Characterization of Streptomyces spp. isolated from the rhizosphere of oil palm and evaluation of their ability to suppress basal stem rot disease in oil palm seedlings when applied as powder formulations in a glasshouse trial

Streptomyces albidoflavus Strain CARA17 as a Biocontrol Agent against Fungal Soil-Borne Pathogens of Fennel Plants

Fennel crop is a horticultural plant susceptible to several soil-borne fungal pathogens responsible for yield losses. The control of fungal diseases occurring on fennel crops is very difficult with conventional and/or integrated means; although several chemical fungicides are able to contain specific fungal diseases, they are not registered for fennel crops. The intensive use of some fungicides causes public concern over the environment and human health. The main aims of this study were to assess the ability of a strain of Streptomyces albidoflavus CARA17 to inhibit the growth of fungal soil-borne pathogens, and to protect fennel plants against severe fungal soil-borne pathogens such as Athelia rolfsii, Fusarium oxysporum, Plectosphaerella ramiseptata, Sclerotinia sclerotiorum and Verticillium dahliae. This study confirmed that the CARA17 strain has been able to inhibit the mycelium growth of pathogens in vitro conditions with significant inhibition degrees, where S. sclerotiorum resulted in being the most controlled. The strain CARA17 was also able to significantly protect the fennel seedlings against fungal soil-borne pathogens used in vivo conditions, where the treatment with an antagonist strain by dipping resulted in being more effective at limiting the disease severity of each fungal soil-borne pathogen. Moreover, any treatment with the CARA17 strain, carried out by dipping or after transplanting, produced benefits for the biomass of fennel seedlings, showing significant effects as a promoter of plant growth. Finally, the results obtained showed that CARA17 is a valid strain as a biocontrol agent (BCA) against relevant fungal soil-borne pathogens, although further studies are recommended to confirm these preliminary results. Finally, this study allowed for first time worldwide the association of Plectosphaerella ramiseptata with fennel plants as a severe pathogen.

Diversity and Ecological Guild Analysis of the Oil Palm Fungal Microbiome Across Root, Rhizosphere, and Soil Compartments

The rhizosphere microbiome is a major determinant of plant health, which can interact with the host directly and indirectly to promote or suppress productivity. Oil palm is one of the world’s most important crops, constituting over a third of global vegetable oil production. Currently there is little understanding of the oil palm microbiome and its contribution to plant health and productivity, with existing knowledge based almost entirely on culture dependent studies. We investigated the diversity and composition of the oil palm fungal microbiome in the bulk soil, rhizosphere soil, and roots of 2-, 18-, and 35-year old plantations in Selangor, Malaysia. The fungal community showed substantial variation between the plantations, accounting for 19.7% of community composition, with compartment (root, rhizosphere soil, and bulk soil), and soil properties (pH, C, N, and P) contributing 6.5 and 7.2% of community variation, respectively. Rhizosphere soil and roots supported distinct communities compared to the bulk soil, with significant enrichment of Agaricomycetes, Glomeromycetes, and Lecanoromycetes in roots. Several putative plant pathogens were abundant in roots in all the plantations, including taxa related to Prospodicola mexicana and Pleurostoma sp. The mycorrhizal status and dependency of oil palm has yet to be established, and using 18S rRNA primers we found considerable between-site variation in Glomeromycotinian community composition, accounting for 31.2% of variation. There was evidence for the selection of Glomeromycotinian communities in oil palm roots in the older plantations but compartment had a weak effect on community composition, accounting for 3.9% of variation, while soil variables accounted for 9% of community variation. While diverse Mucoromycotinian fungi were detected, they showed very low abundance and diversity within roots compared to bulk soil, and were not closely related to taxa which have been linked to fine root endophyte mycorrhizal morphology. Many of the fungal sequences showed low similarity to established genera, indicating the presence of substantial novel diversity with significance for plant health within the oil palm microbiome.

