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Plant physiological status is the interaction between the plant genome and the prevailing growth conditions. Accurate characterization of plant physiology is, therefore, fundamental to effective plant phenotyping studies; particularly those focused on identifying traits associated with improved yield, lower input requirements, and climate resilience. Here, we outline the approaches used to assess plant physiology and how these techniques of direct empirical observations of processes such as photosynthetic CO2 assimilation, stomatal conductance, photosystem II electron transport, or the effectiveness of protective energy dissipation mechanisms are unsuited to high-throughput phenotyping applications. Novel optical sensors, remote/proximal sensing (multi- and hyperspectral reflectance, infrared thermography, sun-induced fluorescence), LiDAR, and automated analyses of below-ground development offer the possibility to infer plant physiological status and growth. However, there are limitations to such indirect approaches to gauging plant physiology. These methodologies that are appropriate for the rapid high temporal screening of a number of crop varieties over a wide spatial scale do still require calibration or validation with direct empirical measurement of plant physiological status. The use of deep-learning and artificial intelligence approaches may enable the effective synthesis of large multivariate datasets to more accurately quantify physiological characters rapidly in high numbers of replicate plants. Advances in automated data collection and subsequent data processing represent an opportunity for plant phenotyping efforts to fully integrate fundamental physiological data into vital efforts to ensure food and agro-economic sustainability.

Tuberaceae is one of the most diverse lineages of symbiotic truffle-forming fungi. To understand the molecular underpinning of the ectomycorrhizal truffle lifestyle, we compared the genomes of Piedmont white truffle (Tuber magnatum), Périgord black truffle (Tuber melanosporum), Burgundy truffle (Tuber aestivum), pig truffle (Choiromyces venosus) and desert truffle (Terfezia boudieri) to saprotrophic Pezizomycetes. Reconstructed gene duplication/loss histories along a time-calibrated phylogeny of Ascomycetes revealed that Tuberaceae-specific traits may be related to a higher gene diversification rate. Genomic features in Tuber species appear to be very similar, with high transposon content, few genes coding lignocellulose-degrading enzymes, a substantial set of lineage-specific fruiting-body-upregulated genes and high expression of genes involved in volatile organic compound metabolism. Developmental and metabolic pathways expressed in ectomycorrhizae and fruiting bodies of T. magnatum and T. melanosporum are unexpectedly very similar, owing to the fact that they diverged ~100 Ma. Volatile organic compounds from pungent truffle odours are not the products of Tuber-specific gene innovations, but rely on the differential expression of an existing gene repertoire. These genomic resources will help to address fundamental questions in the evolution of the truffle lifestyle and the ecology of fungi that have been praised as food delicacies for centuries.

Orchids are highly dependent on their mycorrhizal fungal partners for nutrient supply, especially during early developmental stages. In addition to organic carbon, nitrogen (N) is probably a major nutrient transferred to the plant because orchid tissues are highly N-enriched. We know almost nothing about the N form preferentially transferred to the plant or about the key molecular determinants required for N uptake and transfer. We identified, in the genome of the orchid mycorrhizal fungus Tulasnella calospora, two functional ammonium transporters and several amino acid transporters but found no evidence of a nitrate assimilation system, in agreement with the N preference of the free-living mycelium grown on different N sources. Differential expression in symbiosis of a repertoire of fungal and plant genes involved in the transport and metabolism of N compounds suggested that organic N may be the main form transferred to the orchid host and that ammonium is taken up by the intracellular fungus from the apoplatic symbiotic interface. This is the first study addressing the genetic determinants of N uptake and transport in orchid mycorrhizas, and provides a model for nutrient exchanges at the symbiotic interface, which may guide future experiments.

Summary: Arbuscular (AM) and orchid (OrM) mycorrhiza are the most widespread mycorrhizal symbioses among flowering plants, formed by distinct fungal and plant species. They are both endosymbioses because the fungal hyphae can enter inside the plant cell to develop intracellular fungal structures that are surrounded by the plant membrane. The symbiotic plant–fungus interface is considered to be the major site of nutrient transfer to the host plant. We summarize recent data on nutrient transfer in OrM and compare the development and function of the arbuscules formed in AM and the pelotons formed in OrM in order to outline differences and conserved traits. We further describe the unexpected similarities in the form and function of the intracellular mycorrhizal fungal structures observed in orchids and in the roots of mycoheterotrophic plants forming AM. We speculate that these similarities may be the result of convergent evolution of mycorrhizal types in mycoheterotrophic plants and highlight knowledge gaps and new research directions to explore this scenario. [ABSTRACT FROM AUTHOR]

This document is an editorial published in the journal Frontiers in Plant Science. It discusses the use of omics techniques to optimize plant-microbe interactions under climate change. The editorial highlights the importance of understanding these interactions and their impact on crop yield and quality in the face of environmental stresses. It also mentions the application of biostimulants based on microorganisms to improve plant growth and stress tolerance, as well as the use of agronomic and genetic approaches to enhance crop yields. The document emphasizes the need for multi-omics approaches to further explore plant-microbe interactions and their potential for improving plant survival under changing climate conditions. [Extracted from the article]