National Institute of Agricultural Botany

Previous studies showed that dipping rice roots in a formulation of Trichoderma asperellum at the transplanting stage or applying the strain as a foliar spray post transplanting led to a statistically significant reduction in rice blast (caused by Magnaporthe oryzae) and increased grain yield in Tanzania. We investigated the effect of dipping at transplanting or post-transplanting spray application on the root-associated microbiome or leaf epiphytes via amplicon sequencing, and on plant responses via RNA-seq. Both root dipping and foliar application with T. asperellum spore suspension only had a limited impact on the leaf epiphytes and root/rhizosphere microbiome after 1 and 4 weeks of treatment, respectively. However, both treatments led to notable and persistent changes in plant responses in leaves. Moreover, root dipping led to greater and more persistent changes in plant responses than foliar spraying. About 3.3% and 4.3% of plant genes showed statistically significant differential expressions because of foliar spray and root dipping treatments, respectively. The foliar spray treatment led to changes in two out of the five identified gene modules, comprised of 216 and 890 genes, respectively. Root dipping led to changes in 24 out of the 32 identified gene modules. Although both treatments led to increased grain yield in previous field studies, many of the induced plant response changes in terms of directional changes of differentially expressed genes differed between root dipping and foliar spraying, particularly those related to chloroplast activities. The large non-overlapping induced plant changes between root dipping and foliar spraying explain the additive effects of the two treatments in increasing grain yield in previous field studies. The present results also suggest that reduction of blast because of foliar application of T. asperellum is unlikely because of direct antagonism against M. oryzae, but more likely via induced plant defence responses.

Clip-and-burn is a forestry and land management technique common in China and other tropical regions worldwide to clear land for agriculture or to manage vegetation. However, the dynamics of carbon and nitrogen in karst regions following clip-and-burn practices remain largely unknown. Here, we evaluate the impact of clip-and-burn management practices on carbon and nitrogen cycling in the Karst region of China. The treatments included high-intensity fire (HIF), low-intensity fire (LIF), clipping and fire (CF), clipping (CP), and control (CK). Soil samples were collected one year after treatment application. Clipping-and-burning significantly influenced soil organic carbon (SOC), total nitrogen (TN), nitrate (NO3-), and ammonium (NH4+) levels compared to the control. Clipping-and-burning treatments significantly (p < 0.05) reduced SOC, soil organic matter, TN, and NO3- compared to CK. In contrast, NH4+ content increased substantially under clip-and-burn treatments compared to CK, suggesting it potentially affects soil fertility and the recovery of plant life in the post-fire environment. Clipping-and-burning treatments showed higher Acidobacteria and Proteobacteria, likely driving C and N cycling, with Proteobacteria involved in N transformations. The higher bacterial diversity in LIF indicates more active nutrient cycling, with Actinobacteria indicating the importance of organic matter availability and nutrient balance. Moreover, CP significantly (p < 0.05) enhanced the metabolic potential for various N cycle processes, including N fixation, N uptake, and assimilatory NO3- reduction. On the other hand, CP also showed higher gene levels for N fixation than other treatments, indicating its effectiveness in promoting N assimilation in the soil. In addition, microbial biomass C, microbial biomass N, and microbial biomass P were significantly (p < 0.05) increased (by 10.70 %, 11.90 %, 25.60 % respectively) under CP treatment compared to CK. The changes in bacterial composition and diversity could have important implications for soil fertility, nutrient availability, and ecosystem functioning, particularly in terms of C sequestration and N availability in plants in the karst landscape. It suggests that careful fire management and selective clipping could enhance soil health and ecosystem productivity.

