Comparative and population genomic landscape of Phellinus noxius: A hypervariable fungus causing root rot in trees

The order Hymenochaetales of white rot fungi contain some of the most aggressive wood decayers causing tree deaths around the world. Despite their ecological importance and the impact of diseases they cause, little is known about the evolution and transmission patterns of these pathogens. Here, we sequenced and undertook comparative genomic analyses of Hymenochaetales genomes using brown root rot fungus Phellinus noxius, wood‐decomposing fungus Phellinus lamaensis, laminated root rot fungus Phellinus sulphurascens and trunk pathogen Porodaedalea pini. Many gene families of lignin‐degrading enzymes were identified from these fungi, reflecting their ability as white rot fungi. Comparing against distant fungi highlighted the expansion of 1,3‐beta‐glucan synthases in P. noxius, which may account for its fast‐growing attribute. We identified 13 linkage groups conserved within Agaricomycetes, suggesting the evolution of stable karyotypes. We determined that P. noxius has a bipolar heterothallic mating system, with unusual highly expanded ~60 kb A locus as a result of accumulating gene transposition. We investigated the population genomics of 60 P. noxius isolates across multiple islands of the Asia Pacific region. Whole‐genome sequencing showed this multinucleate species contains abundant poly‐allelic single nucleotide polymorphisms with atypical allele frequencies. Different patterns of intra‐isolate polymorphism reflect mono‐/heterokaryotic states which are both prevalent in nature. We have shown two genetically separated lineages with one spanning across many islands despite the geographical barriers. Both populations possess extraordinary genetic diversity and show contrasting evolutionary scenarios. These results provide a framework to further investigate the genetic basis underlying the fitness and virulence of white rot fungi.     

A Polycephalomyces hyperparasite of Ophiocordyceps sinensis leads to shortened duration of production and reduced numbers of host ascospores

Ophiocordyceps sinensis, an entomopathogenic fungus of the Tibetan Plateau is one of the most valuable traditional Chinese medicines. A fungal pathogen of O. sinensis, Polycephalomyces sp. GIMCC 3.570 (isolate 2010A-0818) was characterized by morphology, related to sequences of six genes (SSU, ITS, LSU, TEF1-α, RPB1 and ATP6) found in a BLAST search and five genes (SSU, LSU, TEF1, RPB1 and RPB2) by phylogenetic analysis using maximum parsimony, maximum likelihood and Bayesian methods. The results strongly support placement of P. sp. GIMCC 3.570 in the genus Polycephalomyces. To determine the influence of P. sp. GIMCC 3.570 on the reproduction of its host, 30 artificially infected O. sinensis samples were compared with 30 uninfected controls. In the infected fungus, the life span of the stroma was significantly shorter and significantly fewer ascospores were produced compared with uninfected O. sinensis (p < 0.01).     

Evaluation of the rust fungus Puccinia rapipes for biological control of Lycium ferocissimum (African boxthorn) in Australia: Life cycle,taxonomy and pathogenicity

Fungal plant pathogens are increasingly recognised as being among the most effective and safe agents in classical weed biological control programs worldwide. Suitability of the rust fungus P. rapipes as a classical biological control agent for Lycium ferocissimum (African boxthorn) in Australia was assessed using a streamlined agent selection framework. Studies with P. rapipes were undertaken to elucidate its life cycle, confirm its taxonomic placement and determine its pathogenicity to L. ferocissimum and seven closely-related Solanaceae species that occur in Australia. Field surveys in the native range of South Africa, experiments in a containment facility in Australia and DNA sequencing confirmed that P. rapipes is macrocyclic and autoecious, producing all five spore stages on L. ferocissimum. The stages not previously encountered, spermogonia and aecia, are described. Sequencing also confirmed that P. rapipes is sister to Puccinia afra, in the ‘Old World Lineage’ of Puccinia species on Lycieae. Two purified isolates of the fungus, representing the Eastern and Western Cape distributions of P. rapipes in South Africa, were cultured in the containment facility for use in pathogenicity testing. L. ferocissimum and all of the Lycium species of Eurasian origin tested ‒ Lycium barbarum (goji berry), Lycium chinense (goji berry ‘chinense’) and Lycium ruthenicum (black goji berry) – were susceptible to both isolates of P. rapipes. The Australian native L. australe and three more distantly related species in different genera tested were resistant to both isolates. The isolate from the Western Cape was significantly more pathogenic on L. ferocissimum from Australia, than the Eastern Cape isolate. Our results indicate that P. rapipes may be sufficiently host specific to pursue as a biological control agent in an Australian context, should regulators be willing to accept damage to the Eurasian goji berries being grown, albeit to a limited extent, in Australia.     

