We've launched the Legume Genomics Research Platform version 2 (LGRPv2), now with 413 genomes including 144 legumes and Tamarindus indica. It offers browsing tools, annotations for 18,050,760 protein-coding genes, synteny analyses, and identification of paralogs, orthologs, and trait genes. New tools like DotView, SynView, DecoBrowse, and AncVisual enhance exploration. Integrated resources include a species encyclopedia, omics data, and a comparative genomics toolbox with 58 tools (31 new). Our aim with LGRPv2 is to be a comprehensive resource for legume genomics. Additionally, it offers intuitive query, analysis, and visualization tools, along with statistical charts, user manuals, communities, and submission portals, ensuring usability for all users, making it a vital asset for legume genomics research.

Plants possess a unique class of heterotrimeric Gα subunits called extra-large GTPases (XLGs) which contribute to numerous developmental and stress responses. In addition to the canonical Gα domain, XLGs have an uncharacterized N-terminal domain and functions that are distinct from conventional Gα subunits. In this study, we identified homologs of XLG3 in Lotus japonicus responsive to rhizobial and mycorrhizal symbiosis. However, these proteins were approximately one-third the size of conventional XLGs and only aligned to the N-terminal domain, containing a putative nuclear localization signal and a cysteine-rich domain of unknown function. Multiple sequence alignment and phylogenetic analysis determined these small XLGs (SXLGs) did not share domains with other mono– or heterotrimeric G-protein classes and exhibited a pattern of duplication and neofunctionalization typical of genes involved in symbiotic signaling pathways. Transient expression of LjSXLGs in tobacco demonstrated their potential for localization to the plasma membrane, nucleus, and nucleolus. Analysis of L. japonicus sxlg2 mutants revealed transient impairment of immature nodule formation in a destructive experimental setup and inhibition of infection events in a nutrient-limited non-destructive experimental setup, with a delayed onset of established infection events and a potential impact on nodule maturation rate. Additionally, sxlg2 mutants showed a potential impairment of the root growth response in N-limited conditions. We discuss the potential utility of SXLGs in better understanding the evolution of XLGs and their possible function as transcriptional regulators, as well as the likelihood SXLGs are involved in the establishment of rhizobial and mycorrhizal symbioses through influencing membrane reorganization, such as during infection thread development.

Plant roots are the site of dynamic and complex interactions between a variety of microorganisms, such as fungi, bacteria, and archaea. Plant Growth-Promoting Rhizobacteria (PGPR) is one of those that are important for improving the health and growth of plants. Bacteria are among the most abundant and diverse microorganisms in the rhizosphere. These bacteria contribute to various processes, including nitrogen fixation, phosphate solubilization, and production of plant growth-promoting substances, thereby enhancing plant nutrient uptake and growth. Fungi are another important component of the rhizosphere microbiota. These microbes are used as bioinoculants in the agricultural field, replacing the traditional use of pesticides. Bioinoculants do not show any detrimental impact on the soil's plant and animal life as they are eco-friendly, highly efficient, and can be utilized as bio-pesticides that do not have any harmful influence on plant products. Understanding the composition and functions of rhizosphere microbiota is crucial for developing sustainable agricultural practices that harness the beneficial interactions between plants and microorganisms to enhance soil fertility and crop productivity while minimizing environmental impacts. This review examines the emerging use of microorganisms in the agricultural field, which can replace the chemical fertilizers that are proven hazardous if used extensively over crops, specifically regarding the important micronutrients required by the plant. The current study addresses the gap in the effectiveness of these microorganisms as bio-inoculants in the rhizosphere and future aspects of the microbes for crop productivity.

Rhizobia are soil-dwelling proteobacteria that can enter into symbiotic nitrogen-fixing relationships with compatible leguminous plants. Taxonomically, rhizobia are divided into alpha-rhizobia, which belong to the class Alpharoteobacteria, and beta-rhizobia, which belong to the class Betaproteobacteria. To date, all bona fide alpha-rhizobia belong to the order Hyphomicrobiales. However, a recent study suggested that Sphingomonas sediminicola DSM 18106T is also a rhizobium and is capable of nodulating pea plants (Pisum sativum), which would expand the known taxonomic distribution of alpha-rhizobia to include the order Sphingomonadales. Here, we attempted to replicate the results of that previous study. Resequencing and computational analysis of the genome of S. sediminicola DSM 18106T failed to identify genes encoding proteins involved in legume nodulation or nitrogen fixation. In addition, experimental plant assays indicated that S. sediminicola DSM 18106T is unable to nodulate the two cultivars of pea tested in our study, unlike the rhizobium Rhizobium johnstonii 3841T. Taken together, and in contrast to the previous study, these results suggest that S. sediminicola DSM 18106T is not capable of inducing root nodule formation on pea, meaning that the taxonomic distribution of all known alpha-rhizobia remains limited to the class Hyphomicrobiales.

