Polar Genomics

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Population and Evolutionary Genetics and Genomics".

Deadline for manuscript submissions: closed (23 December 2022) | Viewed by 38834

Special Issue Editors


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Guest Editor
Department of Animal Behaviour, Bielefeld University, 33501 Bielefeld, Germany
Interests: population genetics; evolutionary genetics; conservation genetics; inbreeding depression; genetic diversity; climate change; local adaptation; Antarctic marine organisms

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Guest Editor
British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK
Interests: environmental genomics; adaptation to extreme cold; thermal stress tolerance; transcriptomics; heat shock proteins; multi-omics approaches; calcium regulation; epigenetics

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Guest Editor
Applied Ecology and Phycology, Institute for Biological Sciences, University of Rostock, 18059 Rostock, Germany
Interests: taxonomy & systematics; phylogenetics; biodiversity; marine & terrestrial algae; introduced species; diseases of algae

Special Issue Information

Dear Colleagues,

Rapid advances in genomics are creating unprecedented opportunities to advance our understanding of the biology of polar organisms.  From reduced representation sequencing through transcriptomics, metagenomics, and proteomics to whole-genome and methylome sequencing, advanced molecular tools are providing increasingly detailed insights into patterns of biological diversity, adaptation to extreme environments, and responses to environmental change. This Special Issue of Genes is associated with a topic workshop on Polar Genomics organized by the Deutsche Forschungsgemeinschaft (DFG, German Science Foundation) Priority Programme 1158, “Antarctic Research with Comparative Investigations in Arctic Ice Areas”, which is planned for May 2022.  We invite articles that use genome-scale datasets to address relevant topics including but not restricted to the ones listed below.

With best wishes,

Prof. Dr. Joe Hoffman
Prof. Dr. Melody Clark
Dr. Svenja Heesch
Guest Editors

Manuscript Submission Information

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Keywords

  • population and evolutionary genomics of polar organisms
  • phylogenomics of polar organisms
  • climate change adaptation in polar regions
  • genetics of adaptation to extreme polar environments
  • transcriptomic responses of polar organisms to environmental stress
  • phenotypic plasticity and epigenetics of polar biota
  • structure and function of polar prokaryotic and eukaryotic communities
  • annotated draft genomes of polar organisms
  • systems biology of polar organisms

Published Papers (16 papers)

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Editorial

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5 pages, 210 KiB  
Editorial
Editorial: Polar Genomics in a Changing World
by Joseph Ivan Hoffman, Svenja Heesch and Melody Susan Clark
Genes 2023, 14(7), 1395; https://doi.org/10.3390/genes14071395 - 3 Jul 2023
Viewed by 1004
Abstract
Polar regions play critical roles in the function of the Earth’s climate system, many of which are underpinned by their endemic biota [...] Full article
(This article belongs to the Special Issue Polar Genomics)