A new fungal pathogen of the scavenger mite,Tydeus gloveri

A new fungal pathogen, Hirsutella tydeicola, was found causing epizootics in populations of the scavenger mite, Tydeus gloveri, during the summer of 1979 and 1980 on citrus in Florida. The fungus is described in association with its host using light and scanning electron microscopy. H. tydeicola is compared with a closely related species, H. thompsonii, a coexisting pathogen of the citrus rust mite. All attempts to isolate the fungus on various agar media failed.     

The Genetic Structure of Phellinus noxius and Dissemination Pattern of Brown Root Rot Disease in Taiwan

Since the 1990s, brown root rot caused by Phellinus noxius (Corner) Cunningham has become a major tree disease in Taiwan. This fungal pathogen can infect more than 200 hardwood and softwood tree species, causing gradual to fast decline of the trees. For effective control, we must determine how the pathogen is disseminated and how the new infection center of brown root rot is established. We performed Illumina sequencing and de novo assembly of a single basidiospore isolate Daxi42 and obtained a draft genome of ~40 Mb. By comparing the 12,217 simple sequence repeat (SSR) regions in Daxi42 with the low-coverage Illumina sequencing data for four additional P. noxius isolates, we identified 154 SSR regions with potential polymorphisms. A set of 13 polymorphic SSR markers were then developed and used to analyze 329 P. noxius isolates collected from 73 tree species from urban/agricultural areas in 14 cities/counties all around Taiwan from 1989 to 2012. The results revealed a high proportion (~98%) of distinct multilocus genotypes (MLGs) and that none of the 329 isolates were genome-wide homozygous, which supports a possible predominant outcrossing reproductive mode in P. noxius. The diverse MLGs exist as discrete patches, so brown root rot was most likely caused by multiple clones rather than a single predominant strain. The isolates collected from diseased trees near each other tend to have similar genotype(s), which indicates that P. noxius may spread to adjacent trees via root-to-root contact. Analyses based on Bayesian clustering, F _ST statistics, analysis of molecular variance, and isolation by distance all suggest a low degree of population differentiation and little to no barrier to gene flow throughout the P. noxius population in Taiwan. We discuss the involvement of basidiospore dispersal in disease dissemination.     

Rust disease of eucalypts,caused by Puccinia psidii,did not originate via host jump from guava in Brazil

The rust fungus, Puccinia psidii, is a devastating pathogen of introduced eucalypts (Eucalyptus spp.) in Brazil where it was first observed in 1912. This pathogen is hypothesized to be endemic to South and Central America and to have first infected eucalypts via a host jump from native guava (Psidium guajava). Ten microsatellite markers were used to genotype 148 P. psidii samples from eucalypts and guava plus five additional myrtaceous hosts across a wide geographic range of south‐eastern Brazil and Uruguay. Principal coordinates analysis, a Bayesian clustering analysis and a minimum‐spanning network revealed two major genetic clusters among the sampled isolates, one associated with guava and another associated with eucalypts and three additional hosts. Multilocus genotypes infecting guava differed by multiple mutational steps at eight loci compared with those infecting eucalypts. Approximate Bayesian computation revealed that evolutionary scenarios involving a coalescence event between guava‐ and eucalypt‐associated pathogen populations within the past 1000 years are highly unlikely. None of the analyses supported the hypothesis that eucalypt‐infecting P. psidii in Brazil originated via host jump from guava following the introduction of eucalypts to Brazil approximately 185 years ago. The existence of host‐associated biotypes of P. psidii in Brazil indicates that this diversity must be considered when assessing the invasive threat posed by this pathogen to myrtaceous hosts worldwide.     

