Posts Tagged 'molecular biology'

Regional and species level responses of Scleractinian corals under global change within the Caribbean Sea

Human-induced global change has caused rapid increases in ocean temperature (warming) and declines in seawater pH (acidification), and are expected to have negative impacts on tropical reef-building corals globally. Abnormally high seawater temperatures disrupt the symbiosis between corals and their algal endosymbiont in a process known as ‘coral bleaching.’ During such bleaching events, calcification rates decline and physiological processes deteriorate. Additionally, corals rely heavily on elevated seawater pH in order to support and maintain production of their calcium carbonate skeletons. Together, changes in ocean temperatures and seawater pH pose serious threats to coral reefs, foundational ecosystems that provide habitat for countless essential fisheries, while also acting as natural buffers from storms and providing major economic support for tropical coastal communities. Identifying how these global scale stressors impact Caribbean coral reefs is critical in understanding community composition and coral abundance on future reefs. This dissertation employs an interdisciplinary suite of techniques to assess the impacts of ocean acidification and warming on the growth and physiology of Caribbean corals to improve understandings of the responses of coral under projected global change, and provide a framework for similar future studies. Through the use of a meta-analysis (Chapter 1), I identified trends in coral calcification throughout the Greater Caribbean Sea in response to experimental ocean acidification and warming, and performed quantitative assessment of experimental design effects on coral calcification rates. I then conducted a 93- day simulated ocean acidification and warming mesocosm experiment to identify growth (Chapter 2, 4) and physiological (Chapter 3) responses of several species of common Caribbean corals. The results from this work highlight the diversity of responses of Caribbean corals to projected global change at individual and species levels, as well as between the coral host and algal endosymbiont. Overall, the variation in growth and physiological responses of these important Caribbean coral species under ocean acidification and warming is critical in predicting the future ‘winners’ and ‘losers’ of Caribbean reefs as global change unfolds.

Continue reading ‘Regional and species level responses of Scleractinian corals under global change within the Caribbean Sea’

Unique genomic and phenotypic responses to extreme and variable pH conditions in purple urchin larvae

Environmental variation experienced by a species across space and time can promote the maintenance of genetic diversity that may be adaptive in future global change conditions. Selection experiments have shown that purple sea urchin, Strongylocentrotus purpuratus, populations have adaptive genetic variation for surviving pH conditions at the “edge” (pH 7.5) of conditions experienced in nature. However, little is known about whether populations have genetic variation for surviving low-pH events beyond those currently experienced in nature or how variation in pH conditions affects organismal and genetic responses. Here, we quantified survival, growth, and allele frequency shifts in experimentally selected developing purple sea urchin larvae in static and variable conditions at three pH levels: pH 8.1 (control), pH 7.5 (edge-of-range), and pH 7.0 (extreme). Variable treatments recovered body size relative to static treatments, but resulted in higher mortality, suggesting a potential tradeoff between survival and growth under pH stress. However, within each pH level, allele frequency changes were overlapping between static and variable conditions, suggesting a shared genetic basis underlying survival to mean pH regardless of variability. In contrast, genetic responses to pH 7.5 (edge) versus pH 7.0 (extreme) conditions were distinct, indicating a unique genetic basis of survival. In addition, loci under selection were more likely to be in exonic regions than regulatory, indicating that selection targeted protein-coding variation. Loci under selection in variable pH 7.5 conditions, more similar to conditions periodically experienced in nature, performed functions related to lipid biosynthesis and metabolism, while loci under selection in static pH 7.0 conditions performed functions related to transmembrane and mitochondrial processes. While these results are promising in that purple sea urchin populations possess genetic variation for surviving extreme pH conditions not currently experienced in nature, they caution that increased acidification does not result in a linear response but elicits unique physiological stresses and survival mechanisms.

Continue reading ‘Unique genomic and phenotypic responses to extreme and variable pH conditions in purple urchin larvae’

Effects of ocean acidification on Antarctic microbial communities

Antarctic waters are amongst the most vulnerable in the world to ocean acidification due to their cold temperatures, naturally low levels of calcium carbonate and upwelling that brings deep CO2-rich waters to the surface. A meta-analysis demonstrated groups of Antarctic marine biota in waters south of 60!S have a range of tolerances to ocean acidification. Invertebrates and phytoplankton showed negative effects above 500 μatm and 1000 μatm CO2 respectively, while bacteria appear tolerant to elevated CO2. Phytoplankton studied as part of a natural microbial community were found to be more
sensitive than those studied as a single species in culture. This highlights the importance of community and ecosystem level studies, which incorporate the interaction and competition among species and trophic levels, to accurately assess the effects of ocean acidification on the Antarctic ecosystem.

