Rich microbial and depolymerising diversity in Antarctic krill gut.

With almost a quadrillion individuals, the Antarctic krill processes five million tons of organic carbon every day during austral summer. This high carbon flux requires a broad range of hydrolytic enzymes to decompose the diverse food-derived biopolymers. While krill itself possesses numerous such enzymes, it is unclear, to what extent the endogenous microbiota contribute to the hydrolytic potential of the gut environment. Here we applied amplicon sequencing, shotgun metagenomics, cultivation, and physiological assays to characterize the krill gut microbiota. The broad bacterial diversity (273 families, 919 genera, and 2,309 species) also included a complex potentially anaerobic sub-community. Plate-based assays with 198 isolated pure cultures revealed widespread capacities to utilize lipids (e.g., tributyrin), followed by proteins (casein) and to a lesser extent by polysaccharides (e.g., alginate and chitin). While most isolates affiliated with the genera Pseudoalteromonas and Psychrobacter, also Rubritalea spp. (Verrucomicrobia) were observed. The krill gut microbiota growing on marine broth agar plates possess 13,012 predicted hydrolyses; 15-fold more than previously predicted from a transcriptome-proteome compendium of krill. Cultivation-independent and -dependent approaches indicated members of the families Flavobacteriaceae and Pseudoalteromonadaceae to dominate the capacities for lipid/protein hydrolysis and to provide a plethora of carbohydrate-active enzymes, sulfatases, and laminarin- or porphyrin-depolymerizing hydrolases. Notably, also the potential to hydrolyze plastics such as polyethylene terephthalate and polylactatide was observed, affiliating mostly with Moraxellaceae. Overall, this study shows extensive microbial diversity in the krill gut, and suggests that the microbiota likely play a significant role in the nutrient acquisition of the krill by enriching its hydrolytic enzyme repertoire.IMPORTANCEThe Antarctic krill (Euphausia superba) is a keystone species of the Antarctic marine food web, connecting the productivity of phyto- and zooplankton with the nutrition of the higher trophic levels. Accordingly, krill significantly contributes to biomass turnover, requiring the decomposition of seasonally varying plankton-derived biopolymers. This study highlights the likely role of the krill gut microbiota in this ecosystem function by revealing the great number of diverse hydrolases that microbes contribute to the krill gut environment. The here resolved repertoire of hydrolytic enzymes could contribute to the overall nutritional resilience of krill and to the general organic matter cycling under changing environmental conditions in the Antarctic sea water. Furthermore, the krill gut microbiome could serve as a valuable resource of cold-adapted hydrolytic enzymes for diverse biotechnological applications.

At second glance: The importance of strict quality control - A case study on microplastic in the Southern Ocean key species Antarctic krill, Euphausia superba.

The stomach content of 60 krill specimens from the Southern Ocean were analyzed for the presence of microplastic (MP), by testing different sample volumes, extraction approaches, and applying hyperspectral imaging Fourier-transform infrared spectroscopy (µFTIR). Strict quality control was applied on the generated results. A high load of residual materials in pooled samples hampered the analysis and avoided a reliable determination of putative MP particles. Individual krill stomachs displayed reliable results, however, only after re-treating the samples with hydrogen peroxide. Before this treatment, lipid rich residues of krill resulted in false assignments of polymer categories and hence, false high MP particle numbers. Finally, MP was identified in 4 stomachs out of 60, with only one MP particle per stomach. Our study highlights the importance of strict quality control to verify results before coming to a final decision on MP contamination in the environment to aid the establishment of suitable internationally standardized protocols for sampling and analysis of MP in organisms including their habitats in Southern Ocean and worldwide.

Gene expression patterns of Salpa thompsoni reveal remarkable differences in metabolism and reproduction near the Antarctic Polar Front.

Salpa thompsoni is an important grazer in the Southern Ocean and most abundant in the Antarctic Polar Front (APF) region. During recent decades, their distribution expanded southwards. However, it is unclear whether salps can maintain their populations in the high Antarctic regions throughout the year owing to a poor understanding of their physiological responses to changing environmental conditions. We examined gene expression signatures of salps collected in two geographically close regions south of the APF that differed in water mass composition and productivity. The observed differences in the expression of genes related to reproductive, cellular and metabolic processes reflect variations in water temperature and food supply between the two regions studied here. Our study contributes to a better understanding of the physiological responses of S. thompsoni to changing environmental conditions, and how the species may adapt to a changing environment through potential geographical population shifts under future climate change scenarios.

Variations of intact phospholipid compositions in the digestive system of Antarctic krill, Euphausia superba, between summer and autumn.