Association Genetics Reveals Three Novel Avirulence Genes from the Rice Blast Fungal Pathogen Magnaporthe oryzae

To subvert rice (Oryza sativa) host defenses, the devastating ascomycete fungus pathogen Magnaporthe oryzae produces a battery of effector molecules, including some with avirulence (AVR) activity, which are recognized by host resistance (R) proteins resulting in rapid and effective activation of innate immunity. To isolate novel avirulence genes from M. oryzae, we examined DNA polymorphisms of secreted protein genes predicted from the genome sequence of isolate 70-15 and looked for an association with AVR activity. This large-scale study found significantly more presence/absence polymorphisms than nucleotide polymorphisms among 1032 putative secreted protein genes. Nucleotide diversity of M. oryzae among 46 isolates of a worldwide collection was extremely low (θ = 8.2 × 10⁻⁵), suggestive of recent pathogen dispersal. However, no association between DNA polymorphism and AVR was identified. Therefore, we used genome resequencing of Ina168, an M. oryzae isolate that contains nine AVR genes. Remarkably, a total of 1.68 Mb regions, comprising 316 candidate effector genes, were present in Ina168 but absent in the assembled sequence of isolate 70-15. Association analyses of these 316 genes revealed three novel AVR genes, AVR-Pia, AVR-Pii, and AVR-Pik/km/kp, corresponding to five previously known AVR genes, whose products are recognized inside rice cells possessing the cognate R genes. AVR-Pia and AVR-Pii have evolved by gene gain/loss processes, whereas AVR-Pik/km/kp has evolved by nucleotide substitutions and gene gain/loss.     

Responses of different geographic populations of two potato tuber moth species to genetic variants of Phthorimaea operculella granulovirus

Phthorimaea operculella granulovirus (PhopGV) belongs to the genus Betabaculovirus of the arthropod‐infecting Baculoviridae. PhopGV is able to infect several gelechiid species. Among them are the potato tuber moths Phthorimaea operculella Zeller and Tecia solanivora Povolny (both Lepidoptera: Gelechiidae). In various South American countries, PhopGV‐based biopesticides are used to control either P. operculella or T. solanivora. Many trials have indicated that a particular viral isolate can exhibit very distinct pathogenicity when infecting different host species or different populations of one host species. In this study, we compared host–pathogen interactions using various PhopGV isolates and various populations of P. operculella and T. solanivora. Virus isolates from P. operculella were more pathogenic against their original host species than against T. solanivora. A PhopGV isolated from T. solanivora was less efficient against P. operculella. In addition, virus isolates differed in pathogenicity toward their hosts (i.e., lethal concentrations of isolates ranged from low to high). Unexpectedly, we also found that host populations of one species from distinct geographic origins did not differ significantly in susceptibility to the same PhopGV isolate. This was the case for both host species and for five PhopGV isolates. Comparative restriction fragment length polymorphism (RFLP) analyses of 11 isolates including those used in bio‐assays indicated three main regions of variation in the genome of PhopGV, corresponding to the regions of open reading frame PhopGV046, gene PhopGV129 (egt), and repeat 9 (located between open reading frames PhopGV083 and PhopGV084). Comparison of the nucleotide sequences of the insertions/deletions present in these regions were carried out for the most variable isolate, JLZ9f. The results are discussed in the context of the production and use of PhopGV as a biological agent against these two pest species.     

Survival of Phytophthora cinnamomi and Fusarium verticillioides in commercial potting substrates for ornamental plants

Live plants, particularly when accompanied by soil or potting substrates, are considered the main pathway for international spread of plant pathogens. Modern, rapid shipping technologies for international plant trade increase the probability of plant pathogen survival during transport and the subsequent chances of disease outbreaks in new locations. The survival of two model pathogens, an Oomycete, Phytophthora cinnamomi, and a filamentous fungus, Fusarium verticillioides, was studied in two different commercial potting substrates (peat and peat‐free) under glasshouse conditions in the absence of a plant host. Survival rates were analysed at 2, 7, 12 and 17 months after substrate inoculation. Fusarium verticillioides had the longest survival rate, and was still present at 17 months. In contrast, P. cinnamomi survived up to 7 months but was not recovered after 12 or 17 months. There was no significant difference in the number of colony‐forming units (CFUs) of either pathogen in the two substrates, except at 2 months, when higher numbers were recovered from peat substrates.     

Identification of a New Race of Sporisorium reilianum and Characterization of the Reaction of Sorghum Lines to Four Races of the Head Smut Pathogen

Sporisorium reilianum is the causal agent of head smut on sorghum and maize. In order to effectively utilize host resistance to control this important disease in crops, it is necessary to monitor changes in disease dynamics and virulence of the pathogen. An outbreak of head smut was recently observed in a sorghum field, near Gaoping, Shanxi, China, and research was undertaken to characterize a putative new race of S. reilianum. A set of differential sorghum lines with resistance to several conventional races was used to characterize the newly collected isolate of S. reilianum. The reactions of differential cultivars/germplasm lines to the new isolate indicate that it is a new physiological race of S. reilianum. The new race is highly virulent on sorghum line A₂V4 and its hybrid, Jinza 12, that are known as resistant to all existing Chinese races of S. reilianum, including races 1, 2, and 3. The new isolate of S. reilianum is different from all of the described races of the pathogen; thus, it is designated as race 4 of S. reilianum. Furthermore, a collection of 34 sorghum genotypes including commercial cultivars and germplasm lines was evaluated for disease reaction to the newly described race and the three known races of the pathogen.     