Antarctic marine microbes (comprising phytoplankton, protozoa and bacteria) drive ocean productivity, nutrient cycling and mediate trophodynamics and the biological pump. While they appear vulnerable to changes in ocean chemistry, little is known about the nature and magnitude of their responses to ocean acidification, especially for natural communities. To address this lack of information, a six level, dose-response ocean acidification experiment was conducted in Prydz Bay, East Antarctica, using 650 L incubation tanks (minicosms). The minicosms were filled with Antarctic nearshore water and adjusted to a gradient of carbon dioxide (CO2) from 343 to 1641 μatm. Microscopy
and phylogenetic marker gene sequence analysis found the microbial community
composition altered at CO2 levels above approximately 1000 μatm. The CO2-
induced responses of microeukaryotes (>20 μm) and nanoeukaryotes (2 to 20 μm) were taxon-specific. For diatoms the response of taxa was related to cell size with micro-sized diatoms (>20 μm) increasing in abundance with moderate CO2 (506 to 634 μatm), while above this level their abundance declined. In contrast, nano-size diatoms (<20 μm) tolerated elevated CO2. Like large diatoms, Phaeocystis antarctica increased in abundance between 343 to 634 μatm CO2 but fell at higher levels. 18S and 16S rDNA sequencing showed that picoeukaryotic and prokaryotic composition was unaffected by CO2, despite having higher abundances at CO2 levels !634 μatm. This was likely due to the lower abundance of heterotrophic nanoflagellates at CO2 levels exceeding 953 μatm, which reduced the top-down control of their pico- and nanoplanktonic prey. As a result of the differences in the tolerance of individual taxa/size categories, CO2 caused a
significant change in the microbial community structure to one dominated by nano-sized diatoms, picoeukaryotes and prokaryotes.

Based on the CO2-induced changes in the microbial community, modelling was performed to investigate the future effects of different levels of elevated CO2 on the structure and function of microbial communities in Antarctic coastal systems. These models indicate CO2 levels predicted toward the end of the century under a “business as usual scenario” elicit changes in microbial composition, significantly altering trophodynamic pathways, reducing energy transfer to higher trophic levels and favouring respiration of carbon within the microbial loop. Such responses would alter elemental cycles, jeopardise the productivity that underpins the wealth and diversity of life for which Antarctica is renowned. In addition, it would reduce carbon sequestration in coastal Antarctic waters thereby having a positive feedback on global climate change.

Continue reading ‘Effects of ocean acidification on Antarctic microbial communities’

Transcriptional changes of Pacific oyster Crassostrea gigas reveal essential role of calcium signal pathway in response to CO2-driven acidification


•Totally 501 and 2728 DEGs were identified in oyster after short- and long-term CO2 exposure, respectively.

•A series of calcium-binding genes were up-regulated in oyster after long-term CO2 exposure.

•The intracellular calcium concentration decreased after short-time CO2 exposure but recovered to normal levels after long-term treatment.

•The oxidative stress level increased significantly after short-time CO2 exposure but recovered to normal level after long-term treatment.


There is increasing evidence that ocean acidification (OA) has a significant impact on marine organisms. However, the ability of most marine organisms to acclimate to OA and the underlying mechanisms are still not well understood. In the present study, whole transcriptome analysis was performed to compare the impacts of short- (7 days, named as short group) and long- (60 days, named as long group) term CO2 exposure (pH 7.50) on Pacific oyster Crassostrea gigas. The responses of C. gigas to short- and long-term CO2 exposure shared common mechanisms in metabolism, membrane-associated transportation and binding processes. Long-term CO2 exposure induced significant expression of genes involved in DNA or RNA binding, indicating the activated transcription after long-term CO2 exposure. Oysters in the short-term group underwent significant intracellular calcium variation and oxidative stress. In contrast, the intracellular calcium, ROS level in hemocytes and H2O2 in serum recovered to normal levels after long-term CO2 exposure, suggesting the compensation of physiological status and mutual interplay between calcium and oxidative level. The compensation was supported by the up-regulation of a series of calcium binding proteins (CBPs) and calmodulins (CaMs) related signal pathway. The results provided valuable information to understand the molecular mechanism underlying the responses of Pacific oyster to the acidified ocean and might have implications for predicting the possible effects of global climate changes on oyster aquaculture.

