scholarly journals Within-Arctic horizontal gene transfer as a driver of convergent evolution in distantly related microalgae

2021 ◽  
Author(s):  
Richard G Dorrell ◽  
Alan Kuo ◽  
Zoltan Fussy ◽  
Elisabeth H Richardson ◽  
Asaf Salamov ◽  
...  
Keyword(s):  
Sequence Data ◽  
Sequence Similarity ◽  
Algal Species ◽  
Gene Families ◽  
The Arctic ◽  
Arctic Water ◽  
Diverse Range ◽  
Binding Domains ◽  
Ice Binding ◽  
Ice Conditions

The Arctic Ocean is being impacted by warming temperatures, increasing freshwater and highly variable ice conditions. The microalgal communities underpinning Arctic marine food webs, once thought to be dominated by diatoms, include a phylogenetically diverse range of small algal species, whose biology remains poorly understood. Here, we present genome sequences of a cryptomonad, a haptophyte, a chrysophyte, and a pelagophyte, isolated from the Arctic water column and ice. Comparing protein family distributions and sequence similarity across a densely-sampled set of algal genomes and transcriptomes, we note striking convergences in the biology of distantly related small Arctic algae, compared to non-Arctic relatives; although this convergence is largely exclusive of Arctic diatoms. Using high-throughput phylogenetic approaches, incorporating environmental sequence data from Tara Oceans, we demonstrate that this convergence was partly explained by horizontal gene transfers (HGT) between Arctic species, in over at least 30 other discrete gene families, and most notably in ice-binding domains (IBD). These Arctic-specific genes have been repeatedly transferred between Arctic algae, and are independent of equivalent HGTs in the Antarctic Southern Ocean. Our data provide insights into the specialised Arctic marine microbiome, and underlines the role of geographically-limited HGT as a driver of environmental adaptation in eukaryotic algae.

scholarly journals Analysis of the Sequence Characteristics of Antifreeze Protein

Life ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 520
Author(s):  
Yu-Hang Zhang ◽  
Zhandong Li ◽  
Lin Lu ◽  
Tao Zeng ◽  
Lei Chen ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Active Material ◽  
Antifreeze Protein ◽  
Computational Method ◽  
Acetylneuraminic Acid ◽  
Binding Domains ◽  
Ice Binding ◽  
Surface Active ◽  
Surface Active Material ◽  
Sequence Characteristics

Antifreeze protein (AFP) is a proteinaceous compound with improved antifreeze ability and binding ability to ice to prevent its growth. As a surface-active material, a small number of AFPs have a tremendous influence on the growth of ice. Therefore, identifying novel AFPs is important to understand protein–ice interactions and create novel ice-binding domains. To date, predicting AFPs is difficult due to their low sequence similarity for the ice-binding domain and the lack of common features among different AFPs. Here, a computational engine was developed to predict the features of AFPs and reveal the most important 39 features for AFP identification, such as antifreeze-like/N-acetylneuraminic acid synthase C-terminal, insect AFP motif, C-type lectin-like, and EGF-like domain. With this newly presented computational method, a group of previously confirmed functional AFP motifs was screened out. This study has identified some potential new AFP motifs and contributes to understanding biological antifreeze mechanisms.

scholarly journals Polarella glacialis genomes encode tandem repeats of single-exon genes with functions critical to adaptation of dinoflagellates

2019 ◽  
Author(s):  
Timothy G. Stephens ◽  
Raúl A. González-Pech ◽  
Yuanyuan Cheng ◽  
Amin R. Mohamed ◽  
David W. Burt ◽  
...  
Keyword(s):  
Tandem Repeats ◽  
Genome Structure ◽  
The Arctic ◽  
Genome Comparison ◽  
Long Terminal Repeats ◽  
Transcriptional Responses ◽  
Low Light ◽  
Binding Domains ◽  
Ice Binding ◽  
Genome Assemblies

AbstractDinoflagellates are taxonomically diverse, ecologically important phytoplankton in marine and freshwater environments. Here, we present two draft diploid genome assemblies of the free-living dinoflagellate Polarella glacialis, isolated from the Arctic and Antarctica. For each genome, guided using full-length transcriptome data, we predicted >50,000 high-quality genes. About 68% of the genome is repetitive sequence; long terminal repeats likely contribute to intra-species structural divergence and distinct genome sizes (3.0 and 2.7 Gbp). Of all genes, ∼40% are encoded unidirectionally, ∼25% comprised of single exons. Multi-genome comparison unveiled genes specific to P. glacialis and a common, putatively bacterial, origin of ice-binding domains in cold-adapted dinoflagellates. Our results elucidate how selection acts within the context of a complex genome structure to facilitate local adaptation. Since most dinoflagellate genes are constitutively expressed, Polarella glacialis has enhanced transcriptional responses via unidirectional, tandem duplication of single-exon genes that encode functions critical to survival in cold, low-light environments.