Re‐targeting of a plant defense protease by a cyst nematode effector

Plants mount defense responses during pathogen attacks, and robust host defense suppression by pathogen effector proteins is essential for infection success. 4E02 is an effector of the sugar beet cyst nematode Heterodera schachtii. Arabidopsis thaliana lines expressing the effector‐coding sequence showed altered expression levels of defense response genes, as well as higher susceptibility to both the biotroph H. schachtii and the necrotroph Botrytis cinerea, indicating a potential suppression of defenses by 4E02. Yeast two‐hybrid analyses showed that 4E02 targets A. thaliana vacuolar papain‐like cysteine protease (PLCP) ‘Responsive to Dehydration 21A’ (RD21A), which has been shown to function in the plant defense response. Activity‐based protein profiling analyses documented that the in planta presence of 4E02 does not impede enzymatic activity of RD21A. Instead, 4E02 mediates a re‐localization of this protease from the vacuole to the nucleus and cytoplasm, which is likely to prevent the protease from performing its defense function and at the same time, brings it in contact with novel substrates. Yeast two‐hybrid analyses showed that RD21A interacts with multiple host proteins including enzymes involved in defense responses as well as carbohydrate metabolism. In support of a role in carbohydrate metabolism of RD21A after its effector‐mediated re‐localization, we observed cell wall compositional changes in 4E02 expressing A. thaliana lines. Collectively, our study shows that 4E02 removes RD21A from its defense‐inducing pathway and repurposes this enzyme by targeting the active protease to different cell compartments.     

Streptomyces poriferorum sp. nov., a novel marine sponge-derived Actinobacteria species expressing anti-MRSA activity

Marine sponges represent a rich source of uncharacterized microbial diversity, and many are host to microorganisms that produce biologically active specialized metabolites. Here, a polyphasic approach was used to characterize two Actinobacteria strains, P01-B04^T and P01-F02, that were isolated from the marine sponges Geodia barretti (Bowerbank, 1858) and Antho dichotoma (Esper, 1794), respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains P01-B04^T and P01-F02 are closely related to Streptomyces beijiangensis DSM 41794^T, Streptomyces laculatispora NRRL B-24909^T, and Streptomyces brevispora NRRL B-24910^T. The two strains showed nearly identical 16S rRNA gene sequences (99.93%), and the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) relatedness values were 99.96% and 99.6%, respectively, suggesting that these strains are affiliated with the same species. Chemotaxonomic and culture characteristics of both strains were also consistent with the genus Streptomyces, while phenotypic properties, genome-based comparisons, and phylogenomic analyses distinguished strains P01-B04^T and P01-F02 from their closest phylogenetic relatives. In silico analysis predicted that the 8.9 Mb genome of P01-B04^T contains at least 41 biosynthetic gene clusters (BGCs) encoding secondary metabolites, indicating that this strain could express diverse bioactive metabolites; in support of this prediction, this strain expressed antibacterial activity against Gram-positive bacteria including a clinical isolate of methicillin-resistant Staphylococcus aureus (MRSA) EAMC30. Based on these results, the marine sponge-associated isolates represent a novel species of the genus Streptomyces, for which the name Streptomyces poriferorum sp. nov. is proposed, with P01-B04^T (=DSM 111306^T = CCM 9048^T) as the type strain.     

