Maintaining soil health is fundamental to sustaining agricultural productivity, however, the intricate role of soil microbial diversity in this process is not fully understood. Current research acknowledges that soil microorganisms including bacteria, fungi, and archaea are pivotal in driving essential soil functions such as nutrient cycling, organic matter decomposition, and disease suppression. However, the impacts of global environmental changes and intensive agricultural practices on the diversity of these microorganisms remain a critical gap in the literature. This gap is significant because a decline in microbial diversity could severely compromise soil health, and consequently crop productivity. Here, we provide a comprehensive review of the factors influencing soil microbial diversity and examine their implications for crop performance. We assess both natural factors such as soil pH, moisture, temperature, and vegetation type as well as human-induced factors including tillage systems and fertilizer application. The review synthesizes recent findings on how these factors shape microbial communities and their functional roles in nutrient cycling, soil structure formation, and disease suppression. Our analysis highlights the mechanisms by which microbial diversity enhances plant growth and yield, addressing the gap in understanding the direct links between microbial diversity and agricultural outcomes. Our findings underscore the urgent need for sustainable agricultural practices that protect and enhance microbial diversity to safeguard long-term soil fertility and crop productivity. By addressing the challenges in manipulating soil microbial communities and integrating microbial ecology with crop management practices, this research advances our ability to sustain agricultural systems in the face of global environmental changes.

Current agricultural practices face numerous challenges, including declining soil fertility and heavy reliance on chemical inputs. Rhizosphere microbial metabolites have emerged as promising agents for enhancing crop health and yield in a sustainable manner. These metabolites, including phytohormones, antibiotics, and volatile organic compounds, play critical roles in promoting plant growth, boosting resistance to pathogens, and improving resilience to environmental stresses. This review comprehensively outlines the mechanisms through which rhizosphere microbial metabolites influence crop health, traits, functional components, and yield. It also discusses the potential applications of microbial secondary metabolites in biofertilizers and highlights the challenges associated with their production and practical use. Measures to overcome these challenges are proposed, alongside an exploration of the future development of the functional fertilizer industry. The findings presented here provide a scientific basis for utilizing rhizosphere microbial metabolites to enhance agricultural sustainability, offering new strategies for future crop management. Integrating these microbial strategies could lead to increased crop productivity, improved quality, and reduced dependence on synthetic chemical inputs, thereby supporting a more environmentally friendly and resilient agricultural system.

Insect chemoreception involves many families of genes, including odourant/pheromone binding proteins (OBP/PBPs), chemosensory proteins (CSPs), odourant receptors (ORs), ionotropic receptors (IRs), and sensory neuron membrane proteins (SNMPs), which play irreplaceable roles in mediating insect behaviors such as host location, foraging, mating, oviposition, and avoidance of danger. However, little is known about the molecular mechanism of olfactory reception in Chilo sacchariphagus, which is a major pest of sugarcane. A set of 72 candidate chemosensory genes, including 31 OBPs/PBPs, 15 CSPs, 11 ORs, 13 IRs, and two SNMPs, were identified in four transcriptomes from different tissues and genders of C. sacchariphagus. Phylogenetic analysis was conducted on gene families and paralogs from other model insect species. Quantitative real-time PCR (qRT-PCR) showed that most of these chemosensory genes exhibited antennae-biased expression, but some had high expression in bodies. Most of the identified chemosensory genes were likely involved in chemoreception. This study provides a molecular foundation for the function of chemosensory proteins, and an opportunity for understanding how C. sacchariphagus behaviors are mediated via chemical cues. This research might facilitate the discovery of novel strategies for pest management in agricultural ecosystems.

