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The predicted 80 open reading frames (ORFs) of herpes simplex virus 1 (HSV-1) have been intensively studied for decades. Here, we unravel the complete viral transcriptome and translatome during lytic infection with base-pair resolution by computational integration of multi-omics data. We identify a total of 201 transcripts and 284 ORFs including all known and 46 novel large ORFs. This includes a so far unknown ORF in the locus deleted in the FDA-approved oncolytic virus Imlygic. Multiple transcript isoforms expressed from individual gene loci explain translation of the vast majority of ORFs as well as N-terminal extensions (NTEs) and truncations. We show that NTEs with non-canonical start codons govern the subcellular protein localization and packaging of key viral regulators and structural proteins. We extend the current nomenclature to include all viral gene products and provide a genome browser that visualizes all the obtained data from whole genome to single-nucleotide resolution. Here, using computational integration of multi-omics data, the authors provide a detailed transcriptome and translatome of herpes simplex virus 1 (HSV-1), including previously unidentified ORFs and N-terminal extensions. The study also provides a HSV-1 genome browser and should be a valuable resource for further research.
The fruit fly Drosophila melanogaster is an established model organism in chronobiology, because genetic manipulation and breeding in the laboratory are easy. The circadian clock neuroanatomy in D. melanogaster is one of the best-known clock networks in insects and basic circadian behavior has been characterized in detail in this insect. Another model in chronobiology is the honey bee Apis mellifera, of which diurnal foraging behavior has been described already in the early twentieth century. A. mellifera hallmarks the research on the interplay between the clock and sociality and complex behaviors like sun compass navigation and time-place-learning. Nevertheless, there are aspects of clock structure and function, like for example the role of the clock in photoperiodism and diapause, which can be only insufficiently investigated in these two models. Unlike high-latitude flies such as Chymomyza costata or D. ezoana, cosmopolitan D. melanogaster flies do not display a photoperiodic diapause. Similarly, A. mellifera bees do not go into “real” diapause, but most solitary bee species exhibit an obligatory diapause. Furthermore, sociality evolved in different Hymenoptera independently, wherefore it might be misleading to study the social clock only in one social insect. Consequently, additional research on non-model insects is required to understand the circadian clock in Diptera and Hymenoptera. In this review, we introduce the two chronobiology model insects D. melanogaster and A. mellifera, compare them with other insects and show their advantages and limitations as general models for insect circadian clocks.
Modern agriculture is the basis of human existence, a blessing, but also a curse. It provides nourishment and well-being to the ever-growing human population, yet destroys biodiversity-mediated processes that underpin productivity: ecosystem services such as water filtration, pollination and biological pest control. Ecological intensification is a promising alternative to conventional farming, and aims to sustain yield and ecosystem health by actively managing biodiversity and essential ecosystem services. Here, I investigate opportunities and obstacles for ecological intensification. My research focuses on 1) the relative importance of soil, management and landscape variables for biodiversity and wheat yield (Chapter II); 2) the influence of multi-scale landscape-level crop diversity on biological pest control in wheat (Chapter III) and 3) on overall and functional bird diversity (Chapter IV). I conclude 4) by introducing a guide that helps scientists to increase research impact by acknowledging the role of stakeholder engagement for the successful implementation of ecological intensification (Chapter V).
Ecological intensification relies on the identification of natural pathways that are able to sustain current yields. Here, we crossed an observational field study of arthropod pests and natural enemies in 28 real-life wheat systems with an orthogonal on-field insecticide-fertilizer experiment. Using path analysis, we quantified the effect of 34 factors (soil characteristics, recent and historic crop management, landscape heterogeneity) that directly or indirectly (via predator-prey interactions) contribute to winter wheat yield. Reduced soil preparation and high crop rotation diversity enhanced crop productivity independent of external agrochemical inputs. Concurrently, biological control by arthropod natural enemies could be restored by decreasing average field sizes on the landscape scale, extending crop rotations and reducing soil disturbance. Furthermore, reductions in agrochemical inputs decreased pest abundances, thereby facilitating yield quality.
Landscape-level crop diversity is a promising tool for ecological intensification. However, biodiversity enhancement via diversification measures does not always translate into agricultural benefits due to antagonistic species interactions (intraguild predation). Additionally, positive effects of crop diversity on biological control may be masked by inappropriate study scales or correlations with other landscape variables (e.g. seminatural habitat). Therefore, the multiscale and context-dependent impact of crop diversity on biodiversity and ecosystem services is ambiguous. In 18 winter wheat fields along a crop diversity gradient, insect- and bird-mediated pest control was assessed using a natural enemy exclusion experiment with cereal grain aphids. Although birds did not influence the strength of insect-mediated pest control, crop diversity (rather than seminatural habitat cover) enhanced aphid regulation by up to 33%, particularly on small spatial scales. Crop diversification, an important Greening measure in the European Common Agricultural Policy, can improve biological control, and could lower dependence on insecticides, if the functional identity of crops is taken into account. Simple measures such as ‘effective number of crop types’ help in science communication.
Although avian pest control did not respond to landscape-level crop diversity, birds may still benefit from increased crop resources in the landscape, depending on their functional grouping (feeding guild, conservation status, habitat preference, nesting behaviour). Observational studies of bird functional diversity on 14 wheat study fields showed that non-crop landscape heterogeneity rather than crop diversity played a key role in determining the richness of all birds. Insect-feeding, non-farmland and non-threatened birds increased across multiple spatial scales (up to 3000 m). Only crop-nesting farmland birds declined in heterogeneous landscapes. Thus, crop diversification may be less suitable for conserving avian diversity, but abundant species benefit from overall habitat heterogeneity. Specialist farmland birds may require more targeted management approaches.
Identifying ecological pathways that favour biodiversity and ecosystem services provides opportunities for ecological intensification that increase the likelihood of balancing conservation and productivity goals. However, change towards a more sustainable agriculture will be slow to come if research findings are not implemented on a global scale. During dissemination activities within the EU project Liberation, I gathered information on the advantages and shortcomings of ecological intensification and its implementation. Here, I introduce a guide (‘TREE’) aimed at scientists that want to increase the impact of their research. TREE emphasizes the need to engage with stakeholders throughout the planning and research process, and actively seek and promote science dissemination and knowledge implementation. This idea requires scientists to leave their comfort zone and consider socioeconomic, practical and legal aspects often ignored in classical research.
Ecological intensification is a valuable instrument for sustainable agriculture. Here, I identified new pathways that facilitate ecological intensification. Soil quality, disturbance levels and spatial or temporal crop diversification showed strong positive correlations with natural enemies, biological pest control and yield, thereby lowering the dependence on agrochemical inputs. Differences between functional groups caused opposing, scale-specific responses to landscape variables. Opposed to our predictions, birds did not disturb insect-mediated pest control in our study system, nor did avian richness relate to landscape-level crop diversity. However, dominant functional bird groups increased with non-crop landscape heterogeneity. These findings highlight the value of combining different on-field and landscape approaches to ecological intensification. Concurrently, the success of ecological intensification can be increased by involving stakeholders throughout the research process. This increases the quality of science and reduces the chance of experiencing unscalable obstacles to implementation.