Pseudomonas aeruginosa cytochrome P450 CYP168A1 is a fatty acid hydroxylase that metabolizes arachidonic acid to the vasodilator 19-HETE

Pseudomonas aeruginosa is a Gram-negative opportunistic human pathogen that is highly prevalent in individuals with cystic fibrosis (CF). A major problem in treating CF patients infected with P. aeruginosa is the development of antibiotic resistance. Therefore, the identification of novel P. aeruginosa antibiotic drug targets is of the utmost urgency. The genome of P. aeruginosa contains four putative cytochrome P450 enzymes (CYPs) of unknown function that have never before been characterized. Analogous to some of the CYPs from Mycobacterium tuberculosis, these P. aeruginosa CYPs may be important for growth and colonization of CF patients’ lungs. In this study, we cloned, expressed, and characterized CYP168A1 from P. aeruginosa and identified it as a subterminal fatty acid hydroxylase. Spectral binding data and computational modeling of substrates and inhibitors suggest that CYP168A1 has a large, expansive active site and preferentially binds long chain fatty acids and large hydrophobic inhibitors. Furthermore, metabolic experiments confirm that the enzyme is capable of hydroxylating arachidonic acid, an important inflammatory signaling molecule present in abundance in the CF lung, to 19-hydroxyeicosatetraenoic acid (19-HETE; K_m = 41 μM, V_max = 220 pmol/min/nmol P450), a potent vasodilator, which may play a role in the pathogen’s ability to colonize the lung. Additionally, we found that the in vitro metabolism of arachidonic acid is subject to substrate inhibition and is also inhibited by the presence of the antifungal agent ketoconazole. This study identifies a new metabolic pathway in this important human pathogen that may be of utility in treating P. aeruginosa infections.     

The brown root rot fungus Phellinus noxius affects microbial communities in different root-associated niches of Ficus trees

Brown root rot (BRR) caused by Phellinus noxius is a destructive tree disease in tropical and subtropical areas. To understand how BRR affects the composition of the plant rhizoplane-enriched microbiota, the microbiomes within five root-associated compartments (i.e., bulk soil, old/young root rhizosphere soil, old/young root tissue) of Ficus trees naturally infected by P. noxius were investigated. The level of P. noxius infection was determined by quantitative PCR. Illumina sequencing of the internal transcribed spacer and 16S rRNA revealed that P. noxius infection caused a significant reduction in fungal diversity in the bulk soil, the old root rhizosphere soil, and the old root tissue. Interestingly, Cosmospora was the only fungal genus positively correlated with P. noxius. The abundance and composition of dominant bacterial taxa such as Actinomadura, Bacillus, Rhodoplanes, and Streptomyces differed between BRR-diseased and healthy samples. Furthermore, 838 isolates belonging to 26 fungal and 35 bacterial genera were isolated and tested for interactions with P. noxius. Antagonistic activities were observed for isolates of Bacillus, Pseudomonas, Aspergillus, Penicillium, and Trichoderma. Cellophane overlay and cellulose/lignin utilization assays suggested that Cosmospora could tolerate the secretions of P. noxius and that the degradation of lignin by P. noxius may create suitable conditions for Cosmorpora growth.     

Functional expression,extracellular production,purification, structure modeling and biochemical characterization of Carica papaya lipase 1

Carica papaya latex has been reported to contain lipolytic activity since 1925, nevertheless the efforts to isolate lipolytic enzymes directly from the latex matrix have been unsuccessful. Nowadays papaya genome is known and heterologous expression is an alternative to overcome this problem. Therefore, in this study, Carica papaya lipase 1 sequence (CpLip1) has been identified in papaya genome and for the first time, functionally expressed using Pichia pastoris as host system. Purification of the recombinant enzyme was carried out by affinity chromatography and reached a 7-fold purification factor with 25 U/mg in the purified fraction. Interestingly, homology modeling with lipases of known structure revealed homology with microbial lipases. The biochemical characterization of the purified enzyme shows that CpLip1 hydrolyzed preferentially long-chain triglycerides, it has an optimal pH of 8.5 and an optimal temperature of 35 °C. Finally, the study of its stability in organic solvents showed that, as many lipases, CpLip1 activity is affected in polar solvents. This contribution opens the possibility of studying the catalytic performance of pure CpLip1 in several reactions, and a better understanding of the role of lipases in Carica papaya.     

Effect of three isolates of Pandora neoaphidis from a single population of Sitobion avenae on mortality,speed of kill and fecundity of S. avenae and Rhopalosiphum padi at different temperatures

We studied the effect of three Pandora neoaphidis isolates from one Sitobion avenae population, three temperatures, and two aphid species namely S. avenae and Rhopalosiphum padi on (i) aphid mortality, (ii) time needed to kill aphids, and (iii) aphid average daily and lifetime fecundity. A total of 38% of S. avenae and 7% of R. padi died and supported fungus sporulation. S. avenae was killed 30% faster than R. padi. Average daily fecundity was negatively affected only in S. avenae inoculated with, but not killed by, P. neoaphidis. Nevertheless, lifetime fecundity of both aphid species inoculated and sporulating with P. neoaphidis was halved compared to lifetime fecundity of surviving aphids in the control. Increased temperature resulted in higher mortality rates but did not consistently affect lethal time or fecundity. Results suggest that (i) temperature effects on virulence differ between isolates, even when obtained within the same host population, and (ii) even though an isolate does not kill a host it may reduce its fecundity. Our findings are important for the understanding of P. neoaphidis epizootiology and for use in pest-natural enemy modelling.     

