Читать книгу Phytomicrobiome Interactions and Sustainable Agriculture - Группа авторов - Страница 27

Thus, microbes can be considered for positive exploitation of the plant growth promotion to enhance the growth of the plant. Microbes also make plants sustainable toward the abiotic as well as biotic stresses looking into progressive climate change. There have been many such types of research, where the positive associations have been well characterized using proteomic analysis and have further been utilized for the enhancement of a natural process.

One such aspect of microbial plant growth promotion is when such an association has been utilized for the purpose of phytoremediation. Phytoremediation is of great help in case of heavy metal remediation. The presence of metal‐solubilizing bacteria enhances the ability of the host plant to tolerate metal‐induced stress. The best case scenario can be observed in the bioethanol producers, such as H. tuberosus, a high biomass yielding crop that acquires enhancement in the accumulation and sustenance of a high concentration of zinc and cadmium. Similarly, the microbial population has been found to be colonizing the internal region of the roots as an endophyte, thereby resulting in increased assimilation of cadmium (Montalbán et al. 2017).

Enhancement of drought and salt resistance observed for the enhanced salt and drought resistance owing to the effects of plant growth–promoting bacteria as studied in L. perenne, also known as ryegrass. Unfortunately for this perennially relevant grass as turf and forage, it is highly sensitive to drought‐induced stress and high salinity. However, B. amyloliquefaciens, combined with hydrogels to prevent the soil from eroding, can help the grass sustain the drought‐induced stress by the plant (Su et al. 2017).

In another example, a species of plant growth‐promoting bacteria that have been found to be colonizing the roots, stems, and leaf parts of the sugarcane is the species Gluconacetobacter diazotrophicus. This is one such example where the bacteria serve as a legume endophyte. However, the proteome interaction studies of this bacterium with the sugar cane are still not very deep. A study was performed to investigate the molecular aspects using MS proteomic analysis using N15 metabolic labeling of bacterial, root samples, and co‐cultures. Over 400 proteins were assessed out of which near about 78 combinations of involved proteins appeared relevant among the interaction model. A comparative analysis of the proteomic data thus derived revealed the proteins involved in fundamental roles of protein recognition. Additionally, 30 bacterial active proteins have been identified where 9 were categorically induced by plant signaling pathways. This is the first line of study for the G. diazotrophicus and sugar cane (Schirawski and Perlin 2018).

The microbial action on plants can work both ways. Certain interactions work for the enhancement of the plant, however, some have a negative impact owing to such associations. Any plant maybe rendered vulnerable to disease owing to an undesirable microbial association or any abiotic stress situation which throws the plants defenses out of order. In the case of the pathogen associate disease situation, some events are to happen to manifest a plant's invasion by the pathogen. This series of events may be termed as the disease triangle where disease can manifest due to a pathogen if and only if there is appropriate feedback of the responses for the entry of the pathogen into the plant and for that the environmental conditions must be suitable. Plants' obligation as host to a vast array of pathogens such as bacteria, fungi, nematodes, viruses, etc., is a well‐understood concept (Dangl and Jones 2001).

