Fungal endophytes consortium derived from rubber (Hevea brasiliensis Muell. Arg.) as antagonist against Corynespora cassiicola causing Corynespora leaf fall disease

Solpot T.C., Borja B.T., Prado M.M., Abubakar J.V., Cabasan M.T.

Rubber (Hevea brasiliensis) is a priority tree crop that produces natural rubber (NR), making it an important plantation commodity in the Philippines. However, NR production is confronted with major constraints, including rubber diseases resulting in low latex yield. Twenty-five rubber farms located in five major rubber-producing municipalities (Kidapawan, Antipas, Makilala, Matalam and President Roxas) of Cotabato, Philippines, were surveyed for prevalence of major rubber leaf diseases. Information on farm practices and environmental variables was collected. The majority of rubber farmers were smallholders with hectarage planted ranging between 1 and 15 hectares. The most planted clones are RRIM 600 and PB 260, which are high-yielding yet susceptible to many foliar pathogens. Six leaf diseases, viz. Oidium powdery mildew, Colletotrichum leaf disease, Corynespora leaf fall/spot, Phytophthora leaf blight, bird’s eye spot and algal spot, were documented in this study. Powdery mildew was the most prevalent in Cotabato with the highest percentage and severity of infections in all plantations, followed by Colletotrichum leaf disease. Information on disease prevalence in surveyed areas is important for disease management actions.

Mesny F., Hacquard S., Thomma B.P.

AbstractPlants interact with a diversity of microorganisms that influence their growth and resilience, and they can therefore be considered as ecological entities, namely “plant holobionts,” rather than as singular organisms. In a plant holobiont, the assembly of above‐ and belowground microbiota is ruled by host, microbial, and environmental factors. Upon microorganism perception, plants activate immune signaling resulting in the secretion of factors that modulate microbiota composition. Additionally, metabolic interdependencies and antagonism between microbes are driving forces for community assemblies. We argue that complex plant–microbe and intermicrobial interactions have been selected for during evolution and may promote the survival and fitness of plants and their associated microorganisms as holobionts. As part of this process, plants evolved metabolite‐mediated strategies to selectively recruit beneficial microorganisms in their microbiota. Some of these microbiota members show host‐adaptation, from which mutualism may rapidly arise. In the holobiont, microbiota members also co‐evolved antagonistic activities that restrict proliferation of microbes with high pathogenic potential and can therefore prevent disease development. Co‐evolution within holobionts thus ultimately drives plant performance.

Nascimento Brito V., Lana Alves J., Sírio Araújo K., de Souza Leite T., Borges de Queiroz C., Liparini Pereira O., de Queiroz M.V.

Fungi belonging to the genus Trichoderma have been widely recognized as efficient controllers of plant diseases. Although the majority of isolates currently deployed, thus far, have been isolated from soil, endophytic Trichoderma spp. is considered to be a promising option for application in biocontrol. In this study, 30 endophytic Trichoderma isolates—obtained from the leaves, stems, and roots of wild Hevea spp. in the Brazilian Amazon—were analyzed using specific DNA barcodes: sequences of internal transcribed spacers 1 and 2 of rDNA (ITS region), genes encoding translation elongation factor 1-α (TEF1-α), and the second largest subunit of RNA polymerase II (RPB2). The genealogical concordance phylogenetic species recognition (GCPSR) concept was used for species delimitation. A phylogenetic analysis showed the occurrence of Trichoderma species, such as T. erinaceum, T. ovalisporum, T. koningiopsis, T. sparsum, T. lentiforme, T. virens, and T. spirale. Molecular and morphological features resulted in the discovery of four new species, such as T. acreanum sp. nov., T. ararianum sp. nov., T. heveae sp. nov., and T. brasiliensis sp. nov. The BI and ML analyses shared a similar topology, providing high support to the final trees. The phylograms show three distinct subclades, namely, T. acreanum and T. ararianum being paraphyletic with T. koningiopsis; T. heveae with T. subviride; and T. brasiliensis with T. brevicompactum. This study adds to our knowledge of the diversity of endophytic Trichoderma species in Neotropical forests and reveals new potential biocontrol agents for the management of plant diseases.

Ma H., Song Z., Pan X., Qu Z., Yang Z., Li Y., Zhu A.