Research

Jump to: Editorial, Other

21 pages, 5346 KiB  
Article
Chromosome-Level Genome Assembly and Circadian Gene Repertoire of the Patagonia Blennie Eleginops maclovinus—The Closest Ancestral Proxy of Antarctic Cryonotothenioids
by Chi-Hing Christina Cheng, Angel G. Rivera-Colón, Bushra Fazal Minhas, Loralee Wilson, Niraj Rayamajhi, Luis Vargas-Chacoff and Julian M. Catchen
Genes 2023, 14(6), 1196; https://doi.org/10.3390/genes14061196 - 30 May 2023
Cited by 1 | Viewed by 1601
Abstract
The basal South American notothenioid Eleginops maclovinus (Patagonia blennie or róbalo) occupies a uniquely important phylogenetic position in Notothenioidei as the singular closest sister species to the Antarctic cryonotothenioid fishes. Its genome and the traits encoded therein would be the nearest representatives of [...] Read more.
The basal South American notothenioid Eleginops maclovinus (Patagonia blennie or róbalo) occupies a uniquely important phylogenetic position in Notothenioidei as the singular closest sister species to the Antarctic cryonotothenioid fishes. Its genome and the traits encoded therein would be the nearest representatives of the temperate ancestor from which the Antarctic clade arose, providing an ancestral reference for deducing polar derived changes. In this study, we generated a gene- and chromosome-complete assembly of the E. maclovinus genome using long read sequencing and HiC scaffolding. We compared its genome architecture with the more basally divergent Cottoperca gobio and the derived genomes of nine cryonotothenioids representing all five Antarctic families. We also reconstructed a notothenioid phylogeny using 2918 proteins of single-copy orthologous genes from these genomes that reaffirmed E. maclovinus’ phylogenetic position. We additionally curated E. maclovinus’ repertoire of circadian rhythm genes, ascertained their functionality by transcriptome sequencing, and compared its pattern of gene retention with C. gobio and the derived cryonotothenioids. Through reconstructing circadian gene trees, we also assessed the potential role of the retained genes in cryonotothenioids by referencing to the functions of the human orthologs. Our results found E. maclovinus to share greater conservation with the Antarctic clade, solidifying its evolutionary status as the direct sister and best suited ancestral proxy of cryonotothenioids. The high-quality genome of E. maclovinus will facilitate inquiries into cold derived traits in temperate to polar evolution, and conversely on the paths of readaptation to non-freezing habitats in various secondarily temperate cryonotothenioids through comparative genomic analyses. Full article
(This article belongs to the Special Issue Polar Genomics)
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16 pages, 4781 KiB  
Article
Temperature-Related Short-Term Succession Events of Bacterial Phylotypes in Potter Cove, Antarctica
by Doris Ilicic, Danny Ionescu, Jason Woodhouse and Hans-Peter Grossart
Genes 2023, 14(5), 1051; https://doi.org/10.3390/genes14051051 - 8 May 2023
Cited by 2 | Viewed by 1572
Abstract
In recent years, our understanding of the roles of bacterial communities in the Antarctic Ocean has substantially improved. It became evident that Antarctic marine bacteria are metabolically versatile, and even closely related strains may differ in their functionality and, therefore, affect the ecosystem [...] Read more.
In recent years, our understanding of the roles of bacterial communities in the Antarctic Ocean has substantially improved. It became evident that Antarctic marine bacteria are metabolically versatile, and even closely related strains may differ in their functionality and, therefore, affect the ecosystem differently. Nevertheless, most studies have been focused on entire bacterial communities, with little attention given to individual taxonomic groups. Antarctic waters are strongly influenced by climate change; thus, it is crucial to understand how changes in environmental conditions, such as changes in water temperature and salinity fluctuations, affect bacterial species in this important area. In this study, we show that an increase in water temperature of 1 °C was enough to alter bacterial communities on a short-term temporal scale. We further show the high intraspecific diversity of Antarctic bacteria and, subsequently, rapid intra-species succession events most likely driven by various temperature-adapted phylotypes. Our results reveal pronounced changes in microbial communities in the Antarctic Ocean driven by a single strong temperature anomaly. This suggests that long-term warming may have profound effects on bacterial community composition and presumably functionality in light of continuous and future climate change. Full article
(This article belongs to the Special Issue Polar Genomics)
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23 pages, 2602 KiB  
Article
