Suppression of Phytophthora Capsici Infection and Promotion of Tomato Growth by Soil Bacteria

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Suppression of Phytophthora capsici infection and promotion of tomato growth by soil bacteria

Sharifah Farhana Syed-Ab-Rahman, Yawen Xiao, Lilia C. Carvalhais, Brett J. Ferguson, Peer M. Schenk

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PII: S2452-2198(18)30139-3 DOI: https://doi.org/10.1016/j.rhisph.2018.11.007 Reference: RHISPH137 To appear in: Rhizosphere Received date: 28 October 2018 Revised date: 25 November 2018 Accepted date: 25 November 2018 Cite this article as: Sharifah Farhana Syed-Ab-Rahman, Yawen Xiao, Lilia C. Carvalhais, Brett J. Ferguson and Peer M. Schenk, Suppression of Phytophthora capsici infection and promotion of tomato growth by soil bacteria, Rhizosphere, https://doi.org/10.1016/j.rhisph.2018.11.007 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting galley proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. Suppression of Phytophthora capsici infection and promotion of tomato growth by soil bacteria

Sharifah Farhana Syed-Ab-Rahman1*, Yawen Xiao1, Lilia C. Carvalhais2, Brett J.

Ferguson3, Peer M. Schenk1

1Plant-Microbe Interactions Laboratory, School of Agriculture and Food Sciences, The

University of Queensland, Brisbane, Queensland 4072 Australia.

2Centre of Horticultural Science, Queensland Alliance for Agriculture and Food Innovation,

The University of Queensland, Ecosciences Precinct, GPO Box 267, Queensland 4001

Australia.

3Australian Research Council Centre of Excellence for Integrative Legume Research, The

University of Queensland, St. Lucia, Queensland 4072, Australia.

*Corresponding author: [email protected]

Abstract

Phytophthora capsici causes root, crown and fruit rot on many plant species including tomato and other solanaceous species. Plant growth promotion and suppression of P. capsici on tomato were assessed for three soil bacterial isolates, namely Bacillus amyloliquefaciens

(UQ154), Bacillus velezensis (UQ156) and Acinetobacter sp. (UQ202). Cultures were applied as seed treatments (pre and post-infection inoculation) plus a soil drench at transplanting. The bacterial isolates significantly promoted growth of seedlings, as measured by root length, total fresh weight, and seedling vigor. We observed a reduction in pathogen load in tomato roots in both treatments using quantitative Polymerase Chain Reaction (qPCR). This work

1 confirms the broad-spectrum activity of these bacterial isolates for our previous findings of biocontrol activity on different plants.

Keywords: Biocontrol; disease suppression; horticulture; Phytophthora capsici; tomato

Phytophthora species cause devastating diseases to crops worldwide and are responsible for major production losses (Roy, 2015). Phytophthora blight caused by P. capsici has caused considerable economic losses to vegetable crops, including tomato, and prevalence of the disease has increased dramatically in the last decade (Lamour et al., 2012, Quesada-Ocampo

& Hausbeck, 2010). The aim of this study was to evaluate the plant growth promotion and biocontrol activities of select soil bacteria against P. capsici in tomato.

Among the high biodiversity of microorganisms, plant growth-promoting rhizobacteria

(PGPR) play a crucial role in plant health and represent a potential alternative for a sustainable management of plant diseases suppression. Disease suppression in plants can occur through microbial antagonism or induction of resistance to pathogen infection (Van

Loon, 2007, Liu et al., 2018, Gómez-Lama Cabanás et al., 2014). In our experience in disease suppression of chilli plants infected with P. capsici, the bacterial antagonists investigated had different modes of action and their application in soil resulted in better disease control (Syed-Ab-Rahman et al., 2018). It has been shown that non-pathogenic plant-associated microorganisms generally protect the plant by rapid colonization and thus exhausting the limited available substrates so that none are available for pathogens to develop (Heydari & Pessarakli, 2010). In most cases, pathogens are antagonized by the presence and activities of other microorganisms that they encounter.

