Webinars are held every first Thursday in the Month starting at 4pm (JST)/9am (CET).
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May 6, 2021
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Role of plant exudates in the microbiome recruitment
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Nejc Stopnisek (NIOO-KNAW, NL)
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Plant metabolites have a significant impact on microbial communities. They take part in the recruitment and selection of microbes from the soil microbial pool but also manipulate their activities. The secretion of plant metabolites does not follow a simple continuum, but it is rather dynamic, changing in quantities and qualities depending on plants' needs. It is well known that biotic and abiotic stresses can cause drastic changes in exudates. Moreover, plant development and even circadian rhythms have significant effects on exudate profiles. Plant domestication and selective breeding have resulted in genetic bottleneck events in these plants but to what extent these events affect root exudation and consequently, microbiome composition is less clear. I will discuss my current project in which I am investigating the following questions: 1) how domestication affects plant exudates, 2) and if these metabolites are directly involved in microbial recruitment.
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Diurnal cycle of isoflavone biosynthesis in soybean roots and exploration of isoflavone transporters
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Hinako Matsuda (Kyoto University, JP)
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Isoflavones function as signals for soybean-rhizobia symbiosis and in shaping microbial assemblages in the soybean rhizosphere. Despite these functions in the rhizosphere, isoflavone secretion mechanisms are still to be characterized at the molecular level. It has been revealed that the amount and components of isoflavone in root exudates change throughout the developmental stages, but their diurnal variations remain unknown. We investigated the diurnal metabolic regulation of isoflavones in hydroponically grown soybean by RNA-seq and LC-MS. GmMYB176, a transcription factor gene for isoflavone biosynthesis, was upregulated from 6 a.m. to 12 a.m. in roots. Gene expression levels of isoflavone biosynthetic genes were high at noon and low at night. Besides, the contents of isoflavone aglycones in roots showed a diurnal change following the biosynthetic gene expression. These results suggest the diurnal cycle of isoflavone biosynthesis in soybean roots. The content of isoflavone aglycones in root exudates had no significant variation throughout the day. The expression level of ICHG (isoflavone conjugate-hydrolyzing β-glucosidase) was high during the night, suggesting a regulatory mechanism to keep isoflavone aglycone secretion at a consistent level. We also found several isoflavone transporter candidate genes which exhibited high correlations with isoflavone biosynthetic genes by diurnal co-expression analysis.
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June 3, 2021
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Biosynthesis Research of Austalides from Penicillium arizonense
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Liu Wei (University of Tokyo, JP)
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Fungi are prolific producers of diverse types of natural product, including hybrid metabolites such as meroterpenoids which consist of polyketide and terpenoid structures. Fungal meroterpenoids possess wide chemical diversity, leading to diverse biological activities. Ones of the meroterpenoids, austalides which contain unique ortho-ester moiety were isolated from Penicillium arizonense. Because some of the austalides are osteoclast differentiation inhibitors, there is some potentia to produce pharmaceutically useful compounds by engineering their biosynthetic reactions. A putative austalide gene cluster, named ast gene cluster, was found and we proposed a biosynthetic pathway for austalides produced in P. arizonense. By heterologous expression and enzymatic reaction, the biosynthetic pathway of austalides was characterized. We determined the structure of each product prepared from large scale reaction by HR-MS and NMR analysis. This research contributes to the construction of new pharmaceutical substance production by utilizing combinatorial biosynthesis.
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Deciphering endophytic microbial functions activated upon pathogen infection
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Xinya Pan (Leiden University)
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Plants can shape their root microbiome upon pathogen infection. In previous studies, we found that specific members of the endophytic root microbiome were enriched and activated upon infection by the fungal root pathogen Rhizoctonia solani (Carrion et al., 2019; Science). Furthermore, a large number of bacterial genes and biosynthetic gene clusters (BGCs) with unknown functions was uncovered in the root endophytic microbiome. Site-directed mutagenesis of one of these BGCs, the novel NRPS-PKS gene cluster BGC298 from endophytic Flavobacterium, revealed its essential role in suppression of infections by R. solani. In my PhD project, I will further investigate 1) the metabolic product of BGC298, 2) how BGC298 is activated and regulated upon root infection by R. solani, 3) and which other BGCs and pathways are involved in plant protection and the lifestyle of root endophytic bacteria.
