Biomineralization changes with food supply confer juvenile scallops (Argopecten purpuratus) resistance to ocean acidification

Future ocean acidification (OA) will affect physiological traits of marine species, with calcifying species being particularly vulnerable. As OA entails high energy demands, particularly during the rapid juvenile growth phase, food supply may play a key role in the response of marine organisms to OA. We experimentally evaluated the role of food supply in modulating physiological responses and biomineralization processes in juveniles of the Chilean scallop, Argopecten purpuratus, that were exposed to control (pH 8.0) and low pH (pH 7.6) conditions using three food supply treatments (high, intermediate, and low). We found that pH and food levels had additive effects on the physiological response of the juvenile scallops. Metabolic rates, shell growth, net calcification, and ingestion rates increased significantly at low pH conditions, independent of food. These physiological responses increased significantly in organisms exposed to intermediate and high levels of food supply. Hence, food supply seems to play a major role modulating organismal response by providing the energetic means to bolster the physiological response of OA stress. On the contrary, the relative expression of chitin synthase, a functional molecule for biomineralization, increased significantly in scallops exposed to low food supply and low pH, which resulted in a thicker periostracum enriched with chitin polysaccharides. Under reduced food and low pH conditions, the adaptive organismal response was to trade-off growth for the expression of biomineralization molecules and altering of the organic composition of shell periostracum, suggesting that the future performance of these calcifiers will depend on the trajectories of both OA and food supply. Thus, incorporating a suite of traits and multiple stressors in future studies of the adaptive organismal response may provide key insights on OA impacts on marine calcifiers.

Planktonic and benthic foraminiferal stable isotopes, SSTs and thermocline temperature, coccoliths and benthic foraminiferal assemblages, and productivity reconstruction for sediment core MD06-3067

We present sea surface, upper thermocline, and benthic d18O data, as well as temperature and paleoproductivity proxy data, from the International Marine Global Change Study Program (IMAGES) Core MD06-3067 (6°31'N, 126°30'E, 1575 m water depth), located in the western equatorial Pacific Ocean within the flow path of the Mindanao Current. Our records reveal considerable glacial-interglacial and suborbital variability in the Mindanao Dome upwelling over the last 160 kyr. Dome activity generally intensified during glacial intervals resulting in cooler thermocline waters, whereas it substantially declined during interglacials, in particular in the early Holocene and early marine oxygen isotope stage (MIS) 5e, when upwelling waters did not reach the thermocline. During MIS 3 and MIS 2, enhanced surface productivity together with remarkably low SST and low upper ocean thermal contrast provide evidence for episodic glacial upwelling to the surface, whereas transient surface warming marks periodic collapses of the Mindanao Dome upwelling during Heinrich events. We attribute the high variability during MIS 3 and MIS 2 to changes in the El Niño Southern Oscillation state that affected boreal winter monsoonal winds and upper ocean circulation. Glacial upwelling intensified when a strong cyclonic gyre became established, whereas El Niño-like conditions during Heinrich events tended to suppress the cyclonic circulation, reducing Ekman transport. Thus, our findings demonstrate that variations in the Mindanao Dome upwelling are closely linked to the position and intensity of the tropical convection and also reflect far-field influences from the high latitudes.

Effects of ocean acidification and global warming on reef bioerosion-lessons from a clionaid sponge

Coral reefs are under threat, exerted by a number of interacting effects inherent to the present climate change, including ocean acidification and global warming. Bioerosion drives reef degradation by recycling carbonate skeletal material and is an important but understudied factor in this context. Twelve different combinations of pCO2 and temperature were applied to elucidate the consequences of ocean acidification and global warming on the physiological response and bioerosion rates of the zooxanthellate sponge Cliona orientalis-one of the most abundant and effective bioeroders on the Great Barrier Reef, Australia. Our results confirm a significant amplification of the sponges' bioerosion capacity with increasing pCO2, which is expressed by more carbonate being chemically dissolved by etching. The health of the sponges and their photosymbionts was not affected by changes in pCO2, in contrast to temperature, which had significant negative impacts at higher levels. However, we could not conclusively explain the relationship between temperature and bioerosion rates, which were slightly reduced at both colder as well as warmer temperatures than ambient. The present findings on the effects of ocean acidification on chemical bioerosion, however, will have significant implications for predicting future reef carbonate budgets, as sponges often contribute the lion's share of internal bioerosion on coral reefs.

