生物被膜在病原细菌与植物识别中的作用

生物被膜是微生物附着在生物或非生物表面所形成的一种三维结构,细胞被其自身所产生的胞外聚合物所包围,生物被膜的形成被认为是微生物应对生物和非生物胁迫时所产生的一种自我防御机制。众多微生物能够在植物叶、维管束和根等组织中生长,并在植物不同组织表面附着形成生物被膜,病原细菌的生物被膜随植物内部环境动态变化是其有效发挥致病作用的关键,研究植物病原细菌生物被膜调控机制是认识植物-病原菌互作的重要方面。文中将系统地介绍植物病原细菌生物被膜特征、组成成分、分子调控机制及最新研究进展。     

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.     

New insights on molecular regulation of biofilm formation in plant-associated bacteria

Biofilms are complex bacterial assemblages with a defined three-dimensional architecture, attached to solid surfaces, and surrounded by a self-produced matrix generally composed of exopolysaccharides, proteins, lipids and extracellular DNA. Biofilm formation has evolved as an adaptive strategy of bacteria to cope with harsh environmental conditions as well as to establish antagonistic or beneficial interactions with their host. Plant-associated bacteria attach and form biofilms on different tissues including leaves, stems,vasculature, seeds and roots. In this review, we examine the formation of biofilms from the plant-associated bacterial perspective and detail the recently-described mechanisms of genetic regulation used by these organisms to orchestrate biofilm formation on plant surfaces. In addition, we describe plant host signals that bacterial pathogens recognize to activate the transition from a planktonic lifestyle to multicellular behavior.     

Nonlegumes, legumes, and root nodules harbor different arbuscular mycorrhizal fungal communities

Legumes are an important plant functional group since they can form a tripartite symbiosis with nitrogen-fixing Rhizobium bacteria and phosphorus-acquiring arbuscular mycorrhizal fungi (AMF). However, not much is known about AMF community composition in legumes and their root nodules. In this study, we analyzed the AMF community composition in the roots of three nonlegumes and in the roots and root nodules of three legumes growing in a natural dune grassland. We amplified a portion of the small-subunit ribosomal DNA and analyzed it by using restriction fragment length polymorphism and direct sequencing. We found differences in AMF communities between legumes and nonlegumes and between legume roots and root nodules. Different plant species also contained different AMF communities, with different AMF diversity. One AMF sequence type was much more abundant in legumes than in nonlegumes (39 and 13%, respectively). Root nodules contained characteristic AMF communities that were different from those in legume roots, even though the communities were similar in nodules from different legume species. One AMF sequence type was found almost exclusively in root nodules. Legumes and root nodules have relatively high nitrogen concentrations and high phosphorus demands. Accordingly, the presence of legume- and nodule-related AMF can be explained by the specific nutritional requirements of legumes or by host-specific interactions among legumes, root nodules, and AMF. In summary, we found that AMF communities vary between plant functional groups (legumes and nonlegumes), between plant species, and between parts of a root system (roots and root nodules).     

Nonlegumes, Legumes, and Root Nodules Harbor Different Arbuscular Mycorrhizal Fungal Communities

Legumes are an important plant functional group since they can form a tripartite symbiosis with nitrogen-fixing Rhizobium bacteria and phosphorus-acquiring arbuscular mycorrhizal fungi (AMF). However, not much is known about AMF community composition in legumes and their root nodules. In this study, we analyzed the AMF community composition in the roots of three nonlegumes and in the roots and root nodules of three legumes growing in a natural dune grassland. We amplified a portion of the small-subunit ribosomal DNA and analyzed it by using restriction fragment length polymorphism and direct sequencing. We found differences in AMF communities between legumes and nonlegumes and between legume roots and root nodules. Different plant species also contained different AMF communities, with different AMF diversity. One AMF sequence type was much more abundant in legumes than in nonlegumes (39 and 13%, respectively). Root nodules contained characteristic AMF communities that were different from those in legume roots, even though the communities were similar in nodules from different legume species. One AMF sequence type was found almost exclusively in root nodules. Legumes and root nodules have relatively high nitrogen concentrations and high phosphorus demands. Accordingly, the presence of legume- and nodule-related AMF can be explained by the specific nutritional requirements of legumes or by host-specific interactions among legumes, root nodules, and AMF. In summary, we found that AMF communities vary between plant functional groups (legumes and nonlegumes), between plant species, and between parts of a root system (roots and root nodules).     