Genomes record past climatic impact on species’ range shifts, admixture, refugial isolation, and adaptative evolution. However, these processes are poorly understood in perennial herbaceous species forming a dominant group of temperate flora. We present a demographic history of the perennial herb woodland strawberry (Fragaria vesca L.) reconstructed from 200 genomes spanning most of its European range. Temporal population structure reveals a strong division into western and eastern genetic clusters along a longitudinal climatic gradient, with eastern core populations showing greater resilience during glaciations. Divergence patterns indicate that postglacial recolonization of western and eastern Europe occurred from distinct refugia in multiple waves. The current largest, admixed populations from the Mediterranean to northern Europe form a continuous chain maintained by east–west gene flow through Central Europe, with historical migration patterns indicating comparable connections during earlier interglacials. Our reconstruction of woodland strawberry’s climatic history with high temporal resolution reveals how the late Pleistocene core-periphery dynamics shaped its survival and genome evolution under climate change. The data points to populations that are essential for maintaining the long term genetic diversity of the species and opens new avenues to understand climatic adaptation of temperate flora. Population genomics of European woodland strawberry reveal distinct western and eastern genetic clusters with contrasting demographic histories across multiple glacial-interglacial cycles.

Top-cutting ('weed-surfing') is a pre-harvest strategy that reduces weed seedbank inputs by mechanically removing weed seed heads before seed shedding. To be effective, it requires weeds to set their inflorescences above the crop canopy. Here, a multi-factor two-year field study was conducted to evaluate the efficacy of this approach for four economically important grass species using two winter wheat varieties. The results demonstrate that efficacy is highly species-specific and dependent on cutting frequency and climatic conditions. While three repeated cutting treatments provided the highest level of control, a single cut, particularly applied at an early reproductive phase, was largely ineffective, removing less than 39 % of heads in the best case. The 'midsingle cutting' and 'two-cutting' treatments demonstrated intermediate and similar efficacy, reaching up to 81.9 %. Avena fatua was the most susceptible, with three cuts removing 92-96 % of seed heads. Lolium multiflorum was also well-controlled (69-80 % removal). The technique offered moderate, yearly variable efficacy against Alopecurus myosuroides (37-75 % removal) and was largely ineffective against Bromus secalinus (4-73 % removal), particularly in a drier year. A shorter-strawed wheat variety consistently improved removal efficacy by 14-35 % for A. myosuroides and B. secalinus. Furthermore, compensatory head production was limited and context-dependent, observed mainly in A. myosuroides and L. multiflorum in the wetter year. While early cutting removed fewer seed heads, it resulted in low seed viability (<8 %) from the cut heads across all species. In contrast, seeds from heads cut later showed high viability for A. myosuroides and B. secalinus (86-97 %) but consistently low for A. fatua and L. multiflorum (<= 44 %). This study demonstrates that top-cutting, when applied once at mid, twice (early and mid), or thrice (early, mid, and late) during the reproductive phase, is a practical approach for minimising seed return, combating herbicide resistance, and a valuable non-chemical component of integrated weed management, particularly for regenerative systems.

Puccinia coronata f. sp. avenae (Pca), a fungal pathogen causing crown rust of oat, demonstrates rapid virulence evolution and adaptation to newly released cultivars. To further capture the genetic variation of Pca, we generated nuclear haplotype-resolved genomes for 10 isolates from Europe, Africa, and the Middle East and compared these with existing references for U.S. and Australian isolates. Of the full collection of 52 haplotypes, 40 were unique. Importantly, the presence of a nearly identical haplotype in a U.K. isolate collected in 1984 and in U.S. isolates from 1990 and 2017 supports the existence of long-lived clonal haplotypes in the global population that have been exchanged between lineages. We identified infrequent recombination between haplotypes from geographically dispersed isolates, hinting toward a globally mobile population of Pca that is mostly composed of persistent clonal lineages with some influence from rare recombination events. One isolate contained an additional scaffold with telomeric and centromeric features, suggesting the presence of a supernumerary chromosome. Whereas the core pan-proteome is enriched for predicted secreted and effector proteins, sequence and expression variation are most prevalent in non-core orthogroups, which also displayed allele-specific expression. We anticipate that this expanded collection of haplotypes will facilitate the development of new surveillance technologies and identification of virulence loci. [Formula: see text] Copyright © 2026 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.