Historical Mitogenomic Diversity and Population Structuring of Southern Hemisphere Fin Whales
by Danielle L. Buss, Lane M. Atmore, Maria H. Zicos, William P. Goodall-Copestake, Selina Brace, Frederick I. Archer, C. Scott Baker, Ian Barnes, Emma L. Carroll, Tom Hart, Andrew C. Kitchener, Richard Sabin, Angela L. Sremba, Caroline R. Weir and Jennifer A. Jackson
Genes 2023, 14(5), 1038; https://doi.org/10.3390/genes14051038 - 3 May 2023
Cited by 1 | Viewed by 3414
Abstract
Fin whales Balaenoptera physalus were hunted unsustainably across the globe in the 19th and 20th centuries, leading to vast reductions in population size. Whaling catch records indicate the importance of the Southern Ocean for this species; approximately 730,000 fin whales were harvested during [...] Read more.
Fin whales Balaenoptera physalus were hunted unsustainably across the globe in the 19th and 20th centuries, leading to vast reductions in population size. Whaling catch records indicate the importance of the Southern Ocean for this species; approximately 730,000 fin whales were harvested during the 20th century in the Southern Hemisphere (SH) alone, 94% of which were at high latitudes. Genetic samples from contemporary whales can provide a window to past population size changes, but the challenges of sampling in remote Antarctic waters limit the availability of data. Here, we take advantage of historical samples in the form of bones and baleen available from ex-whaling stations and museums to assess the pre-whaling diversity of this once abundant species. We sequenced 27 historical mitogenomes and 50 historical mitochondrial control region sequences of fin whales to gain insight into the population structure and genetic diversity of Southern Hemisphere fin whales (SHFWs) before and after the whaling. Our data, both independently and when combined with mitogenomes from the literature, suggest SHFWs are highly diverse and may represent a single panmictic population that is genetically differentiated from Northern Hemisphere populations. These are the first historic mitogenomes available for SHFWs, providing a unique time series of genetic data for this species. Full article
(This article belongs to the Special Issue Polar Genomics)
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21 pages, 4991 KiB  
Article
Metabarcoding of Antarctic Lichens from Areas with Different Deglaciation Times Reveals a High Diversity of Lichen-Associated Communities
by Andreas Beck, Angélica Casanova-Katny and Julia Gerasimova
Genes 2023, 14(5), 1019; https://doi.org/10.3390/genes14051019 - 29 Apr 2023
Cited by 1 | Viewed by 1939
Abstract
Lichens have developed numerous adaptations to optimise their survival under harsh abiotic stress, colonise different substrates, and reach substantial population sizes and high coverage in ice-free Antarctic areas, benefiting from a symbiotic lifestyle. As lichen thalli represent consortia with an unknown number of [...] Read more.
Lichens have developed numerous adaptations to optimise their survival under harsh abiotic stress, colonise different substrates, and reach substantial population sizes and high coverage in ice-free Antarctic areas, benefiting from a symbiotic lifestyle. As lichen thalli represent consortia with an unknown number of participants, it is important to know about the accessory organisms and their relationships with various environmental conditions. To this end, we analysed lichen-associated communities from Himantormia lugubris, Placopsis antarctica, P. contortuplicata, and Ramalina terebrata, collected from soils with differing deglaciation times, using a metabarcoding approach. In general, many more Ascomycete taxa are associated with the investigated lichens compared to Basidiomycota. Given our sampling, a consistently higher number of lichen-associated eukaryotes are estimated to be present in areas with deglaciation times of longer than 5000 years compared to more recently deglaciated areas. Thus far, members of Dothideomycetes, Leotiomycetes, and Arthoniomycetes have been restricted to the Placopsis specimens from areas with deglaciation times longer than 5000 years. Striking differences between the associated organisms of R. terebrata and H. lugubris have also been discovered. Thus, a species-specific basidiomycete, Tremella, was revealed for R. terebrata, as was a member of Capnodiales for H. lugubris. Our study provides further understanding of the complex terricolous lichen-associated mycobiome using the metabarcoding approach. It also illustrates the necessity to extend our knowledge of complex lichen symbiosis and further improve the coverage of microbial eukaryotes in DNA barcode libraries, including more extended sampling. Full article
(This article belongs to the Special Issue Polar Genomics)
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15 pages, 2012 KiB  
Article