Bacterial isolates used in this study were originally obtained from bulk, and rhizosphere soil of Arabidopsis thaliana Col-0 plants grown in a potting mix and have previously been shown to have biocontrol activity in chilli (Capsicum annuum L., cultivar Cayenne) inoculated with

P. capsici, and promoted growth in lettuce (Syed-Ab-Rahman et al., 2018). The isolates were evaluated here for plant growth promotion in tomato (Solanum lycopersicum cultivar Red

Cherry). Seeds were surface-sterilised by washing with 70% (v/v) ethanol (5 min), followed by 5% bleach (sodium hypochlorite) (5 min), and then rinsed five times with distilled water.

Sterilised seeds were inoculated with the bacterial isolates by soaking for 1 h in phosphate

8 –1 buffer bacterial saline (PBS) suspensions containing cells at 1×10 CFU mL (OD600nm of

0.1). The isolates used were Bacillus amyloliquefaciens (UQ154), Bacillus velezensis

(UQ156) and Acinetobacter sp. (UQ202) (Syed-Ab-Rahman et al., 2018). Seeds inoculated with PBS only were used as negative control. Inoculated seeds were planted in 80 mm × 80 mm, 410 mL, pots with three replicates and five pots per treatment. Soil moisture was maintained by spraying distilled water uniformly onto the soil. Trays were incubated in a growth cabinet (short day, eight h light) at 26°C for 21 days.

We conducted pot assays to evaluate the ability of the rhizobacteria to suppress P. capsici infection in tomato. Two treatments were conducted: (i) bacterial inoculation prior to being challenged with the pathogen P. capsici (pre-infection inoculation) and (ii) bacterial inoculation after being challenged with the pathogen (post-infection inoculation). Seeds were inoculated with bacterial suspensions (OD600nm of 0.1) and re-inoculation was conducted (i) before and (ii) after pathogen challenge by soil drenching. Pathogen inoculation was performed by adding P. capsici zoospores solution in the tray at the bottom of the pots.

Zoospores were prepared by placing P. capsici discs (5 mm diameter) of 6-day-old cultures grown on clarified V8 (cV8) agar into a petri dish containing a mixture of sterile distilled water and soil and incubated for three days under constant fluorescent light (40-W) to promote zoospores production (105 swimming zoospores mL−1 under haemocytometer at a

×100 magnification). The trays were filled with distilled water to maintain water-saturated conditions. Plants were harvested two weeks after bacterial/pathogen inoculation (four-week-

3 old) and the disease suppression ability of the bacterial isolates was assessed by real-time quantitative PCR (qPCR) analysis. DNA extraction of the washed root samples without attached soil and P. capsici primers used in this study were performed as we previously described (Syed-Ab-Rahman et al., 2018) and Act (Accession number: BT013707.1) was used as a plant reference gene which was amplified using the primers Act_F (5′-

AGGCAGGATTTGCTGGTGATGATGCT-3) and Act_R (5′-

ATACGCATCCTTCTGTCCCATTCCGA-3′). The relative P. capsici DNA biomass was normalized to Actin using the formula: 2^-(ΔCt P. capsici – ΔCt Actin).

All bacterial isolates significantly increased the length of shoots (Figure 1A) and roots

(Figure 1B), as well as the total fresh weight (Figure 1C) of the tomato plants. Increments of

10.9% in shoot and 45.8% in root lengths were obtained with B. amyloliquefaciens (UQ154)

(Figure 1A) and B. velezensis (UQ156) inoculations, respectively. Only B. amyloliquefaciens

(UQ154) led to a significantly higher total fresh weight compared with the uninoculated control (45.8%) (Figure 1C). Furthermore, all isolates were found to be effective in increasing seed germination rates and seedling vigour, with B. amyloliquefaciens (UQ154) exhibiting the highest effect on seedling vigour (Figure 1D). In general, plants respond differently to bacterial inoculation, often depending on the growth conditions (Asari et al.,

2016). Our results also revealed that plants inoculated with the bacterial isolates harboured a lower pathogen load in roots. Interestingly, plants treated with bacterial isolates after challenge with P. capsici (post-treatment) (Figure 2B) exhibited significantly lower pathogen loads in roots compared to plants treated with bacterial isolates before pathogen challenge

(pre-treatment) (Figure 2A). This suggests that sufficient number of bacteria need to be exposed to the pathogen to either produce bioactive compounds or elicit a response in plant for effective pathogen control.

