1991. Annual recurrence of prokaryotic climax communities in shallow waters of the North MediterraneanMauro Celussi, Vincenzo Manna, Elisa Banchi, Viviana Fonti, Matteo Bazzaro, Vesna Flander-Putrle, Katja Klun, Martina Kralj, Neža Orel, Tinkara Tinta, 2024, original scientific article Abstract: In temperate coastal environments, wide fluctuations of biotic and abiotic factors drive microbiome dynamics. To link recurrent ecological patterns with planktonic microbial communities, we analysed a monthly-sampled 3-year time series of 16S rRNA amplicon sequencing data, alongside environmental variables, collected at two stations in the northern Adriatic Sea. Time series multivariate analyses allowed us to identify three stable, mature communities (climaxes), whose recurrence was mainly driven by changes in photoperiod and temperature. Mixotrophs (e.g., Ca. Nitrosopumilus, SUP05 clade, and Marine Group II) thrived under oligotrophic, low-light conditions, whereas copiotrophs (e.g., NS4 and NS5 clades) bloomed at higher temperatures and substrate availability. The early spring climax was characterised by a more diverse set of amplicon sequence variants, including copiotrophs associated with phytoplankton-derived organic matter degradation, and photo-auto/heterotrophic organisms (e.g., Synechococcus sp., Roseobacter clade), whose rhythmicity was linked to photoperiod lengthening. Through the identification of recurrent climax assemblages, we begin to delineate a typology of ecosystem based on microbiome composition and functionality, allowing for the intercomparison of microbial assemblages among different biomes, a still underachieved goal in the omics era.
Keywords: marine microbial ecology, coastal seas, microbial community analyses, marine biology, marine ecology
Published in DiRROS: 17.05.2024; Views: 666; Downloads: 422
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1992. Discovering unknown Madagascar biodiversity : integrative taxonomy of raft spiders (Pisauridae: Dolomedes)Kuang-Ping Yu, Matjaž Kuntner, 2024, original scientific article Abstract: Madagascar is a global biodiversity hotspot, but its biodiversity continues to be underestimated and understudied. Of raft spiders, genus Dolomedes Latreille, 1804, literature only reports two species on Madagascar. Our single expedition to humid forests of eastern and northern Madagascar, however, yielded a series of Dolomedes exemplars representing both sexes of five morphospecies. To avoid only using morphological diagnostics, we devised and tested an integrative taxonomic model for Dolomedes based on the unified species concept. The model first determines morphospecies within a morphometrics framework, then tests their validity via species delimitation using COI. It then incorporates habitat preferences, geological barriers, and dispersal related traits to form hypotheses about gene flow limitations. Our results reveal four new Dolomedes species that we describe from both sexes as Dolomedes gregoric sp. nov., D. bedjanic sp. nov., D. hydatostella sp. nov., and D. rotundus sp. nov. The range of D. kalanoro Silva & Griswold, 2013, now also known from both sexes, is expanded to eastern Madagascar. By increasing the known raft spider diversity from one valid species to five, our results merely scratch the surface of the true Dolomedes species diversity on Madagascar. Our integrative taxonomic model provides the framework for future revisions of raft spiders anywhere.