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July 1, 2021
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Antimicrobial Compounds in the Volatilome of Social Spider Communities
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Alexander Lammers (NIOO-KNAW)
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Social arthropods such as termites, ants, and bees are among others the most successful animal groups on earth. However, social arthropods face an elevated risk of infections due to the close proximity of individuals, which facilitates pathogen transmission. An interesting hypothesis is that social arthropods are protected by chemical compounds produced by the arthropods themselves, microbial symbionts, or plants they associate with. Stegodyphus dumicola is an African social spider species, inhabiting communal silk nests. Because of the complex three-dimensional structure of the spider nest antimicrobial volatile organic compounds (VOCs) are a promising protection against pathogens, because of their ability to diffuse through air-filled pores. We analyzed the volatilomes of S. dumicola, their nests, and capture webs in three locations in Namibia and assessed their antimicrobial potential. Volatilomes were collected using polydimethylsiloxane (PDMS) tubes and analyzed using GC/Q-TOF. We showed the presence of 199 VOCs and tentatively identified 53 VOCs. More than 40 % of the tentatively identified VOCs are known for their antimicrobial activity. The results indicate the potential relevance of the volatilomes for the ecological success of S. dumicola.
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Biosynthetic studies of natural isocyanide hazimycin A
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Kumiko Imachi (Hokkaido University)
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Isocyanide is a functional group which is present in several different groups of natural products, and plays an important role for the biological activity. Isocyanide-containing natural product hazimycin A was originally discovered from actinobacteria Micromonospora echinospora subsp. challisensis SCC 1411, and recently re-discovered from actinobacteria Kitasatospora purpeofusca HV058, which was isolated from a soil sample collected in Hokkaido Univ. campus. Despite its unique structure and potent antimicrobial activity, the biosynthetic route of hazimycin was unknown. In this study, we aimed to identify the hazimycin A biosynthetic gene cluster and elucidate the mechanism of isocyanide formation in hazimycin A biosynthesis. We sequenced the genome of K. purpofusca HV058 and identified a gene coding for HzmA that is similar to IsnA installing isocyanide moiety onto aromatic amino acids. In the flanking region of hzmA, tyrosine dimerization protein P450 gene hzmB and excretion transporter gene hzmC are also encoded, therefore, we hypothesized that this region as hazimycin biosynthetic gene cluster. Disruption of hzmA abolished the production of hazimycins, showing that it is an isocyanide synthase responsible for biosynthesis of hazimycins.
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August 5, 2021
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α-Tomatine play a role in shaping bacterial communities of tomato rhizosphere in the field
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Kyoko Takamatsu (Kyoto University)
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α-Tomatine is a steroidal glycoalkaloid accumulated in the leaves and roots of tomato and has functions in defense against plant pathogens and herbivores. Recently, it has been reported that tomato root secretes tomatine into the rhizosphere, but the role of tomatine in the tomato rhizosphere is unknown. In this study, to analyze the functions of tomatine in the rhizosphere, we used a tomato mutant jre4 in which a master regulator of the tomatine biosynthesis, Jasmonate-responsive ETHYLENE RESPONSE FACTOR 4, is impaired. We cultivated both wild-type (WT) and jre4-1 mutant tomato in the field and analyzed the tomatine content in tissues and rhizosphere by LC-MS. We also analyzed microbial communities using 16S rRNA sequences. We found that tomatine contents were higher in WT than jre4-1 mutant. In the rhizosphere and root compartment, the relative abundance of Sphingomonadaceae, which is enriched in tomato rhizosphere compared with bulk soil, was significantly decreased in jre4-1 mutant. Together, α-tomatine is not only accumulated in their tissues but also secreted from tomato roots into the rhizosphere to modulate the tomato rhizosphere bacterial communities.
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Exploring the volatiles of arbuscular mycorrhiza fungi
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Ana Shein Lee Diaz (NIOO-KNAW)
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Plants and microbes communicate through chemical cues, and in particular, volatile compounds are suitable for long-distance and inter-species communication. It is known plants can emit volatile compounds for defence or to attract natural enemies and similarly, microbes can use volatiles to communicate with host plants or to defend themselves from other microbes such as pathogens or competitors. Among plant-associated microbes, arbuscular mycorrhiza fungi (AMF) are a widespread plant symbiont known to induce physiological changes in the plant during and upon the establishment of the symbiosis. However, it is not yet known whether volatile compounds produced either by the plant or the AMF could take part in the symbiotic process. In our experiments, we aimed to characterize the volatile profile of roots inoculated with AMF through gas chromatography-mass spectrometry (GC-MS). For that, we trapped volatiles present in the headspaces of in vitro systems containing carrot roots inoculated with AMF. The sampling was done at different time points to assess whether volatile compounds are involved at the early stages of the symbiosis or during the active symbiotic phase. Our results show that some volatiles, in particular a terpene, might have a role during the initial pre-symbiotic phase since that compound was mainly found in carrot roots inoculated with AMF. Thus, volatile compounds can be crucial for the early communication between host plants and symbiont microbes and the establishment of plant-microbe mutualistic interactions.
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