Ocean warming and acidification adjust inter- and intra-specific variability in the functional trait expression of polar invertebrates.

Climate change is known to affect the distribution and composition of species, but concomitant alterations to functionally important aspects of behaviour and species-environment relations are poorly constrained. Here, we examine the ecosystem ramifications of changes in sediment-dwelling invertebrate bioturbation behaviour-a key process mediating nutrient cycling-associated with near-future environmental conditions (+ 1.5 °C, 550 ppm [pCO2]) for species from polar regions experiencing rapid rates of climate change. We find that responses to warming and acidification vary between species and lead to a reduction in intra-specific variability in behavioural trait expression that adjusts the magnitude and direction of nutrient concentrations. Our analyses also indicate that species behaviour is not predetermined, but can be dependent on local variations in environmental history that set population capacities for phenotypic plasticity. We provide evidence that certain, but subtle, aspects of inter- and intra-specific variation in behavioural trait expression, rather than the presence or proportional representation of species per se, is an important and under-appreciated determinant of benthic biogeochemical responses to climate change. Such changes in species behaviour may act as an early warning for impending ecological transitions associated with progressive climate forcing.

Biogeochemical consequences of a changing Arctic shelf seafloor ecosystem.

Unprecedented and dramatic transformations are occurring in the Arctic in response to climate change, but academic, public, and political discourse has disproportionately focussed on the most visible and direct aspects of change, including sea ice melt, permafrost thaw, the fate of charismatic megafauna, and the expansion of fisheries. Such narratives disregard the importance of less visible and indirect processes and, in particular, miss the substantive contribution of the shelf seafloor in regulating nutrients and sequestering carbon. Here, we summarise the biogeochemical functioning of the Arctic shelf seafloor before considering how climate change and regional adjustments to human activities may alter its biogeochemical and ecological dynamics, including ecosystem function, carbon burial, or nutrient recycling. We highlight the importance of the Arctic benthic system in mitigating climatic and anthropogenic change and, with a focus on the Barents Sea, offer some observations and our perspectives on future management and policy.

Reproductive traits and population dynamics of benthic invertebrates indicate episodic recruitment patterns across an Arctic polar front.

Climate-induced changes in the ocean and sea ice environment of the Arctic are beginning to generate major and rapid changes in Arctic ecosystems, but the effects of directional forcing on the persistence and distribution of species remain poorly understood. Here, we examine the reproductive traits and population dynamics of the bivalve Astarte crenata and sea star Ctenodiscus crispatus across a north-south transect that intersects the polar front in the Barents Sea. Both species present large oocytes indicative of short pelagic or direct development that do not differ in size-frequency between 74.5 and 81.3º latitude. However, despite gametogenic maturity, we found low frequencies of certain size classes within populations that may indicate periodic recruitment failure. We suggest that recruitment of A. crenata could occur periodically when conditions are favorable, while populations of C. crispatus are characterized by episodic recruitment failures. Pyloric caeca indices in C. crispatus show that food uptake is greatest at, and north of, the polar front, providing credence to the view that interannual variations in the quantity and quality of primary production and its flux to the seafloor, linked to the variable extent and thickness of sea ice, are likely to be strong determinants of physiological fitness. Our findings provide evidence that the distribution and long-term survival of species is not only a simple function of adaptive capacity to specific environmental changes, but will also be contingent on the frequency and occurrence of years where environmental conditions support reproduction and settlement.

Climate-driven benthic invertebrate activity and biogeochemical functioning across the Barents Sea polar front.