Mitochondrial Heteroplasmy and PCR Amplification Bias Lead to Wrong Species Delimitation with High Confidence in the South American and Antarctic Marine Bivalve Aequiyoldia eightsii Species Complex
by Mariano Martínez, Lars Harms, Doris Abele and Christoph Held
Genes 2023, 14(4), 935; https://doi.org/10.3390/genes14040935 - 18 Apr 2023
Cited by 2 | Viewed by 1270
Abstract
The species delimitation of the marine bivalve species complex Aequiyoldia eightsii in South America and Antarctica is complicated by mitochondrial heteroplasmy and amplification bias in molecular barcoding. In this study, we compare different data sources (mitochondrial cytochrome c oxidase subunit I (COI [...] Read more.
The species delimitation of the marine bivalve species complex Aequiyoldia eightsii in South America and Antarctica is complicated by mitochondrial heteroplasmy and amplification bias in molecular barcoding. In this study, we compare different data sources (mitochondrial cytochrome c oxidase subunit I (COI) sequences; nuclear and mitochondrial SNPs). Whilst all the data suggest that populations on either side of the Drake Passage belong to different species, the picture is less clear within Antarctic populations, which harbor three distinct mitochondrial lineages (p-dist ≈ 6%) that coexist in populations and in a subset of individuals with heteroplasmy. Standard barcoding procedures lead to amplification bias favoring either haplotype unpredictably and thus overestimate the species richness with high confidence. However, nuclear SNPs show no differentiation akin to the trans-Drake comparison, suggesting that the Antarctic populations represent a single species. Their distinct haplotypes likely evolved during periods of temporary allopatry, whereas recombination eroded similar differentiation patterns in the nuclear genome after secondary contact. Our study highlights the importance of using multiple data sources and careful quality control measures to avoid bias and increase the accuracy of molecular species delimitation. We recommend an active search for mitochondrial heteroplasmy and haplotype-specific primers for amplification in DNA-barcoding studies. Full article
(This article belongs to the Special Issue Polar Genomics)
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14 pages, 933 KiB  
Article
Using Next-Generation Sequencing to Disentangle the Diet and Incidence of Intestinal Parasites of Falkland Flightless Steamer Duck Tachyeres brachypterus and Patagonian Crested Duck Lophonetta specularioides Sharing a South Atlantic Island
by Juan F. Masello, Yvonne R. Schumm, Sven Griep and Petra Quillfeldt
Genes 2023, 14(3), 731; https://doi.org/10.3390/genes14030731 - 16 Mar 2023
Cited by 1 | Viewed by 1691
Abstract
Species overlapping in habitat use can cohabit depending on how they exploit resources. To understand segregation in resource use, an exhaustive knowledge of the diet is required. We aimed to disentangle the diet composition of the Falkland Flightless Steamer Duck Tachyeres brachypterus and [...] Read more.
Species overlapping in habitat use can cohabit depending on how they exploit resources. To understand segregation in resource use, an exhaustive knowledge of the diet is required. We aimed to disentangle the diet composition of the Falkland Flightless Steamer Duck Tachyeres brachypterus and the Patagonian Crested Duck Lophonetta specularioides sharing a coastal environment. Using DNA extracted from scats and Illumina sequencing, we generated a list of molecular operational taxonomic units. Both ducks consumed a variety of invertebrates, frequently overlapping in the taxa consumed. However, only the Falkland Flightless Steamer Ducks consumed fish, which might be indicative of dietary specialization and inter-specific segregation in the restricted space that these birds share. Moreover, the female and male Falkland Flightless Steamer Ducks consumed different fish prey, with almost one-third of the fish taxa being consumed by females only and another similar number consumed by males only. This result might suggest a case of intra-specific competition, triggering sexual segregation. Additionally, we detected parasitic Platyelminthes (Cestoda and Trematoda), with different frequencies of occurrence, probably related to the different diet compositions of the ducks. This study provides the necessary baseline for future investigations of the ecological segregation of these ducks. Full article
(This article belongs to the Special Issue Polar Genomics)
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18 pages, 2025 KiB  
Article
Winners and Losers of Atlantification: The Degree of Ocean Warming Affects the Structure of Arctic Microbial Communities
by Antonia Ahme, Anabel Von Jackowski, Rebecca A. McPherson, Klara K. E. Wolf, Mario Hoppmann, Stefan Neuhaus and Uwe John
Genes 2023, 14(3), 623; https://doi.org/10.3390/genes14030623 - 1 Mar 2023
Cited by 5 | Viewed by 2162
Abstract
