Posts Tagged 'molecular biology'

Diversity and stability of coral endolithic microbial communities at a naturally high pCO2 reef

The health and functioning of reef-building corals is dependent on a balanced association with prokaryotic and eukaryotic microbes. The coral skeleton harbours numerous endolithic microbes, but their diversity, ecological roles and responses to environmental stress, including ocean acidification (OA), are not well characterized. This study tests whether pH affects the diversity and structure of prokaryotic and eukaryotic algal communities associated with skeletons of Porites spp. using targeted amplicon (16S rRNA gene, UPA and tufA) sequencing. We found that the composition of endolithic communities in the massive coral Porites spp. inhabiting a naturally high pCO2 reef (avg. pCO2 811 μatm) is not significantly different from corals inhabiting reference sites (avg. pCO2 357 μatm), suggesting that these microbiomes are less disturbed by OA than previously thought. Possible explanations may be that the endolithic microhabitat is highly homeostatic or that the endolithic micro-organisms are well adapted to a wide pH range. Some of the microbial taxa identified include nitrogen-fixing bacteria (Rhizobiales and cyanobacteria), algicidal bacteria in the phylum Bacteroidetes, symbiotic bacteria in the family Endozoicomoniaceae, and endolithic green algae, considered the major microbial agent of reef bioerosion. Additionally, we test whether host species has an effect on the endolithic community structure. We show that the endolithic community of massive Porites spp. is substantially different and more diverse than that found in skeletons of the branching species Seriatopora hystrix and Pocillopora damicornis. This study reveals highly diverse and structured microbial communities in Porites spp. skeletons that are possibly resilient to OA.

Continue reading ‘Diversity and stability of coral endolithic microbial communities at a naturally high pCO2 reef’

Target gene expression studies on Platynereis dumerilii and Platynereis cfr massiliensis at the shallow CO2 vents off Ischia, Italy

Many studies predict negative effects of ocean acidification on marine organisms, potentially leading to loss of biodiversity and ecosystem function. Research on species inhabiting naturally high pCO2 environments, such as volcanic CO2 vents, offers an opportunity to understand the molecular mechanisms involved in high pCO2 regulation. Here we investigate the relative expression of NADH dehydrogenase, sodium-hydrogen antiporter (NHE), carbonic anhydrase (CA) and paramyosin genes from two non-calcifying sibling Nereididae polychaetes species, Platynereis cfr massiliensis, collected in the shallow CO2 vents off Ischia (Italy; 40°43′52.0″N 13°57′46.2″E and 40°43′55.5″N 13°57′48.4″E), and P. dumerilii collected in an area nearby (40°43′34.51″N; 13°57′35.7″E). The origin of the worms was confirmed using restriction enzyme digest. NHE and paramyosin expressions were both significantly increased in P. dumerilii relative to the P. cfr massiliensis vent populations. Furthermore, a seven day laboratory transfer experiment to lower/higher pCO2 conditions was conducted to investigate the effects on the short term gene expression. The transfer experiment of the non-vent worms to high pCO2 conditions showed no significant effect on any of the genes analysed, however, two genes (NADH dehydrogenase and NHE) from worms of the vent population were significantly down-regulated under low pCO2. These findings will help to gain further insights into the cellular mechanisms affected by pCO2 changes in two polychaete species.

Continue reading ‘Target gene expression studies on Platynereis dumerilii and Platynereis cfr massiliensis at the shallow CO2 vents off Ischia, Italy’

Molecular responses of sponges to climate change

We live in a time of concern regarding predicted environmental damage due to climate change, i.e. sea temperature increase and a reduction in ocean pH. Such changes will have severe consequences for at least some marine organisms. Developments in molecular and genomic techniques allow for genome-wide comparisons of genes and proteins that may be impacted by such changes with knock-on consequences for cell and organism function. Understanding of impacts at the molecular level is important to understand how organisms will respond to changes and to develop conservation strategies accordingly. Despite sponges having a very simple body plan, they possess gene diversity and genome complexity that mirrors other metazoa. The cellular stress response and adaptation of sponges to increased temperature and low pH are varied and diverse with many genes implicated and their expression patterns complex. Survival thresholds differ between species in their tolerance to temperature increase and lowering of ocean pH. The expression patterns of a variety of genes have been investigated particularly with regard to change in temperature but in few sponge species. Likewise genome and transcriptome data exists for few species, and even fewer studies focus on applying these approaches to stress response. Despite the requirement for more studies in this area, existing data suggests that some sponge species will be severely impacted if climate change predictions hold, while other species will adapt and thrive.

