Spatio-temporal patterns of eukaryotic biodiversity in shallow hard-bottom communities from the West Antarctic Peninsula revealed by DNA metabarcoding

Aim: We studied molecular eukaryotic biodiversity patterns in shallow hard-bottom Antarctic benthic communities using community DNA metabarcoding. Polar ecosystems are extremely exposed to climate change, and benthic macroinvertebrate communities have demonstrated rapid response to a range of natural and anthropogenic pressures. However, these rich and diverse ecosystems are poorly studied, revealing how little is known about the biodiversity of the Antarctic benthos associated with hard-bottom habitats. Location: West Antarctic Peninsula and South Shetland Islands. Methods: Using data collected in seven localities along the western Antarctic Peninsula, we calculated spatial patterns of alpha and beta diversities. Furthermore, we analysed temporal changes in benthic composition in one location (Deception Island) over 3 years. We calculated the temporal alpha and beta diversities to reveal changes in this community over time. Results: We obtained a final list of 2057 molecular operational taxonomic units. We found significant differences in benthic community composition between localities and among years. Our dataset revealed a total of 10 different kingdom-level lineages and 34 different phyla in the samples. The most diverse phylum was Arthropoda, followed by Bacillariophyta, and Annelida, while the highest relative read abundances belonged to Annelida, Porifera and Echinodermata. Benthic community compositions changed between 2016 and 2018 in Deception Island, and decreasing species richness was the main component of temporal beta diversity. Main Conclusions: Direct sampling methods are required for monitoring these complex communities. Informative biodiversity patterns can be retrieved even though most of the benthic biodiversity found in Antarctic habitats is yet to be taxonomically described and barcoded. Hard-bottom assemblages exhibit high spatial variability and heterogeneity, not related to depth, which represent a huge challenge for largescale studies in the Southern Ocean. Local patchiness and structure within the communities are probably a consequence of a combination of several biotic and abiotic factors (i.e. ice disturbance, food supply and competition)

Using DNA Metabarcoding to Characterize the Prey Spectrum of Two Co-Occurring Themisto Amphipods in the Rapidly Changing Atlantic-Arctic Gateway Fram Strait

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

DNA metabarcoding reveals the importance of gelatinous zooplankton in the diet of Pandalus borealis, a keystone species in the Arctic

Information about the dietary composition of a species is crucial to understanding their position and role in the food web. Increasingly, molecular approaches such as DNA metabarcoding are used in studying trophic relationships, not least because they may alleviate problems such as low taxonomic resolution or underestimation of digestible taxa in the diet. Here, we used DNA metabarcoding with universal primers for cytochrome c oxidase I (COI) to study the diet composition of the northern shrimp (Pandalus borealis), an Arctic keystone species with large socio-economic importance. Across locations, jellyfish and chaetognaths were the most important components in the diet of P. borealis, jointly accounting for 40%–60% of the total read abundance. This dietary importance of gelatinous zooplankton contrasts sharply with published results based on stomach content analysis. At the same time, diet composition differed between fjord and shelf locations, pointing to different food webs supporting P. borealis in these two systems. Our study underlines the potential of molecular approaches to provide new insights into the diet of marine invertebrates that are difficult to obtain with traditional methods, and calls for a revision of the role of gelatinous zooplankton in the diet of the key Arctic species P. borealis, and in extension, Arctic food webs

Phenotype-environment association of the oxygen transport system in trimorphic European whitefish (Coregonus lavaretus) populations

Replicated adaptive radiation events, typified by phenotypic divergence across resource axes, provide important insight into the eco-evolutionary dynamics that lead to the formation of new species. Here, we show that in trimorphic adaptive radiations of European whitefish (Coregonus lavaretus), divergence of the oxygen transport system has occurred across the pelagic/littoral (shallow)—profundal (deep) resource axis, and at multiple biological scales. Profundal whitefish exhibited significantly larger red blood cells (RBCs), a greater proportion of cathodic hemoglobin protein components, and higher hemoglobin transcript abundance in kidney compared to littoral and pelagic morphs. Hemoglobin transcript abundance in brain and gill, but not kidney, and anodic hemoglobin protein component diversity in blood were also linked to variation at an intronic single nucleotide polymorphism (SNP). As the whitefish morphs differ in population genetic structure at this SNP, hemoglobin transcript and protein divergence between profundal and pelagic/littoral morphs is likely being driven by genetic divergence. Our findings, along with our previous work on lake whitefish, highlight the importance of the oxygen transport system to the postglacial colonization of novel lacustrine environments by whitefish throughout the northern hemisphere

