Posts Tagged 'molecular biology'

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Experimental coral reef communities transform yet persist under mitigated future ocean warming and acidification

Published 31 October 2024 Science Closed
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Significance

Coral reefs are exceptional ecosystems and support hundreds of millions of people around the world, yet they are under severe threat due to ocean warming and acidification. Reefs are predicted to collapse over the next few decades under these climate change stressors, with grave consequences for society. Contrary to predictions of near total destruction, this study shows that with effective climate change mitigation, coral reefs will continue to change, but global reef collapse may still be avoidable.

Abstract

Coral reefs are among the most sensitive ecosystems affected by ocean warming and acidification, and are predicted to collapse over the next few decades. Reefs are predicted to shift from net accreting calcifier-dominated systems with exceptionally high biodiversity to net eroding algal-dominated systems with dramatically reduced biodiversity. Here, we present a two-year experimental study examining the responses of entire mesocosm coral reef communities to warming (+2 °C), acidification (−0.2 pH units), and combined future ocean (+2 °C, −0.2 pH) treatments. Contrary to modeled projections, we show that under future ocean conditions, these communities shift structure and composition yet persist as novel calcifying ecosystems with high biodiversity. Our results suggest that if climate change is limited to Paris Climate Agreement targets, coral reefs could persist in an altered state rather than collapse.

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Chapter 7 – Proteomic analysis of ocean acidification stress in bivalves: a synthesis and implications for aquaculture

Published 23 October 2024 Science Closed
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Ocean acidification (OA) effect on various marine organisms, including shell forming bivalves, has been the subject of numerous studies in the past decade. Most of those studies have been focusing on measuring or predicting the developmental, physiological, and ecological consequences. However, OA stress produced in marine organisms is first reflected at cellular level due to altered expression of OA-responsive genes (transcriptome), proteins (proteome), bioactive peptides (peptidome), metabolites (metabolome), and then finally on phenotype. OA studies may take advantage of studying expression pattern of these genes and their products such as proteins, their modifications including “bioactive” small peptides, in response to OA-induced stress. Differentially expressed genes, proteins, and peptides in response to OA may then be used as potential biomarkers for early detection of OA symptoms. Identification of OA-responsive markers is important for climate change friendly aquaculture of bivalves such as oysters and mussels. Development of genome sequencing, mass spectrometry–based proteomics and bioinformatics tools for multiomics analyses revealed molecular response of several bivalves to OA. This chapter discusses those results and identifies knowledge gaps with an emphasis on potential application of proteomics technologies in the identification of molecular mechanisms underpinning OA effects in various marine organisms in the era of genomics and multiomics.

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Chapter 2 – Effects of ocean acidification on the reproduction of marine mollusks

Published 18 October 2024 Science Closed
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Studies suggest that ocean acidification (OA) adversely affects various biological processes in marine organisms, including reproductive capacity, larval development, biocalcification, metabolism, immune and antipredator responses, and behavioral changes. Mollusks, particularly the classes Gastropoda and Bivalvia, are notably sensitive to OA. This chapter also explores the disruption of reproductive processes in mollusks due to elevated CO2 levels, focusing on hatching, fertilization, and larval development, and discusses how genetic expression analysis provides insights into the reproductive impacts of OA on mollusks. Finally, it addresses the adaptive reproductive strategies of mollusks in response to acidification pressures and the cultivation of stress-resistant varieties to cope with changing marine environmental conditions.

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Exploring the leaf regeneration cycles response of Zostera japonica to ocean acidification

Published 16 October 2024 Science Closed
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Highlights

  • The leaf regeneration cycles response of Z. japonica to OA was conducted.
  • 10 d represented a critical response node, 100 d was a critical adaptation point.
  • From response to adaptation, Z. japonica increased production and carbon fixation.
  • High‑carbon fixation of Z. japonica owed to three carbon acquisition strategies.

