INORGANIC CARBON ACQUISITION BY CHRYSOPHYTES(1)

Rapid diversification of a free-living protist is driven by adaptation to climate and habitat

Microbial eukaryotes (protists) have major functional roles in aquatic ecosystems, including the biogeochemical cycling of elements as well as occupying various roles in the food web. Despite their importance for ecosystem function, the factors that drive diversification in protists are not known. Here, we aimed to identify the factors that drive differentiation and, subsequently, speciation in a free-living protist, Synura petersenii (Chrysophyceae). We sampled five different geographic areas and utilized population genomics and quantitative trait analyses. Habitat and climate were the major drivers of diversification on the local geographical scale, while geography played a role over longer distances. In addition to conductivity and temperature, precipitation was one of the most important environmental drivers of differentiation. Our results imply that flushing episodes (floods) drive microalgal adaptation to different niches, highlighting the potential for rapid diversification in protists.

Browning affects pelagic productivity in northern lakes by surface water warming and carbon fertilization

Global change impacts important environmental drivers for pelagic gross primary production (GPP) in northern lakes, such as temperature, light, nutrient, and inorganic carbon availability. Separate and/or synergistic impacts of these environmental drivers on pelagic GPP remain largely unresolved. Here, we assess key drivers of pelagic GPP by combining detailed depth profiles of summer pelagic GPP with environmental and climatic data across 45 small and shallow lakes across northern Sweden (20 boreal, 6 subarctic, and 19 arctic lakes). We found that across lakes summer pelagic GPP was strongest associated with lake water temperatures, lake carbon dioxide (CO₂ ) concentrations impacted by lake water pH, and further moderated by dissolved organic carbon (DOC) concentrations influencing light and nutrient conditions. We further used this dataset to assess the extent of additional DOC-induced warming of epilimnia (here named internal warming), which was especially pronounced in shallow lakes (decreasing 0.96°C for every decreasing m in average lake depth) and increased with higher concentrations of DOC. Additionally, the total pools and relative proportion of dissolved inorganic carbon and DOC, further influenced pelagic GPP with drivers differing slightly among the boreal, subarctic and Arctic biomes. Our study provides novel insights in that global change affects pelagic GPP in northern lakes not only by modifying the organic carbon cycle and light and nutrient conditions, but also through modifications of inorganic carbon supply and temperature. Considering the large-scale impacts and similarities of global warming, browning and recovery from acidification of lakes at higher latitudes throughout the northern hemisphere, these changes are likely to operate on a global scale.

Evidence for evolutionary adaptation of mixotrophic nanoflagellates to warmer temperatures

Mixotrophs, organisms that combine photosynthesis and heterotrophy to gain energy, play an important role in global biogeochemical cycles. Metabolic theory predicts that mixotrophs will become more heterotrophic with rising temperatures, potentially creating a positive feedback loop that accelerates carbon dioxide accumulation in the atmosphere. Studies testing this theory have focused on phenotypically plastic (short-term, non-evolutionary) thermal responses of mixotrophs. However, as small organisms with short generation times and large population sizes, mixotrophs may rapidly evolve in response to climate change. Here, we present data from a 3-year experiment quantifying the evolutionary response of two mixotrophic nanoflagellates to temperature. We found evidence for adaptive evolution (increased growth rates in evolved relative to acclimated lineages) in the obligately phototrophic strain, but not in the facultative phototroph. All lineages showed trends of increased carbon use efficiency, flattening of thermal reaction norms, and a return to homeostatic gene expression. Generally, mixotrophs evolved reduced photosynthesis and higher grazing with increased temperatures, suggesting that evolution may act to exacerbate mixotrophs' effects on global carbon cycling.

Mitochondrial phosphoenolpyruvate carboxylase contributes to carbon fixation in the diatom Phaeodactylum tricornutum at low inorganic carbon concentrations

Photosynthetic carbon fixation is often limited by CO₂ availability, which led to the evolution of CO₂ concentrating mechanisms (CCMs). Some diatoms possess CCMs that employ biochemical fixation of bicarbonate, similar to C₄ plants, but whether biochemical CCMs are commonly found in diatoms is a subject of debate. In the diatom Phaeodactylum tricornutum, phosphoenolpyruvate carboxylase (PEPC) is present in two isoforms, PEPC1 in the plastids and PEPC2 in the mitochondria. We used real-time quantitative polymerase chain reaction, Western blots, and enzymatic assays to examine PEPC expression and PEPC activity, under low and high concentrations of dissolved inorganic carbon (DIC). We generated and analyzed individual knockout cell lines of PEPC1 and PEPC2, as well as a PEPC1/2 double-knockout strain. While we could not detect an altered phenotype in the PEPC1 knockout strains at ambient, low or high DIC concentrations, PEPC2 and the double-knockout strains grown under ambient air or lower DIC availability conditions showed reduced growth and photosynthetic affinity for DIC while behaving similarly to wild-type (WT) cells at high DIC concentrations. These mutants furthermore exhibited significantly lower ¹³ C/¹² C ratios compared to the WT. Our data imply that in P. tricornutum at least parts of the CCM rely on biochemical bicarbonate fixation catalyzed by the mitochondrial PEPC2.