Continue reading ‘Transcriptional changes of Pacific oyster Crassostrea gigas reveal essential role of calcium signal pathway in response to CO2-driven acidification’

Transcriptional analysis reveals physiological response to acute acidification stress of barramundi Lates calcarifer (Bloch) in coastal areas

To understand the physiological response of estuarine fish to acidification, barramundi (Lates calcarifer) juveniles were exposed to acidified seawater in experimental conditions. The molecular response of barramundi to acidification stress was assessed by RNA-seq analysis. A total of 2188 genes were identified as differential expression genes. The gene ontology classification system and Kyoto Encyclopedia of Genes and Genomes database analysis showed that acidification caused differential expressions of genes and pathways in the gills of barramundi. Acidification had a great influence on the signal transduction pathway in cell process. Furthermore, we detected that numerous unigenes involved in the pathways associated with lipid metabolism, carbohydrate metabolism, amino acid metabolism, glycan biosynthesis and metabolism specific and non-specific immunity were changed. This study indicates that the physiological responses in barramundi especially the immune system and energy allocation correspond to the variation of environmental pH. This study reveals the necessity for assessment of the potential of estuarine fishes to cope with acidification of the environment and the need to develop strategies for fish conservation in coastal areas.

Continue reading ‘Transcriptional analysis reveals physiological response to acute acidification stress of barramundi Lates calcarifer (Bloch) in coastal areas’

Fish embryo vulnerability to combined acidification and warming coincides with a low capacity for homeostatic regulation

The vulnerability of fish embryos and larvae to environmental factors is often attributed to a lack of adult-like organ systems (gills) and thus insufficient homeostatic capacity. However, experimental data supporting this hypothesis are scarce. Here, by using Atlantic cod (Gadus morhua) as a model, the relationship between embryo vulnerability (to projected ocean acidification and warming) and homeostatic capacity was explored through parallel analyses of stage-specific mortality and in vitro activity and expression of major ion pumps (ATP-synthase, Na+/K+-ATPase, H+-ATPase) and co-transporters (NBC1, NKCC1). Immunolocalization of these transporters was used to study ionocyte morphology in newly hatched larvae. Treatment-related embryo mortality until hatching (+20% due to acidification and warming) occurred primarily during an early period (gastrulation) characterized by extremely low ion transport capacity. Thereafter, embryo mortality decreased in parallel with an exponential increase in activity and expression of all investigated ion transporters. Significant changes in transporter activity and expression in response to acidification (+15% activity) and warming (−30% expression) indicate some potential for short-term acclimatization, although this is probably associated with energetic trade-offs. Interestingly, whole-larvae enzyme activity (supported by abundant epidermal ionocytes) reached levels similar to those previously measured in gill tissue of adult cod, suggesting that early-life stages without functional gills are better equipped in terms of ion homeostasis than previously thought. This study implies that the gastrulation period represents a critical transition from inherited (maternal) defenses to active homeostatic regulation, which facilitates enhanced resilience of later stages to environmental factors.

Continue reading ‘Fish embryo vulnerability to combined acidification and warming coincides with a low capacity for homeostatic regulation’

Ocean acidification induces subtle shifts in gene expression and DNA methylation in mantle tissue of the Eastern oyster (Crassostrea virginica)

Early evidence suggests that DNA methylation can mediate phenotypic responses of marine calcifying species to ocean acidification (OA). Few studies, however, have explicitly studied DNA methylation in calcifying tissues through time. Here, we examined the phenotypic and molecular responses in the extrapallial fluid and mantle (fluid and tissue at the calcification site) in the Eastern oyster (Crassostrea virginica) exposed to experimental OA over 80 days. Oysters were reared under three experimental pCO2 treatments (‘control’, 580 uatm; ‘moderate OA’, 1000 uatm; ‘high OA’, 2800 uatm) and sampled at 6 time points (24 hours – 80 days). We found that high OA initially induced changes in the pH of the extrapallial fluid (pHEPF) relative to the external seawater, but the magnitude of this difference was highest at 9 days and diminished over time. Calcification rates were significantly lower in the high OA treatment compared to the other treatments. To explore how oysters regulate their extrapallial fluid, gene expression and DNA methylation were examined in the mantle-edge tissue of oysters from day 9 and 80 in the control and high OA treatments. Mantle tissue mounted a significant global molecular response (both in the transcriptome and methylome) to OA that shifted through time. Although we did not find individual genes that were significantly differentially expressed to OA, the pHEPF was correlated with the eigengene expression of several co-expressed gene clusters. A small number of OA-induced differentially methylated loci were discovered, which corresponded with a weak association between OA-induced changes in genome-wide gene body DNA methylation and gene expression. Gene body methylation, however, was not significantly correlated with the eigengene expression of pHEPF correlated gene clusters. These results suggest that in C. virginica, OA induces a subtle response in a large number of genes, but also indicates that plasticity at the molecular level may be limited. Our study highlights the need to re-assess the plasticity of tissue-specific molecular responses in marine calcifiers, as well as the role of DNA methylation and gene expression in mediating physiological and biomineralization responses to OA.

