Grasslands play an important role in conserving natural biodiversity and providing ecosystem functions and services for societies. Soil fertility is an important property in grassland, and the monitoring of soil fertility can provide crucial information to optimize ecosystem productivity and sustainability. Testing various soil physiochemical properties related to fertility usually relies on traditional measures, such as destructive sampling, pre-test treatments, labor-intensive procedures, and costly laboratory measurements, which are often difficult to perform. However, soil enzyme activity reflecting the intensity of soil biochemical reactions is a reliable indicator of soil properties and thus enzyme assays could be an efficient alternative to evaluate soil fertility. Here, we review the latest research on the features and functions of enzymes catalyzing the biochemical processes that convert organic materials to available plant nutrients, increase soil carbon and nutrient cycling, and enhance microbial activities to improve soil fertility. We focus on the complex relationships among soil enzyme activities and functions, microbial biomass, physiochemical properties, and soil/crop management practices. We highlight the biochemistry of enzymes and the rationale for using enzyme activities to indicate soil fertility. Finally, we discuss the limits and disadvantages of the potential new molecular tool and provide suggestions to improve the reliability and feasibility of the proposed alternative.

A vast majority of terrestrial plants are dependent on arbuscular mycorrhizal fungi (AMF) for their nutrient acquisition. AMF act as an extension of the root system helping phosphate uptake. In agriculture, harnessing the symbiosis can potentially increase plant growth. Application of the AMF Rhizophagus irregularis has been demonstrated to increase the yields of various crops. However, there is a paradigm that AMF colonization of roots, as well as the plant benefits afforded by inoculation with AMF, decreases with increasing phosphorus (P) supply in the soil. The paradigm suggests that when fertilized with sufficient P, inoculation of crops would not be beneficial. However, the majority of experiments demonstrating the paradigm were conducted in sterile conditions without a background AMF or soil microbial community. Interestingly, intraspecific variation in R. irregularis can greatly alter the yield of cassava even at a full application of the recommended P dose. Cassava is a globally important crop, feeding 800 million people worldwide, and a crop that is highly dependent on AMF for P uptake. In this study, field trials were conducted at three locations in Kenya and Tanzania using different AMF and cassava varieties under different P fertilization levels to test if the paradigm occurs in tropical field conditions. We found that AMF colonization and inoculation responsiveness of cassava does not always decrease with an increased P supply as expected by the paradigm. The obtained results demonstrate that maximizing the inoculation responsiveness of cassava is not necessarily only in conditions of low P availability, but that this is dependent on cassava and fungal genotypes. Thus, the modeling of plant symbiosis with AMF under different P levels in nature should be considered with caution.

SUMMARY: Communities of microorganisms (microbiota) are present in all habitats on Earth and are relevant for agriculture, health, and climate. Deciphering the mechanisms that determine microbiota dynamics and functioning within the context of their respective environments or hosts (the microbiomes) is crucially important. However, the sheer taxonomic, metabolic, functional, and spatial complexity of most microbiomes poses substantial challenges to advancing our knowledge of these mechanisms. While nucleic acid sequencing technologies can chart microbiota composition with high precision, we mostly lack information about the functional roles and interactions of each strain present in a given microbiome. This limits our ability to predict microbiome function in natural habitats and, in the case of dysfunction or dysbiosis, to redirect microbiomes onto stable paths. Here, we will discuss a systematic approach (dubbed the N + 1/N−1 concept) to enable step-by-step dissection of microbiome assembly and functioning, as well as intervention procedures to introduce or eliminate one particular microbial strain at a time. The N+1/N−1 concept is informed by natural invasion events and selects culturable, genetically accessible microbes with well-annotated genomes to chart their proliferation or decline within defined synthetic and/or complex natural microbiota. This approach enables harnessing classical microbiological and diversity approaches, as well as omics tools and mathematical modeling to decipher the mechanisms underlying N+1/N−1 microbiota outcomes. Application of this concept further provides stepping stones and benchmarks for microbiome structure and function analyses and more complex microbiome intervention strategies.