The biochemical composition of Antarctic krill, Euphausia superba, is largely determined by their feeding behaviour. As they supply energy for animals of a higher trophic level and are also commercialized for human consumption, the interest in research on the species is high. Lipids, especially phospholipids, make up a high proportion of dry weight in krill. Seasonal changes are well documented in the fingerprint of free fatty acids analysed after hydrolysis of phospholipids, but the underlying intact polar lipids are rarely considered. In this study, we evaluated the compositions of intact phospholipids (IPLs) in the stomach, digestive gland and hind gut of Antarctic krill caught in summer and autumn at the Antarctic Peninsula region. Using high-resolution mass spectrometry, the fatty acid composition of 179 intact phospholipids could be resolved. Most IPLs were phosphatidylcholines, followed by phosphatidylethanolamines. Several very long chain polyunsaturated fatty acids up to 38:8, which have not been reported in krill before, were identified. The composition shifted to higher molecular weight IPLs with a higher degree of unsaturation for summer samples, especially for samples of the digestive gland. The data supplied in this paper provides new insights into lipid dynamics between summer and autumn usually described by free fatty acid biomarkers.

Driving forces of Antarctic krill abundance.

Antarctic krill, crucial to the Southern Ocean ecosystem and a vital fisheries resource, is endangered by climate change. Identifying drivers of krill biomass is therefore essential for determining catch limits and designating protection zones. We present a modeling approach to pinpointing effects of sea surface temperature, ice cover, chlorophyll levels, climate indices, and intraspecific competition. Our study reveals that larval recruitment is driven by both competition among age classes and chlorophyll levels. In addition, while milder ice and temperature in spring and summer favor reproduction and early larval survival, both larvae and juveniles strongly benefit from heavier ice and colder temperatures in winter. We conclude that omitting top-down control of resources by krill is only acceptable for retrospective or single-year prognostic models that use field chlorophyll data but that incorporating intraspecific competition is essential for longer-term forecasts. Our findings can guide future krill modeling strategies, reinforcing the sustainability of this keystone species.

Plasticity and seasonality of the vertical migration behaviour of Antarctic krill using acoustic data from fishing vessels.

Understanding the vertical migration behaviour of Antarctic krill is important for understanding spatial distribution, ecophysiology, trophic interactions and carbon fluxes of this Southern Ocean key species. In this study, we analysed an eight-month continuous dataset recorded with an ES80 echosounder on board a commercial krill fishing vessel in the southwest Atlantic sector of the Southern Ocean. Our analysis supports the existing hypothesis that krill swarms migrate into deeper waters during winter but also reveals a high degree of variability in vertical migration behaviour within seasons, even at small spatial scales. During summer, we found that behaviour associated with prolonged surface presence primarily occurred at low surface chlorophyll a concentrations whereas multiple ascent-descent cycles per day occurred when surface chlorophyll a concentrations were elevated. The high plasticity, with some krill swarms behaving differently in the same location at the same time, suggests that krill behaviour is not a purely environmentally driven process. Differences in life stage, physiology and type of predator are likely other important drivers. Finally, our study demonstrates new ways of using data from krill fishing vessels, and with the routine collection of additional information in potential future projects, they have great potential to significantly advance our understanding of krill ecology.

An intercomparison of models predicting growth of Antarctic krill (Euphausia superba): The importance of recognizing model specificity.

Antarctic krill (Euphausia superba) is a key species of the Southern Ocean, impacted by climate change and human exploitation. Understanding how these changes affect the distribution and abundance of krill is crucial for generating projections of change for Southern Ocean ecosystems. Krill growth is an important indicator of habitat suitability and a series of models have been developed and used to examine krill growth potential at different spatial and temporal scales. The available models have been developed using a range of empirical and mechanistic approaches, providing alternative perspectives and comparative analyses of the key processes influencing krill growth. Here we undertake an intercomparison of a suite of the available models to understand their sensitivities to major driving variables. This illustrates that the results are strongly determined by the model structure and technical characteristics, and the data on which they were developed and validated. Our results emphasize the importance of assessing the constraints and requirements of individual krill growth models to ensure their appropriate application. The study also demonstrates the value of the development of alternative modelling approaches to identify key processes affecting the dynamics of krill. Of critical importance for modelling the growth of krill is appropriately assessing and accounting for differences in estimates of food availability resulting from alternative methods of observation. We suggest that an intercomparison approach is particularly valuable in the development and application of models for the assessment of krill growth potential at circumpolar scales and for future projections. As another result of the intercomparison, the implementations of the models used in this study are now publicly available for future use and analyses.