The plant's defense system is highly complex and sophisticated. Many microbial species bombard the plant system, some for symbiosis and some for their exploitative tendencies. On the breach by any pathogen, a plant's pathogen‐associated molecular patterns (PAMPs) guided basic resistance is activated or cell wall degrading enzymes (CWDE) play their role (Jones and Dangl 2006). Certain pathogens have ascertained methods of evading or suppressing the plant defense which makes the host plant vulnerable to further infection. Sometimes there is a provision of resistance generation of protein expression in certain host plants to safeguard them against the pathogenic attack thereby activating specific resistance mechanisms. Such mechanisms have been deciphered by the proteomic studies. Proteomic analysis of host plant pathogen reveals the protein interaction profile of the proteins expressed during the plant pathogenesis. The plant–pathogen interactions have been categorized into two types depending upon the eventuality of the outcome of the pathogenesis. The first category is the compatible interaction. This is where the pathogen completes its cycle of pathogenesis and the plant is unable to mount an anti‐defense response. The second category is the incompatible interaction where the plant mounts a series of complex immune defense responses against the pathogen thereby forestalling the pathogenic progression (Mehta et al. 2008). The progression of the phytopathogenesis can be assessed into three stages: perception or detection, signaling to breach successfully, and response generated by the host of the perceived signals of the pathogens. As the pathogen comes in the vicinity of the host, it generates some signal metabolites which are sensed by the plant system and further communicated to the plant nucleus for feedback. The defense mounted in response to these signals is of two types: the local response which is initiated by the sensation of the elicitor produced by the pathogenic intervention and the other is systemic‐acquired resistance (SARs). The intent of the local response is to ameliorate the intervention at the periphery of the first interception. Responses are mediated by innate plant resistance proteins which elicits a rapid yet reliable response. These are high‐effect defense mechanisms thereby leading to mobilization of the ion fluxes across the plasma membrane of the host plant, leading to cell wall reinforcement. This subsequently initiates MAP kinase activation and generation of reactive oxygen species thereby causing the programmed cellular death. This type of response is also known as the hypersensitive response (Heath 2000; Jones 2000; Greenberg and Yao 2004).

The second category of defense response is also known as systemic acquired resistance (SARs). The features of this type of response are where the plant gears up the whole system from the localized region to the far distal end against the pathogen entry (Schneider et al. 1996). SARs deals with the phenomenon of raising the immunity guards to defend against the pathogens and also take proactive measures to aid the plant recovery from the damage post an immunogenic response. SARs activation is initiated by the presence of the endogenous salicylic acids (SA) which in turn increases the expression and assimilation of nitric oxides, ethylene, and jasmonic acid thereby eliciting various downstream pathways as cascade (Ryals et al. 1996). Such information regarding the plant‐pathogen interactions has been thoroughly substantiated by the genomic, post‐genomic, and proteomic analysis. Such studies, therefore, assimilate the validated information pertaining to the pathogenic strategies as well as behavior influenced by the host plant responses. Thus, proteomic studies empower with the most basic functional information regarding the recognition and characterization of the proteins functioning under specific conditions. Proteomics thus assesses the translated protein complement of the gene sequence derived experimentally corresponding to the protein profile of a specified tissue under consideration with a variable growth and treatment conditions (Mehta et al. 2008). Proteomics has helped in elucidating the distinct pathogenic pathways of a plethora of pathogens with their corresponding host plants. Proteomics has helped in elucidating the distinct pathogenic pathways of a plethora of pathogens with their corresponding host plants. Pathogens such as viruses, fungi, and bacteria have special notoriety in causing widespread devastation among the crops and have gained a special place in the study owing to the ease of handling their proteome and trying to establish their methods of pathogenesis. The virus is one of the notorious pathogens which have evolved ways of establishing itself within the host system. It manipulates the host defenses for its benefits. The prime condition for a viral infection is to succeed in entering the host system; viral particles must first be capable of making it through the innate barriers of the host plant cell either using a carrier or through cell receptors. This is followed by its replication within the specified host cell. Once replication occurs it is then transported to the neighboring cell through plasmodesmata to eventually make its way into the vascular tissue of phloem to infect the host systemically. The viral interactions modulate the host genome and proteome to establish an infection and influence the defense proteins to respond to the infection (Whitham et al. 2006; Mehta et al. 2008).

According to a study where the infection caused by the tobacco mosaic virus (TMV) on the hot pepper plant was analyzed. It was found that this cultivar was resistant against TMV‐P0 and susceptible to the TMV‐P1.2 strain. Upon proteome analysis using 2DE followed by MALDI‐TOF MS, it was found that certain proteins present in hot pepper provided defense against the 26S proteasome RPN7 subunit of TMV=P0. The defenses generated were to initiate Rab 11 GTPase responsible membrane trafficking, i.e. exo and endocytosis, RNA metabolism interference caused to mRNA binding protein, and activation of program cell death pathways (Lee et al. 2009).

