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This study was part of an in vivo investigation of methane (CH4) abatement feed on local Menz breed sheep in Ethiopia, conducted over 90 days period using a randomized complete block design. Sheep were subjected to four dietary treatments: Control, Acacia (Acacia nilotica), BSG (Brewer's Spent Grain), and Ziziphus (Ziziphus spina-christi). The aim of the study was to investigate the rumen microbial community composition, diversity, and their relationships with CH4 intensity. Rumen fluid was collected on days 0 (SD_0), 45 (SD_45), and 90 (SD_90), using an esophageal tube. The dynamics of the bacterial and archaeal domains were assessed by 16S rRNA gene sequencing. The sequencing results showed that 92.9% of ASVs were Bacteria, and 0.05% Archaea. At the genus level, Rikenellaceae RC9 gut group (18%), Prevotella (17%), and Candidatus Saccharimonas (8.9%) were the most abundant Bacteria, while Methanobrevibacter (88%) dominated the Archaeal genera across all treatment groups. Treatment feed significantly altered microbial profiles, notably reducing Methanobrevibacter abundance in CH4 abatement diets and increasing the presence of Methanosphaera. Shannon diversity increased in the abatement diet and decreased when the sheep were fed BSG. CH4 intensity was most strongly associated with the archaeal genus Methanomicrobium, but did not associate strongly with any other Bacteria or Archaea, although Methanobrevibacter and Methanosphaera were correlated negatively (r = –0.97). CH4 intensity also did not covary with volatile fatty acids (VFAs), of which Acacia yielded the highest acetate (772 mmol/mol) and BSG the highest propionate (172 mmol/mol) concentration. The volatile fatty acids (VFAs) showed a strong correlation: a positive correlation between acetate and butyrate (r = 0.80) and a strong negative correlation between acetate and propionate (r = –0.92). These findings highlight the complex relationship between diet, rumen microbiota, and fermentation products, with implications for CH4 mitigation strategies in sheep.

The characterization of the seasonal dynamics of endophytic bacteria in beech leaves can be hindered by co-amplification of chloroplast and mitochondrial plant DNA. This study applies established peptide nucleic acid (PNA) clamps to suppress host-derived amplification while resolving bacterial succession across the vegetative season. Chloroplast- and mitochondrion-specific PNAs inverted the proportion of host to bacterial reads, enabled the recovery of bacterial sequence variants, and increased alpha diversity accordingly. Beta-diversity analyses showed that, once host contamination was removed, samples displayed a clear seasonal trajectory. Early-season leaves contained high abundances of Pseudomonas together with taxa likely introduced through plant–insect–microbe interactions. As leaves matured, the microbiome shifted toward a more stable composition dominated by well-established genera. The transition from early transient taxa to the later enrichment of phyllosphere-adapted and nutrient-cycling genera demonstrates that beech leaves host a temporally structured microbiome shaped by leaf development and seasonal environmental stress.

Background: Nickel (Ni) contamination is a significant constraint to agricultural sustainability and medicinal plant productivity, leading to oxidative stress, nutrient imbalance, and disruption of secondary metabolism. Dopamine (DA) has been reported as a stress-mitigating agent in plants. Still, its role in shaping antioxidants and phenolic responses to Ni toxicity in medicinal species, such as Salvia officinalis, remains poorly understood.

Results: Exposure to increasing Ni concentrations (0–1000 µM) significantly reduced biomass (-46%), chlorophyll b (-57%), and shoot Ca and Fe contents (-50% and − 63%, respectively), while elevating oxidative markers (hydrogen peroxide (H2O2), malondialdehyde (MDA); 2.6-fold increase). Foliar DA application (0-100 µM) partially alleviated these effects by restoring biomass (+ 42%), enhancing Ca and Fe translocation (up to 1.7-fold), and maintaining carotenoid levels at nearly twice the control level under moderate stress. DA reduced oxidative markers by 16–24% and moderated the over-accumulation of superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD) activities. Significantly, DA promoted phenolic-based antioxidant responses, increasing phenylalanine ammonia-lyase (PAL) (3.8-fold) and tyrosine aminotransferase (TAT) (1.5-fold) activities and stimulating rosmarinic acid accumulation (up to 91% above control). Multivariate analyses (principal component analysis (PCA), heatmap clustering, correlation networks, random forest) supported these findings, indicating that DA-treated plants clustered with low-stress phenotypes and shifted their defense balance toward phenolic rather than enzyme-dominated strategies.