Meeting global food demands by 2050 requires a 45–60% increase in agricultural production. Plasticulture has emerged as a pivotal yet controversial solution. Here we perform a meta-analysis synthesizing the findings of global studies and reveal that plastic mulch enhances crop yields by 28.7% and water use efficiency by 48.9% under diversified systems. In China (2015–2024), plasticulture contributed an additional 189 million tons (Mt) of staple food, conserved 33.5 million hectares of arable land, and reduced emissions by 438 Mt CO₂-equivalent. However, persistent plastic residues degrade soils, and nanoplastics infiltrate food chains, posing ecological and health risks. Despite global negotiations (2024–2025), a binding UN treaty on plastic pollution remains stalled due to disparities among players. To reconcile productivity with sustainability, we propose six evidence-based priorities: (1) scaling integrated eco-farming systems with AI-driven precise application of soil mulches; (2) accelerating material innovation, focusing on biodegradable films and organic-based alternatives; (3) deploying blockchain-enabled circular economies for plastic waste; (4) improving reuse and recycling infrastructure; (5) implementing localized incentive mechanisms to support plastic-free farming; and (6) integrating plastic management into UN carbon trading frameworks. These strategies can pivot plasticulture toward a climate-resilient, ecologically sustainable model—balancing food security with environmental stewardship in an era of climate uncertainty.

Early-diverging fungi (EDF) are distinct from Dikarya and other eukaryotes, exhibiting high N6-methyldeoxyadenine (6mA) contents, rather than 5-methylcytosine (5mC). As plants transitioned to land the EDF sub-phylum, arbuscular mycorrhizal fungi (AMF; Glomeromycotina) evolved a symbiotic lifestyle with 80% of plant species worldwide. Here we show that these fungi exhibit 5mC and 6mA methylation characteristics that jointly set them apart from other fungi. The model AMF, R. irregularis, evolved very high levels of 5mC and greatly reduced levels of 6mA. However, unlike the Dikarya, 6mA in AMF occurs at symmetrical ApT motifs in genes and is associated with their transcription. 6mA is heterogeneously distributed among nuclei in these coenocytic fungi suggesting functional differences among nuclei. While far fewer genes are regulated by 6mA in the AMF genome than in EDF, most strikingly, 6mA methylation has been specifically retained in genes implicated in components of phosphate regulation; the quintessential hallmark defining this globally important symbiosis.

Horizontal gene transfer (HGT) is an important mechanism in the evolution of many living organisms particularly in Prokaryotes where genes are frequently dispersed between taxa. Although, HGT has been reported in Eukaryotes, its accumulative effect and its frequency has been questioned. Arbuscular mycorrhizal fungi (AMF) are an early diverged fungal lineage belonging to phylum Glomeromycota, whose phylogenetic position is still under debate. The history of AMF and land plant symbiosis dates back to at least 460 Ma. However, Glomeromycota are estimated to have emerged much earlier than land plants. In this study, we surveyed genomic and transcriptomic data of the model arbuscular mycorrhizal fungus Rhizoglomus irregulare (synonym Rhizophagus irregularis) and its relatives to search for evidence of HGT that occurred during AMF evolution. Surprisingly, we found a signature of putative HGT of class I ribonuclease III protein-coding genes that occurred from autotrophic cyanobacteria genomes to R. irregulare. At least one of two HGTs was conserved among AMF species with high levels of sequence similarity. Previously, an example of intimate symbiosis between AM fungus and cyanobacteria was reported in the literature. Ribonuclease III family enzymes are important in small RNA regulation in Fungi together with two additional core proteins (Argonaute/piwi and RdRP). The eukaryotic RNA interference system found in AMF was conserved and showed homology with high sequence similarity in Mucoromycotina, a group of fungi closely related to Glomeromycota. Prior to this analysis, class I ribonuclease III has not been identified in any eukaryotes. Our results indicate that a unique acquisition of class I ribonuclease III in AMF is due to a HGT event that occurred from cyanobacteria to Glomeromycota, at the latest before the divergence of the two Glomeromycota orders Diversisporales and Glomerales.