Review Update on the Life Cycle, Plant–Microbe Interaction, Genomics, Detection and Control Strategies of the Oil Palm Pathogen Ganoderma boninense

Plant pathogens are key threats to agriculture and global food security, causing various crop diseases that lead to massive economic losses. Palm oil is a commodity export of economic importance in Southeast Asia, especially in Malaysia and Indonesia. However, the sustainability of oil palm plantations and production is threatened by basal stem rot (BSR), a devastating disease predominantly caused by the fungus Ganoderma boninense Pat. In Malaysia, infected trees have been reported in nearly 60% of plantation areas, and economic losses are estimated to reach up to ~USD500 million a year. This review covers the current knowledge of the mechanisms utilized by G. boninense during infection and the methods used in the disease management to reduce BSR, including cultural practices, chemical treatments and antagonistic microorganism manipulations. Newer developments arising from multi-omics technologies such as whole-genome sequencing (WGS) and RNA sequencing (RNA-Seq) are also reviewed. Future directions are proposed to increase the understanding of G. boninense invasion mechanisms against oil palm. It is hoped that this review can contribute towards an improved disease management and a sustainable oil palm production in this region.

Antifungal Peptides from a Burkholderia Strain Suppress Basal Stem Rot Disease of Oil Palm

Basal stem rot (BSR) is the most common disease of oil palm (Elaeis guineensis) in Southeast Asia. BSR is caused by a white-rot fungus Ganoderma boninense. The disease is difficult to manage. Therefore, development of novel and environmentally safe approaches to control the disease is important. Species of Burkholderia are known to have diverse lifestyles, some of which can benefit plants by suppressing diseases or increasing plant growth. In the present study, antifungal peptides produced by a bacterial strain isolated from the rhizosphere of an oil palm tree, Burkholderia sp. strain CP01, exhibited strong growth inhibition on G. boninense. A loss-of-function mutant of CP01 was generated, and it has enabled the identification of a 1.2-kDa peptide and its variants as the active antifungal compounds. High-resolution mass spectrometry revealed six analogous compounds with monoisotopic masses similar to the previously reported cyclic lipopeptides occidiofungin and burkholdine. The antifungal compounds of CP01 were secreted into media, and we sought to use CP01 culture extract without living cells to control BSR disease. Glasshouse experiments showed that CP01 culture extract suppressed BSR disease in oil palm seedlings. The ability of CP01 to produce an antifungal substance and suppress plant disease suggests its potential applications as a biofungicide in agriculture.

Utilization of palm oil mill effluent as a novel substrate for the production of antifungal compounds by Streptomyces philanthi RM-1-138 and evaluation of its efficacy in suppression of three strains of oil palm pathogen

AIMS

This study aimed to use palm oil mill effluent (POME) as a renewable resource for the production of antifungal compounds by Streptomyces philanthi RM-1-138 against Ganoderma boninense, Ceratocystis paradoxa and Curvularia oryzae.

METHODS AND RESULTS

The efficacy of antifungal compounds RM-1-138 against the three strains of fungal oil palm pathogen was evaluated both in vitro and on oil palm leaf segments. In vitro studies using confrontation tests on glucose yeast-malt extract (GYM) agar plates indicated that the strain RM-1-138 inhibited the growth of all three fungal pathogenic strains. The antifungal compounds produced in the GYM medium exhibited significantly higher inhibition (79%-100%) against the three fungal pathogens than using the diluted POME (50%) medium (80%-83% inhibition). The optimum condition for the production of antifungal compounds from the strain RM-1-138 was as following: POME of 47,966 mg L^-1 chemical oxygen demand (COD), the initial pH at 7.0 and supplemented with yeast extract (0.4%). Meanwhile, severe morphological and internal abnormalities in C. oryzae hyphae were observed under a scanning electron microscope and transmission electron microscope. In vivo experiment on oil palm leaf segments indicated that the efficacy of the antifungal compounds RM-1-138 (DSI = 1.3) were not significantly difference in the suppression of Curvularia leaf spot compared with the two commercial chemical fungicides of mancozeb^® (DSI = 1.0) and tetraconazole^® (DSI = 1.3).

CONCLUSIONS

Antifungal compounds produced by S. philanthi RM-1-138 grown in POME have the potential to inhibit fungal pathogens.