GmbHLHm1 is a basic Helix-Loop-Helix membrane (bHLHm1) DNA binding transcription factor localized to the symbiosome membrane and nucleus in soybean (Glycine max ) nodules. Overexpression of GmbHLHm1 significantly increased nodule number and size, nitrogen fixation activity,and nitrogen delivery to the shoots. This contrasts with reduced nodule numbers per plant, nitrogen fixation activity and poor plant growth when silenced using RNAi. The promoter of GmbHLHm1 was found to be sensitive to exogenous GA supply, decreasing the level of GUS expression in transformed hairy roots in both nodules and roots and reducing native GmbHLHm1 expression in wild-type nodules. In summary, our study suggests that GmbHLHm1 positively regulates soybean nodulation and nitrogen fixation, and that GA can negatively regulate GmbHLHm1 expression in soybean nodules.

Crops are increasingly exposed to drought and nutrient deficiencies, necessitating enhanced resistance to adverse conditions to meet the growing demands of the global population. While crop productivity has been greatly improved by integrating traits for high yield and stress tolerance through breeding, yield plateaus are now being observed. The rhizosheath, with physical and biological properties distinct from bulk soil, presents a promising target for enhanced tolerance to abiotic stresses such as drought and nutrient deficiencies. This multifunctional region contributes substantially to stress resistance and nutrient cycling, playing a pivotal role in the context of climate change and diminishing supplies of non-renewable fertilisers. We highlight the potential of the rhizosheath as a valuable breeding target to enhance crop productivity under diverse challenging environmental conditions.

Fungi are one of the most diverse and ecologically important groups of organisms on Earth. They exhibit remarkable diversity in their ecological roles, ranging from decomposers to mutualistic symbionts to parasites. They have a wide array of lifestyles, which reflect their diverse ecological roles and evolutionary adaptations to marine, aquatic, and terrestrial ecosystems. Fungi are osmotrophs that grow as filaments of cells (hyphae) into their food, secrete digestive enzymes across their cells’ chitinous walls, and absorb dissolved nutrients. The classification of fungal lifestyles is primarily based on how they obtain nutrients, with the major modes of nutrition being saprotrophy, parasitism, mutualism and commensalism. Here, we briefly explore these various lifestyles, illustrating their significance in ecosystems and their relationships with other organisms, and then discuss how comparative genomics provides novel insights into their evolutionary trajectories.

Legumes are an important and sustainable part of cropping systems due to their ability to form a symbiotic relationship with soil bacteria called rhizobia that can directly fix nitrogen from the atmosphere.
Genetic studies have unravelled the many and varied regulatory mechanisms legumes have evolved to control host–microbe interactions, host infection, and nodule development.
New breeding technologies present an opportunity for the targeted genetic improvement of nitrogen fixation in legumes, in terms of both host and microbe partner.
Challenges remain, however, to identify the optimal approaches considering the large diversity in legume species and agricultural environments.

Background: Soybean is one of the most popular agricultural commodities in Indonesia, but its production is still low. Thus, it is necessary to make efforts to expand its agriculture in the form of marginal land development.
Aims: This study aims to examine the effect and obtain the best treatment dose of arbuscular mycorrhizal fungi (AMF) in ultisol soil to increase the growth of soybean plants (Glycine max (L.) Merill).
Methods: This experimental study employed a complete randomized design (CRD) with the treatment of arbuscular mycorrhizal fungi (AMF). The AMF treatment comprised five levels: no AMF, 4 g/polibag, 8 g/polibag, 12 g/polibag and 16 g/polibag. Each treatment was repeated four times, resulting in 20 experimental units and each experimental unit comprised three polybags so that this study used 60 polybags. The data were analyzed using Analysis of Variance (ANOVA) and continued with Duncan's New Multiple Range Test (DNMRT) at the 5% level.
Result: AMF treatment is able to increase the growth of soybean plants in the parameters of plant height, number of productive branches, flowering age, number of flowers, and harvest age. The AMF treatment dose of 12 g/polybag is proven to give the best results in increasing the growth of soybean plants. The use of AMF can be an effective strategy in optimizing soybean production, especially on marginal lands.

It has been discovered that many phytopathogenic fungi can absorb exogenous double-stranded RNAs (dsRNAs) to silence target genes, inhibiting fungal growth and pathogenicity for plant protection. In our recent report, the beneficial arbuscular mycorrhizal (AM) fungi are capable of acquiring external naked dsRNAs; however, whether the dsRNAs can be delivered into AM fungi through nanocarriers remains to be investigated. Here, we introduce a simple and advanced method for in vitro synthesizing chitosan (CS)/dsRNA polyplex nanoparticles (PNs) to silence the target gene in the AM fungus Rhizophagus irregularis. This method is straightforward, requiring minimal modifications, and is both efficient and eco-friendly, offering potential for rapid application in elucidating gene functions in AM fungi.