Impact of changing carbonate chemistry, temperature, and salinity on growth and test degradation of the benthic foraminifer Ammonia aomoriensis

The present study investigated the combined effects of ocean acidification, temperature, and salinity on growth and test degradation of Ammonia aomoriensis. This species is one of the dominant benthic foraminifera in near-coastal habitats of the southwestern Baltic Sea that can be particularly sensitive to changes in seawater carbonate chemistry. To assess potential responses to ocean acidification and climate change, we performed a fully crossed experiment involving three temperatures (8, 13, and 18°C), three salinities (15, 20, and 25) and four pCO2 levels (566, 1195, 2108, and 3843 µatm) for six weeks. Our results highlight a sensitive response of A. aomoriensis to undersaturated seawater with respect to calcite. The specimens continued to grow and increase their test diameter in treatments with pCO2 <1200 µatm, when Omega calc >1. Growth rates declined when pCO2 exceeded 1200 µatm (Omega calc <1). A significant reduction in test diameter and number of tests due to dissolution was observed below a critical Omega calc of 0.5. Elevated temperature (18°C) led to increased Omega calc, larger test diameter, and lower test degradation. Maximal growth was observed at 18°C. No significant relationship was observed between salinity and test growth. Lowered and undersaturated Omega calc, which results from increasing pCO2 in bottom waters, may cause a significant future decline of the population density of A. aomoriensis in its natural environment. At the same time, this effect might be partially compensated by temperature rise due to global warming.

TEX86H proxy and BIT index of sediment core GeoB9528-3 and reconstructed temperature data from NW Africa surface sediments

Changes in the strength of Atlantic meridional overturning circulation (AMOC) are known to have profound impacts on global climate. Coupled modelling studies have suggested that, on annual to multi-decadal time scales, a slowdown of AMOC causes a deepening of the thermocline in the tropical Atlantic. However, this process has been poorly constrained by sedimentary geochemical records. Here, we reconstruct surface (UK'37 Index) and thermocline (TEX86H) water temperatures from the Guinea Plateau Margin (Eastern tropical Atlantic) over the last two glacial-interglacial cycles (~ 192 kyr). These paleotemperature records show that periods of reduced AMOC, as indicated by the d13 C benthic foraminiferal record from the same core, coincide with a reduction in the near-surface vertical temperature gradient, demonstrating for the first time that AMOC-induced tropical Atlantic thermocline adjustment exists on longer, millennial time scales. Modelling results support the interpretation of the geochemical records and show that thermocline adjustment is particularly pronounced in the eastern tropical Atlantic. Thus, variations in AMOC strength appear to be an important driver of the thermocline structure in the tropical Atlantic from annual to multi-millennial time scales.

Examining wheat yield sensitivity to temperature and precipitation changes for a large ensemble of crop models using impact response surfaces

Impact response surfaces (IRSs) depict the response of an impact variable to changes in two explanatory variables as a plotted surface. Here, IRSs of spring and winter wheat yields were constructed from a 25-member ensemble of process-based crop simulation models. Twenty-one models were calibrated by different groups using a common set of calibration data, with calibrations applied independently to the same models in three cases. The sensitivity of modelled yield to changes in temperature and precipitation was tested by systematically modifying values of 1981-2010 baseline weather data to span the range of 19 changes projected for the late 21st century at three locations in Europe.

Hsf1 and Hsp90 orchestrate temperature-dependent global transcriptional remodelling and chromatin architecture in Candida albicans

We thank Karim Gharbi and Urmi Trivedi for their assistance with RNA sequencing, carried out in the GenePool genomics facility (University of Edinburgh). We also thank Susan Fairley and Eduardo De Paiva Alves (Centre for Genome Enabled Biology and Medicine, University of Aberdeen) for help with the initial bioinformatics analysis. We thank Aaron Mitchell for kindly providing the ALS3 mutant, Julian Naglik for the gift of TR146 cells, and Jon Richardson for technical assistance. We thank the Genomics and Bioinformatics core of the Faculty of Health Sciences for Next Generation Sequencing and Bioinformatics support, the Information and Communication Technology Office at the University of Macau for providing access to a High Performance Computer and Jacky Chan and William Pang for their expert support on the High Performance Computer. Finally, we thank Amanda Veri for generating CaLC2928. M.D.L. is supported by a Sir Henry Wellcome Postdoctoral Fellowship (Wellcome Trust 096072), R.A.F. by a Wellcome Trust-Massachusetts Institute of Technology (MIT) Postdoctoral Fellowship, L.E.C. by a Canada Research Chair in Microbial Genomics and Infectious Disease and by Canadian Institutes of Health Research Grants MOP-119520 and MOP-86452, A.J. P.B. was supported by the UK Biotechnology and Biological Sciences Research Council (BB/F00513X/1) and by the European Research Council (ERC-2009-AdG-249793-STRIFE), KHW is supported by the Science and Technology Development Fund of Macau S.A.R (FDCT) (085/2014/A2) and the Research and Development Administrative Office of the University of Macau (SRG2014-00003-FHS) and R.T.W. by the Burroughs Wellcome fund and NIH R15AO094406. Data availability RNA-sequencing data sets are available at ArrayExpress (www.ebi.ac.uk) under accession code E-MTAB-4075. ChIP-seq data sets are available at the NCBI SRA database (http://www.ncbi.nlm.nih.gov) under accession code SRP071687. The authors declare that all other data supporting the findings of this study are available within the article and its supplementary information files, or from the corresponding author upon request.