Abstract

Ocean acidification is one of the major global environmental problems facing humankind today, and it has far-reaching impacts on marine organisms and the entire marine ecosystem. Zostera japonica, an important supporting species of intertidal seagrass beds, exhibits high photosynthetic productivity and plays an important role in the carbon cycle of nearshore waters. However, little is known about the characteristics, processes, and mechanisms of its response to ocean acidification. In this study, we conducted a 120-day acidification experiment in Z. japonica; here, plants underwent four leaf regeneration cycles to reveal the response mechanism of Z. japonica to ocean acidification (OA). We found that acidification significantly affected the seedling stage of Z. japonica, impacting leaf regeneration cycles by altering physiological and molecular responses. In one leaf regeneration cycle, the short-term exposure to CO2 affected the seagrass parameters, such as the regulation of inorganic carbon uptake modes and the regulation of photosynthesis between the dark and light reactions, with the potential to affect the carbon sinks of the marine organisms. The long-term effects on the regulation of antioxidant enzymes and antioxidant metabolites, caused an improvement in the marine life adaptation to OA. In a comparison of the different leaf regeneration cycles, the response pattern of Z. japonica showed an offset of the acidification during the short cycles and an adaption to the acidification during the long cycles. This study revealed the response mechanism of Z. japonica to OA at different time scales and could provide a theoretical basis for accurately assessing the impact of OA on seagrass and the entire seagrass bed ecosystem.

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Coral reef fish visual adaptations to a changing world

Published 15 October 2024 Science Closed
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  1. Coral reef ecosystems show fluctuations in their prevailing light environment in response to both regular (e.g. between seasons) and more prevalent stochastic events (e.g. human-induced sediment runoff). In these shifting environments, phenotypic plasticity provides an essential mechanism for coral reef fishes to adjust their visual capability to meet changing sensory requirements.
  2. Here, we evaluate the growing area of research that highlights the many genetic and ecological mechanisms that affect the plastic responses of coral reef fish vision to environmental cues.
  3. With an increasing number of disturbances in the marine environment, it is critical to understand the extent and limits of visual plasticity under natural and disturbed conditions. With our current knowledge and drawing upon a large body of work in freshwater fishes, we speculate whether coral reef fishes can adapt to the changes to their visual environment and where the limitations could lie.
  4. Whilst coral reef fishes have shown visual adaptations under different light environments, the degree of plasticity is inconsistent between species. Thus, plasticity may not only be functionally significant in maintaining the performance of visually guided behaviours for single species but, more broadly, is likely key to sustaining ecosystem function.
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Mutligenerational chronic exposure to near future ocean acidification in European sea bass (Dicentrarchus labrax): insights into the regulation of the transcriptome in a sensory organ involved in feed intake, the tongue

Published 10 October 2024 Science Closed
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Highlights

  • Multigenerational exposure to OA has no impact on teeth mineralization in Sea bass.
  • Of the 18703 genes expressed in the tongue, 295 exhibited OA-induced regulation.
  • Genes related to cell stress, immune system and fatty acid sensitivity are regulated.
  • OA impacts the branchial expression of p2ry4 gene involved in gustatory system.

Abstract

In this study, we examined the effect of near future ocean acidification (OA) on the transcriptome of a sensory organ in contact with surrounding water, the tongue in adult European sea bass (Dicentrarchus labrax) by mean of RNAseq experiment. We acquired a total of 14.1 Mb quality-trimmed reads covering 18,703 expressed genes from the tongue of fish reared from two generations at actual (pH 8.0 condition) and predicted near-future seawater pH (pH 7.6 condition). Gene ontologies analyses of expressed genes support the evidence that the tongue exhibits biological processes related to the sensory system, tooth mineralization and immune defences among others. Our data revealed only 295 OA-induced regulated genes with 114 up- and 181 down-regulated by OA. Functions over-represented encompass processes involved in organic substance metabolic process, RNA metabolism and especially RNA methylation which, combined with the regulation of some hsp genes expression, suggest a molecular response to stress which might contribute to lingual cell homeostasis under OA. The immune system process is also found enriched within OA-induced regulated genes. With the exception of one fatty acid receptor, known taste perception effectors were not impacted by OA in the tongue. However, a complementary droplet digital PCR approach dedicated to genes involved in gustatory signal transduction revealed the down regulation by OA of pyrimidinergic receptor (p2ry4) transcript expression in the gills of the fish. Combined with scanning electron microscopy analysis, our RNAseq data revealed that OA has no impact on processes related to teeth development and mineralization. Altogether, our data reveal that multigenerational exposure to OA has not a substantially effect on the tongue transcriptome but emphasis should be placed on investigating the potential physiological consequences related to the regulation of genes related to cell stress, immune system and fatty acid sensitivity to conclude on species resilience in face of OA.