Xylaria, a large and cosmopolitan genus of Ascomycota, plays an important ecological role in forest ecology as wood-decomposers, and serve as a source of bioactive secondary metabolites. The present work concerns a survey of Xylaria from Southwest China. Four new species of Xylaria with pale-colored ascospores associated with fallen fruits and seeds are described and illustrated based on morphological and phylogenetic evidences. The phylogeny inferred from a combined dataset of ITS-RPB2-β-tubulin sequences supports these four species as distinct species. The four new taxa, namely Xylariarogersii, X. schimicola, X. theaceicola, and X. wallichii, are compared and contrasted against morphologically similar species. A dichotomous identification key to all the accepted species of Xylaria associated with fallen fruits and seeds is given.

Brooks S., Klomchit A., Chimthai S., Jaidee W., Bastian A.C.

Over the past decade endophytic fungi have been known as a source of secondary metabolites with the ability to act as a biocontrol agents. Xylaria feejeensis, SRNE2BP a fungal endophyte isolated from a mangrove tree exhibited antagonistic activity against two fungal pathogens of tomato. Crude extract of X. feejeensis SRNE2BP significantly inhibited Fusarium oxysporum MFLUCC 19–0157 growth as shown approximately 60–75% in in vitro and in situ assays. Both assays showed that the endophyte also inhibited mycelium formation of Alternaria solani MFLUCC 19–0093 by 56% and 87%, respectively. The half maximal inhibitory concentration of X. feejeensis SRNE2BP crude extract against A. solani and F. oxysporum was approximately 7 mg/l. Crude extract and mycelium of X. feejeensis SRNE2BP showed potential in controlling early blight and fusarium wilt disease in tomato, respectively. Seedlings from seeds coated with crude extract of X. feejeensis SRNE2BP had lower disease severity (31.71%) of early blight disease compared to un-treated seeds (57.13%). Soil treated with 10% endophytic mycelium not only reduced fusarium wilt in tomato plant (55.55% severity compared with 91.66% in un-treated soil) but also promoted seed emergence and growth of tomato. Structure analysis revealed that 12 secondary metabolites, especially mellein derivatives, are major components of the crude extract of X. feejeensis SRNE2BP. These compounds could be responsible for antifungal activities; however, further study is required. Our findings strongly suggest that colonization with this fungal endophyte can be beneficial to the host plant especially with regards to plant growth promotion and broad antagonistic activity.

Collinge D.B., Bryngelsson T., Gregersen P.L., Smedegaard-Petersen V., Thordal-Christensen H.

Abdelfattah A., Tack A.J., Wasserman B., Liu J., Berg G., Norelli J., Droby S., Wisniewski M.

Plants evolved in association with a diverse community of microorganisms. The effect of plant phylogeny and domestication on host-microbiome co-evolutionary dynamics are poorly understood. Here we examined the effect of domestication and plant lineage on the composition of the endophytic microbiome of 11 Malus species, representing three major groups: domesticated apple (M. domestica), wild apple progenitors, and wild Malus species. The endophytic community of M. domestica and its wild progenitors showed higher microbial diversity and abundance than wild Malus species. Heirloom and modern cultivars harbored a distinct community composition, though the difference was not significant. A community-wide Bayesian model revealed that the endophytic microbiome of domesticated apple is an admixture of its wild progenitors, with clear evidence for microbiome introgression, especially for the bacterial community. We observed a significant correlation between the evolutionary distance of Malus species and their microbiome. This study supports co-evolution between Malus species and their microbiome during domestication. This finding has major implications for future breeding programs and our understanding of the evolution of plants and their microbiomes.

Sinno M., Ranesi M., Di Lelio I., Iacomino G., Becchimanzi A., Barra E., Molisso D., Pennacchio F., Digilio M.C., Vitale S., Turrà D., Harizanova V., Lorito M., Woo S.L.