Keywords: raft spiders, integrative taxonomic model, Madagascar, biodiversity, integrative taxonomy, zoology
Published in DiRROS: 16.05.2024; Views: 596; Downloads: 606
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1993. Bacterial degradation of ctenophore Mnemiopsis leidyi organic matterEduard Fadeev, Jennifer H. Hennenfeind, Chie Amano, Zihao Zhao, Katja Klun, Gerhard J. Herndl, Tinkara Tinta, 2024, original scientific article Abstract: Blooms of gelatinous zooplankton, an important source of protein-rich biomass in coastal waters, often collapse rapidly, releasing large amounts of labile detrital organic matter (OM) into the surrounding water. Although these blooms have the potential to cause major perturbations in the marine ecosystem, their effects on the microbial community and hence on the biogeochemical cycles have yet to be elucidated. We conducted microcosm experiments simulating the scenario experienced by coastal bacterial communities after the decay of a ctenophore (Mnemiopsis leidyi) bloom in the northern Adriatic Sea. Within 24 h, a rapid response of bacterial communities to the M. leidyi OM was observed, characterized by elevated bacterial biomass production and respiration rates. However, compared to our previous microcosm study of jellyfish (Aurelia aurita s.l.), M. leidyi OM degradation was characterized by significantly lower bacterial growth efficiency, meaning that the carbon stored in the OM was mostly respired. Combined metagenomic and metaproteomic analysis indicated that the degradation activity was mainly performed by Pseudoalteromonas, producing a large amount of proteolytic extracellular enzymes and exhibiting high metabolic activity. Interestingly, the reconstructed metagenome-assembled genome (MAG) of Pseudoalteromonas phenolica was almost identical (average nucleotide identity >99%) to the MAG previously reconstructed in our A. aurita microcosm study, despite the fundamental genetic and biochemical differences of the two gelatinous zooplankton species. Taken together, our data suggest that blooms of different gelatinous zooplankton are likely triggering a consistent response from natural bacterial communities, with specific bacterial lineages driving the remineralization of the gelatinous OM.
Keywords: jellyfish, proteases, bacterioplankton, ocean biogeochemistry
Published in DiRROS: 16.05.2024; Views: 497; Downloads: 375
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1994. Contribution to the knowledge of Gongolaria barbata (Sargassaceae, Fucales) from the Mediterranean : insights into infraspecific diversityAnnalisa Falace, Chiara Manfrin, Giovanni Furnari, Sara D’Ambros Burchio, Alberto Pallavicini, Emmanuelle Patricia Descourvières, Sara Kaleb, Ana Lokovšek, Daniele Grech, Giuseppina Alongi, 2024, original scientific article Abstract: Gongolaria barbata (Sargassaceae, Fucales) is a widespread species for which several infraspecific taxa have been described, indicating its polymorphism. This study contributes to the understanding of the molecular, nomenclatural, morphological and ecological aspects of G. barbata in the Mediterranean and sheds light on the infraspecific diversity and its implications for the taxonomy of this species. Molecular analyses were performed using sequencing of the mitochondrial cox1 gene on both haptophytic and pleustophytic forms from different sites in the Adriatic and Tyrrhenian Seas. Vegetative and reproductive morphology was studied on thalli samples from the Adriatic. Our results showed that there are different morphotypes within G. barbata populations related to specific environmental conditions, suggesting infraspecific variation. In contrast, molecular analyses showed no differences between samples, regardless of whether individuals are growing “attached” to a substrate or “unattached”. We also discussed the taxonomic status and nomenclatural issues related to certain infraspecific taxa previously proposed for G. barbata. In particular, the confusion surrounding Cystoseira aurantia is clarified.
Keywords: ecotypes, taxonomy, Northern Adriatic, Cystoseira s.l.
Published in DiRROS: 16.05.2024; Views: 481; Downloads: 175
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1995. Matrix type affects carabid beetle community and trait composition, and intraspecific variation in remnant forestsD. Johan Kotze, Matic Gabor, S. Kohout, Heikki Setälä, 2024, original scientific article Abstract: Aim: The Anthropocene is characterised by urban and agricultural landscapes. Within these landscapes, natural to semi-natural habitats are fragmented, isolated and disturbed to varying degrees. Species associated with these natural habitats have to content with the surrounding landscape, both in terms of level of isolation, and matrix type and quality. We investigated the community structure, trait distribution and individual traits of carabid beetles in boreal forest fragments within three matrices: urban, agricultural and freshwater lake. Location: City of Lahti and its surroundings, southern Finland. Taxon: Coleoptera, Carabidae. Methods: Using pitfall traps from June to October 2019, we collected carabid beetles from eight spruce-dominated forest fragments in the urban matrix, 10 fragments in an agricultural matrix, seven fragments on lake islands and three large control forests at the outskirts of the city. Results: Compared to natural forests, carabid beetles in forest fragments in these matrices showed distinct assemblages, and with beetle diversity the highest in fragments in the agricultural landscape. Fragments in the urban and lake island landscapes were characterised by small-sized species, and those capable of flight. We also found strong intraspecific trait responses in terms of body size, with some generalist species being significantly smaller in urban, agricultural or lake island fragments compared to the controls. Main Conclusions: The matrix has a clear effect on carabid beetle communities, both in terms of taxonomic and trait distribution, and filters for communities of smaller sized species and those capable of flight. Such overall community and intraspecific effects can have considerable effects on populations and community assemblages: As anthropogenic effects intensify in urban and agricultural landscapes, our findings may be the expression of further morphological and physiological responses, and eventually in the adaptation of those species that can cope with the Anthropocene.