Continue reading ‘Molecular responses of sponges to climate change’

Responses of photosynthesis and CO2 concentrating mechanisms of marine crop Pyropia haitanensis thalli to large pH variations at different time scales


• A pH of 4, 5, and 9 resulted in the death of Pyropia haitanensis thalli.
• A pH of 6 and 7 increased the growth of Pyropia haitanensis thalli.
• The CO2 concentrating mechanisms may play a role in intracellular pH homeostasis.
• Actual pH variation needs to be considered in relative studies.

Wild and cultivated populations of Pyropia haitanensis have frequently experienced extremely low pH conditions in the last few decades. This could potentially threaten the development of the aquaculture of this economically important marine crop. To gain a broader perspective, we investigated the short- (4 h) and long- (7 days) term responses of CO2 concentrating mechanisms (CCMs) of P. haitanensis thalli to large variations in pH. Our study found that a pH of 4 and 5, which mimicked the decreased pH caused by acid rain, resulted in decreased photosynthesis and respiration while leading to the death of P. haitanensis thalli. Thus, acid rain would result in a decline in P. haitanensis production and threaten wild seaweed sources. However, a pH of 6 and 7 enhanced the growth of P. haitanensis thalli by > 30%, mainly because increased CO2 levels favored photosynthesis, while the algae need to effectively maintain intracellular pH homeostasis to support rapid growth rates. The contributions of extracellular carbonic anhydrases (eCAs) to photosynthetic rates remained at > 77% when pH ≥ 7, regardless of the treatment time. However, at pH 6, the contribution of eCAs to photosynthesis increased from 25% for a short-term treatment to 66% for a long-term treatment. Thus, except for work on carbon assimilation, this study proposes that the CCMs component involved in the movement and metabolism of inorganic carbon may play an important role in pH homeostasis. In addition, pH 9 also led to the death of P. haitanensis thalli, which is consistent with observations of the natural distribution of this algae and hints that P. haitanensis thalli prefer to use inorganic carbon via eCAs when pH ≥ 7. The present study suggested that the actual variation in pH experienced by marine organisms needs to be considered in the experimental design of related studies.

Continue reading ‘Responses of photosynthesis and CO2 concentrating mechanisms of marine crop Pyropia haitanensis thalli to large pH variations at different time scales’

Nutrient loading fosters seagrass productivity under ocean acidification

The effects of climate change are likely to be dependent on local settings. Nonetheless, the compounded effects of global and regional stressors remain poorly understood. Here, we used CO2 vents to assess how the effects of ocean acidification on the seagrass, Posidonia oceanica, and the associated epiphytic community can be modified by enhanced nutrient loading. P. oceanica at ambient and low pH sites was exposed to three nutrient levels for 16 months. The response of P. oceanica to experimental conditions was assessed by combining analyses of gene expression, plant growth, photosynthetic pigments and epiphyte loading. At low pH, nutrient addition fostered plant growth and the synthesis of photosynthetic pigments. Overexpression of nitrogen transporter genes following nutrient additions at low pH suggests enhanced nutrient uptake by the plant. In addition, enhanced nutrient levels reduced the expression of selected antioxidant genes in plants exposed to low pH and increased epiphyte cover at both ambient and low pH. Our results show that the effects of ocean acidification on P. oceanica depend upon local nutrient concentration. More generally, our findings suggest that taking into account local environmental settings will be crucial to advance our understanding of the effects of global stressors on marine systems.