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Mitochondrial DNA damage, repair and copy number dynamics of Sclerophytum sp. (Anthozoa: Octocorallia) in response to short-term abiotic oxidative stress

Published 4 October 2024 Science Closed
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Highlights

  • Octocorals possess unique mitochondrial genomes with an intrinsic DNA mismatch repair gene, mtMutS.
  • Short-term thermal and low pH stress cause mtDNA damage and variation in mtDNA copy number in the soft coral Sclerophytum sp.
  • mtMutS gene was significantly upregulated during low pH stress.
  • mtDNA damage caused by H2O2 was quickly reversed, suggesting efficient mtMutS DNA repair activity.Higher mtDNA copy number was associated with lower mtDNA damage.

Abstract

As a consequence of global climate change, the increasing frequency of environmental disturbances and surplus oxidative stress experienced by coral reefs will likely contribute to phase shifts from stony to soft corals. Mitochondrial response to reactive oxygen species (ROS) -induced oxidative damage appears pivotal for bioenergetic adaptation and recovery during environmental stress, partly governed by mitochondrial DNA copy number. Unlike other animals, octocorals possess unique mitogenomes with an intrinsic DNA mismatch repair gene, the mtMutS, that is likely to have a role in mitochondrial response and mtDNA damage recovery. Yet, there is a general lack of stress response studies on octocorals from a mitochondrial perspective. Here we evaluate the mitochondrial response of the octocoral Sclerophytum sp. subjected to acute elevated temperature and low pH, and its putative competence to reverse oxidative mtDNA damage caused by exogenous agents like hydrogen peroxide (H2O2). Temporal changes in mtDNA copy number and mtDNA damage and recovery were monitored. Both short-term thermal and low pH stress applied independently instigated mtDNA damage and affected mtDNA copy number differently, while mtMutS gene was significantly upregulated during low pH stress. mtDNA damage caused by H2O2 insult was observed to be promptly reversed in Sclerophytum sp., and a higher mtDNA copy number was associated with lower mtDNA damage. These findings provide insights into the potential role of mtMutS gene in conferring resilience to octocorals, the relevance of mtDNA copy number, and emphasize the importance of better understanding the mitochondrial stress response of cnidarians in the context of climate change.

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Genome of Halimeda opuntia reveals differentiation of subgenomes and molecular bases of multinucleation and calcification in algae

Published 27 September 2024 Science Closed
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Significance

Coral reef ecosystems are undergoing significant degradation and reorganization due to ocean warming and acidification. Calcareous algae, crucial primary producers and reef-builders, exhibit diverse morphologies, lifestyles, and adaptative strategies. A significant gap exists, however, in deciphering the genetic basis of algae positioned at an evolutionary crossroad from unicellular to multicellular, from intracellular calcifying to extracellular calcification, and from acidification-sensitive to acidification-tolerant. Genome analysis of the green alga Halimeda opuntia and other algae shed light on unique genetic features associated with multinucleation, cell fragment regeneration, extracellular calcification, and tolerance of CO2 increases in seawater. Our findings advance the understanding of how calcareous algae respond to environmental changes and have implications in regenerative biology, plant grafting, and coral reef conservation and restoration.