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.     

Cross-kingdom interactions: Candida albicans and bacteria

Bacteria and fungi are found together in a myriad of environments and particularly in a biofilm, where adherent species interact through diverse signaling mechanisms. Yet, despite billions of years of coexistence, the area of research exploring fungal–bacterial interactions, particularly within the context of polymicrobial infections, is still in its infancy. However, reports describing a multitude of wide-ranging interactions between the fungal pathogen Candida albicans and various bacterial pathogens are on the rise. An example of a mutually beneficial interaction is coaggregation, a phenomenon that takes place in oral biofilms where the adhesion of C. albicans to oral bacteria is considered crucial for its colonization of the oral cavity. In contrast, the interaction between C. albicans and Pseudomonas aeruginosa is described as being competitive and antagonistic in nature. Another intriguing interaction is that occurring between Staphylococcus aureus and C. albicans , which although not yet fully characterized, appears to be initially synergistic. These complex interactions between such diverse and important pathogens would have significant clinical implications if they occurred in an immunocompromised host. Therefore, understanding the mechanisms of adhesion and signaling involved in fungal–bacterial interactions may lead to the development of novel therapeutic strategies for impeding microbial colonization and development of polymicrobial disease.     

Plant neighbor effects mediated by rhizosphere factors along a simulated aridity gradient

Aims

We investigated how rhizosphere factors (total rhizosphere, roots, arbuscular mycorrhizal fungal hyphae [AMF], and soil solution) and water availability affect interactions between neighboring Medicago sativa plants.

Methods

A three-compartment mesocosm was used to test the effects of rhizosphere factors on plant–plant interactions. A relative interaction index (RII) was calculated to indicate whether effects of neighbor plant on target plant were positive or negative (facilitative or competitive). Isotope tracers were used to test whether AMF hyphae mediated competition for nitrogen (N) between target and neighbor plants.

Results

The effects of rhizosphere factors on the interactions between neighboring M. sativa plants depended on water availability. The effects of total rhizosphere shifted RII from negative to positive as water availability increased. Interaction with the roots and rhizosphere soil solution of neighbor plants shifted RII from negative to positive as water availability increased but the opposite was true for AMF hyphae. AMF hyphae helped neighbor plants compete for ¹⁵N when water was available but not when water was limiting.

Conclusions

The effect of total rhizosphere on plant–plant interaction of M. sativa shifted from competitive to facilitative as water availability increased. Competition was reduced by neighboring soil solution and roots but was increased by AMF hyphae.     

Rhizosphere: its structure,bacterial diversity and significance

Sustainable agricultural practices are the answer to multifaceted problems that have resulted due to prolonged and indiscriminate use of chemical based agronomic tools to improve crop productions for the last many decades. The hunt for suitable ecofriendly options to replace the chemical fertilizers and pesticides has thus been aggravated. Owing to their versatile and unmatchable capacities microbial agents offer an attractive and feasible option to develop the biological tools to replace/supplement the chemicals. Exploring the microorganisms that reside in close proximity to the plant is thus a justified move in the direction to achieve this target. One of the most lucrative options is to look into the rhizosphere. Rhizosphere may be defined as the narrow zone of soil that surrounds and get influenced by the roots of the plants. It is rich in nutrients compared to the bulk soil and hence exhibit intense biological and chemical activities. A wide range of macro and microorganisms including bacteria, fungi, virus, protozoa, algae, nematodes and microarthropods co-exist in rhizosphere and show a variety of interactions between themselves as well as with the plant. Plant friendly bacteria residing in rhizosphere which exert beneficial affect on it are called as plant growth promoting rhizobacteria (PGPR). Here we review the structure and bacterial diversity of the rhizosphere. The major points discussed here are: (1) structure and composition of the rhizosphere (2) range of bacteria found in rhizosphere and their interactions with the plant with a particular emphasis on PGPR (3) mechanisms of plant growth promotion by the PGPR (4) rhizosphere competence.     