Arctic marine ecosystems are undergoing rapid correction in response to multiple expressions of climate change, but the consequences of altered biodiversity for the sequestration, transformation and storage of nutrients are poorly constrained. Here, we determine the bioturbation activity of sediment-dwelling invertebrate communities over two consecutive summers that contrasted in sea-ice extent along a transect intersecting the polar front. We find a clear separation in community composition at the polar front that marks a transition in the type and amount of bioturbation activity, and associated nutrient concentrations, sufficient to distinguish a southern high from a northern low. While patterns in community structure reflect proximity to arctic versus boreal conditions, our observations strongly suggest that faunal activity is moderated by seasonal variations in sea ice extent that influence food supply to the benthos. Our observations help visualize how a climate-driven reorganization of the Barents Sea benthic ecosystem may be expressed, and emphasize the rapidity with which an entire region could experience a functional transformation. As strong benthic-pelagic coupling is typical across most parts of the Arctic shelf, the response of these ecosystems to a changing climate will have important ramifications for ecosystem functioning and the trophic structure of the entire food web. This article is part of the theme issue 'The changing Arctic Ocean: consequences for biological communities, biogeochemical processes and ecosystem functioning'.

Interrogation of highly structured RNA with multicomponent deoxyribozyme probes at ambient temperatures.

Molecular analysis of RNA through hybridization with sequence-specific probes is challenging due to the intrinsic ability of RNA molecules to form stable secondary and tertiary structures. To overcome the energy barrier toward the probe-RNA complex formation, the probes are made of artificial nucleotides, which are more expensive than their natural counterparts and may still be inefficient. Here, we propose the use of a multicomponent probe based on an RNA-cleaving deoxyribozyme for the analysis of highly structured RNA targets. Efficient interrogation of two native RNA from Saccharomyces cerevisiae-a transfer RNA (tRNA) and 18S ribosomal RNA (rRNA)-was achieved at ambient temperature. We achieved detection limits of tRNA down to ∼0.3 nM, which is two orders of magnitude lower than that previously reported for molecular beacon probes. Importantly, no probe annealing to the target was required, with the hybridization assay performed at 37°C. Excess of nonspecific targets did not compromise the performance of the probe, and high interrogation efficiency was maintained by the probes even in complex matrices, such as cell lysate. A linear dynamic range of 0.3-150 nM tRNA was demonstrated. The probe can be adapted for differentiation of a single mismatch in the tRNA-probe complex. Therefore, this study opens a venue toward highly selective, sensitive, robust, and inexpensive assays for the interrogation of biological RNA.

Cascade of deoxyribozymes for the colorimetric analysis of drug resistance in Mycobacterium tuberculosis.

A visual cascade detection system has been applied to the detection and analysis of drug-resistance profile of Mycobacterium tuberculosis complex (MTC), a causative agent of tuberculosis. The cascade system utilizes highly selective split RNA-cleaving deoxyribozyme (sDz) sensors. When activated by a complementary nucleic acid, sDz releases the peroxidase-like deoxyribozyme apoenzyme, which, in complex with a hemin cofactor, catalyzes the color change of the sample's solution. The excellent selectivity of the cascade has allowed for the detection of point mutations in the sequences of the MTC rpoB, katG, and gyrA genes, which are responsible for resistance to rifampin, isoniazid, and fluoroquinolone, respectively. When combined with isothermal nucleic acid sequence based amplification (NASBA), the assay was able to detect amplicons of 16S rRNA and katG mRNA generated from 0.1 pg and 10 pg total RNA taken for NASBA, respectively, in less than 2 h, producing a signal detectable with the naked eye. The proposed assay may become a prototype for point-of-care diagnosis of drug resistant bacteria with visual signal output.

Selective Determination of Isothermally Amplified Zika Virus RNA Using a Universal DNA-Hairpin Probe in Less than 1 Hour.