Abstract

Algae mostly occur either as unicellular (microalgae) or multicellular (macroalgae) species, both being uninucleate. There are important exceptions, however, as some unicellular algae are multinucleate and macroscopic, some of which inhabit tropical seas and contribute to biocalcification and coral reef robustness. The evolutionary mechanisms and ecological significance of multinucleation and associated traits (e.g., rapid wound healing) are poorly understood. Here, we report the genome of Halimeda opuntia, a giant multinucleate unicellular chlorophyte characterized by interutricular calcification. We achieve a high-quality genome assembly that shows segregation into four subgenomes, with evidence for polyploidization concomitant with historical sea level and climate changes. We further find myosin VIII missing in H. opuntia and three other unicellular multinucleate chlorophytes, suggesting a potential mechanism that may underpin multinucleation. Genome analysis provides clues about how the unicellular alga could survive fragmentation and regenerate, as well as potential signatures for extracellular calcification and the coupling of calcification with photosynthesis. In addition, proteomic alkalinity shifts were found to potentially confer plasticity of H. opuntia to ocean acidification (OA). Our study provides crucial genetic information necessary for understanding multinucleation, cell regeneration, plasticity to OA, and different modes of calcification in algae and other organisms, which has important implications in reef conservation and bioengineering.

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Widespread scope for coral adaptation under combined ocean warming and acidification

Published 27 September 2024 Science Closed
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Reef-building coral populations are at serious risk of collapse due to the combined effects of ocean warming and acidification. Nonetheless, many corals show potential to adapt to the changing ocean conditions. Here we examine the broad sense heritability (H2) of coral calcification rates across an ecologically and phylogenetically diverse sampling of eight of the primary reef-building corals across the Indo-Pacific. We show that all eight species exhibit relatively high heritability of calcification rates under combined warming and acidification (0.23–0.56). Furthermore, tolerance to each factor is positively correlated and the two factors do not interact in most of the species, contrary to the idea of trade-offs between temperature and pH sensitivity, and all eight species can co-evolve tolerance to elevated temperature and reduced pH. Using these values together with historical data, we estimate potential increases in thermal tolerance of 1.0–1.7°C over the next 50 years, depending on species. None of these species are probably capable of keeping up with a high global change scenario and climate change mitigation is essential if reefs are to persist. Such estimates are critical for our understanding of how corals may respond to global change, accurately parametrizing modelled responses, and predicting rapid evolution.

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Induction of lipid production through controlled acidification: a transcriptional insight into the metabolism of Scenedesmus obtusiusculus AT-UAM

Published 20 September 2024 Science Closed
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Highlights

  • Maximum lipid content and productivity were 62 % and 85.9 mg L−1d−1, respectively.
  • Controlled acidification altered gene expression during nitrogen depletion.
  • Up-regulation of genes in energy metabolism was observed in the conditions studied.
  • Down-regulation of lipid degradation and carbohydrate synthesis was observed.
  • ANIm analysis confirmed the identity of Scenedesmus obtusiusculus AT-UAM.

Abstract

Scenedesmus obtusiusculus AT-UAM was able to accumulate up to 62 % of lipids when controlled acidification was applied to a nitrogen-deplete culture. Under these conditions, up-regulation of genes related to lipid synthesis and central carbon metabolism (glycolysis, the tricarboxylic acid cycle, and the pentose phosphate pathway) was recorded. Additionally, genes related to photosynthesis were up-regulated in the nitrogen depletion and nitrogen depletion with controlled acidification conditions with respect to the control samples analyzed under nutritional sufficiency. The Pyani program was used to establish pairwise ANI values between reported and annotated NCBI genomes to uphold genomics similarity. ANI analysis confirms the previously observed identity of S. obtusiusculus AT-UAM with the 18S rRNA and ITS2 regions, and also provides a solid framework for understanding the genetic stability and lineage of the strain. Results obtained are encouraging for integrating biofuel production processes and carbon capture technologies. Specifically, the up-regulation of genes related to both lipid synthesis and photosynthesis under controlled conditions indicates the potential of S. obtusiusculus AT-UAM for efficient biofuel production while simultaneously sequestering carbon. These biochemical properties make this strain a promising candidate for sustainable energy solutions and environmental mitigation strategies.

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Evolution of chitin-synthase in molluscs and their response to ocean acidification

Published 17 September 2024 Science Closed
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Highlights

  • The metazoan chitin synthase (CHS) gene family is highly extended in bivalves.
  • CHS gene number is not related to the presence of a mineralized exoskeleton.
  • The tissue distribution of CHS genes is coherent with diverse biological functions.
  • The effect of OA on shell formation is not through a direct action on CHS.

