The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

A genomic database of all Earth’s eukaryotic species could contribute to many scientific discoveries; however, only a tiny fraction of species have genomic information available. In 2018, scientists across the world united under the Earth BioGenome Project (EBP), aiming to produce a database of high-quality reference genomes containing all ~1.5 million recognized eukaryotic species. As the European node of the EBP, the European Reference Genome Atlas (ERGA) sought to implement a new decentralised, equitable and inclusive model for producing reference genomes. For this, ERGA launched a Pilot Project establishing the first distributed reference genome production infrastructure and testing it on 98 eukaryotic species from 33 European countries. Here we outline the infrastructure and explore its effectiveness for scaling high-quality reference genome production, whilst considering equity and inclusion. The outcomes and lessons learned provide a solid foundation for ERGA while offering key learnings to other transnational, national genomic resource projects and the EBP.info:eu-repo/semantics/publishedVersio

Perceptions of the appropriate response to norm violation in 57 societies

An Author Correction to this article: DOI: 10.1038/s41467-021-22955-x.Norm enforcement may be important for resolving conflicts and promoting cooperation. However, little is known about how preferred responses to norm violations vary across cultures and across domains. In a preregistered study of 57 countries (using convenience samples of 22,863 students and non-students), we measured perceptions of the appropriateness of various responses to a violation of a cooperative norm and to atypical social behaviors. Our findings highlight both cultural universals and cultural variation. We find a universal negative relation between appropriateness ratings of norm violations and appropriateness ratings of responses in the form of confrontation, social ostracism and gossip. Moreover, we find the country variation in the appropriateness of sanctions to be consistent across different norm violations but not across different sanctions. Specifically, in those countries where use of physical confrontation and social ostracism is rated as less appropriate, gossip is rated as more appropriate.Peer reviewe

The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.

ABSTRACT: A global genome database of all of Earth’s species diversity could be a treasure trove of scientific discoveries. However, regardless of the major advances in genome sequencing technologies, only a tiny fraction of species have genomic information available. To contribute to a more complete planetary genomic database, scientists and institutions across the world have united under the Earth BioGenome Project (EBP), which plans to sequence and assemble high-quality reference genomes for all ∼1.5 million recognized eukaryotic species through a stepwise phased approach. As the initiative transitions into Phase II, where 150,000 species are to be sequenced in just four years, worldwide participation in the project will be fundamental to success. As the European node of the EBP, the European Reference Genome Atlas (ERGA) seeks to implement a new decentralised, accessible, equitable and inclusive model for producing high-quality reference genomes, which will inform EBP as it scales. To embark on this mission, ERGA launched a Pilot Project to establish a network across Europe to develop and test the first infrastructure of its kind for the coordinated and distributed reference genome production on 98 European eukaryotic species from sample providers across 33 European countries. Here we outline the process and challenges faced during the development of a pilot infrastructure for the production of reference genome resources, and explore the effectiveness of this approach in terms of high-quality reference genome production, considering also equity and inclusion. The outcomes and lessons learned during this pilot provide a solid foundation for ERGA while offering key learnings to other transnational and national genomic resource projects.info:eu-repo/semantics/publishedVersio

Changes in social norms during the early stages of the COVID-19 pandemic across 43 countries

The emergence of COVID-19 dramatically changed social behavior across societies and contexts. Here we study whether social norms also changed. Specifically, we study this question for cultural tightness (the degree to which societies generally have strong norms), specific social norms (e.g. stealing, hand washing), and norms about enforcement, using survey data from 30,431 respondents in 43 countries recorded before and in the early stages following the emergence of COVID-19. Using variation in disease intensity, we shed light on the mechanisms predicting changes in social norm measures. We find evidence that, after the emergence of the COVID-19 pandemic, hand washing norms increased while tightness and punishing frequency slightly decreased but observe no evidence for a robust change in most other norms. Thus, at least in the short term, our findings suggest that cultures are largely stable to pandemic threats except in those norms, hand washing in this case, that are perceived to be directly relevant to dealing with the collective threat

Anger and disgust shape judgments of social sanctions across cultures, especially in high individual autonomy societies

When someone violates a social norm, others may think that some sanction would be appropriate. We examine how the experience of emotions like anger and disgust relate to the judged appropriateness of sanctions, in a pre-registered analysis of data from a large-scale study in 56 societies. Across the world, we find that individuals who experience anger and disgust over a norm violation are more likely to endorse confrontation, ostracism and, to a smaller extent, gossip. Moreover, we find that the experience of anger is consistently the strongest predictor of judgments of confrontation, compared to other emotions. Although the link between state-based emotions and judgments may seem universal, its strength varies across countries. Aligned with theoretical predictions, this link is stronger in societies, and among individuals, that place higher value on individual autonomy. Thus, autonomy values may increase the role that emotions play in guiding judgments of social sanctions

Endophytes in the buds of Scots pine (<em>Pinus sylvestris</em> L.)