Conclusions: This study provides integrative physiological and metabolic evidence that DA enhances Ni tolerance in sage by reducing oxidative damage, supporting nutrient uptake, and reinforcing phenolic metabolism. These results highlight DA as a promising candidate biostimulant under controlled conditions, with relevance to the sustainable cultivation of medicinal plants in metal-contaminated soils, pending further validation.

This book explores the emerging field of plant molecular farming, highlighting its potential in producing biopharmaceuticals, combating diseases, and advancing sustainable agriculture. It covers diverse topics, including plant-based biopharmaceuticals, transient expression systems, antiviral plant extracts, nanogene delivery, and the role of AI in biopharmaceutical production. With contributions from leading experts, the chapters provide in-depth insights into innovative strategies and technologies shaping this field. This book is a valuable resource for researchers, academicians, and professionals in biotechnology, agriculture, and pharmaceutical sciences, as well as policymakers and students seeking to understand the future of plant-based innovations.

Potato is the world's third most important food crop, yet its production relies heavily on pesticides, creating a need for sustainable alternatives. We assessed how straw mulching, a practice known to improve soil fertility, enrich microbial activity, and suppress diseases, affects below-ground bacterial community structure and functional potential across different potato-associated sample types. A field experiment was conducted in northern Sweden using two potato cultivars under mulched and control soil conditions. Samples from the rhizosphere, root, soil, and tuber peel were analyzed using 16S ribosomal RNA (rRNA) gene sequencing (Illumina platform) to assess bacterial diversity and community composition. Straw mulching significantly increased bacterial richness and altered community structure across sample types and cultivars. Copiotrophic genera, which thrive in nutrient-rich environments, included Rhodanobacter, Mucilaginibacter, Flavobacterium, and Pseudomonas, and were enriched in rhizosphere, root, and tuber peel. Oligotrophs such as Bryobacter and Candidatus Solibacter dominated the soil and are known to contribute to organic matter turnover and plant growth. Notably, in the peel of one cultivar (King Edward), the abundance of Pseudomonas increased 5–7-fold, correlating with elevated starch and ascorbic acid contents of the tubers. In conclusion, the effect of straw mulching on soil bacterial communities and tuber quality appears to be diverse and cultivar dependent. Long-term and large-scale studies are needed to evaluate cumulative impacts on soil health, yield, and resilience.

Plants are associated with microbial communities, which are inherited through the seed and acquired from the environment. These microbiomes influence plant physiology, chemistry, and functioning. Yet, we lack insights into how seed origin and the environmental microbiome jointly influence the leaf metabolome. We used untargeted metabolomics (gas chromatography/mass spectrometry) on leaves of pedunculate oak (Quercus robur) seedlings to examine metabolic responses to different seed origins and environmental microbiomes, as well as home and away environments. For this, acorns were collected from three mother trees and grown in a multifactorial design with soil and canopy microbiomes originating from the local mother tree (i.e., the home treatment) and neighbouring trees (i.e., the away treatment). We also measured two plant traits—plant height and leaf chlorophyll content—to examine relationships between plant traits and the metabolome. The leaf metabolome did not differ significantly between plants growing with different soil and canopy microbiomes. However, the leaf metabolome differed among acorn origins and between seedlings growing in home vs. away treatments. We found no clear link between plant traits and the leaf metabolome. This study is one of the first to disentangle the combined effects of seed origin and environmental microbiomes on plant leaf chemistry, and the home vs. away framework provides novel insights into local adaptation effects on plant metabolomes within forest ecosystems. These findings have practical implications for the use of local genotypes and the development of microorganism-based management practices in sustainable forestry and agriculture.

