Rhizosphere bacterial interactions and impact on plant health

Rhizosphere -plant root-soil interface, is home to diverse microorganisms such as bacteria, archaea, fungi, nematodes, protozoa, invertebrates, and other organisms that interact with each other .The plant rhizosphere is a dynamic environment in which many parameters may influence the population structure, diversity and activity of the microbial community. 

1. Welcome 10-03-2025 Dept. of Plant Pathology 1

2. Rhizosphere bacterial interactions and impact on plant health UNIVERSITY OF AGRICULTURAL SCIENCES, BANGALORE College of Agriculture V.C Farm, Mandya SHWETHA G S PAMM1028 Dept. of Plant Pathology Seminar - 2 10-03-2025 Dept. of Plant Pathology 2

3. FLOW OF SEMINAR 10-03-2025 Dept. of Plant Pathology 3

4. Holobiont Pathobiome 10-03-2025 Dept. of Plant Pathology 4

5. Rhizosphere -plant root-soil interface, is home to diverse microorganisms such as bacteria, archaea, fungi, nematodes, protozoa, invertebrates, and other organisms that interact with each other Rhizosphere The plant rhizosphere is a dynamic environment in which many parameters may influence the population structure, diversity and activity of the microbial community.  10-03-2025 Dept. of Plant Pathology 5

6. Pseudomonas Rhizobium Bacillus Azospirillium Actinobacteria Enterobacter Firmicutes Cyanobacteria Rhizosphere bacteria Common and major rhizobacteria 10-03-2025 Dept. of Plant Pathology 6

7. Root exduates Nutrients availability Environmental factors Plant-microbe interactions Plant species Soil type Agricultural practices Factors affecting rhizobacteria in rhizosphere 10-03-2025 Dept. of Plant Pathology 7

8. Negative interactions Positive interactions Neutral interactions Interactions 10-03-2025 Dept. of Plant Pathology 8

9. Positive effect of Rhizosphere bacteria on Plants 10-03-2025 Dept. of Plant Pathology 9

10. Objectives : The aim to develop an effective indigenous PGPR consortium to enhance the growth, yield and nutrient acquisition in wheat crop under greenhouse and field conditions 10-03-2025 Dept. of Plant Pathology 10 Ashok et al. (2021)

11. Plant growth promoting properties of isolated bacterial strains under in vitro conditions 10-03-2025 Dept. of Plant Pathology 11 Ashok et al. (2021) Ashby broth medium- Kjeldahl method Pikovskaya’s broth- Molybdenum blue method

12. Effect of PGPR strains on growth, yield and test weight of wheat under pot and field 10-03-2025 Dept. of Plant Pathology 12 Ashok et al. (2021)

13. Negative effect of Rhizosphere bacteria on Plants M icroorganisms compete with the plants for water, nutrient, and space. It act as plant pathogens, resulting plant diseases. Competition between the microorganisms community in result in the loss of beneficial microorganisms. 10-03-2025 Dept. of Plant Pathology 13

14. Undisputed guardians 10-03-2025 Dept. of Plant Pathology 14

15. How the plant influences or recruits beneficial bacteria in the rhizosphere How the interactions between bacteria influence rhizosphere microbial structure and in turn, how this impacts plant health. 10-03-2025 Dept. of Plant Pathology 15

16. Plant and rhizosphere bacteria 10-03-2025 Dept. of Plant Pathology 16

17. Plant Growth Promoting Rhizobacteria (PGPR) Bacteria function as biofertilizers, biocontrol agents and nutrient cycler Group of bacteria that actively colonize plant roots and enhance plant growth and yield via various plant growth promoting substances Pseudomonas,  Azospirillum , Mycobacterium, Azotobacter, Bacillus, Burkholderia , Enterobacter, Rhizobium, Mesorhizobium , Flavobacterium , etc. 10-03-2025 Dept. of Plant Pathology 17

18. Beneficial rhizosphere bacteria can benefit the plant directly or indirectly by Assisting plants to acquire nutrients from the soil. 2)Suppression of plant pathogens. 3)Enhancing plant immunity through induced systemic resistance (ISR). 10-03-2025 Dept. of Plant Pathology 18

