1,721,255 research outputs found
Patterns of Rare and Abundant Marine Microbial Eukaryotes
No full textLogares, Ramiro ... et. al.-- 9 pages, 5 figures, 1 tableBackground. Biological communities are normally composed of a few abundant and many rare species. This pattern is particularly prominent in microbial communities, in which most constituent taxa are usually extremely rare. Although abundant and rare subcommunities may present intrinsic characteristics that could be crucial for understanding community dynamics and ecosystem functioning, microbiologists normally do not differentiate between them. Here, we investigate abundant and rare subcommunities of marine microbial eukaryotes, a crucial group of organisms that remains among the least-explored biodiversity components of the biosphere. We surveyed surface waters of six separate coastal locations in Europe, independently considering the picoplankton, nanoplankton, and microplankton/mesoplankton organismal size fractions.
Results. Deep Illumina sequencing of the 18S rRNA indicated that the abundant regional community was mostly structured by organismal size fraction, whereas the rare regional community was mainly structured by geographic origin. However, some abundant and rare taxa presented similar biogeography, pointing to spatiotemporal structure in the rare microeukaryote biosphere. Abundant and rare subcommunities presented regular proportions across samples, indicating similar species-abundance distributions despite taxonomic compositional variation. Several taxa were abundant in one location and rare in other locations, suggesting large oscillations in abundance. The substantial amount of metabolically active lineages found in the rare biosphere suggests that this subcommunity constitutes a diversity reservoir that can respond rapidly to environmental change.
Conclusions. We propose that marine planktonic microeukaryote assemblages incorporate dynamic and metabolically active abundant and rare subcommunities, with contrasting structuring patterns but fairly regular proportions, across space and timeWe thank the Biodiversity of Marine euKaryotes (BioMarKs, http://www. biomarks.eu) consortium, which was funded by the European Union ERANet program BiodivERsA (2008-6530). Extra financial support was provided by the Marie Curie Intra-European Fellowship (PIEF-GA-2009-235365) and Juan de la Cierva (JCI-2010-06594) programmes to R.L. and FLAME (CGL2010-16304, MICINN, Spain) to R.M. The Barcelona Supercomputing Center (BSC) provided access to the MareNostrum supercomputer (grants BCV-2011-2-0003/3-0005 and 2012-1-0006/2-0002 to R.L. and R.M.)Peer reviewe
Global comparative analysis of prokaryotic and eukaryotic diversity contributing to oceanic photosynthesis using data from Tara Oceans and Malaspina expeditions
No full textTrabajo final presentado por Laura Rubinat Ripoll para un Máster de la Universitat Pompeu Fabra (UPF), realizado bajo la dirección del Dr. Ramiro Logares del Institut de Ciències del Mar (ICM-CSIC)Peer Reviewe
Ecologia e taxonomia de protistas planctônicos em zonas de surfe de praias arenosas brasileirs em latitudes equatorial, tropical e subtropical
No full textMemoria de tesis doctoral presentada por Andréa de Oliveira da Rocha Franco para obtener el título de Doctora por la Universidade Federal do Rio Grande, realizada bajo la dirección del Dr. Ramiro Logares del Institut de Ciències del Mar (ICM-CSIC
Comparative genomics of unculturable marine flagellates: new insights using Co-assembled single-amplified genomes from the MAST-4 group
No full textTrabajo final presentado por Francisco Latorre Pérez para un Máster de la Universitat Pompeu Fabra (UPF), realizado bajo la dirección del Dr. Ramiro Logares del Institut de Ciències del Mar (ICM-CSIC).-- 7 pages, 3 figures, 2 tablesMotivation: Previous Co-assemblies of marine microeukaryotic flagellates MAST-4 (clades A and E) based on single-cell MDA data may present DNA contamination from other eukaryotes or prokaryotes which has proven to be difficult to detect. Decontaminated assemblies are needed in order to study the role of these relatively abundant and ubiquitous organisms in the ocean, as well as to determine their genomic composition. Comparative genomics can help linking gene composition and ecological success in MAST-4 as well as to determine the degree of genomic differentiation between clades A and E.