The enormous repetitive Antarctic krill genome reveals environmental adaptations and population insights.

Antarctic krill (Euphausia superba) is Earth's most abundant wild animal, and its enormous biomass is vital to the Southern Ocean ecosystem. Here, we report a 48.01-Gb chromosome-level Antarctic krill genome, whose large genome size appears to have resulted from inter-genic transposable element expansions. Our assembly reveals the molecular architecture of the Antarctic krill circadian clock and uncovers expanded gene families associated with molting and energy metabolism, providing insights into adaptations to the cold and highly seasonal Antarctic environment. Population-level genome re-sequencing from four geographical sites around the Antarctic continent reveals no clear population structure but highlights natural selection associated with environmental variables. An apparent drastic reduction in krill population size 10 mya and a subsequent rebound 100 thousand years ago coincides with climate change events. Our findings uncover the genomic basis of Antarctic krill adaptations to the Southern Ocean and provide valuable resources for future Antarctic research.

Antarctic marine life under pressure.

Next week, the Convention on the Conservation of Antarctic Marine Living Resources (CCAMLR) convenes in Hobart, Tasmania, to examine the state of marine life in the Southern Ocean. As part of the Antarctic Treaty System, this convention entered into force in 1982, and its focus on the region's environmental integrity has never been more important, given the increasing effects of climate change and commercial fishing. An important focus over the past 40 years has been Antarctic krill, Euphausia superba (hereafter krill), a keystone species that helps to hold this marine ecosystem together. Climate and fishing stresses should prompt the CCAMLR to address whether management of krill fishing is at a level that protects the Southern Ocean from losing its overall balance of marine life and the oceanic processes that regulate global climate.

Transcriptome-proteome compendium of the Antarctic krill (Euphausia superba): Metabolic potential and repertoire of hydrolytic enzymes.

The Antarctic krill (Euphausia superba Dana) is a keystone species in the Southern Ocean that uses an arsenal of hydrolases for biomacromolecule decomposition to effectively digest its omnivorous diet. The present study builds on a hybrid-assembled transcriptome (13,671 ORFs) combined with comprehensive proteome profiling. The analysis of individual krill compartments allowed detection of significantly more different proteins compared to that of the entire animal (1464 vs. 294 proteins). The nearby krill sampling stations in the Bransfield Strait (Antarctic Peninsula) yielded rather uniform proteome datasets. Proteins related to energy production and lipid degradation were particularly abundant in the abdomen, agreeing with the high energy demand of muscle tissue. A total of 378 different biomacromolecule hydrolysing enzymes were detected, including 250 proteases, 99 CAZymes, 14 nucleases and 15 lipases. The large repertoire in proteases is in accord with the protein-rich diet affiliated with E. superba's omnivorous lifestyle and complex biology. The richness in chitin-degrading enzymes allows not only digestion of zooplankton diet, but also the utilisation of the discharged exoskeleton after moulting.

Return of large fin whale feeding aggregations to historical whaling grounds in the Southern Ocean.

Fin whales (Balaenoptera physalus quoyi) of the Southern Hemisphere were brought to near extinction by twentieth century industrial whaling. For decades, they had all but disappeared from previously highly frequented feeding grounds in Antarctic waters. Our dedicated surveys now confirm their return to ancestral feeding grounds, gathering at the Antarctic Peninsula in large aggregations to feed. We report on the results of an abundance survey and present the first scientific documentation of large fin whale feeding aggregations at Elephant Island, Antarctica, including the first ever video documentation. We interpret high densities, re-establishment of historical behaviours and the return to ancestral feeding grounds as signs for a recovering population. Recovery of a large whale population has the potential to augment primary productivity at their feeding grounds through the effects of nutrient recycling, known as 'the whale pump'. The recovery of fin whales in that area could thus restore ecosystem functions crucial for atmospheric carbon regulation in the world's most important ocean region for the uptake of anthropogenic CO2.

A thorough annotation of the krill transcriptome offers new insights for the study of physiological processes.