Prévoir les variations saisonnières de la glace de mer arctique et leurs impacts sur le climat

2020 ◽  
pp. 024
Author(s):  
Rym Msadek ◽  
Gilles Garric ◽  
Sara Fleury ◽  
Florent Garnier ◽  
Lauriane Batté ◽  
...  
Keyword(s):  
Sea Ice ◽  
Arctic Region ◽  
Arctic Sea Ice ◽  
Climate Impacts ◽  
The Arctic ◽  
Recent Effort ◽  
Sea Ice Thickness ◽  
Arctic Sea ◽  
Ice Conditions ◽  
Upper Level

L'Arctique est la région du globe qui s'est réchauffée le plus vite au cours des trente dernières années, avec une augmentation de la température de surface environ deux fois plus rapide que pour la moyenne globale. Le déclin de la banquise arctique observé depuis le début de l'ère satellitaire et attribué principalement à l'augmentation de la concentration des gaz à effet de serre aurait joué un rôle important dans cette amplification des températures au pôle. Cette fonte importante des glaces arctiques, qui devrait s'accélérer dans les décennies à venir, pourrait modifier les vents en haute altitude et potentiellement avoir un impact sur le climat des moyennes latitudes. L'étendue de la banquise arctique varie considérablement d'une saison à l'autre, d'une année à l'autre, d'une décennie à l'autre. Améliorer notre capacité à prévoir ces variations nécessite de comprendre, observer et modéliser les interactions entre la banquise et les autres composantes du système Terre, telles que l'océan, l'atmosphère ou la biosphère, à différentes échelles de temps. La réalisation de prévisions saisonnières de la banquise arctique est très récente comparée aux prévisions du temps ou aux prévisions saisonnières de paramètres météorologiques (température, précipitation). Les résultats ayant émergé au cours des dix dernières années mettent en évidence l'importance des observations de l'épaisseur de la glace de mer pour prévoir l'évolution de la banquise estivale plusieurs mois à l'avance. Surface temperatures over the Arctic region have been increasing twice as fast as global mean temperatures, a phenomenon known as arctic amplification. One main contributor to this polar warming is the large decline of Arctic sea ice observed since the beginning of satellite observations, which has been attributed to the increase of greenhouse gases. The acceleration of Arctic sea ice loss that is projected for the coming decades could modify the upper level atmospheric circulation yielding climate impacts up to the mid-latitudes. There is considerable variability in the spatial extent of ice cover on seasonal, interannual and decadal time scales. Better understanding, observing and modelling the interactions between sea ice and the other components of the climate system is key for improved predictions of Arctic sea ice in the future. Running operational-like seasonal predictions of Arctic sea ice is a quite recent effort compared to weather predictions or seasonal predictions of atmospheric fields like temperature or precipitation. Recent results stress the importance of sea ice thickness observations to improve seasonal predictions of Arctic sea ice conditions during summer.

scholarly journals Predicting bacteriophage hosts based on sequences of annotated receptor-binding proteins

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Dimitri Boeckaerts ◽  
Michiel Stock ◽  
Bjorn Criel ◽  
Hans Gerstmans ◽  
Bernard De Baets ◽  
...  
Keyword(s):  
Machine Learning ◽  
Predictive Model ◽  
Receptor Binding ◽  
Bacterial Infections ◽  
Sequence Data ◽  
Sequence Similarity ◽  
Area Under The Curve ◽  
Local Alignment ◽  
Search Tool ◽  
Different Levels

AbstractNowadays, bacteriophages are increasingly considered as an alternative treatment for a variety of bacterial infections in cases where classical antibiotics have become ineffective. However, characterizing the host specificity of phages remains a labor- and time-intensive process. In order to alleviate this burden, we have developed a new machine-learning-based pipeline to predict bacteriophage hosts based on annotated receptor-binding protein (RBP) sequence data. We focus on predicting bacterial hosts from the ESKAPE group, Escherichia coli, Salmonella enterica and Clostridium difficile. We compare the performance of our predictive model with that of the widely used Basic Local Alignment Search Tool (BLAST). Our best-performing predictive model reaches Precision-Recall Area Under the Curve (PR-AUC) scores between 73.6 and 93.8% for different levels of sequence similarity in the collected data. Our model reaches a performance comparable to that of BLASTp when sequence similarity in the data is high and starts outperforming BLASTp when sequence similarity drops below 75%. Therefore, our machine learning methods can be especially useful in settings in which sequence similarity to other known sequences is low. Predicting the hosts of novel metagenomic RBP sequences could extend our toolbox to tune the host spectrum of phages or phage tail-like bacteriocins by swapping RBPs.