Abstract Although microbes are generally found as endophytes in many plant tissues, the plant shoot meristems have been considered virtually sterile. Plant tissue culture, which utilizes mostly the meristems, has nevertheless given numerous references to microbial existence in these tissues. Since the bud-derived tissue cultures of Scots pine (Pinus sylvestris L.) also become easily occupied by microbes, microbial presence was considered to be one potential cause of the low regeneration capacity of tissues from mature trees. The origin of the microbes occurring in tissue cultures of buds of Scots pine was established in this study. One of the microbes, classified as Hormonema dematioides (Ascomycota), was localized in the scale tissues of a bud. Several other microbes were detected, and were associated especially with the meristematic tissues of Scots pine buds. This group was comprised of the yeast Rhodotorula minuta, and bacteria belonging to Methylobacterium spp., the Pseudomonas fluorescens subgroup, and a Mycobacterium sp. These endophytes were located particularly in the outermost cells of meristems, in the epithelial cells of resin ducts, and in the cells of the developing stem, in the vicinity of the meristems. These endophytes were less frequently found in the vascular tissue or in the intercellular spaces of cells, which are typical locations for the previously known endophytic bacteria. The meristem-associated endophytes were discovered to affect growth of pine tissues, and some of them produced substances that are suitable as precursors for phytohormone synthesis. Additionally, pure cultures of both bacterial and fungal endophytes showed antagonism in vitro against pathogens. When the correlation between the presence endophytes and the degeneration of bud-derived tissue cultures of Scots pine was studied, it was discovered that the endophytes grew uncontrollably once a tissue culture was initiated from the bud. A high level of chitinase production was also detected in these tissue cultures, which was considered to be indicative of a defense reaction. However, the endophytes were not found to colonize excessively in every tissue, but all bud-derived tissue cultures of Scots pine eventually degenerate. Therefore, it was concluded that the endophytes may not exclusively be considered responsible for the degeneration of the cultures

Biofertilizers and biocontrol agents for agriculture:how to identify and develop new potent microbial strains and traits

Abstract Microbiological tools, biofertilizers, and biocontrol agents, which are bacteria and fungi capable of providing beneficial outcomes in crop plant growth and health, have been developed for several decades. Currently we have a selection of strains available as products for agriculture, predominantly based on plant-growth-promoting rhizobacteria (PGPR), soil, epiphytic, and mycorrhizal fungi, each having specific challenges in their production and use, with the main one being inconsistency of field performance. With the growing global concern about pollution, greenhouse gas accumulation, and increased need for plant-based foods, the demand for biofertilizers and biocontrol agents is expected to grow. What are the prospects of finding solutions to the challenges on existing tools? The inconsistent field performance could be overcome by using combinations of several different types of microbial strains, consisting various members of the full plant microbiome. However, a thorough understanding of each microbiological tool, microbial communities, and their mechanisms of action must precede the product development. In this review, we offer a brief overview of the available tools and consider various techniques and approaches that can produce information on new beneficial traits in biofertilizer and biocontrol strains. We also discuss innovative ideas on how and where to identify efficient new members for the biofertilizer and biocontrol strain family

Fungi originating from tree leaves contribute to fungal diversity of litter in streams

Abstract Biomass production and decomposition are key processes in ecology, where plants are primarily responsible for production and microbes act in decomposition. Trees harbor foliar microfungi living on and inside leaf tissues, epiphytes, and endophytes, respectively. Early researchers hypothesized that all fungal endophytes are parasites or latent saprophytes, which slowly colonize the leaf tissues for decomposition. While this has been proven for some strains in the terrestrial environment, it is not known whether foliar microfungi from terrestrial origin can survive or perform decomposition in the aquatic environment. On the other hand, aquatic hyphomycetes, fungi which decompose organic material in stream environments, have been suggested to have a plant-associated life phase. Our aim was to study how much the fungal communities of leaves and litter submerged in streams overlap. Ergosterol content on litter, which is an estimator of fungal biomass, was 5–14 times higher in submerged litter than in senescent leaves, indicating active fungal colonization. Leaves generally harbored a different microbiome prior to than after submergence in streams. The Chao1 richness was significantly higher (93.7 vs. 60.7, p = 0.004) and there were more observed operational taxonomic units (OTUs) (78.3 vs. 47.4, p = 0.004) in senescent leaves than in stream-immersed litter. There were more Leotiomycetes (9%, p = 0.014) in the litter. We identified a group of 35 fungi (65%) with both plant- and water-associated lifestyles. Of these, eight taxa had no previous references to water, such as lichenicolous fungi. Six OTUs were classified within Glomeromycota, known as obligate root symbionts with no previous records from leaves. Five members of Basidiomycota, which are rare in aquatic environments, were identified in the stream-immersed litter only. Overall, our study demonstrates that foliar microfungi contribute to fungal diversity in submerged litter