Evolutionary trends in RuBisCO kinetics and their co-evolution with CO2 concentrating mechanisms

RuBisCO-catalyzed CO₂ fixation is the main source of organic carbon in the biosphere. This enzyme is present in all domains of life in different forms (III, II, and I) and its origin goes back to 3500 Mya, when the atmosphere was anoxygenic. However, the RuBisCO active site also catalyzes oxygenation of ribulose 1,5-bisphosphate, therefore, the development of oxygenic photosynthesis and the subsequent oxygen-rich atmosphere promoted the appearance of CO₂ concentrating mechanisms (CCMs) and/or the evolution of a more CO₂ -specific RuBisCO enzyme. The wide variability in RuBisCO kinetic traits of extant organisms reveals a history of adaptation to the prevailing CO₂ /O₂ concentrations and the thermal environment throughout evolution. Notable differences in the kinetic parameters are found among the different forms of RuBisCO, but the differences are also associated with the presence and type of CCMs within each form, indicative of co-evolution of RuBisCO and CCMs. Trade-offs between RuBisCO kinetic traits vary among the RuBisCO forms and also among phylogenetic groups within the same form. These results suggest that different biochemical and structural constraints have operated on each type of RuBisCO during evolution, probably reflecting different environmental selective pressures. In a similar way, variations in carbon isotopic fractionation of the enzyme point to significant differences in its relationship to the CO₂ specificity among different RuBisCO forms. A deeper knowledge of the natural variability of RuBisCO catalytic traits and the chemical mechanism of RuBisCO carboxylation and oxygenation reactions raises the possibility of finding unrevealed landscapes in RuBisCO evolution.

Comparative Plastid Genomics of Non-Photosynthetic Chrysophytes: Genome Reduction and Compaction

Spumella-like heterotrophic chrysophytes are important eukaryotic microorganisms that feed on bacteria in aquatic and soil environments. They are characterized by their lack of pigmentation, naked cell surface, and extremely small size. Although Spumella-like chrysophytes have lost their photosynthetic ability, they still possess a leucoplast and retain a plastid genome. We have sequenced the plastid genomes of three non-photosynthetic chrysophytes, Spumella sp. Baeckdong012018B8, Pedospumella sp. Jangsampo120217C5 and Poteriospumella lacustris Yongseonkyo072317C3, and compared them to the previously sequenced plastid genome of "Spumella" sp. NIES-1846 and photosynthetic chrysophytes. We found the plastid genomes of Spumella-like flagellates to be generally conserved with respect to genome structure and housekeeping gene content. We nevertheless also observed lineage-specific gene rearrangements and duplication of partial gene fragments at the boundary of the inverted repeat and single copy regions. Most gene losses correspond to genes for proteins involved in photosynthesis and carbon fixation, except in the case of petF. The newly sequenced plastid genomes range from ~55.7 kbp to ~62.9 kbp in size and share a core set of 45 protein-coding genes, 3 rRNAs, and 32 to 34 tRNAs. Our results provide insight into the evolutionary history of organelle genomes via genome reduction and gene loss related to loss of photosynthesis in chrysophyte evolution.

Subtropical freshwater phytoplankton show a greater response to increased temperature than to increased pCO2

Global increases in atmospheric CO₂ and temperatures will impact aquatic systems, with freshwater habitats being affected. Some studies suggest that these conditions will promote cyanobacterial dominance. There is a need for a clearer picture of how algal species and strains within species will respond to higher temperatures and CO₂, especially in combination. This study examined two chlorophytes (Monoraphidium and Staurastrum), and two strains of the cyanobacterium Raphidiopsis raciborskii (straight S07 and coiled C03), to determine how the combination of higher temperature and CO₂ levels will affect their growth and maximum cell concentrations. Continuous cultures were used to compare the steady state cell concentrations at 28 °C and 30 °C, and CO₂ partial pressures (pCO₂), 400 and 750 ppm for all cultures, and in addition 1000 ppm at 28 °C for R. raciborskii strains. This study showed that, for all species, water temperature had a greater effect than higher pCO₂ on cell concentrations. There were clear differences in response between the chlorophyte species, with Monoraphidium preferring 28 °C and Staurastrum preferring 30 °C. There were also differences in response of the R. raciborskii strains to increasing temperature and pCO₂, with S07 having a greater increase in cell concentration. Genome analysis of R. raciborskii showed that the straight strain has five additional carbon acquisition genes (β-CA, chpY, cmpB, cmpD and NdhD4), indicative of increased carbon metabolism. These differences in the strains' response to elevated pCO₂ will lead to changes in the species population structure and distribution in the water column. This study shows that it is important to examine the effects of both pCO₂ and temperature, and to consider strain variation, to understand how species composition of natural systems may change under future climate conditions.

Carbon limitation of lake productivity

Phytoplankton productivity in lakes controls the rate of synthesis of organic matter that drives energy flow through the food webs and regulates the transparency and oxygen conditions in the water. Limitation of phytoplankton productivity and biomass by nutrients and light availability is an established paradigm for lake ecosystems, whereas invasion of atmospheric CO2 has been assumed to cover the high demands of dissolved inorganic carbon (DIC) during intense organic productivity. We challenge this paradigm, and show up to a 5-fold stimulation of phytoplankton productivity and biomass in outdoor mesocosms enriched with DIC, compared to mesocosms with lower DIC concentrations. High DIC supported phytoplankton productivity by direct algal uptake of bicarbonate, through the release of CO2 coupled to calcification and by inducing high pH that greatly enhances atmospheric CO2 invasion. Comparisons of 204 natural Danish lakes supported mesocosm experiments showing higher phytoplankton biomass and pH levels in hard water than soft water lakes for the same nutrient and light availabilities. The most productive lakes are nutrient-rich, hard water lakes that attain surface pHs of 10-11 and chemically enhance atmospheric CO2 uptake 10-15-fold. Our results will help understand natural variations of lake productivity along gradients in nutrients, DIC and pH.