DNA metabarcoding unveils niche overlapping and competition among Caribbean sea urchins

Detailed information of trophic interactions among consumer-resources in food webs is usually limited due to the lack of accurate identification of eaten food resources. The use of DNA-metabarcoding has been proven useful for molecular identification of the numerous taxa present in stomach contents. Here, we characterize the diet and trophic behavior of four sea urchin species inhabiting shallow waters of Puerto Rico using this molecular technique. We extracted, sequenced, and analyzed DNA from the gut content of a total of 60 individuals collected at three sites at the northeastern coast of Puerto Rico. Our results demonstrated that seaweeds were the dominant food source for the four sea urchin species at all three sites, but also small protists, fungi and metazoans were important components of sea urchin's diet. Interspecific differences in diet were also found among sites. PERMANOVA analysis detected significant differences among species (Pseudo-F 1.755, p < 0.001), and among sites (Pseudo-F 2.52, p < 0.001). A SIMPER analysis showed that in all cases the main taxa causing differences between species and sites were macroalgae (Rhodophyta, Chlorophyta and Ochrophyta) with some contribution of small eukaryotes (Apicomplexa and Bacillariophyta). This diet characterization in sea urchins revealed a generalist omnivore behavior, but with a clear dominance of algae as a main dietary component. Thus, we found a potential inter-specific competition due to niche overlapping, which seems to be more common than initially thought

Terrestrial Inputs Shape Coastal Bacterial and Archaeal Communities in a High Arctic Fjord (Isfjorden, Svalbard)

The Arctic is experiencing dramatic changes including increases in precipitation, glacial melt, and permafrost thaw, resulting in increasing freshwater runoff to coastal waters. During the melt season, terrestrial runoff delivers carbon- and nutrient-rich freshwater to Arctic coastal waters, with unknown consequences for the microbial communities that play a key role in determining the cycling and fate of terrestrial matter at the land-ocean interface. To determine the impacts of runoff on coastal microbial (bacteria and archaea) communities, we investigated changes in pelagic microbial community structure between the early (June) and late (August) melt season in 2018 in the Isfjorden system (Svalbard). Amplicon sequences of the 16S rRNA gene were generated from water column, river and sediment samples collected in Isfjorden along fjord transects from shallow river estuaries and glacier fronts to the outer fjord. Community shifts were investigated in relation to environmental gradients, and compared to river and marine sediment microbial communities. We identified strong temporal and spatial reorganizations in the structure and composition of microbial communities during the summer months in relation to environmental conditions. Microbial diversity patterns highlighted a reorganization from rich communities in June toward more even and less rich communities in August. In June, waters enriched in dissolved organic carbon (DOC) provided a niche for copiotrophic taxa including Sulfitobacter and Octadecabacter. In August, lower DOC concentrations and Atlantic water inflow coincided with a shift toward more cosmopolitan taxa usually associated with summer stratified periods (e.g., SAR11 Clade Ia), and prevalent oligotrophic marine clades (OM60, SAR92). Higher riverine inputs of dissolved inorganic nutrients and suspended particulate matter also contributed to spatial reorganizations of communities in August. Sentinel taxa of this late summer fjord environment included taxa from the class Verrucomicrobiae (Roseibacillus, Luteolibacter), potentially indicative of a higher fraction of particle-attached bacteria. This study highlights the ecological relevance of terrestrial runoff for Arctic coastal microbial communities and how its impacts on biogeochemical conditions may make these communities susceptible to climate change

Speciation reversal in European whitefish (Coregonus lavaretus (L.)) caused by competitor invasion