Abstract

Chitin-synthase (CHS) is found in most eukaryotes and has a complex evolutionary history. Research into CHS has mainly been in the context of biomineralization of mollusc shells an area of high interest due to the consequences of ocean acidification. Exploration of CHS at the genomic level in molluscs, the evolution of isoforms, their tissue distribution, and response to environmental challenges are largely unknown. Exploiting the extensive molecular resources for mollusc species it is revealed that bivalves possess the largest number of CHS genes (12–22) reported to date in eukaryotes. The evolutionary tree constructed at the class level of molluscs indicates four CHS Type II isoforms (A-D) probably existed in the most recent common ancestor, and Type II-A (Type II-A-1/Type II-A-2) and Type II-C (Type II-C-1/Type II-C-2) underwent further differentiation. Non-specific loss of CHS isoforms occurred at the class level, and in some Type II (B-D groups) isoforms the myosin head domain, which is associated with shell formation, was not preserved and highly species-specific tissue expression of CHS isoforms occurred. These observations strongly support the idea of CHS functional diversification with shell biomineralization being one of several important functions. Analysis of transcriptome data uncovered the species-specific potential of CHS isoforms in shell formation and a species-specific response to ocean acidification (OA). The impact of OA was not CHS isoform-dependent although in Mytilus, Type I-B and Type II-D gene expression was down-regulated in both M. galloprovincialis and M. coruscus. In summary, during CHS evolution the gene family expanded in bivalves generating a large diversity of isoforms with different structures and with a ubiquitous tissue distribution suggesting that chitin is involved in many biological functions. These findings provide insight into CHS evolution in molluscs and lay the foundation for research into their function and response to environmental changes.

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Effects of ocean acidification on nitrogen metabolism of Skeletonema costatum

Published 16 September 2024 Science Closed
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Ocean acidification (OA), caused by the rising concentration of atmospheric CO2, leads to changes in the marine carbonate system. This, in turn, affects the physiological processes of phytoplankton. In response to increased pCO2 levels, marine microalgae modulate their physiological responses to meet their energy and metabolic requirements. Nitrogen metabolism is a critical metabolic pathway, directly affecting the growth and reproductive capacity of marine microorganisms. Understanding the molecular mechanisms that regulate nitrogen metabolism in microalgae under OA conditions is therefore crucial. This study aimed to investigate how OA affects the expression profiles of key genes in the nitrogen metabolic pathway of the marine diatom Skeletonema costatum. Our findings indicate that OA upregulates key genes involved in the nitrogen metabolic pathway, specifically those related to nitrate assimilation and glutamate metabolism. Moreover, pCO2 has been identified as the predominant factor affecting the expression of these genes, with a more significant impact than pH variations in S. costatum. This research not only advances our understanding of the adaptive mechanisms of S. costatum in response to OA but also provides essential data for predicting the ecological consequences of OA on marine diatoms.

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Nearshore microbial communities of the Pacific Northwest coasts of Canada and the U.S.

Published 6 September 2024 Science Closed
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A survey of marine pelagic coastal microbial communities was conducted over a large geographic latitude range, from Cape Mendocino in northern California USA to Queen Charlotte Sound in British Columbia Canada, during the spring to summer transition. DNA metabarcoding and flow cytometry were used to characterize microbial communities. Physical and chemical oceanography indicated moderate conditions during the survey with no widespread upwelling, marine heat wave, or other extreme conditions. However, four locations displayed features approaching acidified conditions: Heceta Head, Newport, Copalis Beach, and Cape Flattery. Although bacterial and archaeal communities at the Juan de Fuca canyon and northward had high similarity, those south of the Juan de Fuca canyon were well differentiated from each other. In contrast, eukaryotic microbial communities exhibited stronger geographic differentiation than bacterial and archaeal communities across the extent of the survey. Seawater parameters that were best predictors of bacterial and archaeal community structure were temperature, pH, and dissolved inorganic nutrients (nitrate, phosphate, silicate), while those that were best predictors of eukaryotic microbial community structure were salinity, dissolved oxygen, total alkalinity, and dissolved inorganic nutrients (nitrite, silicate). Although five bacterial and archaeal indicators for potentially corrosive waters were identified (Colwellia, Nitrosopumilus, Nitrosopelagicus, Sup05 cluster, Sva0996 marine group), no eukaryotic microbial indicators were found. Potentially pathogenic taxa detected in the survey included four disease-causing bacteria for mammals, finfish, and/or shellfish (Coxiella, Flavobacterium, Francisella, Tenacibaculum), sixteen genera of microalgae capable of producing biotoxins, and fifteen parasitic species. This study demonstrates the value of coordinating microbial sampling and analysis with broad-scale oceanographic surveys to generate insights into community structures of these important pelagic trophic levels.