Carbon acquisition characteristics of six microalgal species isolated from a subtropical reservoir: potential implications for species succession

CO₂ levels in freshwater systems can fluctuate widely, potentially influencing photosynthetic rates and growth of phytoplankton. Given the right conditions, this can lead to bloom formation and affect water quality. This study investigated the acquisition of dissolved inorganic carbon (DIC) by six species of microalgae, a cyanobacterium Cylindrospermopsis raciborskii, the diatoms Cyclotella sp., Nitzschia sp., and the green algae Stichococcus sp., Staurastrum sp., and Monoraphidium sp., all isolated from a subtropical reservoir in Australia. Carbon acquisition characteristics, specifically the affinity for DIC, internal pH, and internal DIC concentrations were measured. Affinities for CO₂ ( K0.5(CO2) ) ranged between 0.7 and 6 μM CO₂ . This was considerably lower than air-equilibrated surface water CO₂ concentrations, and below reported affinities for CO₂ of RuBisCO suggesting operation of active carbon dioxide concentrating mechanisms (CCMs) in all species. Internal pH was lowest for Cyclotella sp. at 7.19, and highest for Staurastrum sp., at 7.71. At 180 μM external DIC, ratios of internal:external CO₂ ranged from 2.5 for Nitzschia sp. to 14 in C. raciborskii. Internal HCO₃^- concentration showed a linear relationship with surface area to biovolume ratio (SA:Vol). We hypothesized that species with a higher SA:Vol suffer more from diffusive escape of CO₂ , thus storage of DIC as bicarbonate is favored in these strains. For C. raciborskii, under stratified summer conditions, its strong CCM, and resilient photosynthetic characteristics may contribute to its bloom forming capacity.

Carbonate Disequilibrium in the External Boundary Layer of Freshwater Chrysophytes: Implications for Contaminant Uptake

The interplay between biological and chemical reactions in the freshwater phytoplankton phycosphere and the resulting modulations of contaminant speciation and uptake is poorly characterized. Here we modeled the effect of algal C and N uptake on carbonate cycling and speciation of selected contaminants in the phycosphere (external boundary layer) of chrysophytes, a key phytoplankton group in oligotrophic systems. We calculated an enrichment in H⁺ concentration relative to that in the bulk solution (pH 7.0) of approximately 40% or a depletion of approximately 30% for NH₄⁺ or NO₃^--grown cells, respectively, at the algal membrane surface of a 5-μm radius cell. Such changes are mainly due to direct H⁺ uptake or release at the plasmalemma if NO₃^- or NH₄⁺ is the N source, respectively. Due to these pH changes in the external boundary layer, competition between H⁺ and metals for uptake is enhanced, for NH₄⁺-grown cells which contributes to a decrease in potential metal uptake. Our model suggests that the uptake of protonated weakly acidic organic acids (HA) is greater in NH₄⁺-grown cells compared to that in NO₃^--grown cells. The account of chemical reactions in the algal external boundary layer could improve ecological risk assessments for a wide range of contaminants.

High planktonic diversity in mountain lakes contains similar contributions of autotrophic, heterotrophic and parasitic eukaryotic life forms

A rich eukaryotic planktonic community exists in high-mountain lakes despite the diluted, oligotrophic and cold, harsh prevailing conditions. Attempts of an overarching appraisal have been traditionally hampered by observational limitations of small, colorless, and soft eukaryotes. We aimed to uncover the regional eukaryotic biodiversity of a mountain lakes district to obtain general conclusions on diversity patterns, dominance, geographic diversification, and food-web players common to oligotrophic worldwide distributed freshwater systems. An unprecedented survey of 227 high-altitude lakes comprising large environmental gradients was carried out using Illumina massive tag sequencing of the 18S rRNA gene. We observed a large Chrysophyceae dominance in richness, abundance and novelty, and unveiled an unexpected richness in heterotrophic phagotrophs and parasites. In particular, Cercozoa and Chytridiomycota showed diversity features similar to the dominant autotrophic groups. The prominent beta-dispersion shown by parasites suggests highly specific interactions and a relevant role in food webs. Interestingly, the freshwater Pyrenean metacommunity contained more diverse specific populations than its closest marine oligotrophic equivalent, with consistently higher beta-diversity. The relevance of unseen groups opens new perspectives for the better understanding of planktonic food webs. Mountain lakes, with remarkable environmental idiosyncrasies, may be suitable environments for the genetic diversification of microscopic eukaryotic life forms.

A tale of two mixotrophic chrysophytes: Insights into the metabolisms of two Ochromonas species (Chrysophyceae) through a comparison of gene expression

Ochromonas spp. strains CCMP1393 and BG-1 are phagotrophic phytoflagellates with different nutritional strategies. Strain CCMP1393 is an obligate phototroph while strain BG-1 readily grows in continuous darkness in the presence of bacterial prey. Growth and gene expression of strain CCMP1393 were investigated under conditions allowing phagotrophic, mixotrophic, or phototrophic nutrition. The availability of light and bacterial prey led to the differential expression of 42% or 45–59% of all genes, respectively. Data from strain CCMP1393 were compared to those from a study conducted previously on strain BG-1, and revealed notable differences in carbon and nitrogen metabolism between the 2 congeners under similar environmental conditions. Strain BG-1 utilized bacterial carbon and amino acids through glycolysis and the tricarboxylic acid cycle, while downregulating light harvesting and carbon fixation in the Calvin cycle when both light and bacteria were available. In contrast, the upregulation of genes related to photosynthesis, light harvesting, chlorophyll synthesis, and carbon fixation in the presence of light and prey for strain CCMP1393 implied that this species is more phototrophic than strain BG-1, and that phagotrophy may have enhanced phototrophy. Cellular chlorophyll a content was also significantly higher in strain CCMP1393 supplied with bacteria compared to those without prey. Our results thus point to very different physiological strategies for mixotrophic nutrition in these closely related chrysophyte species.

