CAB International

Here, we describe AgMicrobiomeBase as an output of the UK Crop Microbiome Cryobank (UKCMCB) project, including details of the underlying meta-barcode sequence-based methods and three microbiome analysis case studies. The UKCMCB links genomic datasets and associated soil metadata with a cryobank collection of samples, for six economically significant crops: fava bean (Vicia faba), oil seed rape (Brassica napus), spring barley (Hordeum vulgare), spring oats (Avena sativa), spring wheat (Triticum aestivum) and sugar beet (Beta vulgaris). The crops were grown in nine agricultural soils from the UK, representing three major soil texture classes. The UKCMCB is a scalable sequence-based data catalogue linked to a cryo-preserved sample collection. The focus of this paper is the amplicon sequencing, associated bioinformatics workflows, and development of the project data catalogue. Short-read amplicon sequencing (16 S rRNA gene and ITS region) was implemented to describe the rhizosphere and bulk soil communities, for the multiple crop-soil combinations. Three case studies illustrate how different biological questions in phytobiome research can be addressed using this data resource. The three case studies illustrate how to (1) determine the impact of soil texture and location on microbiome composition, (2) determine a core microbiome for a single crop across different soil types, and (3) analyse a single genus, Fusarium within a single crop microbiome. The UKCMCB data catalogue AgMicroBiomeBase ( https://agmicrobiomebase.org/data ) links the sequence-based data with soil metadata and to cryopreserved samples. The UKCMCB provides baseline data and resources to enable researchers to assess the impact of soil type, location and crop type variables on crop soil microbiomes. The resource can be used to address biological questions and cross-study comparisons. Development of the UKCMCB will continue with the addition of metagenome and bacterial isolate genomic sequence data and has the potential to integrate additional data types including microbial phenotypes and synthetic microbial communities.

Abstract Background: Climate change poses critical challenges to global livestock systems, threatening productivity, food security, and environmental sustainability. The ruminant microbiome, particularly the rumen microbial community, plays a vital role in animal health, nutrition, and productivity, while also contributing to greenhouse gas emissions. Framing the microbiome within a One Health perspective highlights its importance for animal well-being, human nutrition, and environmental resilience. Methods: This review synthesizes evidence on the impacts of climate-related stressors, including heat, drought, and feed scarcity on the livestock microbiome. It examines interventions such as probiotics, prebiotics, fecal microbiota transplantation, dietary modifications, and synthetic biology approaches, alongside strategies to inhibit methanogenic archaea. Advances in microbiome analytics, including omics platforms, sensors, and machine learning, are discussed in relation to precision livestock farming and monitoring of animal health and emissions. Results: Findings indicate that microbiome shifts under climate stressors influence both livestock productivity and methane emissions. Meta-analyses and field trials demonstrate that feed and microbial additives and methanogenesis inhibitors can decrease enteric methane emissions by 20–80%, enhance feed conversion efficiency by 5–15%, and sustain milk production under heat stress conditions. While technological innovations enable more precise monitoring, significant gaps remain in understanding host–microbe–climate interactions, and barriers such as technical limitations, regulatory hurdles, and farmer adoption challenges persist. Integrated multi-omics methodologies now elucidate key genes and pathways that regulate fermentation resilience, facilitating precise microbiome engineering via probiotics, bacteriophages, and CRISPR-mediated modulation of methanogens. Beyond biological innovation, microbiome-focused approaches are consistent with international One Health frameworks (FAO–WHO–WOAH), facilitating the mitigation of antimicrobial resistance (AMR), reduction of zoonotic risks, and reporting of greenhouse gas emissions within climate-smart agricultural initiatives. Integrating microbiome metrics into national livestock, AMR, and climate policies can elevate them from experimental instruments to quantifiable sustainability strategies. Conclusion: Overall, this review demonstrates that harnessing the ruminant microbiome has the potential to reduce global agricultural methane emissions by up to 40%, while simultaneously enhancing animal resilience and productivity – positioning the microbiome as a critical biological and policy frontier for climate-smart, One Health-oriented livestock transformation. Microbiome-based strategies offer a promising pathway toward climate-smart livestock systems. Achieving this will require harmonized research methodologies, systems-based multi-omics approaches, cross-sectoral collaboration, and supportive policy frameworks. Integrating microbiome innovations into climate adaptation strategies can strengthen livestock productivity, improve food security, and support environmental resilience. One Health impact statement This review underscores the centrality of the ruminant microbiome at the interface of animal, human, and environmental health. By shaping livestock productivity, methane emissions, and antimicrobial resistance dynamics, microbial communities act as critical levers for sustainable food systems. Integrating microbiome science into livestock management contributes to safer food, reduced zoonotic and AMR risks, and lower greenhouse gas outputs, thereby aligning with the global One Health agenda. Advancing microbiome-based interventions through selective breeding, dietary strategies, and precision livestock farming, offers practical opportunities to strengthen climate resilience, improve animal welfare, and safeguard public health.