Phytoplankton of the Calanus Expeditions in Hudson Bay, 1953 and 1954

1961 ◽  
Vol 18 (1) ◽  
pp. 51-83 ◽  
Author(s):  
Adam Bursa
Keyword(s):  
Surface Wind ◽  
The Arctic ◽  
Phytoplankton Production ◽  
Hudson Bay ◽  
Population Exchange ◽  
Taxonomic Descriptions ◽  
Hydrographic Structure ◽  
Plankton Production ◽  
Water Temperature Data ◽  
Ice Conditions

Phytoplankton samples, collected in 1953 and 1954 by the Calanus expeditions, were examined by the quantitative sedimentation method in an attempt to determine the ecological aspects of phytoplankton production in Hudson Bay and Strait. During the period July to September of both years, water temperature data, and salinity, oxygen and quantitative phytoplankton samples were collected at the surface and from depths of 10, 25, 50 and 100 metres. Numerically, the most abundant, heterogeneous phytoplankton populations were found in the mouth of Hudson Bay. The lower production of phytoplankton in the surface layer can be explained by the greater amplitude of temperature and salinity, dependent upon ice conditions and surface wind drift. The most productive layer was at a depth of 10 m. Large phytoplankton populations in waters supersaturated with oxygen were still found at 25 m, indicating light conditions favourable for photosynthesis. The relatively high plankton production in the area joining Hudson Bay and Hudson Strait is probably due to the hydrographic structure and the supply of nutrients resulting from the mixing of water masses which originate in other geographical areas. The preponderance of diatoms over flagellated groups, which is more marked in Hudson Strait than in Hudson Bay, is typical for the arctic. The composition of phytoplankton in these areas shows a great similarity in the main to that found on both sides of the Atlantic. Apart from locally produced plankton populations, there is a population exchange which follows water movements. To supplement the meagreness of existing taxonomic descriptions, attention is here focussed on the identification of plankters and their individual importance in the general ecology of the phytoplankton.

Co-producing Sea-Ice Predictions with Stakeholders Using Simulation

2021 ◽  
Keyword(s):  
Sea Ice ◽  
Local Community ◽  
Economic Value ◽  
Arctic Region ◽  
Production Model ◽  
The Arctic ◽  
Simulation Game ◽  
Climate Services ◽  
Diverse Range ◽  
Uncertainty Information

Abstract Forecasts of sea-ice evolution in the Arctic region for several months ahead can be of considerable socio-economic value for a diverse range of marine sectors and for local community supply logistics. However, subseasonal-to-seasonal (S2S) forecasts represent a significant technical challenge, while translating user needs into scientifically manageable procedures and robust user confidence requires collaboration among a range of stakeholders. We developed and tested a novel, transdisciplinary co-production approach that combined socio-economic scenarios and participatory, research-driven simulation-gaming to test a new S2S sea-ice forecast system with experienced mariners in the cruise tourism sector. Our custom-developed computerized simulation-game ICEWISE integrated sea-ice parameters, forecast technology and human factors, as a participatory environment for stakeholder engagement. We explored the value of applications-relevant S2S sea-ice prediction and linked uncertainty information. Results suggest that the usefulness of S2S services is currently most evident in schedule-dependent sectors but expected to increase due to anticipated changes in the physical environment and continued growth in Arctic operations. Reliable communication of uncertainty information in sea-ice forecasts must be demonstrated and trialed before users gain confidence in emerging services and technologies. Mariners’ own intuition, experience, and familiarity with forecast service provider reputation impact the extent to which sea-ice information may reduce uncertainties and risks for Arctic mariners. Our insights into the performance of the combined foresight/simulation co-production model in brokering knowledge across a range of domains demonstrates promise. We conclude with an overview of the potential contributions from S2S sea-ice predictions and from experiential co-production models to the development of decision-driven and science-informed climate services.