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Transcriptional plasticity and environmental change in marine fishes

Published 14 August 2024 Science Closed
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How organisms respond to environmental changes is crucial for their survival, especially in the face of rapid climate change. One of the mechanisms facilitating acclimation to novel environments is phenotypic plasticity, the ability of a single genotype to produce multiple phenotypes in different environments. Phenotypic plastic responses are influenced by various factors like environmental stability, parental experiences, and genetic factors and can be classified as acute, developmental, or intergenerational responses based on the timeframe involved. This dissertation investigates molecular basis of all these three types of plasticity in marine fishes in response to changes in their physical and social environment. Physical environmental changes mediated by ocean acidification negatively affects various fish species however, some thrive in naturally occurring CO2 seeps, potentially benefiting from habitat shifts induced by reduced pH levels. In the anemone goby, a species that has increased population density at CO2 seeps in Vulcano Island, Italy, differential regulation of key pathways resulting in acclimation to acidified waters, potentially mediated by developmental plasticity, were identified. While overall increase in CO2 levels elicits molecular responses in fish, the stability of CO2 concentration is crucial. Exposure of spiny damselfish to both stable and fluctuating CO2 conditions resulted in loss of natural rhythmic splicing events however, fish in fluctuating CO2 conditions alone showed increased capability of time-dependent regulation of splicing events in genes associated with synaptic plasticity and neuronal functioning. This might be mediated by the observed amplitude change in circadian rhythm genes in the fluctuating CO2 treatment enabling the fish to coordinate biological processes in anticipation of periodic changes in CO2 levels. Furthermore, the spiny damselfish showed molecular signatures of intergenerational plasticity to ocean acidification conditions, particularly in the brain and liver. Specifically, within-generation transcriptional responses indicating altered neural signaling in the brain and metabolic depression in the liver returned to control levels when parents were also exposed to elevated CO2 conditions. Interestingly, these signatures indicating intergenerational acclimation were predominant in offspring of parents behaviourally tolerant to elevated CO2 conditions. This shows that parental phenotype and parental environment play a role in mediating offspring transcriptional response to ocean acidification. An organisms’ environment encompasses not only its physical environment but also the social environment. The last chapter of this thesis explores molecular processes underlying plastic responses of organisms to changes in their social environment by using the anemone-anemonefish mutualistic system. Significant changes in the transcriptome of both species were identified during the acclimation period of mutualistic association. Anemonefish showed activation of sensory pathways in response to cues received from the anemone, while the anemone showed upregulation of genes associated with nematocyst discharge and venom production, potentially in response to sensing fish movements. This study reveals an interplay of molecular events underlying mutualistic association in both partners. Taken together, the findings reported in this thesis furthers our understanding of the molecular processes underlying various types of phenotypic plastic responses to environmental changes and provides key information regarding the acclimation potential of marine fishes to global change.

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miRNA-mRNA joint analysis reveals the response mechanism of Ruditapes philippinarum to CO2-driven ocean acidification

Published 9 August 2024 Science Closed
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Highlights

  • Combined mRNA-miRNA analysis of the effects of seawater acidification on Philippine clams.
  • The response of Philippine clams to seawater acidification is mainly reflected in the immune response.
  • Philippine clams alleviate the stress caused by seawater acidification by regulating the expression of miR-184–3p.