The krill species Euphausia superba plays a critical role in the food chain of the Antarctic ecosystem. Significant changes in climate conditions observed in the Antarctic Peninsula region in the last decades have already altered the distribution of krill and its reproductive dynamics. A deeper understanding of the adaptation capabilities of this species is urgently needed. The availability of a large body of RNA-seq assays allowed us to extend the current knowledge of the krill transcriptome. Our study covered the entire developmental process providing information of central relevance for ecological studies. Here we identified a series of genes involved in different steps of the krill moulting cycle, in the reproductive process and in sexual maturation in accordance with what was already described in previous works. Furthermore, the new transcriptome highlighted the presence of differentially expressed genes previously unknown, playing important roles in cuticle development as well as in energy storage during the krill life cycle. The discovery of new opsin sequences, specifically rhabdomeric opsins, one onychopsin, and one non-visual arthropsin, expands our knowledge of the krill opsin repertoire. We have collected all these results into the KrillDB2 database, a resource combining the latest annotation of the krill transcriptome with a series of analyses targeting genes relevant to krill physiology. KrillDB2 provides in a single resource a comprehensive catalog of krill genes; an atlas of their expression profiles over all RNA-seq datasets publicly available; a study of differential expression across multiple conditions. Finally, it provides initial indications about the expression of microRNA precursors, whose contribution to krill physiology has never been reported before.

Annual transcriptome of a key zooplankton species, the copepod Calanus finmarchicus.

The copepod Calanus finmarchicus (Crustacea, Copepoda) is a key zooplanktonic species with a crucial position in the North Atlantic food web and significant contributor to ocean carbon flux. Like many other high latitude animals, it has evolved a programmed arrested development called diapause to cope with long periods of limited food supply, while growth and reproduction are timed to take advantage of seasonal peaks in primary production. However, anthropogenic warming is inducing changes in the expected timing of phytoplankton blooms, suggesting phenological mismatches with negative consequences for the N. Atlantic ecosystem. While diapause mechanisms are mainly studied in terrestrial arthropods, specifically on laboratory model species, such as the fruit fly Drosophila, the molecular investigations of annual rhythms in wild marine species remain fragmentary. Here we performed a rigorous year-long monthly sampling campaign of C. finmarchicus in a Scottish Loch (UK; 56.45°N, 5.18°W) to generate an annual transcriptome. The mRNA of 36 samples (monthly triplicate of 25 individuals) have been deeply sequenced with an average depth of 137 ± 4 million reads (mean ± SE) per sample, aligned to the reference transcriptome, and filtered. We detail the quality assessment of the datasets and provide a high-quality resource for the investigation of wild annual transcriptomic rhythms (35,357 components) in a key diapausing zooplanktonic species.

Krill and salp faecal pellets contribute equally to the carbon flux at the Antarctic Peninsula.

Krill and salps are important for carbon flux in the Southern Ocean, but the extent of their contribution and the consequences of shifts in dominance from krill to salps remain unclear. We present a direct comparison of the contribution of krill and salp faecal pellets (FP) to vertical carbon flux at the Antarctic Peninsula using a combination of sediment traps, FP production, carbon content, microbial degradation, and krill and salp abundances. Salps produce 4-fold more FP carbon than krill, but the FP from both species contribute equally to the carbon flux at 300 m, accounting for 75% of total carbon. Krill FP are exported to 72% to 300 m, while 80% of salp FP are retained in the mixed layer due to fragmentation. Thus, declining krill abundances could lead to decreased carbon flux, indicating that the Antarctic Peninsula could become a less efficient carbon sink for anthropogenic CO2 in future.

Selective feeding in Southern Ocean key grazers-diet composition of krill and salps.

Over the past decades, two key grazers in the Southern Ocean (SO), krill and salps, have experienced drastic changes in their distribution and abundance, leading to increasing overlap of their habitats. Both species occupy different ecological niches and long-term shifts in their distributions are expected to have cascading effects on the SO ecosystem. However, studies directly comparing krill and salps are lacking. Here, we provide a direct comparison of the diet and fecal pellet composition of krill and salps using 18S metabarcoding and fatty acid markers. Neither species' diet reflected the composition of the plankton community, suggesting that in contrast to the accepted paradigm, not only krill but also salps are selective feeders. Moreover, we found that krill and salps had broadly similar diets, potentially enhancing the competition between both species. This could be augmented by salps' ability to rapidly reproduce in favorable conditions, posing further risks to krill populations.

Salp fecal pellets release more bioavailable iron to Southern Ocean phytoplankton than krill fecal pellets.