BACKGROUND: Fungal pathogens are major contributors to global losses of crop yields. Despite large-scale efforts to develop fungicides and resistant plant genotypes, disease outbreaks still pose severe risks to food security due to fungicide resistance and high adaptability of fungal pathogens. Genetic mechanisms behind the acquisition of resistance and renewed virulence have been uncovered by genome sequencing, especially of pathogens of main crops targeted by major control programs. Here, we investigate the use of comparative genomics of historical isolates to investigate how the wider community of fungal plant pathogens evolved during agricultural intensification. RESULTS: We analysed historical cryopreserved fungal isolates from three species that were collected in the UK between 1950 and 2000. Comparative genomics of 32 genomes was used to identify variable genome regions that represent putative targets of strong selection during this period, focusing especially on targets of fungicides and putative effector genes that might underpin changes in virulence. Using methods suitable for isolate rather than population sampling, we found evidence of rapid changes in single nucleotide polymorphism frequency in a suite of genes involved in pathogenesis, which overlapped partly between two of the species. We also found turnover in effector gene content in the UK during the period, but generally conserved evolution of fungicide target genes. Sample time and host explained similar amounts of variation in both single nucleotide polymorphism (SNP) changes and variation in effector gene content. CONCLUSIONS: The described approach could be scaled up in the future to reconstruct the evolution of hundreds of species and samples held in historical fungal collections worldwide throughout the course of the Green Revolution.

Climate change has resulted in the emergence of several plant pathogens, which have caused a huge yield loss to crops globally. Among them, a soil-borne necrotrophic fungus Macrophomina phaseolina (Tassi) Goid is an economically important pathogen because of its wide host range and geographic distribution. The pathogen causes dry root rot of chickpeas, a serious disease threatening chickpea production in Ethiopia. Isolates of M. phaseolina were obtained from symptomatic chickpea roots from ten districts across three zones in Central Ethiopia. The isolates were examined for variability in their morpho-genetic and pathogenic characteristics. A significant variation in colony growth and sclerotia traits was observed among the isolates. At 72 h after incubation, 21 isolates were rated as fast-growing, six as medium-growing, and two isolates as slow-growing. The isolates had a colony growth rate ranging from 9.4 to 17.1 mm day(-1). The isolates had four colony pigmentations: pale-grey, grey, black, and greenish-grey. Four isolates were classified as having small-sized sclerotia, whereas five were medium, and 20 isolates were large-sized. The sclerotia of the isolates exhibited four morphotypes: round, oblong, ovoid, and irregular. Principal component analysis (PCA) revealed that morphological characters accounted for the greatest variation among the isolates. The pathogenicity of the isolates varied from strongly to highly virulent on chickpeas. Using morphological and pathogenicity traits, principal coordinate analysis clustered the isolates into four groups, whereas hierarchical cluster analysis into ten groups. The isolates revealed 99.7-100 % ITS and LSU rDNA sequence identity to several reference isolates deposited in GenBank. This study documented basic information for designing management strategies for this emerging pathogen in Ethiopia.

Biological invasions are one of the major drivers of biodiversity decline and have been shown to have far-reaching consequences for society and the economy. Preventing the introduction and spread of alien species represents the most effective solution to reducing their impacts on nature and human well-being. However, implementing effective solutions requires a good understanding of where the species are established and how biological invasions develop over time. Knowledge of the status and trends of biological invasions is thus key for guiding research efforts, informing stakeholders and policymakers, for targeted management efforts, and preparing for the future. However, information about the status and trends of alien species is scattered, patchy, and highly incomplete, making it difficult to assess. Published reports for individual regions and taxonomic groups are available, but large-scale overviews are scarce. A global assessment therefore requires a review of available knowledge with careful consideration of sampling and reporting biases. This paper provides a comprehensive global assessment of the status and trends of alien species for major taxonomic groups [Bacteria, Protozoa, Stramenopila, Alveolata, and Rhizaria (SAR), fungi, plants, and animals] for Intergovernmental Panel of Biodiversity and Ecosystem Services (IPBES) regions. The review provides irrefutable evidence that alien species have been introduced to all regions worldwide including Antarctica and have spread to even the most remote islands. The numbers of alien species are increasing within all taxa and across all regions, and are often even accelerating. Large knowledge gaps exist, particularly for taxonomic groups other than vascular plants and vertebrates, for regions in Africa and Central Asia, and for aquatic realms. In fact, for inconspicuous species, such as Bacteria, Protozoa, and to some degree SAR and fungi, we found records for very few species and regions. Observed status and trends are thus highly influenced by research effort. More generally, it is likely that all lists for alien species of any taxonomic group and region are incomplete. The reported species numbers therefore represent minima, and we can expect additions to all lists in the near future. We identified six key challenges which need to be addressed to reduce knowledge gaps and to improve our ability to assess trends and status of biological invasions.