571. |
572. Poročilo o preskusu št.: LVG 2024-063 : vzorec št. 2024/00185Tine Hauptman, Špela Hočevar, Barbara Piškur, 2024, expertise, arbitration decision Keywords: varstvo gozdov, morfološke analize, program preiskav, Geosmithia morbida, bolezen tisočerih rakov, vektorji, rtPCR Published in DiRROS: 23.07.2024; Views: 152; Downloads: 0 This document has many files! More... |
573. Who cares about ocean acidification in the Plasticene?Rachel Tiller, Francisco Arenas, Charles Galdies, Francisco Leitão, Alenka Malej, Beatriz Martinez Romera, Cosimo Solidoro, Robert Stojanov, Valentina Turk, Roberta Guerra, 2019, original scientific article Abstract: Plastics is all the rage, and mitigating marine litter is topping the agenda for nations pushing issues such as ocean acidification, or even climate change, away from the public consciousness. We are personally directly affected by plastics and charismatic megafauna is dying from it, and it is something that appears to be doable. So, who cares about the issue of ocean acidification anymore? We all should. The challenge is dual in the fact that is both invisible to the naked eye and therefore not felt like a pressing issue to the public, thereby not reaching the top of the agenda of policy makers; but also that it is framed in the climate change narrative of fear - whereby it instills in a fight-or-flight response in the public, resulting in their avoidance of the issue because they feel they are unable to take action that have results. In this article, we argue that the effective global environmental governance of ocean acidification, though critical to address, mitigate against and adapt to, is hindered by the both this lack of perception of urgency in the general public, fueled by a lack of media coverage, as well as a fight-or-flight response resulting from fear. We compare this to the more media friendly and plastics problem that is tangible and manageable. We report on a media plots of plastics and ocean acidification coverage over time and argue that the issue needs to be detangled from climate change and framed as its own issue to reach the agenda at a global level, making it manageable to assess and even care about for policy makers and the public alike? Keywords: oceans, acidification, plastics Published in DiRROS: 23.07.2024; Views: 148; Downloads: 79
Full text (1,03 MB) This document has many files! More... |
574. Genomic characterisation of the new Dickeya fangzhongdai species regrouping plant pathogens and environmental isolatesŠpela Alič, Jacques Pédron, Tanja Dreo, Frédérique van Gijsegem, 2019, original scientific article Abstract: Background
The Dickeya genus is part of the Pectobacteriaceae family that is included in the newly described enterobacterales order. It comprises a group of aggressive soft rot pathogens with wide geographic distribution and host range. Among them, the new Dickeya fangzhongdai species groups causative agents of maceration-associated diseases that impact a wide variety of crops and ornamentals. It affects mainly monocot plants, but D. fangzhongdai strains have also been isolated from pear trees and water sources. Here, we analysed which genetic novelty exists in this new species, what are the D. fangzhongdai-specific traits and what is the intra-specific diversity.
Results
The genomes of eight D. fangzhongdai strains isolated from diverse environments were compared to 31 genomes of strains belonging to other Dickeya species. The D. fangzhongdai core genome regroups approximately 3500 common genes, including most genes that encode virulence factors and regulators characterised in the D. dadantii 3937 model strain. Only 38 genes are present in D. fangzhongdai and absent in all other Dickeyas. One of them encodes a pectate lyase of the PL10 family of polysaccharide lyases that is found only in a few bacteria from the plant environment, soil or human gut. Other D. fangzhongdai-specific genes with a known or predicted function are involved in regulation or metabolism.
The intra-species diversity analysis revealed that seven of the studied D. fangzhongdai strains were grouped into two distinct clades. Each clade possesses a pool of 100–150 genes that are shared by the clade members, but absent from the other D. fangzhongdai strains and several of these genes are clustered into genomic regions. At the strain level, diversity resides mainly in the arsenal of T5SS- and T6SS-related toxin-antitoxin systems and in secondary metabolite biogenesis pathways.
Conclusion
This study identified the genome-specific traits of the new D. fangzhongdai species and highlighted the intra-species diversity of this species. This diversity encompasses secondary metabolites biosynthetic pathways and toxins or the repertoire of genes of extrachromosomal origin. We however didn’t find any relationship between gene content and phenotypic differences or sharing of environmental habitats.