Interactions among endophytic bacteria and fungi: Effects and potentials

Plants benefit extensively by harbouring endophytic microbes. They promote plant growth and confer enhanced resistance to various pathogens. However, the way the interactions among endophytes influence the plant productivity has not been explained. Present study experimentally showed that endophytes isolated from rice (Oryza sativa) used as the test plant produced two types of interactions; biofilms (bacteria attached to mycelia) and mixed cultures with no such attachments. Acidity, as measured by pH in cultures with biofilms was higher than that of fungi alone, bacteria alone or the mixed cultures. Production of indoleacetic acid like substances (IAAS) of biofilms was higher than that of mixed cultures, fungi or bacteria. Bacteria and fungi produced higher quantities of IAAS than mixed cultures. In mixed cultures, the potential of IAAS production of resident microbes was reduced considerably. There was a negative relationship between IAAS and pH of the biofilms, indicating that IAAS was the main contributor to the acidity. However, such a relationship was not observed in mixed cultures. Microbial acid production is important for suppressing plant pathogens. Thus the biofilm formation in endophytic environment seems to be very important for healthy and improved plant growth. However, it is unlikely that an interaction among endophytes takes place naturally in the endophytic environment, due to physical barriers of plant tissues. Further, critical cell density dependant quorum sensing that leads to biofilm formation may not occur in the endophytic environment as there is a limited space. As suchin vitro production and application of beneficial biofilmed inocula of endophytes are important for improved plant production in any agro-ecosystem. The conventional practice of plant inoculation with monocultures or mixed cultures of effective microbes may not give the highest microbial effect, which may only be achieved by biofilm formation.     

Interaction between Earthworms and Arbuscular Mycorrhizal Fungi in Plants: A Review

Different kinds of soil animals and microorganisms inhabit the plant rhizosphere, which function closely to plant roots. Of them, arbuscular mycorrhizal fungi (AMF) and earthworms play a critical role in sustaining the soil-plant health. Earthworms and AMF belong to the soil community and are soil beneficial organisms at different trophic levels. Both of them improve soil fertility and structural development, collectively promoting plant growth and nutrient acquisition capacity. Earthworm activities redistribute mycorrhizal fungi spores and give diversified effects on root mycorrhizal fungal colonization. Dual inoculation with both earthworms and AMF strongly magnifies the response on plant growth through increased soil enzyme activities and changes in soil nutrient availability, collectively mitigating the negative effects of heavy metal pollution in plants and soils. This thus enhances phytoremediation and plant disease resistance. This review simply outlines the effects of earthworms and AMF on the soil-plant relationship. The effects of earthworms on root AMF colonization and activities are also analyzed. This paper also summarizes the interaction between earthworms and AMF on plants along with suggested future research.     

基于菌植互作的植物根际细菌钝化镉作用和机制研究进展

土壤重金属镉(Cd)污染严重危害农产品安全生产,植物根际细菌在钝化土壤Cd和帮助作物抵御Cd胁迫方面发挥重要作用。本文首先概括在修复Cd污染土壤中得到广泛应用的植物根际细菌种类,并从根际细菌直接吸附Cd、调整土壤理化特性、调控土壤微生物群落和其他作用4方面阐述了植物根际细菌对Cd的钝化作用,其次从菌植互作角度阐述植物根系分泌物与根际细菌群落相互影响对土壤Cd的钝化作用。最后展望重金属胁迫下植物根际钝化Cd核心菌群的构建,以在新兴学科与技术的快速发展中探明植物根系-微生物互作体系的分子机制,深入开展植物根际细菌钝化修复重金属污染土壤的理论研究和实践。     

Unravelling rhizosphere-microbial interactions: opportunities and limitations

The rhizosphere is a biologically active zone of the soil around plant roots that contains soil-borne microbes including bacteria and fungi. Plant-microbe interactions in the rhizosphere can be beneficial to the plant, the microbes or to neither of them. One of the major difficulties that plant biologists and microbiologists face when studying these interactions is that many groups of microbes that inhabit this zone are not cultivable in the laboratory. Recent developments in molecular biology methods are shedding some light on rhizospheric microbial diversity. This review discusses recent findings and future challenges in the study of plant-microbe interactions in the rhizosphere.     