Arctic microbial communities (i.e., protists and bacteria) are increasingly subjected to an intrusion of new species via Atlantification and an uncertain degree of ocean warming. As species differ in adaptive traits, these oceanic conditions may lead to compositional changes with functional implications for [...] Read more.
Arctic microbial communities (i.e., protists and bacteria) are increasingly subjected to an intrusion of new species via Atlantification and an uncertain degree of ocean warming. As species differ in adaptive traits, these oceanic conditions may lead to compositional changes with functional implications for the ecosystem. In June 2021, we incubated water from the western Fram Strait at three temperatures (2 °C, 6 °C, and 9 °C), mimicking the current and potential future properties of the Arctic Ocean. Our results show that increasing the temperature to 6 °C only minorly affects the community, while an increase to 9 °C significantly lowers the diversity and shifts the composition. A higher relative abundance of large hetero- and mixotrophic protists was observed at 2 °C and 6 °C compared to a higher abundance of intermediate-sized temperate diatoms at 9 °C. The compositional differences at 9 °C led to a higher chlorophyll a:POC ratio, but the C:N ratio remained similar. Our results contradict the common assumption that smaller organisms and heterotrophs are favored under warming and strongly indicate a thermal limit between 6 °C and 9 °C for many Arctic species. Consequently, the magnitude of temperature increase is a crucial factor for microbial community reorganization and the ensuing ecological consequences in the future Arctic Ocean. Full article
(This article belongs to the Special Issue Polar Genomics)
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15 pages, 3911 KiB  
Article
Biogeography and Genetic Diversity of Terrestrial Mites in the Ross Sea Region, Antarctica
by Gemma E. Collins, Monica R. Young, Peter Convey, Steven L. Chown, S. Craig Cary, Byron J. Adams, Diana H. Wall and Ian D. Hogg
Genes 2023, 14(3), 606; https://doi.org/10.3390/genes14030606 - 28 Feb 2023
Cited by 3 | Viewed by 3282
Abstract
Free-living terrestrial mites (Acari) have persisted through numerous glacial cycles in Antarctica. Very little is known, however, of their genetic diversity and distribution, particularly within the Ross Sea region. To redress this gap, we sampled mites throughout the Ross Sea region, East Antarctica, [...] Read more.
Free-living terrestrial mites (Acari) have persisted through numerous glacial cycles in Antarctica. Very little is known, however, of their genetic diversity and distribution, particularly within the Ross Sea region. To redress this gap, we sampled mites throughout the Ross Sea region, East Antarctica, including Victoria Land and the Queen Maud Mountains (QMM), covering a latitudinal range of 72–85 °S, as well as Lauft Island near Mt. Siple (73 °S) in West Antarctica and Macquarie Island (54oS) in the sub-Antarctic. We assessed genetic diversity using mitochondrial cytochrome c oxidase subunit I gene sequences (COI-5P DNA barcode region), and also morphologically identified voucher specimens. We obtained 130 sequences representing four genera: Nanorchestes (n = 30 sequences), Stereotydeus (n = 46), Coccorhagidia (n = 18) and Eupodes (n = 36). Tree-based analyses (maximum likelihood) revealed 13 genetic clusters, representing as many as 23 putative species indicated by barcode index numbers (BINs) from the Barcode of Life Datasystems (BOLD) database. We found evidence for geographically-isolated cryptic species, e.g., within Stereotydeus belli and S. punctatus, as well as unique genetic groups occurring in sympatry (e.g., Nanorchestes spp. in QMM). Collectively, these data confirm high genetic divergence as a consequence of geographic isolation over evolutionary timescales. From a conservation perspective, additional targeted sampling of understudied areas in the Ross Sea region should be prioritised, as further diversity is likely to be found in these short-range endemic mites. Full article
(This article belongs to the Special Issue Polar Genomics)
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20 pages, 6854 KiB  
Article
Genetic and Structural Diversity of Prokaryotic Ice-Binding Proteins from the Central Arctic Ocean
by Johanna C. Winder, William Boulton, Asaf Salamov, Sarah Lena Eggers, Katja Metfies, Vincent Moulton and Thomas Mock
Genes 2023, 14(2), 363; https://doi.org/10.3390/genes14020363 - 30 Jan 2023
Cited by 6 | Viewed by 2363
Abstract
Ice-binding proteins (IBPs) are a group of ecologically and biotechnologically relevant enzymes produced by psychrophilic organisms. Although putative IBPs containing the domain of unknown function (DUF) 3494 have been identified in many taxa of polar microbes, our knowledge of their genetic and structural [...] Read more.