Background
Soft rot Pectobacteriaceae are Enterobacterales responsible for considerable economic losses in several important crops and ornamental plants [1,2,3]. Their virulence is mainly due to the production and secretion of a battery of plant cell wall degrading enzymes (PCWDEs) that cause maceration of the plant tissue; however, several other virulence factors have also been characterized [2, 4]. These bacteria often exhibit a very broad host range, and recent outbreaks in potato, for example, resulted from the action of a cohort of bacteria belonging to different Pectobacteriaceae species in a complex population dynamics history [5]. The Pectobacteriaceae family includes two genera comprising soft rot bacteria, Pectobacterium and Dickeya. The Dickeya genus was formed in 2005 by the reclassification of former Erwinia chrysanthemi into six species [6]. It has recently undergone multiple phylogenetic changes, including the addition of three new species, Dickeya solani [7], Dickeya aquatica [8] and, more recently, Dickeya fangzhongdai [9].
The description of this last new species was based on three isolates from pear trees in China with bleeding canker necrosis [9], but it was extended by a large number of strains isolated from monocot plants from Japan [10, 11]. D. fangzhongdai strains were associated with soft rot symptoms of many ornamental and economically important staple food plants [10, 12, 13], thereby highlighting the broad host range of the species.
While there is little information regarding associated economic damages and the extent of its occurrence in different host plants outside of Asia, Alič et al. [14] recently identified D. fangzhongdai as the causative agent of soft rot of orchids in commercial production in Europe, starting with material from Asia [11]. Moreover, as previously reported, bacteriophages of different families, and active against D. fangzhongdai, were isolated from a wastewater treatment plant not associated to the orchid production site. This would suggest that D. fangzhongdai bacteria may be more widespread in nature than could currently be concluded on the basis of symptoms in plants. Its occurrence in water would suggest that it may potentially have a wider ecological niche than genomically close Dickeya spp., that is, Dickeya dadantii, Dickeya dianthicola, and D. solani.
Previous experience with D. solani has shown that novel species or isolates can lead to clonal spread and high losses in affected host plants [15]. Together with repeated introductions of D. fangzhongdai, the co-occurrence of genetically and phenotypically diverse strains on the same plants (e.g., B16 and S1 on orchids, as reported by Alič et al. [11]) increases the probability of the development of recombined strains with novel pathogenic potential and may present a risk to agriculturally important plants. Their aggressiveness, high maceration potential on various plant tissues, and persistence in potato plants further exacerbate the risk for agriculture.
Therefore, in this paper, we analysed the genomic characteristics of the D. fangzhongdai species, compared it to the other Dickeya species and determine the inter- and intra- species diversity. The study addressed the question whether the presence of the isolates in a specific environment is associated to a specific set of genes (water vs plant symptoms, monocots vs dicots, different geographical origin). We also analysed the virulence gene arsenal, in order to evaluate the virulence potential of this species.
Methods
Dickeya strain selection
All D. fangzhongdai genomes publicly available in the NCBI database were included in this study. These genomes were compared to five D. solani, four D. dadantii, five D. dianthicola, five D. chrysanthemi, seven D. zeae, one D. aquatica, two D. paradisiaca and two unassigned Dickeya genomes extracted from the NCBI database. Information on the provenance and genomic data of the D. fangzhongdai strains used in this study are summarized in Table 1. The accession numbers and phylogenetic position of the other Dickeya strains used for the SiLix analyses are presented in Additional file 1: Figure S1. Keywords: T5SS, T6SS, NRPS/PKS, zeamine, oocydin A, plant-bacteria interactions, plasmid, Dickeya fangzhongdai Published in DiRROS: 23.07.2024; Views: 169; Downloads: 122
Full text (2,95 MB) This document has many files! More... |
575. Poročilo o preskusu št.: LVG 2024-055 : vzorec št. 2024/00136Tine Hauptman, Špela Hočevar, Zina Devetak, Barbara Piškur, 2024, expertise, arbitration decision Keywords: varstvo gozdov, morfološke analize, program preiskav, Geosmithia morbida, bolezen tisočerih rakov, vektorji, rtPCR Published in DiRROS: 23.07.2024; Views: 157; Downloads: 0 This document has many files! More... |