19. 1. Assisting plants to acquire nutrients Example 1. Rhizosphere-facilitated nutrient uptake is iron by coumarins 2. Terpenes and benzoxazinoids play a pivotal role increasing beneficial soil microbes. 3. Nitrogen fixation. 4. Phosphate solubilization. Fe Fe The plant host plays an important role in recruiting or attracting beneficial bacteria through secreted root exudates 10-03-2025 Dept. of Plant Pathology 19

20. Modulation of plant hormones Chemical messengers playing key role in plant physiology and development. Rhizosphere microbes produce phytohormones which modulate plant response, promote plant growth and development Auxin - IAA, Cytokinins . 10-03-2025 Dept. of Plant Pathology 20 Mitigate the deleterious effect of biotic and abiotic stress

21. Objectives Isolate and characterize auxin-producing bacteria showing a high plant growth-promoting (PGP) potential. Evaluate the PGPR effects on the growth of Medicago sativa L under salinity stress (130 mM NaCl) 10-03-2025 Dept. of Plant Pathology 21 Zhu et al. (2020)

22. Auxin production of the isolates and effect of different concentrations of NaCl on the growth of bacteria 10-03-2025 Dept. of Plant Pathology 22 Zhu et al. (2020) liquid LB medium-indole acetic acid (IAA) standard curve

23. Evaluation of different plant growth promoting parameters to show the effect of three strains inoculation on seedlings under non-saline and saline conditions. 10-03-2025 Dept. of Plant Pathology 23 Zhu et al. (2020)

24. Plant growth-promoting characteristics of isolate strains 10-03-2025 Dept. of Plant Pathology 24 Zhu et al. (2020) Peptone water culture medium- Spectrophotometer Pikovskaya’s broth- Molybdenum blue method Aleksandrov medium- flame photometer Universal Chrome Azurol -S (CAS) colorimetric assay

25. Suppression of plant pathogens Example: Rhizosphere bacteria suppress the bacterial pathogen, Ralstonia solanacearum, by siderophore-mediated competition for iron. Production of antimicrobial compounds or by competing with pathogens within an ecological niche. Production of siderophores Siderophores are iron chelating compounds that have the potential to provide iron for plant use. 10-03-2025 Dept. of Plant Pathology 25 Disruptions of ISR eliciting Firmicutes and Actinobacteria in tomato plant rhizosphere increased incidences of bacterial wilt.

26. Antibiosis Antibiotics are secondary metabolites produced by PGPB in response to plant exudates, low nutrient or pathogen attack Ex : 2, 4- Diacetylphloroglucinol (DAPG), from Pseudomonads, DAPG acts on Pythium sp. by damaging their membranes and preventing zoospore formation 10-03-2025 Dept. of Plant Pathology 26 Pal and Gardener (2006)

27. Lytic enzyme production Lytic or cell-wall degrading enzymes destroy the integrity and stability of pathogen cell walls, preventing the development of the pathogens. 10-03-2025 Dept. of Plant Pathology 27 Lipases, phosphatases, proteases, glucanase , and chitinases against Sclerotium rolfsii , Botrytis cinerea, Fusarium oxysporum , Pythium ultimum , Phytophthora sp . and Rhizoctonia solani Olanrewaju and Babola (2019)

28. Wheat plants inoculated with Rhizoctonia solani anastomosis group 8 (AG8) were - Chitinophaga , Pseudomonas, Chryseobacterium , and Flavobacterium , and nitrogen-fixing microbes that act in consortium to antagonize soil-borne pathogens . 10-03-2025 Dept. of Plant Pathology 28

29. Enhancing plant immunity through induced systemic resistance (ISR) Pathogen attack, the plant cell receptors perceive a stressor issuing a ‘cry for help’ 10-03-2025 Dept. of Plant Pathology 29 Ex: Pseudomonas Fluorescens in Arabidopsis. Zhou and Zhang (2018)