Keywords: biogeography, ground beetle, urban lake, agricultural lake, freshwater lake, zoology
Published in DiRROS: 16.05.2024; Views: 499; Downloads: 509
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1996. Lizard host abundances and climatic factors explain phylogenetic diversity and prevalence of blood parasites on an oceanic islandRodrigo Megía-Palma, Gemma Palomar, Javier Martínez, Bernardo Antunes, Katarzyna Dudek, Anamarija Žagar, Nina Guerra Serén, Miguel A. Carretero, Wiesław Babik, Santiago Merino, 2024, original scientific article Abstract: Host abundance might favour the maintenance of a high phylogenetic diversity of some parasites via rapid transmission rates. Blood parasites of insular lizards represent a good model to test this hypothesis because these parasites can be particularly prevalent in islands and host lizards highly abundant. We applied deep amplicon sequencing and analysed environmental predictors of blood parasite prevalence and phylogenetic diversity in the endemic lizard Gallotia galloti across 24 localities on Tenerife, an island in the Canary archipelago that has experienced increasing warming and drought in recent years. Parasite prevalence assessed by microscopy was over 94%, and a higher proportion of infected lizards was found in warmer and drier locations. A total of 33 different 18s rRNA parasite haplotypes were identified, and the phylogenetic analyses indicated that they belong to two genera of Adeleorina (Apicomplexa: Coccidia), with Karyolysus as the dominant genus. The most important predictor of between-locality variation in parasite phylogenetic diversity was the abundance of lizard hosts. We conclude that a combination of climatic and host demographic factors associated with an insular syndrome may be favouring a rapid transmission of blood parasites among lizards on Tenerife, which may favour the maintenance of a high phylogenetic diversity of parasites.
Keywords: Canary Islands, climate change, next-generation sequencing, phylogenetic analyses, zoology, ecology
Published in DiRROS: 16.05.2024; Views: 463; Downloads: 470
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1998. Exploring the mesoscale connectivity of phytoplankton periodic assemblages' succession in northern Adriatic pelagic habitatsIvano Vascotto, Fabrizio Bernardi Aubry, Mauro Bastianini, Patricija Mozetič, Stefania Finotto, Janja Francé, 2024, original scientific article Abstract: An appropriate model for phytoplankton distribution patterns is critical for understanding biogeochemical cycles and trophic interactions in the oceans and seas. Because phytoplankton dynamics in coastal waters are more complex due to shallow depth and proximity to land, more accurate models applied to the correct spatial and temporal scales are needed. Our study investigates the role of the atmosphere and hydrosphere in pelagic habitat by modelling phytoplankton assemblages at two Long Term Ecological Research sites in the northern Adriatic Sea using niche-forming environmental variables (wind, temperature, salinity, river discharge, rain, and water column stratification). To study the synchronization between the phytoplankton community and these environmental variables at the two LTER sites, we applied current linear and nonlinear numerical methods for ecological modelling. The aim was to use periodic and/or non-periodic properties of the environmental variables to classify the phytoplankton assemblages at one LTER site (Gulf of Trieste - Slovenia) and then predict them at another LTER site 100 km away (Gulf of Venice - Italy). We found that periodicity played a role in the explanatory and predictive power of the environmental variables and that it was more important than non-periodic events in defining the common structure of the two pelagic habitats. The non-linear classification functions of the neural networks further increased the predictive power of these variables. We observed partial synchronization of communities at the mesoscale and differences between the original and predicted assemblages under similar environmental conditions. We conclude that mesoscale connectivity plays an important role in phytoplankton communities in the northern Adriatic. However, the loss of periodicity of niche-forming variables due to more frequent extreme meteorological and hydrological events could loosen these connections and affect the temporal succession of phytoplankton assemblages.