Terrestrial adaptation of green algae Klebsormidium and Zygnema (Charophyta) involves diversity in photosynthetic traits but not in CO2 acquisition

The basal streptophyte Klebsormidium and the advanced Zygnema show adaptation to terrestrialization. Differences are found in photoprotection and resistance to short-term light changes, but not in CO ₂ acquisition. Streptophyte green algae colonized land about 450-500 million years ago giving origin to terrestrial plants. We aim to understand how their physiological adaptations are linked to the ecological conditions (light, water and CO₂) characterizing modern terrestrial habitats. A new Klebsormidium isolate from a strongly acidic environment of a former copper mine (Schwarzwand, Austria) is investigated, in comparison to Klebsormidium cf. flaccidum and Zygnema sp. We show that these genera possess different photosynthetic traits and water requirements. Particularly, the Klebsormidium species displayed a higher photoprotection capacity, concluded from non-photochemical quenching (NPQ) and higher tolerance to high light intensity than Zygnema. However, Klebsormidium suffered from photoinhibition when the light intensity in the environment increased rapidly, indicating that NPQ is involved in photoprotection against strong and stable irradiance. Klebsormidium was also highly resistant to cellular water loss (dehydration) under low light. On the other hand, exposure to relatively high light intensity during dehydration caused a harmful over-reduction of the electron transport chain, leading to PSII damages and impairing the ability to recover after rehydration. Thus, we suggest that dehydration is a selective force shaping the adaptation of this species towards low light. Contrary to the photosynthetic characteristics, the inorganic carbon (C _i ) acquisition was equivalent between Klebsormidium and Zygnema. Despite their different habitats and restriction to hydro-terrestrial environment, the three organisms showed similar use of CO₂ and HCO₃^- as source of C_i for photosynthesis, pointing out a similar adaptation of their CO₂-concentrating mechanisms to terrestrial life.

Acquisition and metabolism of carbon in the Ochrophyta other than diatoms

The acquisition and assimilation of inorganic C have been investigated in several of the 15 clades of the Ochrophyta other than diatoms, with biochemical, physiological and genomic data indicating significant mechanistic variation. Form ID Rubiscos in the Ochrophyta are characterized by a broad range of kinetics values. In spite of relatively high K0.5CO2 and low CO2 : O2 selectivity, diffusive entry of CO2 occurs in the Chrysophyceae and Synurophyceae. Eustigmatophyceae and Phaeophyceae, on the contrary, have CO2 concentrating mechanisms, usually involving the direct or indirect use of [Formula: see text] This variability is possibly due to the ecological contexts of the organism. In brown algae, C fixation generally takes place through a classical C3 metabolism, but there are some hints of the occurrence of C4 metabolism and low amplitude CAM in a few members of the Fucales. Genomic data show the presence of a number of potential C4 and CAM genes in Ochrophyta other than diatoms, but the other core functions of many of these genes give a very limited diagnostic value to their presence and are insufficient to conclude that C4 photosynthesis is present in these algae.This article is part of the themed issue 'The peculiar carbon metabolism in diatoms'.

Disturbance-induced phytoplankton regime shifts and recovery of cyanobacteria dominance in two subtropical reservoirs

Many countries in the world still suffer from high toxic cyanobacterial blooms in inland waters used for human consumption. Regional climate change and human activities within watersheds exert a complex and diverse influence on aquatic ecosystem structure and function across space and time. However, the degree to which these factors may contribute to the long-term dynamics of plankton communities is still not well understood. Here, we explore the impacts of multiple disturbance events (e.g. human-resettlement, temperature change, rainfall, water level fluctuations), including six combined disturbances, on phytoplankton and cyanobacteria in two subtropical reservoirs over six years. Our data showed that combined environmental disturbances triggered two apparent and abrupt switches between cyanobacteria-dominated state and non-cyanobacterial taxa-dominated state. In late 2010, the combined effect of human-resettlement (emigration) and natural disturbances (e.g. cooling, rainfall, water level fluctuations) lead to a 60-90% decrease in cyanobacteria biomass accompanied by the disappearance of cyanobacterial blooms, in tandem with an abrupt and persistent shift in phytoplankton community. After summer 2014, however, combined weather and hydrological disturbances (e.g. warming, rainfall, water level fluctuations) occurred leading to an abrupt and marked increase of cyanobacteria biomass, associated with a return to cyanobacteria dominance. These changes in phytoplankton community were strongly related to the nutrient concentrations and water level fluctuations, as well as water temperature and rainfall. As both extreme weather events and human disturbances are predicted to become more frequent and severe during the twenty-first century, prudent sustainable management will require consideration of the background limnologic conditions and the frequency of disturbance events when assessing the potential impacts on reservoir biodiversity and ecosystem functioning and services.

The algal pyrenoid: key unanswered questions

The confinement of Rubisco in a chloroplast microcompartment, or pyrenoid, is a distinctive feature of most microalgae, and contributes to perhaps ~30 Pg of carbon fixed each year, yet our understanding of pyrenoid composition, regulation, and function remains fragmentary. Recently, significant progress in understanding the pyrenoid has arisen from studies using mutant lines, mass spectrometric analysis of isolated pyrenoids, and advanced ultrastructural imaging of the microcompartment in the model alga Chlamydomonas. The emergence of molecular details in other lineages provides a comparative framework for this review, and evidence that most pyrenoids function similarly, even in the absence of a common ancestry. The objective of this review is to explore pyrenoid diversity throughout key algal lineages and discuss whether common ultrastructural and cellular features are indicative of common functional processes. By characterizing pyrenoid origins in terms of mechanistic and structural parallels, we hope to provide key unanswered questions which will inform future research directions.