30. Example: Effectors of Type III secretion system ( R. solanacearum ) Pathogens encode large amounts of secreted effector proteins, functions of many effectors in terms of host plant manipulation remain unknown. Potential modulator of microbiome compositions. Effectors as exquisite tools for interaction 10-03-2025 Dept. of Plant Pathology 30 Wu et al ., (2019)

31. Plant plays an important role in rhizosphere bacteria selection to enhance beneficial microbes which promote plant health ,other microbes can change the host cell and use it to reconfigure plant microbiota 10-03-2025 Dept. of Plant Pathology 31

32. Bacteria competition influences rhizosphere microbiota 10-03-2025 Dept. of Plant Pathology 32

33. Competition mechanisms play a fundamental role in shaping rhizosphere microbial composition, subsequently influencing the host plant Engineering strategies - improvement of plant health Exploitative competition - compete for scarce resources and the winner limits nutrient availability from competitors Interference competition mediated by production of antibacterial compounds or lethal effector proteins, function between physically separated bacteria 10-03-2025 Dept. of Plant Pathology 33

34. Overcome iron depletion, bacteria produce siderophores which locks iron away from competitors that do not have matching receptors. Exploitative competition- ‘An offensive operation’ High demand of the same nutrients by members of a microbial community. One indirectly outcompetes its rivals by utilizing limiting nutrients like carbon, phosphorus, iron, and nitrogen, which are essential for bacterial growth. Xanthomonas oryzae pv . oryzicola can improve iron uptake through gene editing in a ferric siderophore receptor. Fe 10-03-2025 Dept. of Plant Pathology 34 Friman et al. (2020)

35. Cooperation is an ‘expensive affair’ due to exploitation by ‘cheaters’ ,with time the ‘cheaters’ outcompete producers in the population. Siderophore nonproducers have shown to evolve receptors that match the modified siderophores via Horizontal gene transfer Ex : Pseudomonas sp. isolates from soil and freshwater habitats. 10-03-2025 Dept. of Plant Pathology 35

36. Lack of understanding of how sharing of public goods between plant- associated bacteria influences microbial community and improves plant health. Bacteria compete to colonize a niche/enhance access to a given space through the formation of a biofilm Biofilm-forming bacteria can survive under environmental stresses. Biofilms formed by some bacteria produce volatile compounds Competing for space 10-03-2025 Dept. of Plant Pathology 36

37. Example: Maize recruits bacteria with fewer beneficial properties than those with many. Bacterium with fewer beneficial functions in a consortium is more productive for those given functions. Cooperation in microbial communities can be harnessed for development of better consortia of plant-beneficial microbes 10-03-2025 Dept. of Plant Pathology 37

38. Interference competition 10-03-2025 Dept. of Plant Pathology 38

39. Shoot to kill or disable: Interference competition Plant rhizosphere is highly populated with plant pathogenic, beneficial, and commensal bacteria. To tackle intra- and interspecific competition. Production of Antibiotics Bacteriolytic enzymes Bacteriocins 10-03-2025 Dept. of Plant Pathology 39 Hass and Delago (2005)

40. Antibiotics producing bacteria such as Bacillus subtilis can discriminate self from nonself when self-produced antibiotics are involved in self-recognition Antibiotic production enhanced Competing against phylogenetically distant species The rival cells are sensitive to a specific class of antibiotics. Antibiotics are broad-spectrum metabolites produced by multienzyme complexes. 10-03-2025 Dept. of Plant Pathology 40 Lyons et al . (2017)

41. Bacteriocins Bacteriocins are ribosomally synthesized narrow spectrum proteinous substances, capable of killing closely related rival bacteria. Production favored - UV irradiation, nutrient limitation, and production of antimicrobial compounds by other bacteria. 10-03-2025 Dept. of Plant Pathology 41 Plantibiotics Mezaache et al. (2016)

42. Mode of activity Pore formation in the cell membrane D egradation of cellular DNA. Cleavage of r RNA 16S or t -RNA. Inhibition of peptidoglycan synthesis resulting in cell death. Different types of bacteriocins in rhizobacteria R-, F-, S-, and M-type pyocins 10-03-2025 Dept. of Plant Pathology 42 Mojgani (2017)