Endophytic fungi (EF) can enhance both plant growth and defense barriers against pests and pathogens, contributing to the reduction of chemical pesticides and fertilizers use in agriculture. Beauveria bassiana is an entomopathogenic fungus showing endophytism in several crops, often associated with a good capacity to limit the development of pests and disease agents. However, the diversity of the protective efficacy and plant response to different strains can be remarkable and needs to be carefully assessed for the successful and predictable use of these beneficial microorganisms. This study aims to select B. bassiana strains able to colonize tomato plants as endophytes as well as to control two important disease agents, Botrytis cinerea and Alternaria alternata, and the pest aphid, Macrosiphum euphorbiae. Nine wild-type isolates and one commercial strain were screened for endophytism, then further characterized for plant-growth promotion plus inhibition of disease development and pest infestation. Four isolates proved to have a good control activity against the biotic stressors tested, but only Bb716 was also able to promote plant growth. This work provides a simple workflow for the selection of beneficial EF, paving the way towards more effective use of B. bassiana in Integrate Pest Management (IPM) of tomato.

Li B., Yang Y., Cai J., Liu X., Shi T., Li C., Chen Y., Xu P., Huang G.

Rubber tree Corynespora leaf fall (CLF) disease, caused by the fungus Corynespora cassiicola, is one of the most damaging diseases in rubber tree plantations in Asia and Africa, and this disease also threatens rubber nurseries and young rubber plantations in China. C. cassiicola isolates display high genetic diversity, and virulence profiles vary significantly depending on cultivar. Although one phytotoxin (cassicolin) has been identified, it cannot fully explain the diversity in pathogenicity between C. cassiicola species, and some virulent C. cassiicola strains do not contain the cassiicolin gene. In the present study, we report high-quality gapless genome sequences, obtained using short-read sequencing and single-molecule long-read sequencing, of two Chinese C. cassiicola virulent strains. Comparative genomics of gene families in these two stains and a virulent CPP strain from the Philippines showed that all three strains experienced different selective pressures, and metabolism-related gene families vary between the strains. Secreted protein analysis indicated that the quantities of secreted cell wall-degrading enzymes were correlated with pathogenesis, and the most aggressive CCP strain (cassiicolin toxin type 1) encoded 27.34% and 39.74% more secreted carbohydrate-active enzymes (CAZymes) than Chinese strains YN49 and CC01, respectively, both of which can only infect rubber tree saplings. The results of antiSMASH analysis showed that all three strains encode ~60 secondary metabolite biosynthesis gene clusters (SM BGCs). Phylogenomic and domain structure analyses of core synthesis genes, together with synteny analysis of polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) gene clusters, revealed diversity in the distribution of SM BGCs between strains, as well as SM polymorphisms, which may play an important role in pathogenic progress. The results expand our understanding of the C. cassiicola genome. Further comparative genomic analysis indicates that secreted CAZymes and SMs may influence pathogenicity in rubber tree plantations. The findings facilitate future exploration of the molecular pathogenic mechanism of C. cassiicola.

N. Rondon M., Lawrence K.

Mahendran T.R., Thottathil G.P., Surendran A., Nagao H., Sudesh K.

The pathogenic fungi, Rigidoporus microporus and Corynespora cassiicola are among the major agents of root and leaf disease of rubber tree (Hevea brasiliensis). In this study, endophytic fungi were...

Trivedi P., Leach J.E., Tringe S.G., Sa T., Singh B.K.

Healthy plants host diverse but taxonomically structured communities of microorganisms, the plant microbiota, that colonize every accessible plant tissue. Plant-associated microbiomes confer fitness advantages to the plant host, including growth promotion, nutrient uptake, stress tolerance and resistance to pathogens. In this Review, we explore how plant microbiome research has unravelled the complex network of genetic, biochemical, physical and metabolic interactions among the plant, the associated microbial communities and the environment. We also discuss how those interactions shape the assembly of plant-associated microbiomes and modulate their beneficial traits, such as nutrient acquisition and plant health, in addition to highlighting knowledge gaps and future directions. In this Review, Trivedi and colleagues explore the interactions between plants, their associated microbial communities and the environment, and also discuss how those interactions shape the assembly of plant-associated microbiomes and modulate their beneficial traits.

Benucci G.M., Burnard D., Shepherd L.D., Bonito G., Munkacsi A.B.