576. Biogeography of the Caribbean Cyrtognatha spidersKlemen Čandek, Ingi Agnarsson, Greta Binford, Matjaž Kuntner, 2019, original scientific article Abstract: Island systems provide excellent arenas to test evolutionary hypotheses pertaining to gene flow and diversification of dispersal-limited organisms. Here we focus on an orbweaver spider genus Cyrtognatha (Tetragnathidae) from the Caribbean, with the aims to reconstruct its evolutionary history, examine its biogeographic history in the archipelago, and to estimate the timing and route of Caribbean colonization. Specifically, we test if Cyrtognatha biogeographic history is consistent with an ancient vicariant scenario (the GAARlandia landbridge hypothesis) or overwater dispersal. We reconstructed a species level phylogeny based on one mitochondrial (COI) and one nuclear (28S) marker. We then used this topology to constrain a time-calibrated mtDNA phylogeny, for subsequent biogeographical analyses in BioGeoBEARS of over 100 originally sampled Cyrtognatha individuals, using models with and without a founder event parameter. Our results suggest a radiation of Caribbean Cyrtognatha, containing 11 to 14 species that are exclusively single island endemics. Although biogeographic reconstructions cannot refute a vicariant origin of the Caribbean clade, possibly an artifact of sparse outgroup availability, they indicate timing of colonization that is much too recent for GAARlandia to have played a role. Instead, an overwater colonization to the Caribbean in mid-Miocene better explains the data. From Hispaniola, Cyrtognatha subsequently dispersed to, and diversified on, the other islands of the Greater, and Lesser Antilles. Within the constraints of our island system and data, a model that omits the founder event parameter from biogeographic analysis is less suitable than the equivalent model with a founder event. Keywords: biogeography, spiders Published in DiRROS: 23.07.2024; Views: 158; Downloads: 122
Full text (1,62 MB) This document has many files! More... |
577. Stress-tolerant yeasts : opportunistic pathogenicity versus biocontrol potentialJanja Zajc, Cene Gostinčar, Anja Černoša, Nina Gunde-Cimerman, 2019, original scientific article Abstract: Stress-tolerant fungi that can thrive under various environmental extremes are highly desirable for their application to biological control, as an alternative to chemicals for pest management. However, in fungi, the mechanisms of stress tolerance might also have roles in mammal opportunism. We tested five species with high biocontrol potential in agriculture (Aureobasidium pullulans, Debayomyces hansenii, Meyerozyma guilliermondii, Metschnikowia fructicola, Rhodotorula mucilaginosa) and two species recognized as emerging opportunistic human pathogens (Exophiala dermatitidis, Aureobasidium melanogenum) for growth under oligotrophic conditions and at 37 °C, and for tolerance to oxidative stress, formation of biofilms, production of hydrolytic enzymes and siderophores, and use of hydrocarbons as sole carbon source. The results show large overlap between traits desirable for biocontrol and traits linked to opportunism (growth under oligotrophic conditions, production of siderophores, high oxidative stress tolerance, and specific enzyme activities). Based on existing knowledge and these data, we suggest that oligotrophism and thermotolerance together with siderophore production at 37 °C, urease activity, melanization, and biofilm production are the main traits that increase the potential for fungi to cause opportunistic infections in mammals. These traits should be carefully considered when assessing safety of potential biocontrol agents. Keywords: opportunistic pathogen, biocontrol agent, virulence, stress tolerance, secretome, CAZy, protease, thermotolerance, oligotrophism, melanin, siderophore, biofilm Published in DiRROS: 23.07.2024; Views: 167; Downloads: 170
Full text (2,70 MB) This document has many files! More... |