The possible evolution and future of CO2-concentrating mechanisms

CO2-concentrating mechanisms (CCMs), based either on active transport of inorganic carbon (biophysical CCMs) or on biochemistry involving supplementary carbon fixation into C4 acids (C4 and CAM), play a major role in global primary productivity. However, the ubiquitous CO2-fixing enzyme in autotrophs, Rubisco, evolved at a time when atmospheric CO2 levels were very much higher than today and O2 was very low and, as CO2 and O2 approached (by no means monotonically), today's levels, at some time subsequently many organisms evolved a CCM that increased the supply of CO2 and decreased Rubisco oxygenase activity. Given that CO2 levels and other environmental factors have altered considerably between when autotrophs evolved and the present day, and are predicted to continue to change into the future, we here examine the drivers for, and possible timing of, evolution of CCMs. CCMs probably evolved when CO2 fell to 2-16 times the present atmospheric level, depending on Rubisco kinetics. We also assess the effects of other key environmental factors such as temperature and nutrient levels on CCM activity and examine the evidence for evolutionary changes in CCM activity and related cellular processes as well as limitations on continuity of CCMs through environmental variations.

Ecological imperatives for aquatic CO2-concentrating mechanisms

In aquatic environments, the concentration of inorganic carbon is spatially and temporally variable and CO2 can be substantially oversaturated or depleted. Depletion of CO2 plus low rates of diffusion cause inorganic carbon to be more limiting in aquatic than terrestrial environments, and the frequency of species with a CO2-concentrating mechanism (CCM), and their contribution to productivity, is correspondingly greater. Aquatic photoautotrophs may have biochemical or biophysical CCMs and exploit CO2 from the sediment or the atmosphere. Though partly constrained by phylogeny, CCM activity is related to environmental conditions. CCMs are absent or down-regulated when their increased energy costs, lower CO2 affinity, or altered mineral requirements outweigh their benefits. Aquatic CCMs are most widespread in environments with low CO2, high HCO3-, high pH, and high light. Freshwater species are generally less effective at inorganic carbon removal than marine species, but have a greater range of ability to remove carbon, matching the environmental variability in carbon availability. The diversity of CCMs in seagrasses and marine phytoplankton, and detailed mechanistic studies on larger aquatic photoautotrophs are understudied. Strengthening the links between ecology and CCMs will increase our understanding of the mechanisms underlying ecological success and will place mechanistic studies in a clearer ecological context.

Autotrophic and heterotrophic acquisition of carbon and nitrogen by a mixotrophic chrysophyte established through stable isotope analysis

Collectively, phagotrophic algae (mixotrophs) form a functional continuum of nutritional modes between autotrophy and heterotrophy, but the specific physiological benefits of mixotrophic nutrition differ among taxa. Ochromonas spp. are ubiquitous chrysophytes that exhibit high nutritional flexibility, although most species generally fall towards the heterotrophic end of the mixotrophy spectrum. We assessed the sources of carbon and nitrogen in Ochromonas sp. strain BG-1 growing mixotrophically via short-term stable isotope probing. An axenic culture was grown in the presence of either heat-killed bacteria enriched with ¹⁵N and ¹³C, or unlabeled heat-killed bacteria and labeled inorganic substrates (¹³C-bicarbonate and ¹⁵N-ammonium). The alga exhibited high growth rates (up to 2 divisions per day) only until heat-killed bacteria were depleted. NanoSIMS and bulk IRMS isotope analyses revealed that Ochromonas obtained 84-99% of its carbon and 88-95% of its nitrogen from consumed bacteria. The chrysophyte assimilated inorganic ¹³C-carbon and ¹⁵N-nitrogen when bacterial abundances were very low, but autotrophic (photosynthetic) activity was insufficient to support net population growth of the alga. Our use of nanoSIMS represents its first application towards the study of a mixotrophic alga, enabling a better understanding and quantitative assessment of carbon and nutrient acquisition by this species.

Ecophysiology matters: linking inorganic carbon acquisition to ecological preference in four species of microalgae (Chlorophyceae)

The effect of CO₂ supply is likely to play an important role in algal ecology. Since inorganic carbon (C_i ) acquisition strategies are very diverse among microalgae and C_i availability varies greatly within and among habitats, we hypothesized that C_i acquisition depends on the pH of their preferred natural environment (adaptation) and that the efficiency of C_i uptake is affected by CO₂ availability (acclimation). To test this, four species of green algae originating from different habitats were studied. The pH-drift and C_i uptake kinetic experiments were used to characterize C_i acquisition strategies and their ability to acclimate to high and low CO₂ conditions and high and low pH was evaluated. Results from pH drift experiments revealed that the acidophile and acidotolerant Chlamydomonas species were mainly restricted to CO₂ , whereas the two neutrophiles were efficient bicarbonate users. CO₂ compensation points in low CO₂ -acclimated cultures ranged between 0.6 and 1.4 μM CO₂ and acclimation to different culture pH and CO₂ conditions suggested that CO₂ concentrating mechanisms were present in most species. High CO₂ acclimated cultures adapted rapidly to low CO₂ condition during pH-drifts. C_i uptake kinetics at different pH values showed that the affinity for C_i was largely influenced by external pH, being highest under conditions where CO₂ dominated the C_i pool. In conclusion, C_i acquisition was highly variable among four species of green algae and linked to growth pH preference, suggesting that there is a connection between C_i acquisition and ecological distribution.