Continue reading ‘Nutrient loading fosters seagrass productivity under ocean acidification’

The impact of elevated CO2 on Prochlorococcus and microbial interactions with ‘helper’ bacterium Alteromonas

Prochlorococcus is a globally important marine cyanobacterium that lacks the gene catalase and relies on ‘helper’ bacteria such as Alteromonas to remove reactive oxygen species. Increasing atmospheric CO2 decreases the need for carbon concentrating mechanisms and photorespiration in phytoplankton, potentially altering their metabolism and microbial interactions even when carbon is not limiting growth. Here, Prochlorococcus (VOL4, MIT9312) was co-cultured with Alteromonas (strain EZ55) under ambient (400p.p.m.) and elevated CO2 (800p.p.m.). Under elevated CO2, Prochlorococcus had a significantly longer lag phase and greater apparent die-offs after transfers suggesting an increase in oxidative stress. Whole-transcriptome analysis of Prochlorococcus revealed decreased expression of the carbon fixation operon, including carboxysome subunits, corresponding with significantly fewer carboxysome structures observed by electron microscopy. Prochlorococcus co-culture responsive gene 1 had significantly increased expression in elevated CO2, potentially indicating a shift in the microbial interaction. Transcriptome analysis of Alteromonas in co-culture with Prochlorococcus revealed decreased expression of the catalase gene, known to be critical in relieving oxidative stress in Prochlorococcus by removing hydrogen peroxide. The decrease in catalase gene expression was corroborated by a significant ~6-fold decrease in removal rates of hydrogen peroxide from co-cultures. These data suggest Prochlorococcus may be more vulnerable to oxidative stress under elevated CO2 in part from a decrease in ecosystem services provided by heterotrophs like Alteromonas. This work highlights the importance of considering microbial interactions in the context of a changing ocean.

Continue reading ‘The impact of elevated CO2 on Prochlorococcus and microbial interactions with ‘helper’ bacterium Alteromonas’

Transcriptomic response of the Antarctic pteropod Limacina helicina antarctica to ocean acidification

Ocean acidification (OA), a change in ocean chemistry due to the absorption of atmospheric CO2 into surface oceans, challenges biogenic calcification in many marine organisms. Ocean acidification is expected to rapidly progress in polar seas, with regions of the Southern Ocean expected to experience severe OA within decades. Biologically, the consequences of OA challenge calcification processes and impose an energetic cost.

In order to better characterize the response of a polar calcifier to conditions of OA, we assessed differential gene expression in the Antarctic pteropod, Limacina helicina antarctica. Experimental levels of pCO2 were chosen to create both contemporary pH conditions, and to mimic future pH expected in OA scenarios. Significant changes in the transcriptome were observed when juvenile L. h. antarctica were acclimated for 21 days to low-pH (7.71), mid-pH (7.9) or high-pH (8.13) conditions. Differential gene expression analysis of individuals maintained in the low-pH treatment identified down-regulation of genes involved in cytoskeletal structure, lipid transport, and metabolism. High pH exposure led to increased expression and enrichment for genes involved in shell formation, calcium ion binding, and DNA binding. Significant differential gene expression was observed in four major cellular and physiological processes: shell formation, the cellular stress response, metabolism, and neural function. Across these functional groups, exposure to conditions that mimic ocean acidification led to rapid suppression of gene expression.

Results of this study demonstrated that the transcriptome of the juvenile pteropod, L. h. antarctica, was dynamic and changed in response to different levels of pCO2. In a global change context, exposure of L. h. antarctica to the low pH, high pCO2 OA conditions resulted in a suppression of transcripts for genes involved in key physiological processes: calcification, metabolism, and the cellular stress response. The transcriptomic response at both acute and longer-term acclimation time frames indicated that contemporary L. h. antarctica may not have the physiological plasticity necessary for adaptation to OA conditions expected in future decades. Lastly, the differential gene expression results further support the role of shelled pteropods such as L. h. antarctica as sentinel organisms for the impacts of ocean acidification.

Continue reading ‘Transcriptomic response of the Antarctic pteropod Limacina helicina antarctica to ocean acidification’

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Ocean acidification in the IPCC AR5 WG II

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