Ice-binding proteins (IBPs) are a group of ecologically and biotechnologically relevant enzymes produced by psychrophilic organisms. Although putative IBPs containing the domain of unknown function (DUF) 3494 have been identified in many taxa of polar microbes, our knowledge of their genetic and structural diversity in natural microbial communities is limited. Here, we used samples from sea ice and sea water collected in the central Arctic Ocean as part of the MOSAiC expedition for metagenome sequencing and the subsequent analyses of metagenome-assembled genomes (MAGs). By linking structurally diverse IBPs to particular environments and potential functions, we reveal that IBP sequences are enriched in interior ice, have diverse genomic contexts and cluster taxonomically. Their diverse protein structures may be a consequence of domain shuffling, leading to variable combinations of protein domains in IBPs and probably reflecting the functional versatility required to thrive in the extreme and variable environment of the central Arctic Ocean. Full article
(This article belongs to the Special Issue Polar Genomics)
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17 pages, 17357 KiB  
Article
Genomic Consequences of Fragmentation in the Endangered Fennoscandian Arctic Fox (Vulpes lagopus)
by Christopher A. Cockerill, Malin Hasselgren, Nicolas Dussex, Love Dalén, Johanna von Seth, Anders Angerbjörn, Johan F. Wallén, Arild Landa, Nina E. Eide, Øystein Flagstad, Dorothee Ehrich, Aleksandr Sokolov, Natalya Sokolova and Karin Norén
Genes 2022, 13(11), 2124; https://doi.org/10.3390/genes13112124 - 15 Nov 2022
Cited by 4 | Viewed by 2776
Abstract
Accelerating climate change is causing severe habitat fragmentation in the Arctic, threatening the persistence of many cold-adapted species. The Scandinavian arctic fox (Vulpes lagopus) is highly fragmented, with a once continuous, circumpolar distribution, it struggled to recover from a demographic bottleneck [...] Read more.
Accelerating climate change is causing severe habitat fragmentation in the Arctic, threatening the persistence of many cold-adapted species. The Scandinavian arctic fox (Vulpes lagopus) is highly fragmented, with a once continuous, circumpolar distribution, it struggled to recover from a demographic bottleneck in the late 19th century. The future persistence of the entire Scandinavian population is highly dependent on the northernmost Fennoscandian subpopulations (Scandinavia and the Kola Peninsula), to provide a link to the viable Siberian population. By analyzing 43 arctic fox genomes, we quantified genomic variation and inbreeding in these populations. Signatures of genome erosion increased from Siberia to northern Sweden indicating a stepping-stone model of connectivity. In northern Fennoscandia, runs of homozygosity (ROH) were on average ~1.47-fold longer than ROH found in Siberia, stretching almost entire scaffolds. Moreover, consistent with recent inbreeding, northern Fennoscandia harbored more homozygous deleterious mutations, whereas Siberia had more in heterozygous state. This study underlines the value of documenting genome erosion following population fragmentation to identify areas requiring conservation priority. With the increasing fragmentation and isolation of Arctic habitats due to global warming, understanding the genomic and demographic consequences is vital for maintaining evolutionary potential and preventing local extinctions. Full article
(This article belongs to the Special Issue Polar Genomics)
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17 pages, 3622 KiB  
Article
Using DNA Metabarcoding to Characterize the Prey Spectrum of Two Co-Occurring Themisto Amphipods in the Rapidly Changing Atlantic-Arctic Gateway Fram Strait
by Annkathrin Dischereit, Owen S. Wangensteen, Kim Præbel, Holger Auel and Charlotte Havermans
Genes 2022, 13(11), 2035; https://doi.org/10.3390/genes13112035 - 4 Nov 2022
Cited by 4 | Viewed by 1595
Abstract
The two congeneric hyperiids Themisto libellula and T. abyssorum provide an important trophic link between lower and higher trophic levels in the rapidly changing Arctic marine ecosystem. These amphipods are characterized by distinct hydrographic affinities and are hence anticipated to be impacted differently [...] Read more.
The two congeneric hyperiids Themisto libellula and T. abyssorum provide an important trophic link between lower and higher trophic levels in the rapidly changing Arctic marine ecosystem. These amphipods are characterized by distinct hydrographic affinities and are hence anticipated to be impacted differently by environmental changes, with major consequences for the Arctic food web. In this study, we applied DNA metabarcoding to the stomach contents of these Themisto species, to comprehensively reveal their prey spectra at an unprecedented-high-taxonomic-resolution and assess the regional variation in their diet across the Fram Strait. Both species feed on a wide variety of prey but their diet strongly differed in the investigated summer season, showing overlap for only a few prey taxa, such as calanoid copepods. The spatially structured prey field of T. libellula clearly differentiated it from T. abyssorum, of which the diet was mainly dominated by chaetognaths. Our approach also allowed the detection of previously overlooked prey in the diet of T. libellula, such as fish species and gelatinous zooplankton. We discuss the reasons for the differences in prey spectra and which consequences these may have in the light of ongoing environmental changes. Full article
