigenous B. cepacia was recovered at higher amounts from the lower parts of root systems of mature plants. As far as total culturable bacteria are concerned, an almost uniform distribution in the root system of mature plants was observed. The release of the exogenous bacterial strain affected mainly the microbial populations of young growing plants rather than mature plants. Indeed it caused only short-term perturbations in the microbial community of maize rhizosphere. Colonization of maize roots by indigenous B. cepacia was not significantly affected by the presence of the exogenous strain.     

西北黄土高原柠条种植区土壤微生物多样性分析

柠条锦鸡儿(Caragana korshinskii)是我国黄土高原区重要的饲用豆科灌木植物。为揭示土壤微生物与柠条种植之间的关系,采用未培养技术提取样品宏基因组DNA,分别构建柠条根表、根际和自然土16SrDNA文库,分析各文库微生物群落的变化。结果显示,随距离柠条根部渐远,微生物数量呈现递减趋势。聚类分析发现,变形杆菌纲是根表土壤区系中的优势微生物种群(70.3%),尤其存在大量α-Proteobacteria类的能诱使植物形成根瘤的根瘤菌和对植物有促生作用的γ-Proteobacteria类微生物;而在根际和自然土中,酸杆菌属(Acidobacteria)和古菌(Archaea)数量较多。柠条根际的多样性指数最高,而根表和自然土微生物类群具有较高的优势度,表现出从根表、根际植物相关微生物到自然土单一简单微生物类群的过渡。说明植物根系和土壤环境与微生物类群具有相互选择性。     

Causes and consequences of plant-associated biofilms

The rhizosphere is the critical interface between plant roots and soil where beneficial and harmful interactions between plants and microorganisms occur. Although microorganisms have historically been studied as planktonic (or free-swimming) cells, most are found attached to surfaces, in multicellular assemblies known as biofilms. When found in association with plants, certain bacteria such as plant growth promoting rhizobacteria not only induce plant growth but also protect plants from soil-borne pathogens in a process known as biocontrol. Contrastingly, other rhizobacteria in a biofilm matrix may cause pathogenesis in plants. Although research suggests that biofilm formation on plants is associated with biological control and pathogenic response, little is known about how plants regulate this association. Here, we assess the biological importance of biofilm association on plants.     

Bacterial communities associated with the rhizosphere of transgenic Bt 176 maize (Zea mays) and its non transgenic counterpart

The effect of transgenic Bt 176 maize on the rhizosphere bacterial community has been studied with a polyphasic approach by comparing the rhizosphere of Bt maize cultivated in greenhouse with that of its non transgenic counterpart grown in the same conditions. In the two plants the bacterial counts of the copiotrophic, oligotrophic and sporeforming bacteria, and the community level catabolic profiling, showed no significant differences; differences between the rhizosphere and bulk soil bacterial communities were evidenced. Automated ribosomal intergenic spacer analysis (ARISA) showed differences also in the rhizosphere communities at different plant ages, as well as between the two plant types. ARISA fingerprinting patterns of soil bacterial communities exposed to root growth solutions, collected from transgenic and non transgenic plants grown in hydroponic conditions, were grouped separately by principal component analysis suggesting that root exudates could determine the selection of different bacterial communities.