Understanding the winning strategies used by the bloom-forming cyanobacterium Cylindrospermopsis raciborskii

The cyanobacterium Cylindrospermopsis raciborskii is a widespread species increasingly being recorded in freshwater systems around the world. It is of particular concern because strains in some geographic areas are capable of producing toxins with implications for human and animal health. Studies of this species have increased rapidly in the last two decades, especially in the southern hemisphere where toxic strains are prevalent. A clearer picture is emerging of the strategies adopted by this species to bloom and out-compete other species. This species has a high level of flexibility with respect to light and nutrients, with higher temperatures and carbon dioxide also promoting growth. There are two types of toxins produced by C. raciborskii: cylindrospermopsins (CYNs) and saxitoxins (STXs). The toxins CYNs are constitutively produced irrespective of environmental conditions and the ecological or physiological role is unclear, while STXs appear to serve as protection against high salinity and/or water hardness. It is also apparent that strains of this species can vary substantially in their physiological responses to environmental conditions, including CYNs production, and this may explain discrepancies in findings from studies in different geographical areas. The combination of a flexible strategy with respect to environmental conditions, and variability in strain response makes it a challenging species to manage. Our ability to improve bloom prediction will rely on a more detailed understanding of the complex physiology of this species.

The ins and outs of CO2

It is difficult to distinguish influx and efflux of inorganic C in photosynthesizing tissues; this article examines what is known and where there are gaps in knowledge. Irreversible decarboxylases produce CO2, and CO2 is the substrate/product of enzymes that act as carboxylases and decarboxylases. Some irreversible carboxylases use CO2; others use HCO3(-). The relative role of permeation through the lipid bilayer versus movement through CO2-selective membrane proteins in the downhill, non-energized, movement of CO2 is not clear. Passive permeation explains most CO2 entry, including terrestrial and aquatic organisms with C3 physiology and biochemistry, terrestrial C4 plants and all crassulacean acid metabolism (CAM) plants, as well as being part of some mechanisms of HCO3(-) use in CO2 concentrating mechanism (CCM) function, although further work is needed to test the mechanism in some cases. However, there is some evidence of active CO2 influx at the plasmalemma of algae. HCO3(-) active influx at the plasmalemma underlies all cyanobacterial and some algal CCMs. HCO3(-) can also enter some algal chloroplasts, probably as part of a CCM. The high intracellular CO2 and HCO3(-) pools consequent upon CCMs result in leakage involving CO2, and occasionally HCO3(-). Leakage from cyanobacterial and microalgal CCMs involves up to half, but sometimes more, of the gross inorganic C entering in the CCM; leakage from terrestrial C4 plants is lower in most environments. Little is known of leakage from other organisms with CCMs, though given the leakage better-examined organisms, leakage occurs and increases the energetic cost of net carbon assimilation.

Changes in gene expression, cell physiology and toxicity of the harmful cyanobacterium Microcystis aeruginosa at elevated CO2

Rising CO2 concentrations may have large effects on aquatic microorganisms. In this study, we investigated how elevated pCO2 affects the harmful freshwater cyanobacterium Microcystis aeruginosa. This species is capable of producing dense blooms and hepatotoxins called microcystins. Strain PCC 7806 was cultured in chemostats that were shifted from low to high pCO2 conditions. This resulted in a transition from a C-limited to a light-limited steady state, with a ~2.7-fold increase of the cyanobacterial biomass and ~2.5-fold more microcystin per cell. Cells increased their chlorophyll a and phycocyanin content, and raised their PSI/PSII ratio at high pCO2. Surprisingly, cells had a lower dry weight and contained less carbohydrates, which might be an adaptation to improve the buoyancy of Microcystis when light becomes more limiting at high pCO2. Only 234 of the 4691 genes responded to elevated pCO2. For instance, expression of the carboxysome, RuBisCO, photosystem and C metabolism genes did not change significantly, and only a few N assimilation genes were expressed differently. The lack of large-scale changes in the transcriptome could suit a buoyant species that lives in eutrophic lakes with strong CO2 fluctuations very well. However, we found major responses in inorganic carbon uptake. At low pCO2, cells were mainly dependent on bicarbonate uptake, whereas at high pCO2 gene expression of the bicarbonate uptake systems was down-regulated and cells shifted to CO2 and low-affinity bicarbonate uptake. These results show that the need for high-affinity bicarbonate uptake systems ceases at elevated CO2. Moreover, the combination of an increased cyanobacterial abundance, improved buoyancy, and higher toxin content per cell indicates that rising atmospheric CO2 levels may increase the problems associated with the harmful cyanobacterium Microcystis in eutrophic lakes.

The biodiversity of carbon assimilation

As all plastids that have been investigated so far can be traced back to endosymbiotic uptake of cyanobacteria by heterotrophic host cells, they accordingly show a high similarity regarding photosynthesis, which includes both the photosystems and the biochemical reactions around the CO2 fixation via the Calvin-Bassham cycle. Major differences between the different algal and plant groups may include the presence or absence of carbon concentrating mechanisms, pyrenoids, Rubisco activases, carbonic anhydrases as well as differences in the regulation of the Calvin-Bassham cycle. This review describes the diversity of primary carbon fixation steps in algae and plants and the respective regulatory mechanisms.