(This article belongs to the Special Issue Polar Genomics)
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27 pages, 6120 KiB  
Article
Photosynthetic, Respirational, and Growth Responses of Six Benthic Diatoms from the Antarctic Peninsula as Functions of Salinity and Temperature Variations
by Lara R. Prelle, Ina Schmidt, Katherina Schimani, Jonas Zimmermann, Nelida Abarca, Oliver Skibbe, Desiree Juchem and Ulf Karsten
Genes 2022, 13(7), 1264; https://doi.org/10.3390/genes13071264 - 16 Jul 2022
Cited by 7 | Viewed by 2167
Abstract
Temperature and salinity are some of the most influential abiotic parameters shaping biota in aquatic ecosystems. In recent decades, climate change has had a crucial impact on both factors—especially around the Antarctic Peninsula—with increasing air and water temperature leading to glacial melting and [...] Read more.
Temperature and salinity are some of the most influential abiotic parameters shaping biota in aquatic ecosystems. In recent decades, climate change has had a crucial impact on both factors—especially around the Antarctic Peninsula—with increasing air and water temperature leading to glacial melting and the accompanying freshwater increase in coastal areas. Antarctic soft and hard bottoms are typically inhabited by microphytobenthic communities, which are often dominated by benthic diatoms. Their physiology and primary production are assumed to be negatively affected by increased temperatures and lower salinity. In this study, six representative benthic diatom strains were isolated from different aquatic habitats at King George Island, Antarctic Peninsula, and comprehensively identified based on molecular markers and morphological traits. Photosynthesis, respiration, and growth response patterns were investigated as functions of varying light availability, temperature, and salinity. Photosynthesis–irradiance curve measurements pointed to low light requirements, as light-saturated photosynthesis was reached at <70 µmol photons m−2 s−1. The marine isolates exhibited the highest effective quantum yield between 25 and 45 SA (absolute salinity), but also tolerance to lower and higher salinities at 1 SA and 55 SA, respectively, and in a few cases even <100 SA. In contrast, the limnic isolates showed the highest effective quantum yield at salinities ranging from 1 SA to 20 SA. Almost all isolates exhibited high effective quantum yields between 1.5 °C and 25 °C, pointing to a broad temperature tolerance, which was supported by measurements of the short-term temperature-dependent photosynthesis. All studied Antarctic benthic diatoms showed activity patterns over a broader environmental range than they usually experience in situ. Therefore, it is likely that their high ecophysiological plasticity represents an important trait to cope with climate change in the Antarctic Peninsula. Full article
(This article belongs to the Special Issue Polar Genomics)
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12 pages, 1396 KiB  
Article
Demographic Reconstruction of Antarctic Fur Seals Supports the Krill Surplus Hypothesis
by Joseph I. Hoffman, Rebecca S. Chen, David L. J. Vendrami, Anna J. Paijmans, Kanchon K. Dasmahapatra and Jaume Forcada
Genes 2022, 13(3), 541; https://doi.org/10.3390/genes13030541 - 18 Mar 2022
Cited by 13 | Viewed by 3757
Abstract
Much debate surrounds the importance of top-down and bottom-up effects in the Southern Ocean, where the harvesting of over two million whales in the mid twentieth century is thought to have produced a massive surplus of Antarctic krill. This excess of krill may [...] Read more.
Much debate surrounds the importance of top-down and bottom-up effects in the Southern Ocean, where the harvesting of over two million whales in the mid twentieth century is thought to have produced a massive surplus of Antarctic krill. This excess of krill may have allowed populations of other predators, such as seals and penguins, to increase, a top-down hypothesis known as the ‘krill surplus hypothesis’. However, a lack of pre-whaling population baselines has made it challenging to investigate historical changes in the abundance of the major krill predators in relation to whaling. Therefore, we used reduced representation sequencing and a coalescent-based maximum composite likelihood approach to reconstruct the recent demographic history of the Antarctic fur seal, a pinniped that was hunted to the brink of extinction by 18th and 19th century sealers. In line with the known history of this species, we found support for a demographic model that included a substantial reduction in population size around the time period of sealing. Furthermore, maximum likelihood estimates from this model suggest that the recovered, post-sealing population at South Georgia may have been around two times larger than the pre-sealing population. Our findings lend support to the krill surplus hypothesis and illustrate the potential of genomic approaches to shed light on long-standing questions in population biology. Full article
