21. Biogeography of the Caribbean Cyrtognatha spidersKlemen Čandek, Ingi Agnarsson, Greta Binford, Matjaž Kuntner, 2019, izvirni znanstveni članek Povzetek: 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.
Ključne besede: biogeography, spiders
Objavljeno v DiRROS: 23.07.2024; Ogledov: 4; Prenosov: 3
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22. Stress-tolerant yeasts : opportunistic pathogenicity versus biocontrol potentialJanja Zajc, Cene Gostinčar, Anja Černoša, Nina Gunde-Cimerman, 2019, izvirni znanstveni članek Povzetek: 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.
Ključne besede: opportunistic pathogen, biocontrol agent, virulence, stress tolerance, secretome, CAZy, protease, thermotolerance, oligotrophism, melanin, siderophore, biofilm
Objavljeno v DiRROS: 23.07.2024; Ogledov: 15; Prenosov: 7
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23. 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, izvirni znanstveni članek Povzetek: 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.
Ključne besede: bacteria, moon jellyfish, Gulf of Trieste, Adriatic sea
Objavljeno v DiRROS: 23.07.2024; Ogledov: 24; Prenosov: 7
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24. 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, izvirni znanstveni članek Povzetek: 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.
Ključne besede: dead wood, insects, invertebrates, restoration, saproxylic, sporocarp
Objavljeno v DiRROS: 23.07.2024; Ogledov: 23; Prenosov: 6
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26. MapMan4 : a refined protein classification and annotation framework applicable to multi-omics data analysisRainer Schwacke, Gabriel Y. Ponce-Soto, Kirsten Krause, Anthony M. Bolger, Borjana Arsova, Asis Hallab, Kristina Gruden, Mark Stitt, Marie E. Bolger, Björn Usadel, 2019, izvirni znanstveni članek Povzetek: Genome sequences from over 200 plant species have already been published, with this number expected to increase rapidly due to advances in sequencing technologies. Once a new genome has been assembled and the genes identified, the functional annotation of their putative translational products, proteins, using ontologies is of key importance as it places the sequencing data in a biological context. Furthermore, to keep pace with rapid production of genome sequences, this functional annotation process must be fully automated. Here we present a redesigned and significantly enhanced MapMan4 framework, together with a revised version of the associated online Mercator annotation tool. Compared with the original MapMan, the new ontology has been expanded almost threefold and enforces stricter assignment rules. This framework was then incorporated into Mercator4, which has been upgraded to reflect current knowledge across the land plant group, providing protein annotations for all embryophytes with a comparably high quality. The annotation process has been optimized to allow a plant genome to be annotated in a matter of minutes. The output results continue to be compatible with the established MapMan desktop application.
Ključne besede: genome sequences, MapMan4
Objavljeno v DiRROS: 23.07.2024; Ogledov: 7; Prenosov: 3
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27. Microscopy of crustacean cuticle : formation of a flexible extracellular matrix in moulting sea slaters Ligia pallasiiJasna Štrus, Magda Tušek-Žnidarič, Urška Repnik, Andrej Blejec, Adam P. Summers, 2019, izvirni znanstveni članek Povzetek: Structural and functional properties of exoskeleton in moulting sea slaters Ligia pallasii from the Eastern Pacific coast were investigated with CT scanning and electron microscopy. Ultrastructure of preecdysial and postecdysial cuticular layers was described in premoult, intramoult and postmoult animals. Cuticle is a flexible extracellular matrix connected to the epidermal cells through pore channels. During premoult epicuticle and exocuticle are formed and during intramoult and postmoult endocuticular lamellae are deposited and the cuticle is progressively constructed by thickening and mineralization. Cuticle permeability, flexibility and waterproofing capacity change accordingly. Elaboration of epicuticular scales connected to an extensive network of nanotubules, establish its anti-adhesive and hydrophobic properties. Labelling with gold conjugated WGA lectins on Tokuyashu thawed cryosections exposes differences in chitin content between exocuticle and endocuticle. Histochemical staining of cuticle shows presence of acidic carbohydrates/glycoconjugates and lipoproteins in epicuticular layer. Chitin microfibrils are formed at the microvillar border of epidermal cells with abundant Golgi apparatus and secretory vesicles. Numerous spherules associated with nanotubules were observed in the ecdysial space in intramoult animals. The mineral component of the cuticle as visualized with CT scanning indicates progressive mineral resorption from the posterior to the anterior half of the body in premoult animals, its translocation from the anterior to posterior part during intramoult and its progressive deposition in the posterior and anterior exoskeleton during postmoult. Cuticle of sea slaters is a unique biocomposite and biodynamic material constantly reconstructed during frequent moults, and adapted to specific physical and biotic conditions of the high intertidal rocky zone.
Ključne besede: cuticle ultrastructure, micro CT scanning, moult cycle, SEM, TEM, terrestrial isopods
Objavljeno v DiRROS: 23.07.2024; Ogledov: 12; Prenosov: 3
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29. Respiration rates in shallow lakes of different types : contribution of benthic microorganisms, macrophytes, plankton and macrozoobenthosJanusz Żbikowski, Tatjana Simčič, Franja Pajk, Małgorzata Poznańska-Kakareko, Tomasz Kakareko, Jarosław Kobak, 2019, izvirni znanstveni članek Povzetek: The determination of the metabolic activity of organisms at various trophic levels is crucial for the proper assessment of the energy flow through the ecosystem, which is the basic process determining ecosystem functioning. We estimated the respiration rate in nine shallow, eutrophic lakes (macrophyte-dominated and phytoplankton-dominated) from north-eastern Poland. Respiratory carbon loss (RCL) through bottom microbial communities, macrophytes, plankton and macrozoobenthos was estimated by measuring the Electron Transport System activity. The shares of the particular ecosystem components in respiration processes differed among the lake types and seasons. The bottom microbial communities contributed most to the RCL (from 50% in the macrophyte-dominated lakes to 90% in the shallower phytoplankton-dominated lakes) except in macrophytes-dominated lakes in summer, where the macrophyte contribution prevailed (80%). The contribution of plankton was considerable only in the deeper phytoplankton-dominated lakes (20%). Macrozoobenthos was important (20%) only in the macrophyte-dominated lakes in spring and autumn. The RCL through bottom microbial communities was substantially higher in the shallow lakes (especially phytoplankton-dominated) than in deep, stratified eutrophic lakes. Shallow eutrophic lakes can be highly productive due to intensive organic matter mineralization at the bottom and rapid flow and cycling of carbon and nutrients resulting from their polymictic character.
Ključne besede: shallow lakes, ETS activity, respiratory carbon loss, abiotic parameters
Objavljeno v DiRROS: 23.07.2024; Ogledov: 6; Prenosov: 4
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