The recent outbreak of the Zika virus (ZIKV) in the Americas and multiple studies that linked the virus to the cases of microcephaly and neurological complications have revealed the need for cost efficient and rapid ZIKV diagnostics tests. Here, a diagnostic platform relying on a four-way junction (4WJ)-based biosensor with electrochemical readout using a Universal DNA-Hairpin (UDH) probe for the selective recognition of an isothermally amplified ZIKV RNA fragment is developed. The 4WJ structure utilizes an electrode-immobilized stem-loop (DNA-hairpin) probe and two DNA adaptor strands complementary to both the stem-loop probe and the targeted fragment of a ZIKV amplicon. One of the adaptor strands is responsible for high selectivity of the target recognition, while another helps unwinding the target secondary structure. The first adaptor strand contains a redox label methylene blue to trigger the current change in response to the target-dependent formation of the 4WJ structure on the surface of the electrode. The amplicon can be analyzed directly from the amplification sample without the need for its purification. The proposed diagnostic methodology exhibits the limit of ZIKV RNA detection of 1.11 fg/µL (∼0.3 fM) and high selectivity that allows for reliable discrimination of ZIKV from West Nile virus and four dengue virus serotypes. Overall, the analysis of ZIKV RNA can be completed in less than 1 h, including amplification and electrochemical detection.

Label-Free Pathogen Detection by a Deoxyribozyme Cascade with Visual Signal Readout.

A colorimetric nucleic acid based test for label-free pathogen detection has been developed and used for the detection of the Zika virus. The test relies on nucleic acid sequence-based amplification (NASBA) of a viral RNA followed by interrogation of the amplicon by a cascade of deoxyribozymes constituting a visual split deoxyribozyme (vsDz) probe. The probe consists of a split phosphodiesterase deoxyribozyme, which forms its catalytic core upon binding to a specific amplicon fragment. The catalytically active complex recognizes and cleaves an inhibited peroxidase-like deoxyribozyme (PDz), thereby activating it. Active PDz catalyzes hydrogen peroxide-mediated oxidation of a colorless substrate into a colored product, thereby generating a visible signal. Viral RNA (106 copies/mL or higher) triggers intense color within 2 hr. The test selectively differentiates between Zika and closely related dengue and West Nile viruses. The reported technology combines isothermal amplification and visual detection and therefore represents a basis for the future development of a cost-efficient and instrument-free method for point-of-care nucleic acid analysis.

Phosphate deficiency promotes coral bleaching and is reflected by the ultrastructure of symbiotic dinoflagellates.

Enrichment of reef environments with dissolved inorganic nutrients is considered a major threat to the survival of corals living in symbiosis with dinoflagellates (Symbiodinium sp.). We argue, however, that the direct negative effects on the symbiosis are not necessarily caused by the nutrient enrichment itself but by the phosphorus starvation of the algal symbionts that can be caused by skewed nitrogen (N) to phosphorus (P) ratios. We exposed corals to imbalanced N:P ratios in long-term experiments and found that the undersupply of phosphate severely disturbed the symbiosis, indicated by the loss of coral biomass, malfunctioning of algal photosynthesis and bleaching of the corals. In contrast, the corals tolerated an undersupply with nitrogen at high phosphate concentrations without negative effects on symbiont photosynthesis, suggesting a better adaptation to nitrogen limitation. Transmission electron microscopy analysis revealed that the signatures of ultrastructural biomarkers represent versatile tools for the classification of nutrient stress in symbiotic algae. Notably, high N:P ratios in the water were clearly identified by the accumulation of uric acid crystals.

Shifting baselines in Antarctic ecosystems; ecophysiological response to warming in Lissarca miliaris at Signy Island, Antarctica.

The Antarctic Peninsula has experienced a rapid increase in atmospheric temperature over the last 50 years. Whether or not marine organisms thriving in this cold stenothermal environment are able to cope with warming is of concern. Here, we present changes to the growth and shell characteristics of the ecologically important, small and short lived brooding bivalve Lissarca miliaris from Signy Island, Antarctica. Using material collected from the 1970's to the present day, we show an increase in growth rate and adult shell deterioration accompanied by a decrease in offspring size, associated with an increase in annual average temperatures. Critical changes to the bivalve's ecology seen today evidence the problem of a shift in baseline since the onset of warming recorded in Antarctica. These small bivalves are demonstrating ecophysiological responses to subtle warming that, provided warming continues, could soon surpass a physiological tipping point, adding to warming associated threats such as increased predatory pressure and ocean acidification.