(This article belongs to the Special Issue Polar Genomics)
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22 pages, 2282 KiB  
Article
Molecular Responses to Thermal and Osmotic Stress in Arctic Intertidal Mussels (Mytilus edulis): The Limits of Resilience
by Nicholas J. Barrett, Jakob Thyrring, Elizabeth M. Harper, Mikael K. Sejr, Jesper G. Sørensen, Lloyd S. Peck and Melody S. Clark
Genes 2022, 13(1), 155; https://doi.org/10.3390/genes13010155 - 15 Jan 2022
Cited by 14 | Viewed by 3996
Abstract
Increases in Arctic temperatures have accelerated melting of the Greenland icesheet, exposing intertidal organisms, such as the blue mussel Mytilus edulis, to high air temperatures and low salinities in summer. However, the interaction of these combined stressors is poorly described at the transcriptional [...] Read more.
Increases in Arctic temperatures have accelerated melting of the Greenland icesheet, exposing intertidal organisms, such as the blue mussel Mytilus edulis, to high air temperatures and low salinities in summer. However, the interaction of these combined stressors is poorly described at the transcriptional level. Comparing expression profiles of M. edulis from experimentally warmed (30 °C and 33 °C) animals kept at control (23‰) and low salinities (15‰) revealed a significant lack of enrichment for Gene Ontology terms (GO), indicating that similar processes were active under all conditions. However, there was a progressive increase in the abundance of upregulated genes as each stressor was applied, with synergistic increases at 33 °C and 15‰, suggesting combined stressors push the animal towards their tolerance thresholds. Further analyses comparing the effects of salinity alone (23‰, 15‰ and 5‰) showed high expression of stress and osmoregulatory marker genes at the lowest salinity, implying that the cell is carrying out intracellular osmoregulation to maintain the cytosol as hyperosmotic. Identification of aquaporins and vacuolar-type ATPase transcripts suggested the cell may use fluid-filled cavities to excrete excess intracellular water, as previously identified in embryonic freshwater mussels. These results indicate that M. edulis has considerable resilience to heat stress and highly efficient mechanisms to acclimatise to lowered salinity in a changing world. Full article
(This article belongs to the Special Issue Polar Genomics)
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9 pages, 591 KiB  
Brief Report
Metagenomics Provides a Deeper Assessment of the Diversity of Bacterial Communities in Polar Soils Than Metabarcoding
by Burkhard Becker and Ekaterina Pushkareva
Genes 2023, 14(4), 812; https://doi.org/10.3390/genes14040812 - 28 Mar 2023
Cited by 4 | Viewed by 2051
Abstract
The diversity of soil bacteria was analyzed via metabarcoding and metagenomic approaches using DNA samples isolated from the biocrusts of 12 different Arctic and Antarctic sites. For the metabarcoding approach, the V3-4 region of the 16S rRNA was targeted. Our results showed that [...] Read more.
The diversity of soil bacteria was analyzed via metabarcoding and metagenomic approaches using DNA samples isolated from the biocrusts of 12 different Arctic and Antarctic sites. For the metabarcoding approach, the V3-4 region of the 16S rRNA was targeted. Our results showed that nearly all operational taxonomic units (OTUs = taxa) found in metabarcoding analyses were recovered in metagenomic analyses. In contrast, metagenomics identified a large number of additional OTUs absent in metabarcoding analyses. In addition, we found huge differences in the abundance of OTUs between the two methods. The reasons for these differences seem to be (1) the higher sequencing depth in metagenomics studies, which allows the detection of low-abundance community members in metagenomics, and (2) bias of primer pairs used to amplify the targeted sequence in metabarcoding, which can change the community composition dramatically even at the lower taxonomic levels. We strongly recommend using only metagenomic approaches when establishing the taxonomic profiles of whole biological communities. Full article
(This article belongs to the Special Issue Polar Genomics)
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