Abstract

To explore the response mechanism of Ruditapes philippinarum to CO2-driven ocean acidification, 540 clams with healthy physique and consistent specifications were randomly divided into 3 groups, with 3 repetitions in each group, and 60 specimens in each repetition. Stress tests were then conducted under different pH conditions (8.0, 7.2, 6.4). After 96 hours of stress, gill tissues were collected for mRNA-seq and miRNA-seq analysis. The results show that when Philippine clams are stimulated by seawater acidification, the gene expression levels in the glycine, serine and threonine metabolism and arachidonic acid metabolism pathways in their gill tissue are increased, thereby inducing the occurrence of inflammation in the body and reducing the body’s immunity and disease resistance. Philippine clams can also alleviate the adverse effects of seawater acidification on the body by regulating the expression of genes such as miR-184–3p. And when Philippine clams are stimulated by seawater acidification, they can also regulate the interferon-inducible GTPase (IIGP) by regulating the expression of Novel-m0002–3p, which ultimately affects the cellular defense mechanism, material transport ability, and ion exchange ability with the external environment.

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Hepatic transcriptomic responsiveness of Polar Cod, Boreogadus saida, to ocean acidification and warming

Published 6 August 2024 Science Closed
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Background: This study was part of a larger comprehensive project (BIOACID) addressing the physiological resilience of Polar cod, Boreogadus saida, to ocean acidification and global warming and aimed to unravel underlying molecular mechanisms of the observed physiological responses. Methods: Fish were acclimated long-term to three CO2 concentrations comprising control conditions (390 ppm) and two projected climate scenarios (780 ppm and 1170 ppm). Each CO2 treatment was combined with four temperatures: 0, 3, 6, and 8 °C. Here, we focused on the hepatic transcriptomic profiles from these previously physiologically characterized fish. Results: Generally, we did not detect signs of a classical stress response. Consistent with functional observations, warming induced much stronger molecular responses compared to elevated PCO2, but an interaction between both factors existed to some extent. Gene ontology analysis revealed a strong response in lipid, amino acid, and protein metabolism. With increasing temperature, we observed a shift away from lipid metabolism, while carbohydrate metabolic pathways remained stable. Conclusions: Although we found Polar cod to be quite resilient to ocean acidification, temperature will remain a critical parameter for this valuable Arctic keystone species, and the question remains as to whether the observed acclimation strategies can be implemented in its natural habitat, especially when food supply is limited.

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Assessing the effects of warming and carbonate chemistry parameters on marine microbes in the Gulf of Mexico through basin-scale DNA metabarcoding

Published 2 August 2024 Science Closed
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Ocean acidification and warming threaten marine life, yet the impact of these processes on microbes remains unclear. Here, we performed basin-scale DNA metabarcoding of prokaryotes (16S V4–V5) and protists (18S V9) in the Gulf of Mexico and applied generalized linear models to reveal group-specific environmental correlates of functionally diverse microbes. Models supported prior physiological trends for some groups, like positive temperature effects on SAR11 and SAR86, and a positive effect of pH on Prochlorococcus that implied a negative response to decreasing pH. New insights were revealed for protists, like Syndiniales and Sagenista (e.g., positive pH effects), which offset positive relationships with temperature and reinforced the importance of considering multiple stressors simultaneously. Indicator analysis revealed phytoplankton, like Ostreococcus sp. and Emiliania huxleyi, that were associated with more acidic waters and may reflect candidate indicators of ocean change. Our findings highlight the need for sustained microbial sampling in marine systems, with implications for carbon export, nutrient cycling, and ecosystem health.

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A chromosome-scale Mytilus edulis genome assembly for aquaculture, marine ecology, and evolution

Published 25 July 2024 Science Closed
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The smooth-shelled blue mussel, Mytilus edulis is part of the Mytilus species complex, encompassing at least three putative species: M. edulis, Mytilus galloprovincialis, and Mytilus trossulus. These three species occur on both sides of the Atlantic and hybridize in nature, and both M. edulis and M. galloprovincialis are important aquaculture species. They are also invasive species in many parts of the world. Here, we present a chromosome-level assembly of M. edulis. We used a combination of PacBio sequencing and Dovetail’s Omni-C technology to generate an assembly with 14 long scaffolds containing 94% of the predicted length of the M. edulis genome (1.6 out of 1.7 Gb). Assembly statistics were as follows: total length = 1.65 Gb, N50 = 116 Mb, L50 = 7, and L90 = 13. BUSCO analysis showed 92.55% eukaryote BUSCOs identified. AB-Initio annotation using RNA-seq from mantle, gills, muscle, and foot predicted 47,128 genes. These gene models were combined with IsoSeq validation resulting in 45,379 full CDS protein sequences and 129,708 isoforms. Using GBS and shotgun sequencing, we also sequenced several eastern Canadian populations of Mytilus to characterize single-nucleotide as well as structural variance. This high-quality genome for M. edulis provides a platform to develop tools that can be used in breeding, molecular ecology and evolution to address questions of both commercial and environmental perspectives.