Continue reading ‘Ocean acidification induces subtle shifts in gene expression and DNA methylation in mantle tissue of the Eastern oyster (Crassostrea virginica)’

Multi-generational mitigating effects of ocean acidification on in vivo endpoints, antioxidant defense, DNA damage response, and epigenetic modification in an asexual monogonont rotifer

Ocean acidification (OA) is caused by changes in ocean carbon chemistry due to increased atmospheric pCO2 and is predicted to have deleterious effects on marine ecosystems. While the potential impacts of OA on many marine species have been studied, the multi-generational effects on asexual organisms remain unknown. We found that low seawater pH induced oxidative stress and DNA damage, decreasing growth rates, fecundity, and lifespans in the parental generation, whereas deleterious effects on in vivo endpoints in F1 and F2 offspring were less evident. The findings suggest multi-generational adaptive effects play a role in antioxidant abilities and other defenses mechanisms. OA-induced DNA damage, including double-strand breaks (DSBs), was fully repaired in F1 offspring of parents exposed to OA for 7 days, indicating that an adaptation mechanism may be the major driving force behind multi-generational adaptive effects. Analysis of epigenetic modification in response to OA involved examination of histone modification of DNA repair genes and a chromatin immunoprecipitation assay, as B. koreanus has no methylation pattern for CpG in its genome. We conclude that DSBs, DNA repair, and histone modification play important roles in multi-generational plasticity in response to OA in an asexual monogonont rotifer.

Continue reading ‘Multi-generational mitigating effects of ocean acidification on in vivo endpoints, antioxidant defense, DNA damage response, and epigenetic modification in an asexual monogonont rotifer’

Decreased motility of flagellated microalgae long-term acclimated to CO2-induced acidified waters

Motility plays a critical role in algal survival and reproduction, with implications for aquatic ecosystem stability. However, the effect of elevated CO2 on marine, brackish and freshwater algal motility is unclear. Here we show, using laboratory microscale and field mesoscale experiments, that three typical phytoplankton species had decreased motility with increased CO2. Polar marine Microglena sp., euryhaline Dunaliella salina and freshwater Chlamydomonas reinhardtii were grown under different CO2 concentrations for 5 years. Long-term acclimated Microglena sp. showed substantially decreased photo-responses in all treatments, with a photophobic reaction affecting intracellular calcium concentration. Genes regulating flagellar movement were significantly downregulated (P < 0.05), alongside a significant increase in gene expression for flagellar shedding (P < 0.05). D. salina and C. reinhardtii showed similar results, suggesting that motility changes are common across flagellated species. As the flagella structure and bending mechanism are conserved from unicellular organisms to vertebrates, these results suggest that increasing surface water CO2 concentrations may affect flagellated cells from algae to fish.

Continue reading ‘Decreased motility of flagellated microalgae long-term acclimated to CO2-induced acidified waters’

Transgenerational plasticity and acclimation of tropical sea urchins to ocean warming and acidification

Anthropogenic CO2 emissions are causing the oceans to simultaneously warm and become increasingly acidic, with rates of change that are putting evolutionary pressure on many marine organisms. As a result, both short-term responses and the ability of organisms to acclimate to rapid environmental change through phenotypic plasticity are expected to play a considerable role in persistence of many species under future ocean change. Evidence is accumulating that non-genetic inheritance and transgenerational plasticity (TGP) may be important mechanisms which may facilitate acclimation to ocean warming and acidification. This thesis tests the overarching hypothesis that TGP and parental acclimation to predicted ocean warming and acidification conditions promote greater resilience in offspring using two tropical sea urchins, Tripneustes gratilla and Echinometra sp. A, as model organisms.

Continue reading ‘Transgenerational plasticity and acclimation of tropical sea urchins to ocean warming and acidification’

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Ocean acidification in the IPCC AR5 WG II

OUP book