Results: We have been able to detect and remove traces of contaminant DNA. Afterwards, our comparative genomic studies showed how both protists have similar functional metabolic routes that link them to their environment. Yet, at the same time, our analyses showed a significant degree of divergence at the protein and whole genome level, indicating that they are evolutionary more distant than expectedPeer Reviewe
Constraining the ecological niche of planktonic foraminifera in the Arctic
No full textThe effects of global warming are especially pronounced in the Arctic: temperatures have increased at a rate twice as fast as in other regions of the world during the past century. This trend implies that the Arctic Ocean will likely become entirely ice-free during the summer before the end of this century. Paleoclimatic studies have shown that abrupt large-volume meltwater discharges into the Arctic Ocean and its surrounding seas, were capable of disturbing the global ocean circulation and triggering further climatic transformations. Hence, a better understanding of the past natural variability of the Arctic Ocean is needed for more accurate model predictions of future climate change. Planktonic foraminifera represent a powerful tool for palaeoceanographic reconstructions. Their fossil assemblages and the chemical composition of their calcite shells allow reconstructing the physical state of the ocean in the past. The correct interpretation of these paleo-reconstructions highly relies on a thorough understanding of species-specific ecology of living planktonic foraminifera in the water column as, for example, preferred depth habitat, calcification conditions, and biotic interactions. In the Arctic Ocean, due to the fragmented observations on this marine group, no consensus exists on the ecological preferences of the different species, hampering the correct interpretation of the paleosignal present in their shells. This thesis aims to extend the understanding of the ecology of Arctic planktonic foraminifera species by focusing on various levels of organismal biology and physiology.
To constrain the environmental and biological factors controlling the vertical distribution of the species Neogloboquadrina pachyderma, a compilation of 104 vertical density profiles from the Arctic Ocean and its marginal seas was investigated using a statistical approach (Chapter 2). Contrary to what has been previously assumed, no significant relationship between N. pachyderma depth habitat and depth of chlorophyll maximum was observed. The depth habitat of the species could instead be predicted with a model including sea-ice concentration, surface chlorophyll concentration, and days since ice-break-up as predictors explaining 33% of the observed variability.
The biotic interactions of N. pachyderma with the eukaryotic pelagic community were assessed using a single-cell metabarcoding approach (Chapter 3). The eukaryotic DNA present in 39 specimens and contextual seawater from the Baffin Bay was extracted, amplified, and sequenced. The analyses revealed that N. pachyderma is omnivorous as it lives and opportunistically feeds on diatom-fuelled aggregates. The data also showed a particularly high occurrence of reads belonging to Syndiniales in the foraminifera samples, suggesting that this widely distributed parasite could infect N. pachyderma and possibly influence its population dynamics.
To test the assumption that planktonic foraminifera can tolerate low salinity and record the chemical signature of past meltwater discharge events in their shells, specimens of Neogloboquadrina incompta were exposed to a gradient of salinities between 35 and 25 PSU (Chapter 4) as part of a culturing study. Survival was monitored over 26 days by measuring the extent of the rhizopodial network. The highest rhizopodial activity occurred at salinity levels between 35 and 31 PSU. The results indicated that the species can survive long-term exposure to salinities as low as 28, but no rhizopodial activity and signs of cytoplasm degradation were observed in all specimens exposed to 25 PSU.
The responsiveness of Arctic planktonic foraminifera to current climate change was investigated by analysing a compilation of 51 species-resolved stratified population profiles collected in the Fram Strait between 1985 and 2015 (Chapter 5). The data revealed an ongoing Atlantification of the community not mirrored by changes in local environmental conditions. The abundance of Atlantic expatriates is instead rising because of processes favouring their growth in the Nordic Seas, the “source” area. On the contrary, the resident species Turborotalita quinqueloba showed declining density and habitat shoaling due to the ongoing extensive sea-ice export from the Arctic and associated cooling in the Fram Strait. These conditions favour the other resident species, the polar N. pachyderma being better adapted to the cold conditions of the area.
These results advance our understanding of the abiotic and biotic processes regulating the ecology of planktonic foraminifera in the Arctic Ocean and can be used to refine palaeoceanographic reconstructions in the polar regions and to improve predictions of future climate change
Functional characterization of a prevalent deep-sea fungi extracted from global metagenomes
No full textTrabajo final presentado por Lidia Montiel Fontanet para un Máster de la Universitat Pompeu Fabra (UPF), realizado bajo la dirección del Dr. Ramiro Logares del Institut de Ciències del Mar (ICM-CSIC)Peer Reviewe
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Co-Evolution and Global Population Structure of Tiny Ocean Predators
No full textSymposium on Aquatic Microbial Ecology - SAME17, From isolation to collaboration, 20-25 August-2023 Tartu, EstoniaUnicellular eukaryotic predators, including the MAST-4 lineage, significantly impact marine ecosystems and food web dynamics. Understanding their evolution, population structure, and adaptation to environmental factors is essential to comprehend the role of protists in marine ecosystems. Our analyses revealed different distributions of MAST-4 species in the global surface ocean and diverse food-degrading genes, pointing to niche adaptations. Specifically, the study of glycoside hydrolases suggested niche diversification tied to prey digestion. We propose that adaptations to temperature and prey type have driven MAST-4's evolutionary diversification. The analysis of MAST-4 population structure revealed varied patterns of genomic divergence in the global surface ocean. Temperature and salinity were the primary factors structuring these populations. Gene clusters under positive selection provided insights into metabolic functions that may be the basis of population adaptation. These findings enhance our understanding of MAST-4's evolutionary diversification and population structure, emphasizing the need for population genomics in protist analysis for a deeper understanding of marine ecosystem
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