Host-microbe signaling shaping the root and nodule microbiota assembly of Lotus japonicus

Research output: Book/anthology/dissertation/reportPh.D. thesis

Leguminous plants can interact with nitrogen-fixing rhizobia and establish symbiotic relationships leading to infection threads (ITs) formation, nodule organogenesis and symbiotic nitrogen fixation. This symbiosis is initiated by glycan perception and signalling by LysM receptors of legumes. In nature legumes-rhizobia interaction is, however more complex-since it establishes concomitantly with the root-associated microbiota. Furthermore, previous studies haven shown that symbiosis signalling is important for legume roots to assembly a taxonomic diverse and healthy microbiota, and the infection threads of legumes induced by symbiotic rhizobia can act as the “route” used by specific non-symbionts to colonize the legume roots. At present, how the binary symbiotic interaction influences and contributes to a healthy and beneficial microbial assembly of legumes, or how root microbiota affects nitrogen fixing symbiosis is poorly understood. Here, to initiate a mechanistic understanding of these questions, we focused on identifying the contribution of rhizobia-induced symbiosis to the establishment of root and rhizosphere microbiota. To this end, we obtained a taxonomically diverse and complex bacterial culture collections that covers 38% of the root microbiota of Lotus japonicus, which we call Lj-RSPHERE. Using representative isolates of Lj-RSPHERE, we constructed tailored synthetic communities (SynComs) by drop-out strategy to perform recolonization experiments on L. japonicus wild-type. We found that elimination of Burkholderia, Bosea or Pseudorhodoferax from the analysed SynCom improves Lotus shoot growth and nitrogen fixation symbiosis, while Dyella has a positive role on Lotus growth. Using isolates from Lj-RSPHERE and At-RSHERE in complex co-inoculation and competition experiments identified signatures of host preference for same-taxa commensals isolated from different host species, and this host preference is not dependent on known immune responses.
To further study the role of symbiosis-induced developmental programs to the establishment of root and rhizosphere microbiota, we investigated the root and rhizosphere microbiota of two L. japonicus mutants in native soil: lhk1nfya1, which forms infection threads (ITs) but is impaired in nodule organogenesis, and nfr5snf1, which forms nodules but no ITs. We found that both developmental programs have major contribution to structuring root-associated microbiota of Lotus. Next, using established Lj-SPHERE, we investigated the role of symbionts in the development of Lotus root-associated microbiota. By constructing “symbiont-free” SymComs, we found fewer bacteria could colonized the endosphere of Lotus compared with “symbiont-present” SynComs, indicating the essential role of symbionts in structuring taxonomic diverse microbiota of Lotus. Our findings provide new insights into the role of legume-rhizobia symbiosis in structuring healthy legume microbiota.
Finally, to identify the role of glycan signalling to the establishment of Lotus root and rhizosphere microbiota, we investigated the root and rhizosphere microbiota of four L. japonicus mutants in nature soil: nfr5, impaired for NFR5 receptor responsible of Nod Factor perception, nfre, impaired for Nod Factor perception at the epidermal cells, chit5, impaired in Nod Factor signalling in the cortex cells, and epr3, impaired in exopolysaccharide perception. We found all the mutants assembly distinct root and rhizosphere microbiota from the wild-type plants, and a gradual reduction of Burkholderiales was observed in the roots of nfre, epr3, chit5 and nfr5. By analysing the relative abundance of individual OTUs presented in the roots and rhizosphere of the four mutants, we observed distinct influence of the impaired Nfre, Epr3, Chit5 and Nfr5 genes on specific bacterial taxa, indicating key role of glycan signalling in assembling specific microbiota in the roots of Lotus. Our results provided genetic evidences enabling legumes to selectively host specific members from the soil microbiota, implying a larger role of glycan signalling than previously described in symbiosis signalling with nitrogen-fixing rhizobia.
Original languageEnglish
PublisherAarhus Universitet
Number of pages177
Publication statusPublished - 2020

Note re. dissertation

Termination date: 14.05.2020

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ID: 176310353