Microbial interactions with plants result in beneficial as well as harmful impacts, which have a major role in ecosystem processes. Negative interactions by microorganisms (bacteria and fungi) end up with plant diseases threatening the agriculture worldwide.

By Hafsa Javaid, Athar Mahmood

On the contrary, positive interactions have beneficial implications useful in pharmaceutical, biotechnological and agricultural applications. From the agricultural point of view, plants and microbes interact in many ways resulting in manifestation of mutualistic or hostile changes. If the interaction is mutualistic, this will be beneficial or advantageous to both organisms like fertile soil composed of a large number of beneficial bacteria and fungi (e.g. rhizobia and mycorrhizas). Such interactions result in beneficial effects like nitrogen fixation as well as uptake of nutrients. Moreover, plants are constantly threatened by a wide range of pathogens (e.g. bacteria, fungi and others), which result in the development of defence mechanisms in plants to combat against pathogens.

The Good: Soil Microbes Positively Affecting Plant Growth

Of the microorganisms colonizing the rhizosoil, Streptomyces species are special. They grow filamentously and can colonize not only soil but also roots and aerial parts of the plants; they are active producers of antibiotics and can save the plant from attack by more dangerous bacteria; and they produce volatile organic compounds that give rise to the typical fragrance of fresh forest soil. As such, they qualify as biocontrol agents in several cropping systems, and strains serving as antagonists of various plant pathogens can be identified. The versatile Streptomyces species also have plant growth-promoting abilities and can be used as biofertilizers. Because of their ability to form spores and survive adverse conditions in the soil, they are also more competitive than other microbes. In addition, they produce various lytic enzymes that can break down insoluble organic polymers and generate nutrients that can be used by plants.


Plant growth-promoting bacteria can also be used in phytoremediation of metal-contaminated soils. The exposing Helianthus tuberosus, a high biomass crop used for bio-ethanol production, to particular plant growth-promoting bacteria that were isolated from plants growing on a  metal-contaminated soil increased the ability of the plant to sustain elevated concentrations of cadmium and zinc. The bacteria were shown to grow endophytically in the root and resulted in a significantly increased cadmium uptake into the plant. In presence of the bacteria, the plant showed a decrease of metal-induced stress and an improved growth. Thus, these plant growthpromoting bacteria can help both in phytoremediation and in sustainable biomass production.

Plant Growth-Promoting Rhizobacteria

Microbes existing in the rhizosphere perform several functions towards host growth and development. Rhizobacteria that facilitate plant growth promotion and resistance to diseases are classified as PGPR (plant growth-promoting rhizobacteria), a class of organisms that enhance plant growth and improve yield via a variety of plant growth-promoting substances, which serve as biofertilizers or bioprotectants. Their plant growth-promoting performance is usually attributed to improved nutrient acquisition through hormonal stimulation. Bacteria residing in the rhizosphere of plants have special role and known to possess plant growthpromoting attributes, which improve nutrient cycling as well as help in reducing the use of chemicals.

Many rhizosphere bacteria are used as biofertilizers extensively in organic farming for sustainable agriculture. It is well established that PGPR are biofertilizers as well as efficient soil-inhabiting bacteria for sustainable agriculture. The PGPR are well-known and commercially harnessed by government and private organizations across the globe. The PGPR are known to produce a number of special metabolites, which are soluble and volatile, and help in inhibiting the growth of pathogenic bacteria by antibiosis or by cell signaling through induction of resistance and tolerance to plants against various pathogenic and environmental stresses. They are also known to enhance the nodulation upon co-inoculating with Bradyrhizobium japonicum leading to enhanced plant development and yield in soybean.

Plant Growth-Promoting Fungi

Fungi residing in various habitats in a plant system (roots, leaves, stem, rhizosphere and phyllosphere) are exploited for their ability to support plant growth promotion, thereby activating several key pathways during plant development or disease resistance during pathogenesis or combating stressful environments. Interactions between plants and their associated fungi in rhizosphere and phyllosphere as endophytes promote the plant development and induction of resistance systemically (ISR) on invading pathogens are known as plant growth-promoting fungi (PGPF). A large number of heterogeneous classes of fungi from different habitats have the capacity to augment plant growth promotion. The important fungal  genera recorded to have the PGPF traits are Aspergillus, Fusarium, Penicillium, Piriformospora, Phoma, Trichoderma and many others.

The PGPF interacts with host plants, and their interactions will positively influence the belowground as well as the above-ground parts. The PGPF are also known to significantly improve the seed germination, seedling vigour, biomass, root hair growth, efficiency of photosynthesis, flowering, yield of seeds and biochemical composition of seeds. Other than these traits, the PGPF are also known to control several foliar pathogens by inducing systemic resistance. It is now known that the PGPF are also capable to control numerous foliar and root pathogens by triggering ISR in the hosts. They enhance the abilities of host plants to increase nutrient uptake and hormone production, which in turn reprogram the gene expression through differential activation of plant signalling pathways. The PGPF have attracted substantial attention as biofertilizers due to their beneficial effects on plant quantity and efficiency of their positive relationship with the environment.

Mycorrhizal Implications in Agriculture

Mycorrhizas are symbiotically associated fungi with plant roots, which enhance the uptake of water and nutrients. The mycorrhizosphere represents a significant environmental niche for exceptionally adapted diverse microbial communities. At present it is known that the density of bacteria in the mycorrhizosphere will be higher (4–5-fold) than the rhizosphere of plant. The arbuscular mycorrhizal (AM) association is the vital mutualistic interaction resulting in significant beneficial impact worldwide, and over 65% of known land plants have this association. The AM fungi associate with plants without morphological modification from the Devonian period (~400 my), and thus the AM fungal mutualism played a crucial role in plant evolution. Nearly 10,000 of ectomycorrhizal fungal species have been recognized, and many of them show host specificity. The mycorrhizal fungi form their extensive hyphal network in soils, and the extra-radical mycelia (ERM) serve as artificial root system to increase the nutrient uptake. The ERM with its mycorrhizosphere act as a vital link of microbial communities as well as host plant species.