Phytoplankton of cold-water lake ecosystems under the influence of natural and anthropogenic factors

2021 ◽  
pp. 42-49
Author(s):  
Andrey N. Sharov
Keyword(s):  
Heavy Metals ◽  
Cold Water ◽  
Arctic Lakes ◽  
Water Bodies ◽  
The Arctic ◽  
Anthropogenic Factors ◽  
Large Lakes ◽  
Arctic Water ◽  
The North ◽  
Natural And Anthropogenic Factors

Based on the study of the spatio-temporal aspects of the development of phytoplankton in the lakes of the North and North-West of the European territory of Russia (large lakes – Imandra, Onega and Chudsko-Pskovskoye and small lakes of the Arctic and Subarctic), the features of its structure and dynamics under the influence of natural and anthropogenic factors (eutrophication, heavy metal pollution, acidification, thermification). The species composition and quantitative characteristics of phytoplankton of large lakes of the North of Russia, small arctic lakes and lakes of subarctic regions are studied. It has been shown that diatoms predominate in arctic water bodies according to species diversity, and green and diatoms predominate in boreal ones. By biomass, diatoms dominate mainly in all cold-water lakes, with the exception of small arctic lakes, where golden algae lead. The features of the reorganization of phytoplankton in response to the action of anthropogenic factors are revealed. It is proved that in the northern water bodies the complex action of heavy metals and nutrients does not lead to inhibition of phytoplankton, and the effect of acidification in combination with heavy metals enhances the toxic effect of the latter. A feature of the response to acidification is an increase in the variability of the dynamics of the biomass of phytoplankton. It has been shown that in different types of lakes of East Antarctica under severe climate conditions under light and biogenic limitation, redistribution of autotrophic components in the formation of the biota of water bodies occurs: against the background of a decrease in the abundance and diversity of phytoplankton, the role of microphytobenthos and periphyton increases.

scholarly journals Distribution of 210Pb and 210Po in the Arctic water column during the 2007 sea-ice minimum: Particle export in the ice-covered basins

2018 ◽  
Vol 142 ◽  
pp. 94-106 ◽  
Author(s):  
Montserrat Roca-Martí ◽  
Viena Puigcorbé ◽  
Jana Friedrich ◽  
Michiel Rutgers van der Loeff ◽  
Benjamin Rabe ◽  
...  
Keyword(s):  
Sea Ice ◽  
Water Column ◽  
The Arctic ◽  
Arctic Water ◽  
Particle Export

scholarly journals Using the Arctic water resources vulnerability index in assessing and responding to environmental change in Alaskan communities

2019 ◽  
Vol 23 ◽  
pp. 19-31 ◽  
Author(s):  
Paula Williams ◽  
Andrew Kliskey ◽  
Molly McCarthy ◽  
Richard Lammers ◽  
Lilian Alessa ◽  
...  
Keyword(s):  
Water Resources ◽  
Environmental Change ◽  
Vulnerability Index ◽  
The Arctic ◽  
Arctic Water ◽  
Water Resources Vulnerability

Identification and analysis of two sequences encoding ice-binding proteins obtained from a putative bacterial symbiont of the psychrophilic Antarctic ciliate Euplotes focardii

2014 ◽  
Vol 26 (5) ◽  
pp. 491-501 ◽  
Author(s):  
Sandra Pucciarelli ◽  
Federica Chiappori ◽  
Raghul Rajan Devaraj ◽  
Guang Yang ◽  
Ting Yu ◽  
...  
Keyword(s):  
Amino Acid Level ◽  
Bacterial Symbiont ◽  
The Arctic ◽  
Glacial Ice ◽  
Mould Fungus ◽  
Lake Vostok ◽  
Ice Binding ◽  
Stigmatella Aurantiaca ◽  
Ice Binding Protein ◽  
The Antarctic

AbstractWe identified two ice-binding protein (IBP) sequences, named EFsymbAFP and EFsymbIBP, from a putative bacterial symbiont of the Antarctic psychrophilic ciliate Euplotes focardii. EFsymbAFP is 57.43% identical to the antifreeze protein (AFP) from the Stigmatella aurantiaca strain DW4/3-1, which was isolated from the Victoria Valley lower glacier. EFsymbIBP is 53.38% identical to the IBP from the Flavobacteriaceae bacterium strain 3519-10, isolated from the glacial ice of Lake Vostok. EFsymbAFP and EFsymbIBP are 31.73% identical at the amino acid level and are organized in tandem on the bacterial chromosome. The relatively low sequence identity and the tandem organization, which appears unique to this symbiont, suggest an occurrence of horizontal gene transfer (HGT). Structurally, EFsymbAFP and EFsymbIBP are similar to the AFPs from the snow mould fungus Typhula ishikariensis and from the Arctic yeast Leucosporidium sp. AY30. A phylogenetic analysis showed that EFsymbAFP and EFsymbIBP cluster principally with the IBP sequences from other Antarctic bacteria, supporting the view that these sequences belong to an Antarctic symbiontic bacterium of E. focardii. These results confirm that IBPs have a complex evolutionary history, which includes HGT events, most probably due to the demands of the environment and the need for rapid adaptation.

Sign in / Sign up

Export Citation Format

Share Document