Exploring agricultural landscape change from the second half of the twentieth century onwards: combining aerial imagery with farmer perspectives.

CONTEXT Anthropogenic landscape change is an important driver shaping our environment. Historical landscape analysis contributes to the monitoring and understanding of these change processes. Such analyses are often focused on specific spatial scales and single research methods, thus covering only limited aspects of landscape change. OBJECTIVES Here, we aim to assess the potential of combining the analysis of historical aerial imagery and local stakeholder interviews for landscape change studies using a standardized mapping and interviewing approach. METHODS We compared six agricultural landscapes across Europe and mapped land-cover using historical aerial imagery (starting between 1930 and 1980, depending on data availability, until recent years) with an object-based image analysis and random forest classification. For local perspectives of landscape change, we conducted oral history interviews (OHIs) with (almost) retired farmers. Comparing recorded landscape changes from both approaches provided insight into advantages of combining these two methods. RESULTS Object-based analysis enabled the identification of high-resolution land-cover dynamics, with scale enlargement and cropland/grassland expansion being the most commonly recurring trends across European landscapes. Perceived landscape changes identified in the OHIs included changes in farm management, landscape structure, and infrastructure. Farmers also reported drivers and personal values associated with landscape change. Combining the two historical landscape analysis tools resulted in a qualitative and quantitative understanding of changes in land-cover, land use, and land management. CONCLUSIONS Comparing physical land-cover change with local farmer perspectives is key to a comprehensive understanding of landscape change. There are different ways the two methods can be combined, leading to different venues for science and policy making. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10980-024-01914-z

Tropical forest patches under pressure - A fieldwork documentary from Africa

Embarking on a journey under the SUSTAINFORESTS project, Prof. Dr. Chinwe Ifejika Speranza and five PhDs, immersed themselves in a six-month exploration across Togo, Benin, Nigeria, and Cameroon. Their mission: unravel the intricacies of tropical forest patches. Armed with a terrestrial laser scanner, drones, and a lot of curiosity, the team conducted ecological forest inventories. They also engaged in enlightening focus group discussions and interviews with local communities. This 18-min film convinces with adventurous motorcycle rides, formidable wildlife, and the vivid realities of African fieldwork

A high fidelity approach to assembling the complex Borrelia genome

BackgroundBacteria of the Borrelia burgdorferi sensu lato (s.l.) complex can cause Lyme borreliosis. Different B. burgdorferi s.l. genospecies vary in their host and vector associations and human pathogenicity but the genetic basis for these adaptations is unresolved and requires completed and reliable genomes for comparative analyses. The de novo assembly of a complete Borrelia genome is challenging due to the high levels of complexity, represented by a high number of circular and linear plasmids that are dynamic, showing mosaic structure and sequence homology. Previous work demonstrated that even advanced approaches, such as a combination of short-read and long-read data, might lead to incomplete plasmid reconstruction. Here, using recently developed high-fidelity (HiFi) PacBio sequencing, we explored strategies to obtain gap-free, complete and high quality Borrelia genome assemblies. Optimizing genome assembly, quality control and refinement steps, we critically appraised existing techniques to create a workflow that lead to improved genome reconstruction. ResultsDespite the latest available technologies, stand-alone sequencing and assembly methods are insufficient for the generation of complete and high quality Borrelia genome assemblies. We developed a workflow pipeline for the de novo genome assembly for Borrelia using several types of sequence data and incorporating multiple assemblers to recover the complete genome including both circular and linear plasmid sequences. ConclusionOur study demonstrates that, with HiFi data and an ensemble reconstruction pipeline with refinement steps, chromosomal and plasmid sequences can be fully resolved, even for complex genomes such as Borrelia. The presented pipeline may be of interest for the assembly of further complex microbial genomes

Repository to Hepner et al. 2023 "A high fidelity approach to assembling the complex <em>Borrelia</em> genome"

The deposited data is part of Hepner, S., Kuleshov, K., Tooming-Kunderud, A. et al. A high fidelity approach to assembling the complex Borrelia genome. BMC Genomics 24, 401 (2023). https://doi.org/10.1186/s12864-023-09500-4 Alignment of PFam32 nucleotide sequences (including pseudogenes) of the plasmids (Hepner_et_al_2023_PFam32_ClustalW_alignment.fasta) and maximum-likelihood tree (Hepner_et_al_2023_PFam32_phylogenetic_tree.nwk, Hepner_et_al_2023_PFam32_phylogenetic_tree.nwk.pdf).</p

Additional file 1 of A high fidelity approach to assembling the complex Borrelia genome

Additional file 1: Table S1. QUAST and Merqury results. Table S2. Detailed information about assembly results after genome reconstruction of PBaeII, PBes and 89B13. Table S3. Summary of mapping statistics of PBaeII. Table S4. Mapping statistics for single genome elements of PBaeII. Table S5. List and characteristics of all isolates. Figures S1-S3. Dot plots B. bavariensis PBaeII. Figure S4. Dot plots B. garinii PBes, lp32-10, microbial assembler. Figure S5. Dot plot B. valaisiana 89B13, lp32-7, IPA. Figure S6. Dot plot B. valaisiana 89B13, lp25, microbial_circulomics. Figure S7. Mapping graphs of B. bavariensis PBaeII