The pathogen biomass in roots treated with the bacterial isolates were significantly lower than the untreated P. capsici-infected plants. Inoculation with P. capsici in the absence of bacterial treatments caused necrosis and brownish lesions throughout the primary root system in both treatments. However, upon inoculation of plants with bacterial isolates, necrosis and brown lesions were less frequent. All the isolates showed a similar reduction of disease severity on chili pepper plants (Table 1).

Our results suggest that the bacterial isolates investigated here enhance plant growth, which can potentially result in higher crop yields. These isolates have previously found to fix nitrogen, solubilize phosphate, siderophore, indoleacetic acid, cell wall degrading enzymes, biofilm and diketopiperazines (DKP) production which could be correlated to the biocontrol activity observed in this study (Syed-Ab-Rahman et al., 2018). Plant growth responses are variable and dependent on the bacterial isolate, inoculum concentration, plant developmental stage, and the growth parameters evaluated (Cakmakçi et al., 2006, Velázquez-Becerra et al.,

2011). Plant protection as conferred by the bacteria used in this study could result from an induction of systemic resistance. This would agree with findings of Wei (1991) who reported that cucumber treated with PGPR strains suppressed anthracnose caused by Collectotrichum orbiculare (Wei et al., 1991). Moreover, bacterial isolates can promote plant growth and enhance biological control over multiple plant diseases through direct antagonisms (Liu et al.,

2017).

Our results and those of our previous studies suggest that inoculation of these broad-spectrum biocontrol activity bacterial isolates may suppress P. capsici-associated diseases and could potentially be applied in multiple horticultural crops. Further investigations aimed at establishing whether bacterial inoculations trigger ISR, act directly by antagonising the

5 pathogen, or provide a combined effect of both, will be of interest to establish the mechanistic nature of the interaction.

Acknowledgements

This research was financially supported by the Australian Research Council (DP1094749,

DP140103363) and International Postgraduate Research Scholarships (IPRS) by The

University of Queensland (to SFSAR). We thank Professor André Drenth for providing P. capsici culture used in this experiment.

References

Abdul-Baki AA, Anderson JD, 1973. Vigor determination in soybean seed by multiple criteria 1. Crop science 13, 630-3. Asari S, Matzén S, Petersen MA, Bejai S, Meijer J, 2016. Multiple effects of Bacillus amyloliquefaciens volatile compounds: plant growth promotion and growth inhibition of phytopathogens. FEMS microbiology ecology 92. Cakmakçi R, Dönmez F, Aydın A, Şahin F, 2006. Growth promotion of plants by plant growth-promoting rhizobacteria under greenhouse and two different field soil conditions. Soil Biology and Biochemistry 38, 1482-7. Gómez-Lama Cabanás C, Schilirò E, Valverde-Corredor A, Mercado-Blanco J, 2014. The biocontrol endophytic bacterium Pseudomonas fluorescens PICF7 induces systemic defense responses in aerial tissues upon colonization of olive roots. Frontiers in microbiology 5, 427. Heydari A, Pessarakli M, 2010. A review on biological control of fungal plant pathogens using microbial antagonists. Journal of Biological Sciences 10, 273-90. Lamour KH, Stam R, Jupe J, Huitema E, 2012. The oomycete broad‐host‐range pathogen Phytophthora capsici. Molecular plant pathology 13, 329-37. Liu K, Mcinroy JA, Hu C-H, Kloepper JW, 2018. Mixtures of Plant-Growth-Promoting Rhizobacteria Enhance Biological Control of Multiple Plant Diseases and Plant-Growth Promotion in the Presence of Pathogens. Plant Disease 102, 67-72. Liu K, Newman M, Mcinroy JA, Hu C-H, Kloepper JW, 2017. Selection and assessment of plant growth-promoting rhizobacteria for biological control of multiple plant diseases. Phytopathology 107, 928-36. Quesada-Ocampo L, Hausbeck M, 2010. Resistance in tomato and wild relatives to crown and root rot caused by Phytophthora capsici. Phytopathology 100, 619-27. Roy SG, 2015. Phytophthora: a member of the sixth kingdom revisited as a threat to food security in the twenty-first century. In. Value Addition of Horticultural Crops: Recent Trends and Future Directions. Springer, 325-37. Syed-Ab-Rahman SF, Carvalhais LC, Schenk P, 2018. Identification of soil bacterial isolates suppressing different Phytophthora spp. and promoting plant growth. Frontiers in Plant Science 9, 1502. Van Loon L, 2007. Plant responses to plant growth-promoting rhizobacteria. In. New Perspectives and Approaches in Plant Growth-Promoting Rhizobacteria Research. Springer, 243-54.

