Diversity of Bacteria Associated with Bursaphelenchus xylophilus and Other Nematodes Isolated from Pinus pinaster Trees with Pine Wilt Disease

The pinewood nematode (PWN), Bursaphelenchus xylophilus, has been thought to be the only causal agent of pine wilt disease (PWD), however, since bacteria have been suggested to play a role in PWD, it is important to know the diversity of the microbial community associated to it. This study aimed to assess the microbial community associated with B. xylophilus and with other nematodes isolated from pine trees, Pinus pinaster, with PWD from three different affected forest areas in Portugal. One hundred and twenty three bacteria strains were isolated from PWN and other nematodes collected from 14 P. pinaster. The bacteria strains were identified by comparative analysis of the 16S rRNA gene partial sequence. All except one Gram-positive strain (Actinobacteria) belonged to the Gram-negative Beta and Gammaproteobacteria. Most isolates belonged to the genus Pseudomonas, Burkholderia and to the family Enterobacteriaceae. Species isolated in higher percentage were Pseudomonas lutea, Yersinia intermedia and Burkholderia tuberum. The major bacterial population associated to the nematodes differed according to the forest area and none of the isolated bacterial species was found in all different forest areas. For each of the sampled areas, 60 to 100% of the isolates produced siderophores and at least 40% produced lipases. The ability to produce siderophores and lipases by most isolates enables these bacteria to have a role in plant physiological response. This research showed a high diversity of the microbial community associated with B. xylophilus and other nematodes isolated from P. pinaster with PWD

Conservation and Diversity of Seed Associated Endophytes in Zea across Boundaries of Evolution, Ethnography and Ecology

Endophytes are non-pathogenic microbes living inside plants. We asked whether endophytic species were conserved in the agriculturally important plant genus Zea as it became domesticated from its wild ancestors (teosinte) to modern maize (corn) and moved from Mexico to Canada. Kernels from populations of four different teosintes and 10 different maize varieties were screened for endophytic bacteria by culturing, cloning and DNA fingerprinting using terminal restriction fragment length polymorphism (TRFLP) of 16S rDNA. Principle component analysis of TRFLP data showed that seed endophyte community composition varied in relation to plant host phylogeny. However, there was a core microbiota of endophytes that was conserved in Zea seeds across boundaries of evolution, ethnography and ecology. The majority of seed endophytes in the wild ancestor persist today in domesticated maize, though ancient selection against the hard fruitcase surrounding seeds may have altered the abundance of endophytes. Four TRFLP signals including two predicted to represent Clostridium and Paenibacillus species were conserved across all Zea genotypes, while culturing showed that Enterobacter, Methylobacteria, Pantoea and Pseudomonas species were widespread, with γ-proteobacteria being the prevalent class. Twenty-six different genera were cultured, and these were evaluated for their ability to stimulate plant growth, grow on nitrogen-free media, solubilize phosphate, sequester iron, secrete RNAse, antagonize pathogens, catabolize the precursor of ethylene, produce auxin and acetoin/butanediol. Of these traits, phosphate solubilization and production of acetoin/butanediol were the most commonly observed. An isolate from the giant Mexican landrace Mixteco, with 100% identity to Burkholderia phytofirmans, significantly promoted shoot potato biomass. GFP tagging and maize stem injection confirmed that several seed endophytes could spread systemically through the plant. One seed isolate, Enterobacter asburiae, was able to exit the root and colonize the rhizosphere. Conservation and diversity in Zea-microbe relationships are discussed in the context of ecology, crop domestication, selection and migration

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

Data availability: The data generated in this study have been deposited in the Open Science Framework (https://doi.org/10.17605/OSF.IO/STKFR). Non-experimental data included in our datasets (i.e., intensity of government response to COVID-19 is the Stringency Index, COVID-19 deaths and cases per million) are taken from the Oxford COVID−19 Government Response Tracker [22 Hale, T. et al. A global panel database of pandemic policies (Oxford COVID−19 Government Response Tracker). Nat. Human Behav. https://doi.org/10.1038/s41562-021-01079-8 (2021).] and Our World in Data [38 Ritchie, H. et al. Coronavirus Pandemic (COVID-19). Our World in Data. https://ourworldindata.org/coronavirus (2020).] (downloaded November 2020). Wave 0 data are from [3 Gelfand, M. J. et al. Differences between tight and loose cultures: a 33-nation study. Science 332, 1100–1104 (2011).[ and Wave 1 data are from [5 Eriksson, K. et al. Perceptions of the appropriate response to norm violation in 57 societies. Nat. Commun. 12, 1481 (2021).].Code availability: The survey and analysis code are available at the Open Science Framework (https://doi.org/10.17605/OSF.IO/STKFR).Supplementary information is available online at: https://www.nature.com/articles/s41467-024-44999-5#Sec40 .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.Knut and Wallenberg Grant “How do human norms form and change?” 2016.0167. (G.An.). The Swedish Research Council grant “Norms & Risk: Do social norms help dealing with collective threats” 2021-06271 (G.An.). Ministero dell’Istruzione dell’Università e della Ricerca, PRIN 2017, prot. 20178TRM3F (D.B.). Universidad de Los Andes, Fondo Vicerrectoría de Investigaciones (J.-C.C.). Ministry of Innovation and Technology of Hungary, National Research, Development and Innovation Fund NKFIH-OTKA K135963 (M.F.). Grant 23-061770 S of the Czech Science Foundation (M.H. and S.G.). RVO: 68081740 of the Institute of Psychology, Czech Academy of Sciences (M.H. and S.G.). RA Science Committee, research project N.20TTSH-070 (A.Gr. and N.Khac.). Open University of Israel, 511687 (R.N.). HSE University Basic Research Program (E.O.). Project BASIC (PID2022-141802NB-I00) funded by MCIN/AEI/10.13039/501100011033 and by “ERDF A way of making Europe” (A.Sá.). US Army Research Office Grant W911NF-19-1-910281 (B.S.). Netherlands Organisation for Scientific Research, 019.183SG.001 (E.S.). Netherlands Organisation for Scientific Research, VI.Veni.201 G.013 (E.S.). European Commission, Horizon 2020-ID 870827 (E.S.). UKRI Grant “Secret Power” No. EP/X02170X/1 awarded under the European Commission’s “European Research Council - STG” Scheme (G.A.T.)