Remodeling of Yeast Genome Expression in Response to Environmental Changes

We used genome-wide expression analysis to explore how gene expression in Saccharomyces cerevisiae is remodeled in response to various changes in extracellular environment, including changes in temperature, oxidation, nutrients, pH, and osmolarity. The results demonstrate that more than half of the genome is involved in various responses to environmental change and identify the global set of genes induced and repressed by each condition. These data implicate a substantial number of previously uncharacterized genes in these responses and reveal a signature common to environmental responses that involves ∼10% of yeast genes. The results of expression analysis with MSN2/MSN4 mutants support the model that the Msn2/Msn4 activators induce the common response to environmental change. These results provide a global description of the transcriptional response to environmental change and extend our understanding of the role of activators in effecting this response.

An evaluation of the performance of cDNA microarrays for detecting changes in global mRNA expression

The cDNA microarray is one technological approach that has the potential to accurately measure changes in global mRNA expression levels. We report an assessment of an optimized cDNA microarray platform to generate accurate, precise and reliable data consistent with the objective of using microarrays as an acquisition platform to populate gene expression databases. The study design consisted of two independent evaluations with 70 arrays from two different manufactured lots and used three human tissue sources as samples: placenta, brain and heart. Overall signal response was linear over three orders of magnitude and the sensitivity for any element was estimated to be 2 pg mRNA. The calculated coefficient of variation for differential expression for all non-differentiated elements was 12–14% across the entire signal range and did not vary with array batch or tissue source. The minimum detectable fold change for differential expression was 1.4. Accuracy, in terms of bias (observed minus expected differential expression ratio), was less than 1 part in 10 000 for all non-differentiated elements. The results presented in this report demonstrate the reproducible performance of the cDNA microarray technology platform and the methods provide a useful framework for evaluating other technologies that monitor changes in global mRNA expression.

Changes of Mitochondrial Properties in Maize Seedlings Associated with Selection for Germination at Low Temperature. Fatty Acid Composition, Cytochrome c Oxidase, and Adenine Nucleotide Translocase Activities1

Mitochondria are affected by low temperature during seedling establishment in maize (Zea mays L.). We evaluated the associated changes in the mitochondrial properties of populations selected for high (C4-H) and low (C4-L) germination levels at 9.5°C. When seedlings of the two populations were grown at 14°C (near the lower growth limit), the mitochondrial inner membranes of C4-H showed a higher percentage of 18-carbon unsaturated fatty acids, a higher fluidity, and a higher activity of cytochrome c oxidase. We found a positive relationship between these properties and the activity of a mitochondrial peroxidase, allowing C4-H to reduce lipid peroxidation relative to C4-L. The specific activity of reconstituted ATP/ADP translocase was positively associated with this peroxidase activity, suggesting that translocase activity is also affected by chilling. The level of oxidative stress and defense mechanisms are differently expressed in tolerant and susceptible populations when seedlings are grown at a temperature near the lower growth limit. Thus, the interaction between membrane lipids and cytochrome c oxidase seems to play a key role in maize chilling tolerance. Furthermore, the divergent-recurrent selection procedure apparently affects the allelic frequencies of genes controlling such an interaction.

Changes in global gene expression patterns during development and maturation of the rat kidney

We set out to define patterns of gene expression during kidney organogenesis by using high-density DNA array technology. Expression analysis of 8,740 rat genes revealed five discrete patterns or groups of gene expression during nephrogenesis. Group 1 consisted of genes with very high expression in the early embryonic kidney, many with roles in protein translation and DNA replication. Group 2 consisted of genes that peaked in midembryogenesis and contained many transcripts specifying proteins of the extracellular matrix. Many additional transcripts allied with groups 1 and 2 had known or proposed roles in kidney development and included LIM1, POD1, GFRA1, WT1, BCL2, Homeobox protein A11, timeless, pleiotrophin, HGF, HNF3, BMP4, TGF-α, TGF-β2, IGF-II, met, FGF7, BMP4, and ganglioside-GD3. Group 3 consisted of transcripts that peaked in the neonatal period and contained a number of retrotransposon RNAs. Group 4 contained genes that steadily increased in relative expression levels throughout development, including many genes involved in energy metabolism and transport. Group 5 consisted of genes with relatively low levels of expression throughout embryogenesis but with markedly higher levels in the adult kidney; this group included a heterogeneous mix of transporters, detoxification enzymes, and oxidative stress genes. The data suggest that the embryonic kidney is committed to cellular proliferation and morphogenesis early on, followed sequentially by extracellular matrix deposition and acquisition of markers of terminal differentiation. The neonatal burst of retrotransposon mRNA was unexpected and may play a role in a stress response associated with birth. Custom analytical tools were developed including “The Equalizer” and “eBlot,” which contain improved methods for data normalization, significance testing, and data mining.