Over the last decades, it has been reported that the habitat of the Southern Ocean (SO) key species Antarctic krill (Euphausia superba) has contracted to high latitudes, putatively due to reduced winter sea ice coverage, while salps as Salpa thompsoni have extended their dispersal to the former krill habitats. To date, the potential implications of this population shift on the biogeochemical cycling of the limiting micronutrient iron (Fe) and its bioavailability to SO phytoplankton has never been tested. Based on uptake of fecal pellet (FP)-released Fe by SO phytoplankton, this study highlights how efficiently krill and salps recycle Fe. To test this, we collected FPs of natural populations of salps and krill, added them to the same SO phytoplankton community, and measured the community's Fe uptake rates. Our results reveal that both FP additions yielded similar dissolved iron concentrations in the seawater. Per FP carbon added to the seawater, 4.8 ± 1.5 times more Fe was taken up by the same phytoplankton community from salp FP than from krill FP, suggesting that salp FP increased the Fe bioavailability, possibly through the release of ligands. With respect to the ongoing shift from krill to salps, the potential for carbon fixation of the Fe-limited SO could be strengthened in the future, representing a negative feedback to climate change.

Facing Southern Ocean warming: Temperature effects on whole animal performance of Antarctic krill (Euphausia superba).

The ongoing environmental changes in the Southern Ocean may cause a dramatic decrease in habitat quality. Due to its central position in the food web, Antarctic krill (Euphausia superba) is a key species of the marine Antarctic ecosystem. It is therefore crucial to understand how increasing water temperatures affect important krill life-cycle processes. Here, a long-term (August - March) laboratory acclimation experiment at different temperature scenarios (0.5 °C, 1.5 °C, 2.5 °C, 3.5 °C, 5 °C, 7 °C) was performed and the effects of elevated temperatures on whole animal parameters (O2 consumption, body length, length of the digestive gland) were analyzed. The response of krill oxygen consumption to different experimental temperatures differed between acute/short-term and long-term acclimation. After 8 months, krill oxygen consumption remained unchanged up to temperatures of 3.5 °C and was significantly higher at temperatures > 3.5 °C. Krill acclimated to temperatures ≥ 3.5 °C were significantly smaller at the end of the experiment. Limited food intake and/or conversion may have contributed to this effect, especially pronounced after the onset of the reproductive period. In addition, the seasonal growth pattern in males differed from that of females. Together, our findings indicate that warming Southern Ocean waters are likely to increase metabolic rate in krill, possibly altering the amount of energy available for other important life-cycle processes, a finding directly related to future population dynamics and fisheries management.

Widely rhythmic transcriptome in Calanus finmarchicus during the high Arctic summer solstice period.

Solar light/dark cycles and seasonal photoperiods underpin daily and annual rhythms of life on Earth. Yet, the Arctic is characterized by several months of permanent illumination ("midnight sun"). To determine the persistence of 24h rhythms during the midnight sun, we investigated transcriptomic dynamics in the copepod Calanus finmarchicus during the summer solstice period in the Arctic, with the lowest diel oscillation and the highest altitude of the sun's position. Here we reveal that in these extreme photic conditions, a widely rhythmic daily transcriptome exists, showing that very weak solar cues are sufficient to entrain organisms. Furthermore, at extremely high latitudes and under sea-ice, gene oscillations become re-organized to include <24h rhythms. Environmental synchronization may therefore be modulated to include non-photic signals (i.e. tidal cycles). The ability of zooplankton to be synchronized by extremely weak diel and potentially tidal cycles, may confer an adaptive temporal reorganization of biological processes at high latitudes.

Seasonal gene expression profiling of Antarctic krill in three different latitudinal regions.

The Antarctic krill, Euphausia superba, has evolved seasonal rhythms of physiology and behaviour to survive under the extreme photoperiodic conditions in the Southern Ocean. However, the molecular mechanisms generating these rhythms remain far from understood. The aim of this study was to investigate seasonal differences in gene expression in three different latitudinal regions (South Georgia, South Orkneys/Bransfield Strait, Lazarev Sea) and to identify genes with potential regulatory roles in the seasonal life cycle of Antarctic krill. The RNA-seq data were analysed (a) for seasonal differences between summer and winter krill sampled from each region, and (b) for regional differences within each season. A large majority of genes showed an up-regulation in summer krill in all regions with respect to winter krill. However, seasonal differences in gene expression were less pronounced in Antarctic krill from South Georgia, most likely due to the milder seasonal conditions of the lower latitudes of this region, with a less extreme light regime and food availability between summer and winter. Our results suggest that in the South Orkneys/Bransfield Strait and Lazarev Sea region, Antarctic krill entered a state of metabolic depression and regressed development (winter quiescence) in winter. Moreover, seasonal gene expression signatures seem to be driven by a photoperiodic timing system that may adapt the flexible behaviour and physiology of Antarctic krill to the highly seasonal environment according to the latitudinal region. However, at the lower latitude South Georgia region, food availability might represent the main environmental cue influencing seasonal physiology.