Lycopods are tracheophytes in the Kingdom Plantae and represent one of the oldest lineages of living vascular plants. Symbiotic interactions between these plants with fungi and bacteria, including fine root endophytes in Endogonales, have been hypothesized to have helped early diverging plant lineages colonize land. However, attempts to study the lycopod rhizobiome in its natural environment are still limited. In this study, we used Illumina amplicon sequencing to characterize fungal and bacterial diversity in nine Lycopodiaceae (club moss) species collected in New Zealand. This was done with generic fungal ITS rDNA primers, as well as Endogonales- and arbuscular mycorrhizal fungi (AMF)-selective primer sets targeting the 18S rDNA, and generic bacterial primers targeting the V4 region of the 16S rDNA. We found that the Lycopodiaceae rhizobiome was comprised of an unexpected high frequency of Basidiomycota and Ascomycota coincident with a low abundance of Endogonales and Glomerales. The distribution and abundance of Endogonales varied with host lycopod, and included a novel taxon as well as a single operational taxonomic unit (OTU) that was detected across all plant species. The Lycopodiaceae species with the greatest number and also most unique OTUs was Phlegmariurus varius, while the plant species that shared the most fungal OTUs were Lycopodiella fastigiatum and Lycopodium scariosum. The bacterial OTU distribution was generally not consistent with fungal OTU distribution. For example, community dissimilarity analysis revealed strong concordance between the evolutionary histories of host plants with the fungal community but not with the bacterial community, indicating that Lycopodiaceae have evolved specific relationships with their fungal symbionts. Notably, nearly 16% of the ITS rDNA fungal diversity detected in the Lycopodiaceae rhizobiome remained poorly classified, indicating there is much plant-associated fungal diversity left to describe in New Zealand.

Pujade-Renaud V., Déon M., Gazis R., Ribeiro S., Dessailly F., Granet F., Chaverri P.

The Corynespora leaf fall disease of rubber trees, caused by the necrotrophic fungus Corynespora cassiicola, is responsible for important yield losses in Asian and African plantations, whereas its impact is negligible in South America. The objective of this study was to identify potential antagonists of C. cassiicola among fungal endophytes (i.e., Pestalotiopsis, Colletotrichum, and Trichoderma spp.) isolated from wild and cultivated rubber trees distributed in the Peruvian Amazon. We first tested the endophytes in dual in vitro confrontation assays against a virulent C. cassiicola isolate (CCP) obtained from diseased rubber trees in the Philippines. All Trichoderma isolates overran the CCP colony, suggesting some antagonistic mechanism, while species from the other genera behaved as mutual antagonists. Trichoderma isolates were then tested through antibiosis assays for their capacity to produce growth-inhibiting molecules. One isolate (LA279), recovered as an endophyte from a wild Hevea guianensis specimen and identified as Trichoderma koningiopsis, showed significant antibiosis capacity. We demonstrated that LA279 was also able to endophytically colonize the cultivated rubber tree species (H. brasiliensis). Under controlled laboratory conditions, rubber plants were inoculated with three Trichoderma strains, including LA279, in combination with the pathogenic CCP. Results showed that 1 week preinoculation with the endophytes differentially reduced CCP mycelial development and symptoms. In conclusion, this study suggests that T. koningiopsis isolate LA279—and derivate compounds—could be a promising candidate for the biological control of the important rubber tree pathogen C. cassiicola.

Segaran G., Sathiavelu M.

Endophytes protect the host plant for their entire life cycle and they have the ability to act as a biocontrol agent. Organisms protect the host plant through antibiosis, parasitism and competition mechanism in the biocontrol process. The improper and excessive use of agrochemicals makes the phytopathogens insensitive and leads to the development of resistant fungal pathogens. Chemical fungicides are expensive and have many negative impacts on the environment. The use of endophyte as the biocontrol agent is effective in controlling the plant disease and to achieve sustainable agriculture. Endophytes have antagonistic activity against disease-causing phytopathogens and also capable to produce antimicrobial, insecticidal, antioxidant, anti-tumor and anti-viral metabolites. Perfumoid, phomoenamide, joxysporidinone, alantrypinene, alantryleunone, (−)-4,6′-anhydrooxysporidinone and (−)-6-deoxyoxysporidinone are the few alkaloid compounds of endophytic fungi. Nidurufin, sterigmatocystin, averantin, 11a-methoxycurvularin 4, 11b-methoxycurvularin, tenellone H, phomopene and 1-chloro-2,4-dihydroxy-5-methoxy-7-methylanthraquinone are the endophytic fungal compounds reported with cytotoxic activity in the year between 2008-2019. The present review concentrates on the antagonistic activity of endophytes towards phytopathogens and their bioactive secondary metabolites with pharmacological properties.