Rhizosphere engineering and management for sustainable agriculture

This paper reviews strategies for manipulating plants and their root-associated microorganisms to improve plant health and productivity. Some strategies directly target plant processes that impact on growth, while others are based on our knowledge of interactions among the components of the rhizosphere (roots, microorganisms and soil). For instance, plants can be engineered to modify the rhizosphere pH or to release compounds that improve nutrient availability, protect against biotic and abiotic stresses, or encourage the proliferation of beneficial microorganisms. Rhizobacteria that promote plant growth have been engineered to interfere with the synthesis of stress-induced hormones such as ethylene, which retards root growth, and to produce antibiotics and lytic enzymes active against soilborne root pathogens. Rhizosphere engineering also can involve the selection by plants of beneficial microbial populations. For example, some crop species or cultivars select for and support populations of antibiotic-producing strains that play a major role in soils naturally suppressive to soil-borne fungal pathogens. The fitness of root-associated bacterial communities also can be enhanced by soil amendment, a process that has allowed the selection of bacterial consortia that can interfere with bacterial pathogens. Plants also can be engineered specifically to influence their associated bacteria, as exemplified by quorum quenching strategies that suppress the virulence of pathogens of the genus Pectobacterium. New molecular tools and powerful biotechnological advances will continue to provide a more complete knowledge of the complex chemical and biological interactions that occur in the rhizosphere, ensuring that strategies to engineer the rhizosphere are safe, beneficial to productivity, and substantially improve the sustainability of agricultural systems.     

Exploiting New Systems-Based Strategies to Elucidate Plant-Bacterial Interactions in the Rhizosphere

The rhizosphere is the site of intense interactions between plant, bacterial, and fungal partners. In plant-bacterial interactions, signal molecules exuded by the plant affect both primary initiation and subsequent behavior of the bacteria in complex beneficial associations such as biocontrol. However, despite this general acceptance that plant-root exudates have an effect on the resident bacterial populations, very little is still known about the influence of these signals on bacterial gene expression and the roles of genes found to have altered expression in plant-microbial interactions. Analysis of the rhizospheric communities incorporating both established techniques, and recently developed “omic technologies” can now facilitate investigations into the molecular basis underpinning the establishment of beneficial plant-microbial interactomes in the rhizosphere. The understanding of these signaling processes, and the functions they regulate, is fundamental to understanding the basis of beneficial microbial–plant interactions, to overcoming existing limitations, and to designing improved strategies for the development of novel Pseudomonas biocontrol strains.     

典型农田土壤中丛枝菌根真菌-根际细菌互作及与氮磷利用的关系

在农业生态系统中,土壤微生物是土壤-作物系统养分循环的重要驱动力,其中丛枝菌根真菌(Arbuscularmycorrhizalfungi,AMF)能够促进作物对养分的吸收,适应逆境胁迫。【目的】进一步揭示AMF和根际细菌群落的跨界网络互作,挖掘与作物氮磷利用显著相关的关键微生物类群,揭示关键类群的生态网络特征。【方法】利用Illumina测序技术对3种典型农田旱地土壤(黑土、潮土和红壤)中AMF和根际细菌群落结构进行分析;构建互作网络并利用偏冗余分析、相关性分析探究了与氮磷利用相关的潜在关键类群。【结果】3种土壤中AMF与根际细菌均以正相互作用为主。不同土壤中AMF与根际细菌互作关系差异明显,在红壤中跨界互作最为密切,其中球囊霉属真菌(Glomus)与根际细菌中的放线菌(Actinobacteria)和变形菌(Proteobacteria)之间的交互作用最多。而在黑土中主要体现为根际细菌的界内互作。与氮磷利用率显著相关的关键微生物类群主要属于球囊霉属真菌、放线菌和α变形菌。【结论】典型旱地土壤中AMF与根际细菌的正相互关系对作物氮磷利用有潜在促进作用,关键类群在有机质和养分贫乏的红壤中可能起到更重要的作用。     

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.     