Background: Ecologically derived synthetic communities can provide robust plant benefits, yet generalizable rules for assembling multifunctional consortia remain limited. We hypothesized that a “top-down” community assembled from an ecological core would yield complementary functions and resilience superior to reductionist mixes. Results: We distilled an eight-member, Bacillus-dominated synthetic community (hereafter referred to as SynCom) from a rice–duckweed agroecosystem by targeting taxa consistently shared across soil, root and shoot niches. Under greenhouse conditions, the SynCom concurrently promoted rice growth and suppressed sheath blight caused by Rhizoctonia solani , reducing the final disease index by 70% without detectable phytotoxicity. Leave-one-member perturbations (−Dx), combined with untargeted LC–MS profiling and qRT-PCR of biosynthetic genes, revealed a division-of-labor architecture: individual strains specialized in auxin production, siderophore-linked iron mobilization, or lipopeptide/polyketide-based antagonism. These complementary yet partially redundant contributions mapped members, metabolite pools, plant outcomes and rendered community performance resilient to single-member loss. Across −Dx contrasts, the complete SynCom uniquely recovered the full suite of plant-growth metabolites (e.g., indole-3-acetic acid, acetoin/2,3-butanediol) together with antimicrobial chemistries (e.g., surfactin, bacillomycin, fengycin, difficidin). We formalize an assembly heuristic, ecological core, complementary functions, redundancy check, that links ecological origin to predictable, multi-trait performance. Conclusions: A top-down, ecology-guided route can generate a multifunction SynCom with demonstrated greenhouse efficacy and mechanistic transparency. By coupling-member perturbations with multi-omics readouts, our study provides a transferable rule for building resilient plant-associated consortia and a tractable framework for future genetic and in-plant chemical confirmations.

Trichogramma is a useful species that is widely applied in biocontrol. Temperature profoundly affects the commercial application of T. chilonis. Different developmental transcriptomes of prepupae and pupae of T. chilonis under 10, 25, and 40°C were obtained from our previous study. In this study, transcriptomic analysis was further conducted to gain a clear understanding of the molecular changes in the prepupae of T. chilonis under different thermal conditions. A total of 37,295 unigenes were identified from 3 libraries of prepupae of T. chilonis, 17,293 of which were annotated. Differential expression analysis showed that 408 and 108 differentially expressed genes (DEGs) were identified after heat and cold treatment, respectively. Under heat stress, the pathway of protein processing in endoplasmic reticulum was found to be active. Most of the genes involved in this pathway were annotated as lethal (2) essential for life [l(2)efl] and heat shock protein genes (hsps), which were both highly upregulated. Nevertheless, most of the genes involved in another significantly enriched pathway of starch and sucrose metabolism were downregulated, including 1 alpha‐glucosidase gene and 2 beta‐glucuronidase genes. Under cold stress, no significantly enriched pathway was found, and the significantly enriched GO terms were related to the interaction with host and immune defenses. Together, these results provide us with a comprehensive view of the molecular mechanisms of T. chilonis in response to temperature stresses and will provide new insight into the mass rearing and utilization of T. chilonis.

Background: Maize kernel colour is an important index for evaluating maize quality and value and mainly entails two natural pigments, carotenoids and anthocyanins. To analyse the genetic mechanism of maize kernel colour and mine single nucleotide polymorphisms (SNPs) related to kernel colour traits, an association panel including 244 superior maize inbred lines was used to measure and analyse the six traits related to kernel colour in two environments and was then combined with the about 3 million SNPs covering the whole maize genome in this study. Two models (Q + K, PCA + K) were used for genome-wide association analysis (GWAS) of kernel colour traits. Results: We identified 1029QTLs, and two SNPs contained in those QTLs were located in coding regions of Y1 and R1 respectively, two known genes that regulate kernel colour. Fourteen QTLs which contain 19 SNPs were within 200 kb interval of the genes involved in the regulation of kernel colour. 13 high-confidence SNPs repeatedly detected for specific traits, and AA genotypes of rs1_40605594 and rs5_2392770 were the most popular alleles appeared in inbred lines with higher levels. By searching the confident interval of the 13 high-confidence SNPs, a total of 95 candidate genes were identified. Conclusions: The genetic loci and candidate genes of maize kernel colour provided in this study will be useful for uncovering the genetic mechanism of maize kernel colour, gene cloning in the future. Furthermore, the identified elite alleles can be used to molecular marker-assisted selection of kernel colour traits.