Advances in molecular interactions on the Rhizoctonia solani-sugar beet pathosystem

Rhizoctonia solani is a soilborne pathogen with a broad host range. An anastomosis group (AG) system based on hyphal fusions has been established to distinguish between different R. solani subgroups in this species complex. Members of the AG2-2IIIB subgroup can cause serious problems in sugar beet production, resulting in Rhizoctonia root and crown rot. In this review, we summarize the current molecular advances in the R. solani sugar beet pathosystem. The draft genome of R. solani AG2-2IIIB has an estimated size of 56.02 Mb, larger than any of the R. solani AGs sequenced to date. The genome of AG2-2IIIB has been predicted to harbor 11,897 protein-encoding genes, including a high number of carbohydrate-active enzymes (CAZymes). The highest number of CAZymes was observed for polysaccharide lyase family 1 (PL-1), glycoside hydrolase family 43 (GH-43), and carbohydrate esterase family 12 (CE-12). Eleven single-effector candidates were predicted based on AG2-2IIIB genome data. The RsLysM, RsRlpA, and RsCRP1 genes were highly induced upon early-stage infection of sugar beet seedlings, and heterologous expression in Cercospora beticola and model plant species demonstrated their involvement in virulence. However, despite the progress achieved thus far on the molecular interactions in this pathosystem, many aspects remain to be elucidated, including the development of efficient transformation systems, important for functional studies, and the silencing of undesirable traits in the sugar beet crop.     

Virulence phenotypes result from interactions between pathogen ploidy and genetic background

Studying fungal virulence is often challenging and frequently depends on many contexts, including host immune status and pathogen genetic background. However, the role of ploidy has often been overlooked when studying virulence in eukaryotic pathogens. Since fungal pathogens, including the human opportunistic pathogen Candida albicans, can display extensive ploidy variation, assessing how ploidy impacts virulence has important clinical relevance. As an opportunistic pathogen, C. albicans causes nonlethal, superficial infections in healthy individuals, but life‐threatening bloodstream infections in individuals with compromised immune function. Here, we determined how both ploidy and genetic background of C. albicans impacts virulence phenotypes in healthy and immunocompromised nematode hosts by characterizing virulence phenotypes in four near‐isogenic diploid and tetraploid pairs of strains, which included both laboratory and clinical genetic backgrounds. We found that C. albicans infections decreased host survival and negatively impacted host reproduction, and we leveraged these two measures to survey both lethal and nonlethal virulence phenotypes across the multiple C. albicans strains. In this study, we found that regardless of pathogen ploidy or genetic background, immunocompromised hosts were susceptible to fungal infection compared to healthy hosts. Furthermore, for each host context, we found a significant interaction between C. albicans genetic background and ploidy on virulence phenotypes, but no global differences between diploid and tetraploid pathogens were observed.     

Specific inactivation of an antifungal bacterial siderophore by a fungal plant pathogen

Bacteria and fungi secrete many natural products that inhibit each other’s growth and development. The dynamic changes in secreted metabolites that occur during interactions between bacteria and fungi are complicated. Pyochelin is a siderophore produced by many Pseudomonas and Burkholderia species that induces systemic resistance in plants and has been identified as an antifungal agent. Through imaging mass spectrometry and metabolomics analysis, we found that Phellinus noxius, a plant pathogen, can modify pyochelin and ent-pyochelin to an esterification product, resulting in reduced iron-chelation and loss of antifungal activity. We also observed that dehydroergosterol peroxide, the fungal metabolite, is only accumulated in the presence of pyochelin produced through bacteria–fungi interactions. For the first time, we show the fungal transformation of pyochelin in the microbial interaction. Our findings highlight the importance of understanding the dynamic changes of metabolites in microbial interactions and their influences on microbial communities.Subject terms: Microbial ecology, Metabolomics