Do mixotrophs grow as photoheterotrophs? Photophysiological acclimation of the chrysophyte Ochromonas danica after feeding

Mixotrophy is increasingly recognized as an important and widespread nutritional strategy in various taxonomic groups ranging from protists to higher plants. We hypothesize that the availability of alternative carbon and energy sources during mixotrophy allows a switch to photoheterotrophic growth, where the photosynthetic apparatus mainly provides energy but not fixed carbon. Because such a change in the function of the photosynthetic machinery is probably reflected in its composition, we compared the photosynthetic machinery in Ochromonas danica during autotrophic and mixotrophic growth. Compared with autotrophic growth, the total pigmentation of O. danica was reduced during mixotrophic growth. Furthermore, the photosystem I (PSI):PSII ratio increased, and the cellular content of Rubisco decreased not only absolutely, but also relative to the content of PSII. The changing composition of the photosynthetic apparatus indicates a shift in its function from providing both carbon and energy during photoautotrophy to mainly providing energy during mixotrophy. This preference for photoheterotrophic growth has interesting implications for the contribution of mixotrophic species to carbon cycling in diverse ecosystems.

The role of C4 metabolism in the marine diatom Phaeodactylum tricornutum

Diatoms are important players in the global carbon cycle. Their apparent photosynthetic affinity for ambient CO(2) is much higher than that of ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco), indicating that a CO(2)-concentrating mechanism (CCM) is functioning. However, the nature of the CCM, a biophysical or a biochemical C(4), remains elusive. Although (14)C labeling experiments and presence of complete sets of genes for C(4) metabolism in two diatoms supported the presence of C(4), other data and predicted localization of the decarboxylating enzymes, away from Rubisco, makes this unlikely. We used RNA-interference to silence the single gene encoding pyruvate-orthophosphate dikinase (PPDK) in Phaeodactylum tricornutum, essential for C(4) metabolism, and examined the photosynthetic characteristics. The mutants possess much lower ppdk transcript and PPDK activity but the photosynthetic K(1/2) (CO(2)) was hardly affected, thus clearly indicating that the C(4) route does not serve the purpose of raising the CO(2) concentration in close proximity of Rubisco in P. tricornutum. The photosynthetic V(max) was slightly reduced in the mutant, possibly reflecting a metabolic constraint that also resulted in a larger lipid accumulation. We propose that the C(4) metabolism does not function in net CO(2) fixation but helps the cells to dissipate excess light energy and in pH homeostasis.

Ecophysiology of photosynthesis in macroalgae

Macroalgae occur in the marine benthos from the upper intertidal to depths of more than 200 m, contributing up to 1 Pg C per year to global primary productivity. Freshwater macroalgae are mainly green (Chlorophyta) with some red (Rhodophyta) and a small contribution of brown (Phaeophyceae) algae, while in the ocean all three higher taxa are important. Attempts to relate the depth distribution of three higher taxa of marine macroalgae to their photosynthetic light use through their pigmentation in relation to variations in spectral quality of photosynthetically active radiation (PAR) with depth (complementary chromatic adaptation) and optical thickness (package effect) have been relatively unsuccessful. The presence (Chlorophyta, Phaeophyceae) or absence (Rhodophyta) of a xanthophyll cycle is also not well correlated with depth distribution of marine algae. The relative absence of freshwater brown algae does not seem to be related to their photosynthetic light use. Photosynthetic inorganic carbon acquisition in some red and a few green macroalgae involves entry of CO(2) by diffusion. Other red and green macroalgae, and brown macroalgae, have CO(2) concentrating mechanisms; these frequently involve acid and alkaline zones on the surface of the alga with CO(2) (produced from HCO(3) (-)) entering in the acid zones, while some macroalgae have CCMs based on active influx of HCO(3) (-). These various mechanisms of carbon acquisition have different responses to the thickness of the diffusion boundary layer, which is determined by macroalgal morphology and water velocity. Energetic predictions that macroalgae growing at or near the lower limit of PAR for growth should rely on diffusive CO(2) entry without acid and alkaline zones, and on NH(4) (+) rather than NO(3) (-) as nitrogen source, are only partially borne out by observation. The impact of global environmental change on marine macroalgae mainly relates to ocean acidification and warming with shoaling of the thermocline and decreased nutrient flux to the upper mixed layer. Predictions of the impact on macroalgae requires further experiments on interactions among increased inorganic carbon, increased temperature and decreased nitrogen and phosphorus supply, and, when possible, studies of genetic adaptation to environmental change.

The impacts of a high CO₂ environment on a bicarbonate user: the cyanobacterium Cylindrospermopsis raciborskii

The potentially toxic cyanobacterium Cylindrospermopsis raciborskii (Wołoszyńska) Seenya et Subba Raju, originally described as a tropical-subtropical species, is increasingly found in temperate regions and its range is expanding. Climate change is hypothesised to be a factor in this expansion. We studied the effects of dissolved inorganic carbon (DIC) and pH on growth and photosynthesis of this species. We prepared six treatments in a continuous culture (turbidostat) grown at high light, two at low light, and eight in batch cultures grown under low light, by manipulating pH, HCO(3)(-) and CO(2) to assess the effect, if any, of these parameters on the growth rate, inorganic carbon acquisition and photosynthetic parameters of C. raciborskii. When the turbidostats were grown at 100 μmol photons (PAR) m(-2) s(-1), HCO(3)(-) concentration and pH had a positive effect on growth rate; the specific growth rate in 6 mM HCO(3)(-), for example, was twice what it was in 0.6 mM HCO(3)(-) (0.84 ± 0.10 and 0.44 ± 0.04 d(-1) respectively). Growth was lower in turbidostats grown at 20 μmol photons (PAR) m(-2) s(-1). Isotope disequilibrium experiments showed that the contribution of HCO(3)(-) to DIC acquisition is proportionately greater at the higher light. The maximum relative electron transport rate (rETR(max)) was significantly higher at the higher light, while the slope of the linear portion of the rETR(max) versus irradiance curve (α) was unchanged. In low light batch cultures, increasing HCO(3)(-) concentration and pH had a negative effect on growth, while CO(2) concentration had a small, positive effect. This species of cyanobacterium has an efficient CCM and under ideal growing conditions gets most of its carbon from HCO(3)(-). It may, therefore, be at a competitive disadvantage in a high CO(2) world.