43. Type-six secretion systems Double-tubular nanomachine found in Gram-negative bacteria capable of penetrating neighboring cells to deliver effectors. Corpse barrier T6SS effectors function as peptidoglycan hydrolases, phospholipases, RNases, and DNases, other functions Short range between the attacking and target cells. Dead cells accumulate to form ‘corpse barriers’ T6SS to deliver lytic toxins that not only kill but also disintegrate target cells . 10-03-2025 Dept. of Plant Pathology 43 Smith et al. (2020)

44. Key player in interkingdom interactions and critical determinant of interbacterial competition. Type-six secretion systems Impact plant health Targeting and undermining plant immunity (anti eukaryotic) Conferring competitive advantage to the producer. Ex: Pseudomonas chlororaphis T6SS bacteria attenuate host immunity 10-03-2025 Dept. of Plant Pathology 44

45. T6SS do not need to be delivered into rival cells to execute killings. 1. Iron-deficient conditions- secrete LPS binding effector to recruit OMVs to confer competitive advantage over rival cells. 2. Anaerobic conditions in P. Aeruginosa for molybdate acquisition. 10-03-2025 Dept. of Plant Pathology 45 Li et al. (2022)

46. Factors regulating in T6SS 10-03-2025 Dept. of Plant Pathology 46 Han et al. (2022)

47. Deployment of resistant gene 10-03-2025 Dept. of Plant Pathology 47

48. Future perspectives: Implication of plant–microbe–microbe virulence mechanisms in disease control 10-03-2025 Dept. of Plant Pathology 48

49. Biological control- microbial communities, single strains, or microbial secondary metabolites offers a sustainable alternative approach to disease control in agriculture. For biological control of plant root pathogens need to understand molecular mechanisms that mediate host–microbe–microbe interactions within the rhizosphere. Advances that allow integration of microbiomics and quantitative plant genetics show promise toward a new generation of microbiome-assisted breeding programs and crops . 10-03-2025 Dept. of Plant Pathology 49

50. Synthetically designed concoctions of beneficial microbes ( SynComs ) Commercial products - consistency of the outcomes needs to be tested and further validated across multiple field trials in regions where aimed to be used. To develop biocontrol products - versatility, combining compatible beneficial microorganisms with complementary effects on different targets Complexity of microbial interactions which better mimic host–microbe–microbe interactions . 10-03-2025 Dept. of Plant Pathology 50 Vorholt et al. (2017)

51. Objectives To evaluate bacteria isolated from the Wheat rhizosphere protect a susceptible wheat cultivar against Rhizoctoni solani AG8 To test if the created Syncoms enhance disease protection 10-03-2025 Dept. of Plant Pathology 51 Yin et al. (2022)

52. 10-03-2025 Dept. of Plant Pathology 52 Yin et al. (2022) TSA medium

53. Inhibition by SynComs on the radial growth of R. Solani in dual culture assays 10-03-2025 Dept. of Plant Pathology 53 Yin et al. (2022) PDA medium

54. Effect of bacteria on wheat root rot on single bacterial and SynComs 10-03-2025 Dept. of Plant Pathology 54 Yin et al. (2022)

55. Effects of bacterial volatiles on the growth of  R. solani  AG8 (inhibition of radial growth of AG8)  10-03-2025 Dept. of Plant Pathology 55 Zhu et al. (2020)

56. Bacteriocin 10-03-2025 Dept. of Plant Pathology 56

57. Ability to outcompete and inhibit plant pathogens Controlling plant pathogens is by disruption of QS systems that regulate T6SS. T6SS Understanding of the molecular mechanisms and regulation of the T6SS should ultimately allow for its application in biocontrol of plant pathogens. Limited competition approaches that use only two bacterial strains per experiment. Modeling studies coupled with experimental studies need to be conducted. 10-03-2025 Dept. of Plant Pathology 57

58. T6SS and OMVs systems are relatively newly discovered, there is still much we do not understand. OMVS could be used to target distant cells T6SS kill in a contact-dependent manner. 10-03-2025 Dept. of Plant Pathology 58

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