Near-Chromosome-Level Genome Assembly of the Dark Septate Endophyte Laburnicola rhizohalophila: A Model for Investigating Root-Fungus Symbiosis

Melanized root-associated fungi: key players in plant-soil systems

Melanized root-associated fungi are a group of fungi that produce melanized structures and form root associations, including different mycorrhizal and endophytic symbioses with plants. They are pervasive across terrestrial ecosystems and play an important role in the prevailing soil carbon (C) and nutrient cycling syndromes through direct and indirect mechanisms, where they may strongly modulate plant-microbe interactions and structure root and soil microbiomes. Furthermore, melanized root-associated fungi can confer on plants an enhanced ability to tolerate abiotic and biotic stressors such as drought, extreme temperatures, heavy metals, and pathogen attacks. We propose that melanized root-associated fungi are a cohesive and ecologically relevant grouping that can be an indicator of plant-soil system functioning, and considering them will advance research on plant-soil interactions.

Intraspecific diploidization of a halophyte root fungus drives heterosis

How organisms respond to environmental stress is a key topic in evolutionary biology. This study focused on the genomic evolution of Laburnicola rhizohalophila, a dark-septate endophytic fungus from roots of a halophyte. Chromosome-level assemblies were generated from five representative isolates from structured subpopulations. The data revealed significant genomic plasticity resulting from chromosomal polymorphisms created by fusion and fission events, known as dysploidy. Analyses of genomic features, phylogenomics, and macrosynteny have provided clear evidence for the origin of intraspecific diploid-like hybrids. Notably, one diploid phenotype stood out as an outlier and exhibited a conditional fitness advantage when exposed to a range of abiotic stresses compared with its parents. By comparing the gene expression patterns in each hybrid parent triad under the four growth conditions, the mechanisms underlying growth vigor were corroborated through an analysis of transgressively upregulated genes enriched in membrane glycerolipid biosynthesis and transmembrane transporter activity. In vitro assays suggested increased membrane integrity and lipid accumulation, as well as decreased malondialdehyde production under optimal salt conditions (0.3 M NaCl) in the hybrid. These attributes have been implicated in salinity tolerance. This study supports the notion that hybridization-induced genome doubling leads to the emergence of phenotypic innovations in an extremophilic endophyte.

Loss of the accessory chromosome converts a pathogenic tree-root fungus into a mutualistic endophyte

Some fungal accessory chromosomes (ACs) may contribute to virulence in plants. However, the mechanisms by which ACs determine specific traits associated with lifestyle transitions along a symbiotic continuum are not clear. Here we delineated the genetic divergence in two sympatric but considerably variable isolates (16B and 16W) of the poplar-associated fungus Stagonosporopsis rhizophilae. We identified a ∼0.6-Mb horizontally acquired AC in 16W that resulted in a mildly parasitic lifestyle in plants. Complete deletion of the AC (Δ16W) significantly altered the fungal phenotype. Specifically, Δ16W was morphologically more similar to 16B, showed enhanced melanization, and established beneficial interactions with poplar plants, thereby acting as a dark septate endophyte. RNA sequencing (RNA-seq) analysis showed that AC loss induced the upregulation of genes related to root colonization and biosynthesis of indole acetic acid and melanin. We observed that the AC maintained a more open status of chromatin across the genome, indicating an impressive remodeling of cis-regulatory elements upon AC loss, which potentially enhanced symbiotic effectiveness. We demonstrated that the symbiotic capacities were non-host-specific through comparable experiments on Triticum- and Arabidopsis-fungus associations. Furthermore, the three isolates generated symbiotic interactions with a nonvascular liverwort. In summary, our study suggests that the AC is a suppressor of symbiosis and provides insights into the underlying mechanisms of mutualism with vascular plants in the absence of traits encoded by the AC. We speculate that AC-situated effectors and other potential secreted molecules may have evolved to specifically target vascular plants and promote mild virulence.