578. Bacteria associated with moon jellyfish during bloom and post-bloom periods in the Gulf of Trieste (northern Adriatic)Maja Kos Kramar, Tinkara Tinta, Davor Lučić, Alenka Malej, Valentina Turk, 2019, original scientific article Abstract: Jellyfish are a prominent component of the plankton community. They frequently form conspicuous blooms which may interfere with different human enterprises. Among the aspects that remain understudied are jellyfish associations with microorganisms having potentially important implications for organic matter cycling. To the best of our knowledge, this study is the first to investigate the bacterial community associated with live moon jellyfish (Aurelia solida, Scyohozoa) in the Adriatic Sea. Using 16S rRNA clone libraries and culture-based methods, we have analyzed the bacterial community composition of different body parts: the exumbrella surface, oral arms, and gastric cavity, and investigated possible differences in medusa-associated bacterial community structure at the time of the jellyfish population peak, and during the senescent phase at the end of bloom. Microbiota associated with moon jellyfish was different from ambient seawater bacterial assemblage and varied between different body parts. Betaproteobacteria (Burkholderia, Cupriavidus and Achromobacter) dominated community in the gastral cavity of medusa, while Alphaproteobacteria (Phaeobacter, Ruegeria) and Gammaproteobacteria (Stenotrophomonas, Alteromonas, Pseudoalteromonas and Vibrio) prevailed on ‘outer’ body parts. Bacterial community structure changed during senescent phase, at the end of the jellyfish bloom, showing an increased abundance of Gammaproteobacteria, exclusively Vibrio. The results of cultured bacterial isolates showed the dominance of Gammaproeteobacteria, especially Vibrio and Pseudoalteromonas in all body parts. Our results suggest that jellyfish associated bacterial community might have an important role for the host, and that anthropogenic pollution in the Gulf of Trieste might affect their community structure. Keywords: bacteria, moon jellyfish, Gulf of Trieste, Adriatic sea Published in DiRROS: 23.07.2024; Views: 174; Downloads: 134
Full text (1,76 MB) This document has many files! More... |
579. Arthropod communities in fungal fruitbodies are weakly structured by climate and biogeography across European beech forestsNicolas Friess, Jörg C. Müller, Pablo Aramendi, Claus Bässler, Martin P. Brändle, Christophe Bouget, Antoine Brin, Heinz Bussler, Kostadin B. Georgiev, Radosław Gil, Martin M. Gossner, Jacob Heilmann-Clausen, Gunnar Isacsson, Anton Krištín, Thibault Lachat, Laurent Larrieu, Elodie Magnanou, Alexander Maringer, Ulrich Mergner, Martin Mikoláš, Lars Opgenoorth, Jürgen Schmidl, Miroslav Svoboda, Simon Thorn, Kris Vandekerkhove, Al Vrezec, Thomas Wagner, Maria-Barbara Winter, Livia Zapponi, Roland Brandl, Sebastian Seibold, 2019, original scientific article Abstract: Aim
The tinder fungus Fomes fomentarius is a pivotal wood decomposer in European beech Fagus sylvatica forests. The fungus, however, has regionally declined due to centuries of logging. To unravel biogeographical drivers of arthropod communities associated with this fungus, we investigated how space, climate and habitat amount structure alpha and beta diversity of arthropod communities in fruitbodies of F. fomentarius.
Location
Temperate zone of Europe.
Taxon
Arthropods.
Methods
We reared arthropods from fruitbodies sampled from 61 sites throughout the range of European beech and identified 13 orders taxonomically or by metabarcoding. We estimated the total number of species occurring in fruitbodies of F. fomentarius in European beech forests using the Chao2 estimator and determined the relative importance of space, climate and habitat amount by hierarchical partitioning for alpha diversity and generalized dissimilarity models for beta diversity. A subset of fungi samples was sequenced for identification of the fungus’ genetic structure.
Results
The total number of arthropod species occurring in fruitbodies of F. fomentarius across European beech forests was estimated to be 600. Alpha diversity increased with increasing fruitbody biomass; it decreased with increasing longitude, temperature and latitude. Beta diversity was mainly composed by turnover. Patterns of beta diversity were only weakly linked to space and the overall explanatory power was low. We could distinguish two genotypes of F. fomentarius, which showed no spatial structuring.
Main conclusion
Fomes fomentarius hosts a large number of arthropods in European beech forests. The low biogeographical and climatic structure of the communities suggests that fruitbodies represent a habitat that offers similar conditions across large gradients of climate and space, but are characterized by high local variability in community composition and colonized by species with high dispersal ability. For European beech forests, retention of trees with F. fomentarius and promoting its recolonization where it had declined seems a promising conservation strategy. Keywords: dead wood, insects, invertebrates, restoration, saproxylic, sporocarp Published in DiRROS: 23.07.2024; Views: 329; Downloads: 96
Full text (1,21 MB) This document has many files! More... |
580. |