The plant–pathogen interaction studies are still quite nascent yet plant fungus interactions have been explored the most through proteomic analysis. Fungal infections are the most prevalent in plant hosts. However, the proteomic study of the fungal proteins encoded by a well‐sequenced genome poses one of the greatest challenges. The fungal system regulates several host defenses to enhance its activity as inferred by proteome analysis (Murad et al. 2006, 2007). The rust disease is one of the leading causes of loss to cereals worldwide. One study was conducted on the wheat leaf rust fungus using proteomic tools to assess the disease progression at the molecular level. Susceptible wheat cultivars were exposed to the virulent strain of Puccinia triticina where 2DE and MS analysis were used to derive the result. Result analysis revealed 22 distinct proteins involved in pathogenesis with functions of some proteins known and the rest were unknown (Rampitsch et al. 2006; Webb and Feller 2006).

Proteomics has given a glimpse into the involvement of various proteins in plant bioprocesses, like stress response, defense responses, photosynthetic regulation, proteins involved in electron transport, and signal transduction. A study conducted by Houterman et al. (2007) assessed the proteome of tomato xylem sap infected with fungal strain Fusarium oxysporum. Thirty‐three proteins were relevant to the pathogenesis using 2DE and MS, out of which 13 proteins were found to be specific to infected plants consisting of enzymes chitinases, peroxidases, polygalacturonase, and a subtilisin‐like protease. These have been found to be involved in rendering protection to the cell structural integrity and the cell wall. An approach has been specifically assigned to study the proteome of the fungal pathogenic species known to secrete out some protein to facilitate pathogenesis. It is known as the secretome approach. A species of phytopathogenic fungus Sclerotinia sclerotiorum secretes the exoproteome. Several CWDE secreted were considered as virulent causative factors, which was derived from liquid culture and further subjected to 2DE and characterized by MALDI‐MS/MS (Yajima and Kav 2006). Some of the interactions of phytomicrobiome deciphered using proteomic approaches have been listed in Table 2.1.

Table 2.1 Proteomic approaches available for detection of plant and microbes along with some examples.

Various Types of Proteomics Approaches	List of Interactions Deciphered Using Various Proteomics Approaches
2 DE (two‐dimensional gel electrophoresis)	Bacillus amyloliquefaciens	Lolium perenne
DIGE (differential gel electrophoresis)	Pseudomonas sp.	Helianthus tuberosus
ITRAQ (Isobaric technique for relative and absolute quantification)	Rhizophagusirregularis	Gossypium (17 sp.)
ICAT (isotope‐coded affinity tag)	M. lychnis‐dioicae	Silene latifolia
Mud PIT (multidimensional protein identification technique)	Fusarium proliferatum	Solanum lycopersicum
SILAC (stable isotope labeling with the aid of amino acids in cell culture)	Gluconacetobacterdiazotrophicus	Saccharum officinarum
2DDIGE (2D fluorescence differential gel electrophoresis)	Fusarium oxysporum	Solanumlycopersicum
MALDI‐TOF (matrix‐assisted laser desorption/ionization‐time‐of‐flight) MS Spectra (tandem mass spectrometry)	Bradyrhizobium japonicum	Glycine max

Bacterial species depict a wide variation of the interaction pathways where pathogenicity is caused by manipulation and translocation of plant host cells. Depending upon the bacterial protein composition, the secretory pathways are classified into various types (Lee and Schneewind 2001). The first secretory pathway, i.e. type‐1 secretions are involved in secretion of phytotoxic substances such as rhizobiocin, hemolysins, etc., which are common to all phytopathogens. Though the majority of secretory pathways follow type 3 in which gram‐negative bacteria are responsible (Agrios 2004; Puhler et al. 2004). This pathway works on the principle where the effector protein is administered directly to the targeted host cell (Galan and Collmer 1999). The type‐2 system of secretion is another imperative pathway for bacterial pathogenicity. It is usually involved in the export of several virulent factors which are usually toxic. Miao and coworkers in their study in 2008 using various transcriptomic and proteomic approaches identified numerous genes and proteins involved in carbon and nitrogen metabolism, plant defense responses, nutrient exchange, and signal transduction that are significantly regulated in Glycine max colonized by Bradyrhizobium japonicum (Brechenmacher et al. 2010). Examples of a few interactions discussed in the chapter are listed in Table 2.2.