Velázquez-Becerra C, Macías-Rodríguez LI, López-Bucio J, Altamirano-Hernández J, Flores-Cortez I, Valencia-Cantero E, 2011. A volatile organic compound analysis from Arthrobacter agilis identifies dimethylhexadecylamine, an amino-containing lipid modulating bacterial growth and Medicago sativa morphogenesis in vitro. Plant and soil 339, 329-40. Wei G, Kloepper JW, Tuzun S, 1991. Induction of systemic resistance of cucumber to Colletotrichum orbiculare by select strains of plant growth-promoting rhizobacteria. Phytopathology 81, 1508-12.

Figures

A B Shoot length Root length 19.5 25 19 * *

18.5 20 * * 18 17.5 * * 15 17

16.5 10 16 15.5

Seedling Seedling shoot length(cm) 5

15 Seedling root length(cm) 14.5 0 UQ154 UQ156 UQ202 Mock UQ154 UQ156 UQ202 Mock Treatment Treatment C D Fresh weight Vigour index 350 3600 *

* 3550

300 3500 250 3450 * * 200 3400

150 3350 3300 100 Seedling vigour index Total fresh Totalfresh weight (mg) 3250 50 3200 0 3150 UQ154 UQ156 UQ202 Mock UQ154 UQ156 UQ202 Mock Treatment Treatment

Figure 1: Effect of bacterial inoculation on tomato after inoculation with PGPR isolates of

21-day-old seedlings. Plant vigour index was calculated as described by Abdul-Baki and

Anderson (1973). Each treatment consisted of five pots with three replicates in a randomized block design. Results were analysed by analysis of variance (ANOVA) using JMP software

(SAS Institute, Cary, NC). For each panel, asterisks (*) indicate (mean ± SE) statistically significant differences compared to the mock (Tukey Kramer’s HSD P < 0.05, n = 15)

A Pre-infection inoculation B Post-infection inoculation

0.9

0.8 1

0.7 0.8

0.6 biomass biomass (pg) biomass biomass (pg) * 0.5 0.6 *

0.4 * * P. P. capsici P. P. capsici 0.4 0.3

0.2

Relative Relative Relative Relative 0.1 * * 0 0 UQ154 UQ156 UQ202 P. capsici Mock UQ154 UQ156 UQ202 P. capsici Mock Treatment Treatment

Figure 2: Quantification of P. capsici DNA in tomato roots via qPCR, (A) bacterial inoculation was done before P. capsici infection (pre-infection inoculation) and (B) bacterial inoculation was done after P. capsici infection (post-infection inoculation). Results were analysed by analysis of variance (ANOVA) using JMP software (SAS Institute, Cary, NC).

Each treatment consisted of five pots with three replicates in a randomized block design.

Asterisks (*) indicate statistically significant differences compared to the P. capsici-infected control (Tukey Kramer’s HSD P < 0.05, n = 15)

Table

Table 1: Disease severity index of tomato pre- and post-infection inoculation

Treatment Disease severity Pre-treatment infection Post-treatment infection UQ154 1.6 ± 0.4 1.1 ± 0.2 UQ156 2.1 ± 0.2 1.7 ± 0.6 UQ202 1.4 ±0.4 1.2 ±0.1 P. capsici 3.8 ± 0.5 3.7 ±0.4 Mock 0 0

Disease severity was monitored by visually estimating the proportion of a root area occupied by brown lesions and were assessed using a scale of 0 –5: 0 = no visible disease symptoms and normal appearing plant; 1– 4 = plants with increasing levels of roots with increasing levels of root lesion and necrosis; 5 = plants with severe lesions. Mean disease severity for a plant was calculated as the mean of disease severity values of roots of that plant. Results were analysed by analysis of variance (ANOVA) followed by Tukey’s HSD Test using JMP software (SAS Institute, Cary, NC).