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SummaryMotivationMicroorganisms have a pivotal role in ecology and human health and form complex networks where different species can interact and exchange a range of different compounds. Flux balance analysis can offer an insight into the production and the absorption of these metabolic compounds, but frequently results are difficult to visualise and interpret. Additionally, a clear understanding of the roles of microbial species in the community requires the integration of different information sources, including relative abundance, taxonomy and compounds exchange rate.ResultsTo fill-in this gap the command-line tool NEMETEX (NEtwork for METabolic Exchanges) was developed to provide a graphical representation of the metabolites exchanged, joined with interactive visualisation of numerical data. This approach can undoubtedly represent an easy way to investigate high-throughput results obtained from metagenomics and flux balance analysis, providing a more direct interpretation of the data.Availability and implementationThis program, accessory utilities, and their documentation are freely available athttps://github.com/palakela/NEMETEX

The recognition of different microbe-associated molecular patterns in the rhizosphere triggers in the plant root the activation of either an immune response or an accommodation program. In both types of responses, Ca2+is a crucial intracellular messenger, mediating the early stages of the respective signalling pathways. In this work, we analysed the cytosolic and nuclear Ca2+changes activated by a set of chitin-related oligomers in different genetic backgrounds ofLotus japonicusroots by using specifically targeted aequorin-based Ca2+reporters. By means of pharmacological and genetic approaches, we dissected the Ca2+signal into two temporally distinct components: a rapid initial transient, followed by a longer and milder elevation in Ca2+concentration. Taking advantage of a complementary analysis using a cameleon-based bioassay inMedicago truncatularoot organ cultures, we showed that the second phase can be interpreted as the Ca2+spiking that is widely described in response to the perception of symbiotic signals. By contrast, the rapid first phase, critically dependent on elicitor concentration, was found to correlate with the activation of plant immunity marker genes. Overall, our study provides novel clues to a better understanding of the subtle boundaries between symbiotic and immunity responses in root-fungus interactions.HighlightIntracellular calcium changes induced inLotus japonicusroots by fungal signals were dissected in two separate phases, relying on distinct genetic programs and differentially mediating plant symbiotic or immunity responses.