This study aims to identify candidate genes involved in the biosynthesis of salicinoid phenolic glycosides (SPGs), a group of specialised metabolites characteristic of the Salicaceae family. While the integration of multi-omics data represents a powerful approach to link genes encoding enzymes and their regulatory factors to metabolite biosynthesis, suitable multi-omics data resources are scarce. We present a comprehensive dataset comprising untargeted liquid chromatography–mass spectrometry (LC–MS) and mRNA-sequencing data from various organs of European aspen (Populus tremula L.) and from genotypes that produce contrasting sets of SPGs. We present a reproducible pipeline for the analysis of the LC–MS data, including predicted annotation of potential novel SPGs. We demonstrate the utility of the resource by identifying candidate genes involved in the biosynthesis of SPGs with a cinnamoyl moiety. By integrating gene and metabolite differential analyses with a gene co-expression network, we identified two HXXXD-type acyltransferase genes and one UDP-glucosyltransferase gene as candidates for future downstream characterisation. The combined gene expression and metabolomics resource is integrated into PlantGenIE.org to facilitate easy access and data mining. All raw data are available in public databases, and all data and results files are available at an associated Figshare repository.

Plant growth-promoting rhizobacteria (PGPRs) play a crucial role in enhancing plant development through a variety of direct and indirect mechanisms. These include the production of phytohormones, nitrogen fixation, phosphate solubilization, siderophore-mediated iron acquisition, and biocontrol of plant pathogens. Predominantly inhabiting the rhizosphere, PGPRs interact with plant roots via complex molecular and ecological processes involving signalling molecules, metabolite exchanges, and modulation of plant immune responses. Such interactions enhance nutrient uptake and stress tolerance but also contribute to long-term plant health and productivity across diverse environmental conditions. This review focuses on the genera Pseudomonas and Bacillus, which are extensively studied for their strong colonization abilities, metabolic versability, and demonstrated potential in improving crop resilience. Advances in microbial genomics, metagenomics, and high-throughput phenotyping have greatly enhanced our ability to identify, characterize, and apply beneficial microbes across a range of crop systems. However, key challenges remain, including limited understanding of native soil microbiotas, the functional outcome of microbiome-soil-plant interactions, and the development of agricultural practices that efficiently integrate microbial solutions. With potato (Solanum tuberosum) as a model crop, this review synthesizes current knowledge on PGRP-mediated growth promotion - primarily by Pseudomonas and Bacillus acting alone or in microbial consortia, identifies critical research gaps, and outlines future directions for the application of PGPRs in sustainable crop production.

Based on discussions within the Northern Tubers of Potato network (N’TOP-net), this review highlights northern Scandinavia’s potential for sustainable, low pest seed potato production. While long transport distances currently limit large-scale supply for consumption or processing, low pest pressure and stricter EU plant protection regulations increase its value for seed production. Climate change is expected to extend the growing season, driving renewed interest in Northern Scandinavia’s role in European food security. Finland exemplifies this potential, and parts of northern and central Sweden—historically suppliers of disease-free seed potatoes, even exported to Brazil—offer expansion opportunities. Nordic potato production, key biotic stressors, and opportunities for regional cooperation are examined, with a focus on novel farming practices, breeding innovations, and disease surveillance to improve resilience and sustainability. Despite shared values in cultivar selection, certification, and potato preferences, Nordic production strategies remain uncoordinated for long-term sustainability. We advocate for transnational, interdisciplinary collaboration to enhance Europe’s food security through joint efforts in three key areas: (1) soil-conserving farming, (2) breeding for adaptation to longer day length and resistance traits, and (3) transnational pest and disease surveillance. A Nordic potato initiative can strengthen European cooperation on sustainable production amid climate change. However, as policies must balance the benefits of longer growing seasons with emerging risks such as pests, droughts, and flooding, coordinated research, regulatory adaptation, and climate resilience investments are essential for safeguarding seed potato quality, food security, and supply chain stability.

Crop pests and diseases increasingly challenge the global food system. To prepare for and detect outbreaks, surveillance plays an important role. Traditional monitoring methods are often organism-specific, making large-scale monitoring of crop pathogens and pests impractical. We here investigate the potential for using shotgun sequencing of airborne eDNA for large-scale surveillance of crop pathogens and pests. We show that it is possible to detect DNA from all types of organisms in air, and that DNA can be classified down to species level. However, the accuracy of the identification is highly dependent on the quality of reference genomes of both the pathogens or pests, and their close relatives present in the region. Finally, we find that observed degree of crop damages correlate with amount of DNA from crop pathogens and pests in air, showing the promise of this approach for surveillance of all types of crop pathogens and pests.