Phosphate transporters play a key role in improving crop yield. In this study, TaPT31-7A is a high-affinity phosphate transporter strongly induced in arbuscular-mycorrhizal (AM) wheat roots. It restores Pi uptake in yeast mutant MB192 and localizes to the plasma membrane. TaPT31-7A overexpression lines accumulated more shoot and root phosphorus than the wild type under both low- and high-Pi conditions. When inoculated with AM in Pi-deficient soil, these overexpression lines displayed enhanced Pi uptake, higher mycorrhization, and improved growth, ultimately increasing the spikelet number per spike, spike length, 1000-grain weight, grain length, and grain width. Transcriptome and coexpression analyses of TaPT31-7A OE lines and control plants showed altered expression of phosphate-starvation and AM-development genes, while docking and yeast two-hybrid assays confirmed its interaction with PP2C phosphatase TaPP2C12-6A. These results establish TaPT31-7A as a central regulator of Pi uptake, AM symbiosis, and productivity in wheat and highlight its potential for breeding phosphorus-efficient cultivars.

Unlike many fungi, arbuscular mycorrhizal (AM) fungi have proven recalcitrant to genetic manipulation due to their obligate biotrophic lifestyle and multinucleate, coenocytic cellular structure. In this review, we examine past attempts at AM fungal transformation, we identify key biological and technical barriers and explore recent advances to overcome them. We focus on techniques never before applied in AM fungi, including CRISPR/Cas9, microinjection, and protoplast-based transformation, and we explore how they provide viable strategies for achieving this elusive goal. We conclude by outlining guidelines for future research, distinguishing between established approaches that are readily applicable to AM fungi and others that first require addressing key outstanding questions in AM fungal cell biology and genetics to ensure success.

Arbuscular mycorrhizal (AM) symbiosis is an important biological breakthrough which assisted plant land colonization over 400 million years ago. This widespread mutualistic interaction between fungi and plants enhances nutrient exchange, ecological sustainability, plant stress resistance, and host plant development. AM symbiosis improves plant nutrition by deriving nutrients through both mycorrhizal pathways and the Plant's own pathways. AMF influence nutrient availability by altering soil properties, microbial populations, and nutrient cycling. Understanding the life cycle of AMF, spore germination, sporulation, colonization, and symbiosis formation are critical for large-scale agricultural applications. Root organ culture (ROC) techniques offer intriguing possibilities to mass producing AMF under in vitro. This review surveys the literature on these topics, focusing on methods for enhancing sporulation in in vitro. Enhancing in vitro sporulation can be achieved by supplementing growth media with phenolic compounds, fatty acids, and phytohormones, and optimizing the media and related factors. These compounds regulate fungal growth and development, leading to increased sporulation and improved AMF inoculant efficacy. Further research is needed to provide quality inoculum and develop crop-specific formulations and delivery methods to harness the potential of AMF in diverse agroecosystems.

Unraveling the mechanisms underlying the maintenance of species diversity is a central pursuit in ecology. It has been hypothesized that ectomycorrhizal (EcM) in contrast to arbuscular mycorrhizal fungi can reduce tree species diversity in local communities, which remains to be tested at the global scale. To address this gap, we analyzed global forest inventory data and revealed that the relationship between tree species richness and EcM tree proportion varied along environmental gradients. Specifically, the relationship is more negative at low latitudes and in moist conditions but is unimodal at high latitudes and in arid conditions. The negative association of EcM tree proportion on species diversity at low latitudes and in humid conditions is likely due to more negative plant-soil microbial interactions in these regions. These findings extend our knowledge on the mechanisms shaping global patterns in plant species diversity from a belowground view.

Globally, invasive plants, animals, and microbes are a dominant threat to biodiversity and ecosystems, inflicting over $1 trillion USD in damage annually. Hundreds of microbial invasive taxa are documented.
Currently, we are inoculating microbes into many environments in enormous numbers to fertilize agricultural soils, remediate contamination, control eutrophication, precipitate minerals, and restore ecosystem functions.
Given the astronomical numbers and myriad environments that are being inoculated with microbes, these manipulations risk creating microbial invasions in much the same way that catastrophic plant and animal invasions have been precipitated by intentional introductions by humans.
A mechanistic understanding and predictive framework for the potential for microbial inoculants to cause invasions is needed to balance their benefits with their risks of causing harmful effects.