Cyanogenic pseudomonads influence multitrophic interactions in the rhizosphere

In the rhizosphere, plant roots cope with both pathogenic and beneficial bacterial interactions. The exometabolite production in certain bacterial species may regulate root growth and other root-microbe interactions in the rhizosphere. Here, we elucidated the role of cyanide production in pseudomonad virulence affecting plant root growth and other rhizospheric processes. Exposure of Arabidopsis thaliana Col-0 seedlings to both direct (with KCN) and indirect forms of cyanide from different pseudomonad strains caused significant inhibition of primary root growth. Further, we report that this growth inhibition was caused by the suppression of an auxin responsive gene, specifically at the root tip region by pseudomonad cyanogenesis. Additionally, pseudomonad cyanogenesis also affected other beneficial rhizospheric processes such as Bacillus subtilis colonization by biofilm formation on A. thaliana Col-0 roots. The effect of cyanogenesis on B. subtilis biofilm formation was further established by the down regulation of important B. subtilis biofilm operons epsA and yqxM. Our results show, the functional significance of pseudomonad cyanogenesis in regulating multitrophic rhizospheric interactions.     

Synthetic biology in biofilms: Tools,challenges, and opportunities

The field of synthetic biology seeks to program living cells to perform novel functions with applications ranging from environmental biosensing to smart cell-based therapeutics. Bacteria are an especially attractive chassis organism due to their rapid growth, ease of genetic manipulation, and ability to persist across many environmental niches. Despite significant progress in bacterial synthetic biology, programming bacteria to perform novel functions outside the well-controlled laboratory context remains challenging. In contrast to planktonic laboratory growth, bacteria in nature predominately reside in the context of densely packed communities known as biofilms. While biofilms have historically been considered environmental and biomedical hazards, their physiology and emergent behaviors could be leveraged for synthetic biology to engineer more capable and robust bacteria. Specifically, bacteria within biofilms participate in complex emergent behaviors such as collective organization, cell-to-cell signaling, and division of labor. Understanding and utilizing these properties can enable the effective deployment of engineered bacteria into natural target environments. Toward this goal, this review summarizes the current state of synthetic biology in biofilms by highlighting new molecular tools and remaining biological challenges. Looking to future opportunities, advancing synthetic biology in biofilms will enable the next generation of smart cell-based technologies for use in medicine, biomanufacturing, and environmental remediation.     

Role of soil microbes in the rhizospheres of plants growing on trace metal contaminated soils in phytoremediation

This article reviews recent developments in in situ bioremediation of trace metal contaminated soils, with particular reference to the microbial dynamics in the rhizospheres of plants growing on such soils and their significance in phytoremediation. In non-agricultural conditions, the natural role of plant growth promoting rhizobacteria (PGPR), P-solubilizing bacteria, mycorrhizal-helping bacteria (MHB) and arbuscular mycorrhizal fungi (AMF) in maintaining soil fertility is more important than in conventional agriculture, horticulture, and forestry where higher use of agrochemicals minimize their significance. These microbes initiate a concerted action when a particular population density is achieved, i.e. quorum sensing. AMF also recognize their host by signals released by host roots, allowing a functional symbiosis. AM fungi produce an insoluble glycoprotein, glomalin, which sequester trace elements and it should be considered for biostabilization leading to remediation of contaminated soils. Conclusions drawn from studies of metal uptake kinetics in solution cultures may not be valid for more complex field conditions and use of some combination of glasshouse and field experiments with organisms that occur within the same plant community is suggested. Phytoextraction strategies, such as inoculation of plants to be used for phytoremediation with appropriate heavy metal adapted rhizobial microflora, co-cropping system involving a non-mycorrhizal hyperaccumulator plant and a non-accumulator but mycorrhizal with appropriate AMF, or pre-cropping with mycotrophic crop systems to optimize phytoremediation processes, merit further field level investigations. There is also a need to improve our understanding of the mechanisms involved in transfer and mobilization of trace elements by rhizosphere microbiota and to conduct research on selection of microbial isolates from rhizosphere of plants growing on heavy metal contaminated soils for specific restoration programmes. This is necessary if we are to improve the chances of successful phytoremediation.