8604 research outputs found
Sort by
Quantitative metagenomics for marine prokaryotes and photosynthetic eukaryotes
Full text linkHigh-throughput sequencing has provided unprecedented insights into microbial biodiversity in marine and other ecosystems. However, most sequencing-based studies report only relative (compositional) rather than absolute abundance, limiting their application in ecological modeling and biogeochemical analyses. Here, we present a metagenomic protocol incorporating genomic internal standards to quantify the absolute abundances of prokaryotes and eukaryotic phytoplankton, which together form the base of the marine food web, in unfractionated seawater. We applied this method to surface waters collected across 50°N to 40°S during the 29th Atlantic Meridional Transect. Using the single-copy recA gene, we estimated an average bacterial abundance of 1.0 × 109 haploid genome equivalents per liter. Leveraging a recent report that the psbO gene is typically single-copy in phytoplankton, we also quantified eukaryotic phytoplankton. Metagenomic estimates closely aligned with flow cytometry data for cyanobacteria (slope = 1.03, Pearson’s r = 0.89) and eukaryotic phytoplankton (slope = 0.72, Pearson’s r = 0.84). Compared to flow cytometry, taxonomic resolution for nano- and picoeukaryotes was greatly improved. Estimates for diatoms, dinoflagellates, and Trichodesmium were considerably higher than microscopy counts, likely reflecting microscopy undercounts and potential ploidy variation. These findings highlight the value of absolute quantification by metagenomics and offer a robust framework for quantitative assessments in microbial oceanography
The genome sequence of the China Limpet, Patella ulyssiponensis Gmelin, 1791 (Patellidae)
No full textWe present a genome assembly from a specimen of Patella ulyssiponensis (China Limpet; Mollusca; Gastropoda; Patellidae). The genome sequence has a total length of 693.56 megabases. Most of the assembly (99.78%) is scaffolded into 8 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 14.94 kilobases. Gene annotation of this assembly on Ensembl identified 21 151 protein-coding gene
The Deep Evolutionary Roots of the Nervous System
No full textThe evolutionary success of animals can, at least in part, be attributed to the presence of neurons that allow long-distance communication between tissues, coordination of movements, and the capacity for learning. However, the evolutionary origin and relationship of neurons to other cell types are fundamental questions that remain unsolved. The first neurons probably evolved shortly after the rise of the first animals over 600 million years ago. Studies on early-diverging animal lineages have provided key insights into the mechanisms underlying the origin of neurons. Recent discoveries in morphology, molecular signatures, and function of neurons in cnidarians and comb jellies, as well as neuron-like cells in nerveless placozoans, sponges, and other eukaryotes, may prompt a redefinition of what constitutes a neuron. Here we review the latest insights into the origin of neurons and nervous systems, while also highlighting exciting technological advancements that not only are accelerating our understanding of nervous system evolution, morphology, and function but also hold the potential to revolutionize the fiel
ParAquaSeq, a Database of Ecologically Annotated rRNA Sequences Covering Zoosporic Parasites Infecting Aquatic Primary Producers in Natural and Industrial Systems
No full textAmplicon sequencing tools such as metabarcoding are commonly used for thorough characterisation of microbial diversity in natural samples. They mostly rely on the amplification of conserved universal markers, mainly ribosomal genes, allowing the taxonomic assignment of barcodes. However, linking taxonomic classification with functional traits is not straightforward and requires knowledge of each taxonomic group to confidently assign taxa to a given functional trait. Zoosporic parasites are highly diverse and yet understudied, with many undescribed species and host associations. However, they can have important impacts on host populations in natural ecosystems (e.g., controlling harmful algal blooms), as well as on industrial-scale algae production, e.g. aquaculture, causing their collapse or economic losses. Here, we present ParAquaSeq, a curated database of available molecular ribosomal sequences belonging to zoosporic parasites infecting aquatic vascular plants, macroalgae and photosynthetic microorganisms, i.e. microalgae and cyanobacteria. These sequences are aligned with ancillary data and other information currently available, including details on their hosts, occurrence, culture availability and associated bibliography. The database includes 1131 curated sequences from marine, freshwater and industrial or artificial environments, and belonging to 13 different taxonomic groups, including Chytridiomycota, Oomycota, Phytomyxea, and Syndiniophyceae. The curated database will allow a comprehensive analysis of zoosporic parasites in molecular datasets to answer questions related to their occurrence and distribution in natural communities. Especially through meta-analysis, the database serves as a valuable tool for developing effective mitigation and sustainable management strategies in the algae biomass industry, but it will also help to identify knowledge gaps for future researc
Evidence of climate change (intertidal indicators)
No full textRocky shore species live in habitats that are exposed to both terrestrial and marine climates during the diurnal tidal cycle, and so provide a unique perspective on the genetic and physiological adaptations to survival in a constantly changing, environmentally challenging ecosystem. Most intertidal animals and seaweed are fixed to the rock or can only move small distances, which places them at the mercy of long-term climate change and extreme events such as heatwaves and storm events that are increasing in frequency and severity. As a result, they have shown some of the fastest responses to global warming in any system on the planet, shifting their geographic distributions to higher latitudes where sea and air temperatures are cooler. The rocky shore is an accessible habitat to study, and scientists have been able to look at the biological pathways by which different creatures respond to changes in climate by carrying out long-term surveys and experiments. The rapid responses to changes in temperature and the large amount of knowledge of their biological processes mean that intertidal species can be used as indicators of the biological effects that climate change is having within the marine real
Intra- and inter-decadal scale variability in kelp population structure reveal both stability and decline in a critical foundation species
No full textAim
Kelp forests support high biodiversity, primary productivity and ecosystem service value but exhibit high levels of spatiotemporal variability, which can complicate management and conservation efforts. A better understanding of multiscale temporal variability is needed to improve understanding of kelp forest dynamics.