Microorganisms use various strategies to establish themselves within an ecological niche while facing keen competition in the environment. Natural products such as antibiotics, quorum sensing molecules, and siderophores are crucial in microbial interactions [1–3]. Certain microorganisms are equipped with uptake systems that enable them to acquire siderophores, even by those that may not produce them [4]. For example, pyochelin is a siderophore produced by many Pseudomonas and Burkholderia strains. Such bacterial strains are commonly found in soils, as endophytes, and from the rhizosphere where they may inhibit plant pathogens [5, 6].Burkholderia cenocepacia 869T2 was isolated as an endophyte and showed beneficial abilities to control banana Fusarium wilt [7]. It harbors many biosynthetic gene clusters of secondary metabolites, such as pyochelin, pyrrolnitrin, and pyrroloquinoline quinone [8]. Recently, we found that this strain could temporarily inhibit the growth of P. noxius, a fungal pathogen of brown root rot disease, which is prevalent in tropical and subtropical regions and has a wide host range covering over 200 plant species [9]. However, in the competition between fungi and bacteria, P. noxius can resist this inhibition and overwhelm bacterial colonies after 1–2 weeks under dual-culture conditions (Fig. S1). These results imply that fungi might have resistance responses and undergo metabolic changes in bacteria–fungi interactions [10]. Here we unveiled metabolic changes in the competitive interaction between B. cenocepacia 869T2 and P. noxius 2252 using the matrix-assisted laser desorption ionization-time of flight imaging mass spectrometry (MALDI-TOF IMS) [11, 12].We specifically monitored the metabolites in the inhibition region of B. cenocepacia 869T2 and P. noxius 2252 dual-culture using MALDI-TOF IMS. Several induced or enzymatically modified metabolites were detected, including m/z 275, 362, 383, and 427 (Fig. 1A). In particular, pyochelin (m/z 325), surrounding the B. cenocepacia 869T2 colony, showed asymmetric distribution in dual-culture samples. Near the P. noxius 2252 mycelia, a new metabolite with m/z 383 was detected with a complementary distribution to pyochelin (Fig. 1A). In LC-MS/MS-based molecular networking analysis [13], we found that this new metabolite structure is an esterification product of pyochelin and glycolic acid, which we named pyochelin-GA (Fig. 1B). We then constructed a pchF-null mutant strain, ΔpchF, which cannot produce pyochelin, and then dual cultured it with P. noxius. Pyochelin and pyochelin-GA were not observed in the MALDI-TOF IMS and LC-MS analysis of dual-culture samples (Fig. 1A and Fig. S2). We further inoculated P. noxius 2252 with pyochelin-GA-free extract harvested from B. cenocepacia 869T2 single culture, and the complementary distribution of pyochelin and pyochelin-GA was observed by MALDI-TOF IMS again (Fig. S3). These results demonstrated that pyochelin-GA was transformed from pyochelin by P. noxius 2252, rather than produced by B. cenocepacia 869T2 under dual-culture conditions.Open in a separate windowFig. 1Metabolic changes in the bacteria–fungi interaction.A Spatial distribution of selected mass signals (m/z) in MALDI-TOF IMS analysis of Phellinus noxius 2252 (Pn2252) dual-cultured with Burkholderia cenocepacia 869T2 (869T2) and a pchF-null mutant strain (Δ pchF). B Molecular networking analysis of pyochelin and analogs from the dual-culture sample. The red node is pyochelin, and the green node is pyochelin-GA. The structures of pyochelin, pyochelin-GA, and dehydroergosterol peroxide (DHEP), together with their mass signals in MALDI-TOF IMS, are shown. C Iron-chelating abilities of pyochelin and pyochelin-GA were evaluated by Chrome Azurol S liquid assay using different concentrations (2.5, 1.25, 0.63, 0.31, and 0.16 mM, n = 3). Proportions of siderophore units are shown in Fig. S14. D Fungal transformation of pyochelin and ent-pyochelin by treating P. noxius 2252 with ethyl acetate crude extracts of B. cenocepacia 869T2, Pseudomonas aeruginosa PAO1, and P. protegens Pf-5 for 8 h. LC-MS was used to monitor the signals of pyochelin (red), ent-pyochelin (blue), and transformation product 383 (black).The chemical structure of pyochelin-GA was further confirmed via total synthesis, NMR, and LC-MS/MS analysis (Supplementary Material and Methods, and Figs. S4–7). The purified pyochelin and pyochelin-GA were also evaluated for their