Background Invasive alien species (IAS) cause significant economic losses in all parts of the world. Although IAS are widespread in Africa and cause serious negative impacts on livelihoods as a result of yield losses and increased labour costs associated with IAS management, few data on the impacts are available in the literature and the magnitude and extent of the costs are largely unknown. We estimated the cost of IAS to agriculture, the most important economic sector in Africa. Methods Data on the monetary costs of IAS to mainland Africa as well as information about the presence and abundance of the most important IAS were collected through literature review and an online survey among a wide variety of stakeholders. Using this and additional data from publicly available sources we estimated yield losses and management costs due to IAS in agriculture for individual countries and the entire continent. Where the data allowed, the costs for selected IAS or crops were estimated separately. The estimates were extrapolated using production and distribution data and/or matching of agro-ecological zones. Results The total estimated annual cost of IAS to agriculture in Africa is USD 3.66 Tn. Yield losses, reductions in livestock derived income and IAS management costs, mainly labour costs, constitute the majority of the estimated cost (ca. 1, < 1 and 99 percent, respectively). The IAS causing the highest yield losses were Phthorimaea absoluta (USD 11.4 Bn) and Spodoptera frugiperda (USD 9.4 Bn). Conclusions This study reveals the extent and scale of the economic impacts of IAS in the agricultural sector in one of the least studied continents. Although the cost estimate presented here is significant, IAS also cause major costs to other sectors which could not be assessed due to data deficit. The results highlight the need for pre-emptive management options, such as prevention and early detection and rapid response to reduce huge potential future costs, as well as measures that contribute to large-scale control of widely established IAS at little cost to farmers and other affected land users, to reduce losses and improve livelihoods.

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The Ascomycota form the largest phylum in the fungal kingdom and show a wide diversity of lifestyles, some involving associations with plants. Genomic data is available for many ascomycetes that are pathogenic to plants, but endophytes, which are asymptomatic inhabitants of plants, are relatively understudied. Here, using short- and long-read technologies, we have sequenced and assembled genomes for 15 endophytic ascomycete strains from CABI’s culture collections. We used phylogenetic analysis to refine the classification of taxa, which revealed that 7 of our 15 genome assemblies are the first for the genus and/or species. We also demonstrated that cytometric genome size estimates can act as a valuable metric for assessing assembly ‘completeness’, which can easily be overestimated when using BUSCOs alone and has broader implications for genome assembly initiatives. In producing these new genome resources, we emphasise the value of mining existing culture collections to produce data that can help to address major research questions relating to plant–fungal interactions.

Soil microbiomes are dynamic systems that respond to biotic and abiotic environmental factors such as those presented at seasonal scales or due to long-term anthropogenic regime shifts. These can affect the composition and function of microbiomes. Investigation of microbiomes can uncover hidden microbial roles in health and disease and discover microbiome-based interventions. Collections of soil samples are kept by various institutions in either a refrigerated or occasionally frozen state, but conditions are not optimised to ensure the integrity of soil microbiome. In this manuscript, we describe cryopreservation with a controlled rate cooler and estimate the genomic content of an exemplar soil sample before and after cryopreservation. The first hypothesis was to test the genomic integrity of the microbiome. We also enriched the soil sample with a liquid medium to estimate the growth of bacteria and compared their growth before and after cryopreservation. Sequence-based rRNA metabarcoding was used to demonstrate that the controlled rate cooler maintains intact the DNA content of the microbiome. Two methods of cryopreservation were applied and compared with control aliquots of soil. An optimised cryopreservation of soil samples is essential for the development of microbiome research in order to retain stable, functionally intact microbiomes. Our results showed that metabarcoding of 16S and ITS rRNA were useful methods to estimate successful cryopreservation. The soil microbiome after enrichment with liquid medium exhibited a similar response of cryopreserved soil and this was estimated with the comparison of the ten most abundant bacterial taxa. These findings support a successful process of cryopreservation and are promising for future use of this technology. To the best of our knowledge, this study is the first report of cryopreservation of soil using a Stirling cycle cooling approach.