Location
West Scotland and southwest England, United Kingdom.
Methods
We utilised high-resolution quantitative historical records from the 1940s and 1980s, combined with robust multiyear contemporary field surveys, to explore intra- and inter-decadal scale variability in population structure of the kelp Laminaria hyperborea in two regions of the UK (‘cool’ conditions in west Scotland, versus ‘warm’ conditions in southwest England).
Results
Over decadal timescales, the abundance (i.e., density, standing stock) of a kelp population in southwest England declined, which aligns with a concurrent increase in sea temperatures above the optimum for the performance of this species. Conversely, a population in western Scotland exhibited stability, with plant density and size remaining consistent over multiple decades. Over shorter timescales (across 10 years of contemporary surveys), kelp populations in both regions exhibited minimal temporal variability, in terms of plant density, cover and standing stock, indicating that this species underpins stable and abundant habitat.
Main Conclusions
Compared to many kelp ecosystems globally, and contrary to the widely accepted highly dynamic nature of these habitats, L. hyperborea populations exhibited marked stability across years and (in the case of west Scotland) decades, although gradual ocean warming is likely eroding the resilience of populations in warmer waters located towards this species upper thermal limit. While historical evidence allowed us to reconstruct ecological baselines, patterns must be interpreted with caution as the number of available sites was very limited. Improved monitoring of these vital coastal habitats is needed to better understand patterns and drivers of temporal variability over multiple time scale
Adaptive traits for chitin utilization in the saprotrophic aquatic chytrid fungus Rhizoclosmatium globosum
No full textThe Chytridiomycota (chytrids) are early diverging fungi, many of which function in ecosystems as saprotrophs; however, associated adaptive traits are poorly understood. We focused on chitin degradation, a common ecosystem function of aquatic chytrids, using the model chitinophilic Rhizoclosmatium globosum and comparison of other chytrid genomes. Zoospores are chemotactic to the chitin monomer N-acetylglucosamine and accelerate development when grown with chitin. The R. globosum secretome is dominated by different glycoside hydrolase (GH) family GH18 chitinases, with abundance matching reciprocal transcriptome mRNA sequences. Models of the secreted chitinases indicate a range of sizes and domain configurations. Along with R. globosum, the genomes of other chitinophilic chytrids also have expanded inventories of GH-encoding genes responsible for chitin processing. Several R. globosum GH18 chitinases have bacteria-like chitin-binding module domains, also present in the genomes of other chitinophilic chytrids yet absent in non-chitinophilic chytrids. Chemotaxis, increased abundance and diversity of secreted chitinases, complemented with the acquisition of novel chitin-binding capability, are probably adaptive traits that facilitate chitin saprotrophy. Our study reveals the underpinning mechanisms that have supported the niche expansion of some chytrids to utilize lucrative chitin-rich particles in aquatic ecosystems and is a demonstration of the adaptive ability of this successful fungal grou
Benchmark workshop on application of Stock Synthesis (SS3) on selected stocks (WKBSS3)
No full textBenchmark workshop on application of Stock Synthesis (SS3) on selected stocks (WKBSS3) is the first dedicated ICES benchmark workshop to stocks assessed using only Stock Synthesis models(SS). Four stocks were included in the ToRs (ank.27.8c9a; Black-bellied anglerfish (Lophius budegassa) in divisions 8.c and 9.a, Cantabrian Sea, Atlantic Iberian waters; mon.27.8c9a; White anglerfish (Lophius piscatorius) in divisions 8.c and 9.a, Cantabrian Sea and Atlantic Iberian waters, pol.27.67; Pollack (Pollachius pollachius) in subareas 6-7; Celtic Seas and the English Channel; sbr.27.9; Blackspot seabream (Pagellus bogaraveo) in Subarea 9; Atlantic Iberian waters. The stocks pertain to three ICES Assessment Working Groups (WGBIE, WGCSE, and WGDEEP) and were selected based on the availability of appropriate data and network capacity
How marine heatwaves are reshaping phytoplankton in the Northeast Pacific
No full textIn 2015 and 2019, the Northeast Pacific has undergone significant heatwave events that strongly disrupted marine ecosystems functioning and services. Here we use the data collected by the Continuous Plankton Recorder (CPR) survey to investigate the changes in summer phytoplankton abundance and morphology and show an increase in prolate (i.e., elongated) taxa during heatwave events, in response to warmer temperatures and declining nitrate. We also investigate the impacts of the morphological shifts on the carbon cycle and show that warmer periods were dominated by prolate cells with high carbon content, whereas cooler periods were dominated by oblate (i.e., flattened) cells with low carbon content. By altering community composition and the overall cells sinking velocity, these morphological shifts likely impacted the carbon cycle, as they were correlated with changes in surface chlorophyll a and particulate organic carbon concentration