The mycorrhizal fungi enhance the nutrient uptake by host plant and are capable to distribute substantial quantities of essential macroelements (N, P, K and S) as well as trace elements (Cu, Zn). Many mycorrhizal fungi also provide benefits beyond nutrition by development of fitness apposing abiotic stresses (e.g. drought, heavy metals and salinity) as well as biotic (pathogens) stresses. Their symbiotic associations with the host plants influence the plant relationships in the ecosystems. However, mycorrhizal fungal mycelia influence the qualitative and  quantitative alterations in the microbial community in rhizosphere. Presence of mycorrhizal hyphae also plays a vital role in the assembly of bacterial community in decomposition process, which facilitates access of carbon to other communities of microbes in the rhizosphere. Schematic illustration of plant microbiome and its exploitation: biotechnological application of plant-microbe interactions (PGPR, PGPF and mycorrhiza) in biocontrol, systemic-acquired resistance, biopesticides and biofertilizers

The Bad: Revealing Mechanistic Strategies of Plant Pathogens

Even though there are several hundreds of important plant pathogens widespread causing significant economic loss and productivity, we attempted to explore the recent developments in plant-pathogen interaction of three major plant pathogens that cause major disease outbreaks in the history of plant pathology. They are

(1) Ceylon coffee rust by Hemileia vastatrix
(2) Late blight of potato by Phytophthora infestans
(3) Stalk rot of maize by Fusarium verticillioides

Hemileia vastatrix

Coffee leaf rust disease caused by Hemileia vastatrix is one of the most prominent diseases in coffee plantations. Commercially viable arabica coffee (Coffea arabica) and robusta coffee  (Coffea canephora) distributions in coffee-growing regions were susceptible to rust infection. The rust pathogen has been reported in multiple outbreaks in several coffee-growing regions which resulted in high yield loss. New races are constantly evolving as evidenced by the presence of fungus in plants that were previously resistant. To understand the nature of their evolution and success of breaking, the resistance of the host plants lies with the genome of pathogen and its interactions with host genome factors. Genomic studies have opened up new approaches to assess the evolution of pathogens over a period of time. However, the fungal genome called secretome deciphered that various traits housed in the pathogen and interact with hosts at various stages of development. Owing to the limited knowledge on the genome of H. vastatrix, identification was possible for only a fraction of secretome.

Phytophthora infestans

The causative agent of late blight Phytophthora infestans occurs on high numbers in solanaceous crops (potato, brinjal, tomato and many other recorded hosts) around the world. Lately a sensational advancement in molecular examinations of P. infestans includes the buildup of novel devices for gene silencing and transformation and the assets for genetic, physical and transcriptional mapping of the genome. Various developmental processes are required for successful cause of disease by P. infestans in host (e.g. development of zoospores, encystment, formation of a germ tube, advancement of appressoria, haustoria, hyphae and sporangiophores). In potato-Phytophthora pathosystem, collections of core RXLR effectors were identified for potential long-lasting late blight-resistant genes. Ten Avr RXLR genes disclosed the genes responsible for resistance (e.g. R2, Rpi-blb2, Rpi-vnt1, Rpi-Smira1 and Rpi-Smira2) in cultivars of potato. Further, investigation on eight SFI (inhibitor of early Flg22- induced response) and RXLR effector genes (e.g. SFI2, SFI3 and SFI4) has shown highly expressive nature in all strains, suggesting their function in the early stages of infection of pathogen.

The first draft genome of P. infestans results from a proliferation of repetitive DNA account about 74% of the genome. The proteome of incompatible and compatible interactions among potato and P. infestans differ and provide valuable information on the role of some important proteins expressed during incompatible reactions, which could be exploited by molecular biologists to develop resistant lines against late-blight fungus.

Fusarium verticillioides

Fusarium verticillioides has dual role in maize as an endophyte without disease symptoms and cause disease as a pathogen (seedlings, stalks, ears and roots). The molecular mechanisms of infection are understood poorly, which hampers breeding programmes. The genetic mechanism underpinning this pathosystem has been recently explored. They showed that striatin-like protein called Fsr1 plays an important role in development of stalk-rot disease. They also explored the NGS technology to record the relative abundance and to infer the co-expression of networks utilizing the preprocessed expression. Further analyzed the RNA-seq data through cointegrationcorrelation-expression, where genes of maize have been jointly analyzed by known virulent genes of F. verticillioides to disclose the genes involved in defense. Using these mechanisms, several computational models have been developed to identify the genetic subnetwork involved in defense response of maize against F. verticillioides. F. verticillioides can synthesize fumonisins at any stage (mycotoxins family similar to the sphingolipid sphinganine). Intake of maize contaminated with fumonisin causes several animal diseases such as cancer in rodents and oesophageal cancer in humans, with some evidence suggesting neural tube defects. There are several challenges that need to be tackled especially to eliminate contamination of fumonisin in maize as well as maize products. Knowledge on such toxins produced during F. verticillioides-maize disease leads to develop suitable strategies to control tissue destruction (by rot) as well as production of fumonisin. To achieve this goal, data on the genomic sequence, expressed sequence tags (EST) along with microarrays, are used  in precise identification of genes of F. verticillioides engaged in the synthesis of toxins involved in pathogenesis.

Authors :  Hafsa Javaid, Athar Mahmood University of Agriculture Faisalabad