iron-chelating ability. Chrome Azurol S assay indicated that pyochelin had the dose-dependent iron-chelating ability, but pyochelin-GA had lower iron-binding efficiency (Fig. 1C, Fig. S8). Pyochelin chelates iron in the extracellular medium and transports it into cells via the specific outer membrane transporter FptA. The X-ray structure of FptA-pyochelin-Fe indicated that the terminal carboxylic acid of pyochelin plays an essential role in the iron uptake ability [14, 15]. Our docking analysis suggested that the glycolic ester moiety of pyochelin-GA would affect the binding pocket shape of FptA and result in different binding properties compared to FptA-pyochelin (Fig. S9).Pyochelin and ent-pyochelin are produced independently by different biosynthetic gene clusters in Pseudomonas species [16]. To determine whether P. noxius 2252 can transform both enantiomers via this esterification process, we treated P. noxius 2252 with the extracts of pyochelin producers (P. aeruginosa PAO1 and B. cenocepacia 869T2) and an ent-pyochelin producer (P. protegens Pf-5). After 8 h of treatment, both pyochelin and ent-pyochelin were converted to pyochelin-GA (or ent-pyochelin-GA) (Fig. 1D), demonstrating this is a non-stereospecific transformation.To better understand the iron-chelating ability of pyochelin, we used pyochelin and pyochelin-GA to treat P. noxius 2252 under iron-deficiency conditions, by adding the iron chelator deferoxamine, and iron-rich conditions by adding FeCl₃ (Fig. 2). Pyochelin-GA did not affect the growth of P. noxius 2252 under all conditions. However, P. noxius 2252 was more sensitive to pyochelin in iron-deficient conditions and more resistant to pyochelin in iron-rich conditions, demonstrating that iron availability directly affected the tolerance of P. noxius 2252 to pyochelin. A similar phenomenon was reported previously for Aspergillus fumigatus [17].Open in a separate windowFig. 2Pyochelin inhibition of mycelial growth of Phellinus noxius 2252 is inversely associated with iron concentration.Pyochelin-GA did not have an inhibition effect on P. noxius 2252. Potato dextrose agar (PDA) with deferoxamine (DFO; 200 and 400 µM) was used to mimic iron-deficiency conditions. Iron-rich conditions was prepared by adding FeCl₃ (200 and 400 µM) in PDA. P. noxius 2252 was treated with 0.03, 0.06, 0.12, and 0.24 µmol of pyochelin or pyochelin-GA at 30 °C for 24 h. The antifungal assay was performed in two biological replicates.Using MALDI-TOF IMS analysis of the dual-culture of B. cenocepacia 869T2 and P. noxius 2252, we observed that several metabolites (e.g., m/z 275, 362, and 427) were only observed in the boundary of fungal mycelia (Fig. 1A). Although those metabolites were not detected in the dual-culture of ΔpchF and P. noxius 2252 (Fig. 1A), they were present when we treated P. noxius 2252 with pyochelin (Fig. S10). We identified the metabolite associated with m/z 427 as dehydroergosterol peroxide (DHEP) (Fig. S11), which was initially oxidized from ergosterol and dehydroergosterol [18]. Pyochelin can enhance intercellular reactive oxygen species (ROS) and ultimately disrupts membrane integrity, leading to cell death [17, 19, 20]. To clarify whether ROS induced the accumulation of DHEP, we treated P. noxius 2252 with pyochelin, pyochelin-GA, and 2,2′-bipyridyl (an iron chelator). Pyochelin and 2,2′-bipyridyl showed antifungal effects on P. noxius 2252 and induced ROS production (Fig. S12). However, the accumulation of DHEP in P. noxius 2252 was only associated with pyochelin treatment (Fig. S13). The induction of ROS in P. noxius 2252 by pyochelin and pyochelin-GA was not significantly different (Fig. S14). Therefore, we predict that pyochelin-induced accumulation of DHEP in P. noxius 2252 is independent of ROS production and iron-deficiency.Overall, we demonstrate that pyochelin transformation by fungi, in the interaction between pyochelin-producing bacteria and the plant pathogen P. noxius transforms pyochelin and ent-pyochelin into pyochelin-GA (and ent-pyochelin-GA). This product no longer functions as an iron chelator and no longer shows antifungal activity. The production of a fungal metabolite, dehydroergosterol peroxide, was induced explicitly by pyochelin through an unknown mechanism. These results highlight the importance of monitoring dynamic changes of metabolites in situ to better understand the functions and influences of metabolites on microbial community interactions.