SIGNIFICANCE AND IMPACT OF THE STUDY

The POME (about 47 mg L^-1 COD) with the initial pH of 7.0 and supplementation of 0.4% nitrogen could be used as a culture medium for the growth and production of antifungal compounds of S. philanthi RL-1-138. In addition, the antifungal compound RM-1-138 could suppress the three strains of oil palm fungal pathogen tested on oil palm leaf segment.

Soil, senescence and exudate utilisation: characterisation of the Paragon var. spring bread wheat root microbiome

BACKGROUND

Conventional methods of agricultural pest control and crop fertilisation are unsustainable. To meet growing demand, we must find ecologically responsible means to control disease and promote crop yields. The root-associated microbiome can aid plants with disease suppression, abiotic stress relief, and nutrient bioavailability. The aim of the present work was to profile the community of bacteria, fungi, and archaea associated with the wheat rhizosphere and root endosphere in different conditions. We also aimed to use 13CO2 stable isotope probing (SIP) to identify microbes within the root compartments that were capable of utilising host-derived carbon.

RESULTS

Metabarcoding revealed that community composition shifted significantly for bacteria, fungi, and archaea across compartments. This shift was most pronounced for bacteria and fungi, while we observed weaker selection on the ammonia oxidising archaea-dominated archaeal community. Across multiple soil types we found that soil inoculum was a significant driver of endosphere community composition, however, several bacterial families were identified as core enriched taxa in all soil conditions. The most abundant of these were Streptomycetaceae and Burkholderiaceae. Moreover, as the plants senesce, both families were reduced in abundance, indicating that input from the living plant was required to maintain their abundance in the endosphere. Stable isotope probing showed that bacterial taxa within the Burkholderiaceae family, among other core enriched taxa such as Pseudomonadaceae, were able to use root exudates, but Streptomycetaceae were not.

CONCLUSIONS

The consistent enrichment of Streptomycetaceae and Burkholderiaceae within the endosphere, and their reduced abundance after developmental senescence, indicated a significant role for these families within the wheat root microbiome. While Streptomycetaceae did not utilise root exudates in the rhizosphere, we provide evidence that Pseudomonadaceae and Burkholderiaceae family taxa are recruited to the wheat root community via root exudates. This deeper understanding crop microbiome formation will enable researchers to characterise these interactions further, and possibly contribute to ecologically responsible methods for yield improvement and biocontrol in the future.

New Antimicrobial Phenyl Alkenoic Acids Isolated from an Oil Palm Rhizosphere-Associated Actinomycete, Streptomyces palmae CMU-AB204T

Basal stem rot (BSR), or Ganoderma rot disease, is the most serious disease associated with the oil palm plant of Southeast Asian countries. A basidiomycetous fungus, Ganoderma boninense, is the causative microbe of this disease. To control BSR in oil palm plantations, biological control agents are gaining attention as a major alternative to chemical fungicides. In the course of searching for effective actinomycetes as potential biological control agents for BSR, Streptomyces palmae CMU-AB204^T was isolated from oil palm rhizosphere soil collected on the campus of Chiang Mai University. The culture broth of this strain showed significant antimicrobial activities against several bacteria and phytopathogenic fungi including G. boninense. Antifungal and antibacterial compounds were isolated by antimicrobial activity-guided purification using chromatographic methods. Their structures were elucidated by spectroscopic techniques, including Nuclear Magnetic Resonance (NMR), Mass Spectrometry (MS), Ultraviolet (UV), and Infrared (IR) analyses. The current study isolated new phenyl alkenoic acids 1-6 and three known compounds, anguinomycin A (7), leptomycin A (8), and actinopyrone A (9) as antimicrobial agents. Compounds 1 and 2 displayed broad antifungal activity, though they did not show antibacterial activity. Compounds 3 and 4 revealed a strong antibacterial activity against both Gram-positive and Gram-negative bacteria including the phytopathogenic strain Xanthomonas campestris pv. oryzae. Compounds 7-9 displayed antifungal activity against Ganoderma. Thus, the antifungal compounds obtained in this study may play a role in protecting oil palm plants from Ganoderma infection with the strain S. palmae CMU-AB204^T.