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Organic matter decay and bacterial community succession in mangroves under simulated climate change scenarios

Published 24 July 2024 Science Closed
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Mangroves are coastal environments that provide resources for adjacent ecosystems due to their high productivity, organic matter decomposition, and carbon cycling by microbial communities in sediments. Since the industrial revolution, the increase of Greenhouse Gases (GHG) released due to fossil fuel burning led to many environmental abnormalities such as an increase in average temperature and ocean acidification. Based on the hypothesis that climate change modifies the microbial diversity associated with decaying organic matter in mangrove sediments, this study aimed to evaluate the microbial diversity under simulated climate change conditions during the litter decomposition process and the emission of GHG. Thus, microcosms containing organic matter from the three main plant species found in mangroves throughout the State of São Paulo, Brazil (Rhizophora mangle, Laguncularia racemosa, and Avicennia schaueriana) were incubated simulating climate changes (increase in temperature and pH). The decay rate was higher in the first seven days of incubation, but the differences between the simulated treatments were minor. GHG fluxes were higher in the first ten days and higher in samples under increased temperature. The variation in time resulted in substantial impacts on α-diversity and community composition, initially with a greater abundance of Gammaproteobacteria for all plant species despite the climate conditions variations. The PCoA analysis reveals the chronological sequence in β-diversity, indicating the increase of Deltaproteobacteria at the end of the process. The GHG emission varied in function of the organic matter source with an increase due to the elevated temperature, concurrent with the rise in the Deltaproteobacteria population. Thus, these results indicate that under the expected climate change scenario for the end of the century, the decomposition rate and GHG emissions will be potentially higher, leading to a harmful feedback loop of GHG production. This process can happen independently of an impact on the bacterial community structure due to these changes.

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Impact of ocean acidification on the intestinal microflora of Sinonovacula constricta

Published 23 July 2024 Science Closed
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The intestinal microflora of host, vital for nutrient absorption and immune regulation, can experience dysbiosis under environmental stress, thereby potentially enhancing host susceptibility to pathogenic invasion.  The impact of ocean acidification on bivalves is substantial, yet its effects on the intestinal microflora remain poorly understood. This study employed high-throughput 16S rRNA sequencing technology to investigate the variations in the intestinal microflora of Sinonovacula constricta between the control group (CON) and the seawater acidification group (OA) at different time points.After exposure to OA, changes in the composition of the intestinal microflora of S. constricta were observed, with no significant difference in α-diversity between the acidified and control groups. At the phylum level, there was an increase in the abundance of Proteobacteria, while Cyanobacteria decreased in the OA14d and OA35d groups. Additionally, the relative abundance of Firmicutes increased in the OA7d and OA35d groups. At the genus level, the relative content of Pseudomonas was lower than that in the control group, while the relative content of Flavobacterium, Acinetobacter, and Enterobacter showed a gradual increasing trendin the OA14d and OA35d groups.. LEfSe analysis identified Serpens as   discriminative biomarkers in the OA7d group, while Enterobacteriales, Rhodobacteraceae and Martvita were biomarker in the OA14d group, and Serpens, Acidibacteria and Aeromonadaceae were biomarker in the OA35d group. Functional prediction results indicated significant enrichment in metabolic pathways at different time points following ocean acidification stress… The pathways involved in biosynthesis in the OA14d group and in sucrose degradation in the OA35d group were significantly disrupted. These results suggest that OA stress can have adverse effects on the intestinal microflora of S. constricta, but it does not cause obvious damage to the digestive system. This study provides new insights into the intestinal microflora of marine bivalves under acidification stress.

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