Keywords: phytoplankton, assemblages, Northern Adriatic, phenology, marine biology, hydrobiology
Published in DiRROS: 16.05.2024; Views: 497; Downloads: 433
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1999. Indicated domination gameBoštjan Brešar, Csilla Bujtás, Vesna Iršič, Douglas F. Rall, Zsolt Tuza, 2024, original scientific article Abstract: Motivated by the success of domination games and by a variation of the coloring game called the indicated coloring game, we introduce a version of domination games called the indicated domination game. It is played on an arbitrary graph $G$ by two players, Dominator and Staller, where Dominator wants to finish the game in as few rounds as possible while Staller wants just the opposite. In each round, Dominator indicates a vertex $u$ of $G$ that has not been dominated by previous selections of Staller, which, by the rules of the game, forces Staller to select a vertex in the closed neighborhood of $u$. The game is finished when all vertices of $G$ become dominated by the vertices selected by Staller. Assuming that both players are playing optimally according to their goals, the number of selected vertices during the game is the indicated domination number, $\gamma_{\rm i}(G)$, of $G$. We prove several bounds on the indicated domination number expressed in terms of other graph invariants. In particular, we find a place of the new graph invariant in the well-known domination chain, by showing that $\gamma_{\rm i}(G)\ge \Gamma(G)$ for all graphs $G$, and by showing that the indicated domination number is incomparable with the game domination number and also with the upper irredundance number. In connection with the trivial upper bound $\gamma_{\rm i}(G)\le n(G)-\delta(G)$, we characterize the class of graphs $G$ attaining the bound provided that $n(G)\ge 2\delta(G)+2$. We prove that in trees, split graphs and grids the indicated domination number equals the independence number. We also find a formula for the indicated domination number of powers of paths, from which we derive that there exist graphs in which the indicated domination number is arbitrarily larger than the upper irredundance number. We provide some partial results supporting the statement that $\gamma_{\rm i}(G)=n(G)/2$ if $G$ is a cubic bipartite graph, and leave this as an open question.
Keywords: domination game, indicated coloring, independence number, upper domination number
Published in DiRROS: 16.05.2024; Views: 561; Downloads: 342
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2000. Quantitative aspects of ToF-SIMS analysis of metals and alloys in a UHV, O2 and H2 atmosphereJernej Ekar, Saša Kos, Janez Kovač, 2024, original scientific article Abstract: Although secondary ion mass spectrometry (SIMS) is a versatile method used in the fields of surface analysis, depth profiling and elemental and molecular mapping, it also lacks quantification capabilities. The main reason for this is the matrix effect, which influences the ionization yield of secondary ions with respect to the substrate from which the analyzed compounds originate. There are several approaches to reduce the matrix effect, and gas flooding is one of the easiest methods to apply. In this work, we have investigated the possibilities of the ToF-SIMS method for the quantification of selected metals and alloys containing these metals in different ratios by reducing the matrix effect in the presence of different atmospheres. The measurements were performed in the ultra-high vacuum (UHV) environment, H2 and O2 atmospheres. H2 flooding shows the most significant improvements compared to the UHV analysis, while O2 is also promising but has some limitations. Improvements are most evident for the transition metals Ti, Cr, Fe, Co and Ni employed in our study, while the p-block elements such as Al and Si do not change so extensively. The deviations from the true atomic ratios of selected transition metals in different alloys reach a maximum of only 46 % when analyzed in the H2 atmosphere. In contrast, these values are 66 and 228 % for the O2 atmosphere and UHV environment, respectively. Our results suggest that gas adsorption and consequent formation of a new matrix on the surface, especially in the case of hydrogen, reduces the differences between the different chemical environments and electronic structures of the surface. In this way, the quantitative aspects of the SIMS method can be improved.
Keywords: ToF-SIMS quantification, H2 and O2 gas flooding, matrix effect reduction, cluster secondary ions
Published in DiRROS: 15.05.2024; Views: 480; Downloads: 280
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