Exploring the potential role of four Rhizophagus irregularis nuclear effectors: opportunities and technical limitations.

Arbuscular mycorrhizal fungi (AMF) are obligate symbionts that interact with the roots of most land plants. The genome of the AMF model species Rhizophagus irregularis contains hundreds of predicted small effector proteins that are secreted extracellularly but also into the plant cells to suppress plant immunity and modify plant physiology to establish a niche for growth. Here, we investigated the role of four nuclear-localized putative effectors, i.e., GLOIN707, GLOIN781, GLOIN261, and RiSP749, in mycorrhization and plant growth. We initially intended to execute the functional studies in Solanum lycopersicum, a host plant of economic interest not previously used for AMF effector biology, but extended our studies to the model host Medicago truncatula as well as the non-host Arabidopsis thaliana because of the technical advantages of working with these models. Furthermore, for three effectors, the implementation of reverse genetic tools, yeast two-hybrid screening and whole-genome transcriptome analysis revealed potential host plant nuclear targets and the downstream triggered transcriptional responses. We identified and validated a host protein interactors participating in mycorrhization in the host.S. lycopersicum and demonstrated by transcriptomics the effectors possible involvement in different molecular processes, i.e., the regulation of DNA replication, methylglyoxal detoxification, and RNA splicing. We conclude that R. irregularis nuclear-localized effector proteins may act on different pathways to modulate symbiosis and plant physiology and discuss the pros and cons of the tools used.

Light-sensitive short hypocotyl genes confer symbiotic nodule identity in the legume Medicago truncatula.

Legumes produce specialized root nodules that are distinct from lateral roots in morphology and function, with nodules intracellularly hosting nitrogen-fixing bacteria. We have previously shown that a lateral root program underpins nodule initiation, but there must be additional developmental regulators that confer nodule identity. Here, we show two members of the LIGHT-SENSITIVE SHORT HYPOCOTYL (LSH) transcription factor family, predominantly known to define shoot meristem complexity and organ boundaries, function as regulators of nodule organ identity. In parallel to the root initiation program, LSH1/LSH2 recruit a program into the root cortex that mediates the divergence into nodules, in particular with cell divisions in the mid-cortex. This includes regulation of auxin and cytokinin, promotion of NODULE ROOT1/2 and Nuclear Factor YA1, and suppression of the lateral root program. A principal outcome of LSH1/LSH2 function is the production of cells able to accommodate nitrogen-fixing bacteria, a key feature unique to nodules.

Seeking the interspecies crosswalk for filamentous microbe effectors.

Both pathogenic and symbiotic microorganisms modulate the immune response and physiology of their host to establish a suitable niche. Key players in mediating colonization outcome are microbial effector proteins that act either inside (cytoplasmic) or outside (apoplastic) the plant cells and modify the abundance or activity of host macromolecules. We compile novel insights into the much-disputed processes of effector secretion and translocation of filamentous organisms, namely fungi and oomycetes. We report how recent studies that focus on unconventional secretion and effector structure challenge the long-standing image of effectors as conventionally secreted proteins that are translocated with the aid of primary amino acid sequence motifs. Furthermore, we emphasize the potential of diverse, unbiased, state-of-the-art proteomics approaches in the holistic characterization of fungal and oomycete effectomes.

Flemish soils contain rhizobia partners for Northwestern Europe-adapted soybean cultivars.

In Europe, soybean (Glycine max) used for food and feed has to be imported, causing negative socioeconomic and environmental impacts. To increase the local production, breeding generated varieties that grow in colder climates, but the yield using the commercial inoculants is not satisfactory in Belgium because of variable nodulation efficiencies. To look for indigenous nodulating strains possibly adapted to the local environment, we initiated a nodulation trap by growing early-maturing cultivars under natural and greenhouse conditions in 107 garden soils in Flanders. Nodules occurred in 18 and 21 soils in the garden and greenhouse experiments respectively. By combining 16S rRNA PCR on single isolates with HiSeq 16S metabarcoding on nodules, we found a large bacterial richness and diversity from different soils. Furthermore, using Oxford Nanopore Technologies sequencing of DNA from one nodule, we retrieved the entire genome of a Bradyrhizobium species, not previously isolated, but profusely present in that nodule. These data highlight the need of combining diverse identification techniques to capture the true nodule rhizobial community. Eight selected rhizobial isolates were subdivided by whole-genome analysis in three genera containing six genetically distinct species that, except for two, aligned with known type strains and were all able to nodulate soybean in the laboratory.