Pervasive associations between dark septate endophytic fungi with tree root and soil microbiomes across Europe

Trees interact with a multitude of microbes through their roots and root symbionts such as mycorrhizal fungi and root endophytes. Here, we explore the role of fungal root symbionts as predictors of the soil and root-associated microbiomes of widespread broad-leaved trees across a European latitudinal gradient. Our results suggest that, alongside factors such as climate, soil, and vegetation properties, root colonization by ectomycorrhizal, arbuscular mycorrhizal, and dark septate endophytic fungi also shapes tree-associated microbiomes. Notably, the structure of root and soil microbiomes across our sites is more strongly and consistently associated with dark septate endophyte colonization than with mycorrhizal colonization and many abiotic factors. Root colonization by dark septate endophytes also has a consistent negative association with the relative abundance and diversity of nutrient cycling genes. Our study not only indicates that root-symbiotic interactions are an important factor structuring soil communities and functions in forest ecosystems, but also that the hitherto less studied dark septate endophytes are likely to be central players in these interactions.

Utilization of halophytes in saline agriculture and restoration of contaminated salinized soils from genes to ecosystem: Suaeda salsa as an example

Halophytes can be used to screen genes for breeding salt-tolerant crops and are of great value in the restoration of salinized or contaminated soils. However, the potential of halophytes in improving saline soils remains limited. In this paper, based on the latest research progress, we use Suaeda salsa L. as an example to evaluate the value of halophytes in developing saline agriculture including: 1) some defined salt-resistance genes and high-affinity nitrate transporter genes in the species for breeding salt-tolerance and nitrogen efficiency crops; 2) the value of S. salsa and microorganisms from S. salsa in remediation of heavy metal contaminated and organic polluted saline soils; and 3) the capacity to remove salts from soils and the application of the species. In conclusion, S. salsa has high value as a candidate to explore the theoretical base and practical application for utilizing halophytes to improve salinized soils from genes to ecosystem.

Trends in Harnessing Plant Endophytic Microbiome for Heavy Metal Mitigation in Plants: A Perspective

Plant microbiomes represent dynamic entities, influenced by the environmental stimuli and stresses in the surrounding conditions. Studies have suggested the benefits of commensal microbes in improving the overall fitness of plants, besides beneficial effects on plant adaptability and survival in challenging environmental conditions. The concept of 'Defense biome' has been proposed to include the plant-associated microbes that increase in response to plant stress and which need to be further explored for their role in plant fitness. Plant-associated endophytes are the emerging candidates, playing a pivotal role in plant growth, adaptability to challenging environmental conditions, and productivity, as well as showing tolerance to biotic and abiotic stresses. In this article, efforts have been made to discuss and understand the implications of stress-induced changes in plant endophytic microbiome, providing key insights into the effects of heavy metals on plant endophytic dynamics and how these beneficial microbes provide a prospective solution in the tolerance and mitigation of heavy metal in contaminated sites.

Two new root endophyte and nematode cyst parasite species of the widely distributed genus Laburnicola

Fungal root endophytes, including the common form group of dark septate endophytes (DSEs), represent different taxonomic groups with potentially diverse life strategies. During surveys of DSE communities and of nematode cysts colonizing fungi, isolates representing Laburnicola (Didymosphaeriaceae, Pleosporales) lineages were discovered. Here we carried out a comprehensive study of the phylogenetic relationships and taxonomy of fungi collected from plant roots in Hungary, Mongolia, and Kazakhstan and from eggs of the cereal cyst nematode Heterodera filipjevi in Turkey. In addition to the study of the morphology and culture characteristics of the strains, four loci (internal transcribed spacer, partial large and small subunit regions of nuclear ribosomal DNA and partial translation elongation factor 1-alpha) were used to infer the molecular phylogenetic relationships of the strains within Laburnicola. The isolates were found to represent two distinct lineages, which are described here as novel species, Laburnicola nematophila and L. radiciphila. The interaction of the strains with plants and nematodes was examined using in vitro bioassays, which revealed endophytic interactions with the plant roots and parasitic interactions with the nematode eggs. Analyses of similar ITS sequences found in public databases revealed that members of the genus Laburnicola are widely distributed characteristic members of the plant microbiome, and they are reported as parasites of plant parasitic cyst nematodes here for the first time.