Invasion of exotic species has caused the loss of biodiversity and imparts evolutionary and ecological changes in the introduced systems. In northern Fennoscandia, European whitefish (Coregonus lavaretus (L.)) is a highly polymorphic species displaying adaptive radiations into partially reproductively isolated and thus genetically differentiated sympatric morphs utilizing the planktivorous and benthivorous food niche in many lakes. In 1993, Lake Skrukkebukta was invaded by vendace (Coregonus albula (L.)) which is a zooplanktivorous specialist. The vendace displaced the densely rakered whitefish from its preferred pelagic niche to the benthic habitat harbouring the large sparsely rakered whitefish. In this study, we investigate the potential influence of the vendace invasion on the breakdown of reproductive isolation between the two whitefish morphs. We inferred the genotypic and phenotypic differentiation between the two morphs collected at the arrival (1993) and 15 years after (2008) the vendace invasion using 16 microsatellite loci and gill raker numbers, the most distinctive adaptive phenotypic trait between them. The comparison of gill raker number distributions revealed two modes growing closer over 15 years following the invasion. Bayesian analyses of genotypes revealed that the two genetically distinct whitefish morphs that existed in 1993 had collapsed into a single population in 2008. The decline in association between the gill raker numbers and admixture values over 15 years corroborates the findings from the Bayesian analysis. Our study thus suggests an apparent decrease of reproductive isolation in a morph-pair of European whitefish within 15 years (. 3 generations) following the invasion of a superior trophic competitor (vendace) in a subarctic lake, reflecting a situation of ‘‘speciation in reverse’’

Meroplankton Diversity, Seasonality and Life-History Traits Across the Barents Sea Polar Front Revealed by High-Throughput DNA Barcoding

In many species of marine benthic invertebrates, a planktonic larval phase plays a critical role in dispersal. Very little is known about the larval biology of most species, however, in part because species identification has historically been hindered by the microscopic size and morphological similarity among related taxa. This study aimed to determine the taxonomic composition and seasonal distribution of meroplankton in the Barents Sea, across the Polar Front. We collected meroplankton during five time points seasonally and used high-throughput DNA barcoding of individual larvae to obtain species-level information on larval seasonality. We found that meroplankton was highly diverse (72 taxa from eight phyla) and present in the Barents Sea year-round with a peak in abundance in August and November, defying the conventional wisdom that peak abundance would coincide with the spring phytoplankton bloom. Ophiuroids, bivalves, and polychaetes dominated larval abundance while gastropods and polychaetes accounted for the bulk of the taxon diversity. Community structure varied seasonally and total abundance was generally higher south of the Polar Front while taxon richness was overall greater to the north. Of the species identified, most were known inhabitants of the Barents Sea. However, the nemertean Cephalothrix iwatai and the brittle star Ophiocten gracilis were abundant in the meroplankton despite never having been previously recorded in the northern Barents Sea. The new knowledge on seasonal patterns of individual meroplanktonic species has implications for understanding environment-biotic interactions in a changing Arctic and provides a framework for early detection of potential newcomers to the system

Seasonal Variability in the Zooplankton Community Structure in a Sub-Arctic Fjord as Revealed by Morphological and Molecular Approaches

Phyto- and zooplankton in Arctic and sub-Arctic seas show very strong seasonal changes in diversity and biomass. Here we document the seasonal variability in the mesozooplankton community structure in a sub-Arctic fjord in Northern Norway based on monthly sampling between November 2018 and February 2020. We combined traditional morphological zooplankton identification with DNA metabarcoding of a 313 base pair fragment of the COI gene. This approach allowed us to provide the most detailed mesozooplankton species list known for this region across an entire year, including both holo- and meroplankton. The zooplankton community was dominated by small copepods throughout the sampling period both in terms of abundance and relative sequence counts. However, meroplankton was the most diverse group, especially within the phylum polychaeta. We identified four distinct periods based on the seasonal analysis of the zooplankton community composition. The pre-spring bloom period (February–March) was characterized by low abundance and biomass of zooplankton. The spring bloom (April) was characterized by the presence of Calanus young stages, cirripedia and krill eggs. The spring-summer period (May–August) was characterized by a succession of meroplankton and a relatively high abundance of copepods of the genus Calanus spp. Finally, the autumn-winter period (September–December) was characterized by a high copepod diversity and a peak in abundance of small copepods (e.g., Oithona similis, Acartia longiremis, Pseudocalanus acuspes, Pseudocalanus elongatus, Pseudocalanus moultoni, Pseudocalanus minutus). During this period, we also observed an influx of boreal warm-water species which were notably absent during the rest of the year. Both the traditional community analysis and metabarcoding were highly complementary and with a few exceptions showed similar trends in the seasonal changes of the zooplankton community structure