Algal evolution in relation to atmospheric CO2: carboxylases, carbon-concentrating mechanisms and carbon oxidation cycles

Oxygenic photosynthesis evolved at least 2.4 Ga; all oxygenic organisms use the ribulose bisphosphate carboxylase-oxygenase (Rubisco)-photosynthetic carbon reduction cycle (PCRC) rather than one of the five other known pathways of autotrophic CO(2) assimilation. The high CO(2) and (initially) O(2)-free conditions permitted the use of a Rubisco with a high maximum specific reaction rate. As CO(2) decreased and O(2) increased, Rubisco oxygenase activity increased and 2-phosphoglycolate was produced, with the evolution of pathways recycling this inhibitory product to sugar phosphates. Changed atmospheric composition also selected for Rubiscos with higher CO(2) affinity and CO(2)/O(2) selectivity correlated with decreased CO(2)-saturated catalytic capacity and/or for CO(2)-concentrating mechanisms (CCMs). These changes increase the energy, nitrogen, phosphorus, iron, zinc and manganese cost of producing and operating Rubisco-PCRC, while biosphere oxygenation decreased the availability of nitrogen, phosphorus and iron. The majority of algae today have CCMs; the timing of their origins is unclear. If CCMs evolved in a low-CO(2) episode followed by one or more lengthy high-CO(2) episodes, CCM retention could involve a combination of environmental factors known to favour CCM retention in extant organisms that also occur in a warmer high-CO(2) ocean. More investigations, including studies of genetic adaptation, are needed.

Algal and aquatic plant carbon concentrating mechanisms in relation to environmental change

Carbon dioxide concentrating mechanisms (also known as inorganic carbon concentrating mechanisms; both abbreviated as CCMs) presumably evolved under conditions of low CO(2) availability. However, the timing of their origin is unclear since there are no sound estimates from molecular clocks, and even if there were, there are no proxies for the functioning of CCMs. Accordingly, we cannot use previous episodes of high CO(2) (e.g. the Palaeocene-Eocene Thermal Maximum) to indicate how organisms with CCMs responded. Present and predicted environmental change in terms of increased CO(2) and temperature are leading to increased CO(2) and HCO(3)(-) and decreased CO(3)(2-) and pH in surface seawater, as well as decreasing the depth of the upper mixed layer and increasing the degree of isolation of this layer with respect to nutrient flux from deeper waters. The outcome of these forcing factors is to increase the availability of inorganic carbon, photosynthetic active radiation (PAR) and ultraviolet B radiation (UVB) to aquatic photolithotrophs and to decrease the supply of the nutrients (combined) nitrogen and phosphorus and of any non-aeolian iron. The influence of these variations on CCM expression has been examined to varying degrees as acclimation by extant organisms. Increased PAR increases CCM expression in terms of CO(2) affinity, whilst increased UVB has a range of effects in the organisms examined; little relevant information is available on increased temperature. Decreased combined nitrogen supply generally increases CO(2) affinity, decreased iron availability increases CO(2) affinity, and decreased phosphorus supply has varying effects on the organisms examined. There are few data sets showing interactions amongst the observed changes, and even less information on genetic (adaptation) changes in response to the forcing factors. In freshwaters, changes in phytoplankton species composition may alter with environmental change with consequences for frequency of species with or without CCMs. The information available permits less predictive power as to the effect of the forcing factors on CCM expression than for their overall effects on growth. CCMs are currently not part of models as to how global environmental change has altered, and is likely to further alter, algal and aquatic plant primary productivity.

Evidence for the occurrence of photorespiration in synurophyte algae

The fluxes of CO(2) and oxygen during photosynthesis by cell suspensions of Tessellaria volvocina and Mallomonas papillosa were monitored mass spectrometrically. There was no rapid uptake of CO(2,) only a slow drawdown to compensation concentrations of 26 μM for T. volvocina and 18 μM for M. papillosa, when O(2) evolution ceased, indicating a lack of active bicarbonate uptake by the cells. Darkening of the cells after a period of photosynthesis did not cause rapid release of CO(2), indicating the absence of an intracellular inorganic carbon pool. However, upon darkening a brief burst of CO(2) was observed similar to the post-illumination burst characteristic of C(3) higher plants. Treatment of the cells of both species with the membrane-permeable carbonic anhydrase inhibitor ethoxyzolamide had no adverse effect on photosynthetic rate, but stimulated the dark CO(2) burst indicating the dark oxidation of a compound formed in the light. In the absence of any active accumulation of inorganic carbon photosynthesis in these species should be inhibited by O(2). This was investigated in four synurophyte species T. volvocina, M. papillosa, Synura petersenii, and Synura uvella: photosynthetic O(2) evolution rates in all four algae, measured by O(2) electrode, were significantly higher (40-50%) in media at low O(2) (4%) than in air-equilibrated (21% O(2)) media, indicating an O(2) inhibition of photosynthesis (Warburg effect) and thus the occurrence of photorespiration in these species.

Reversal in competitive dominance of a toxic versus non-toxic cyanobacterium in response to rising CO2

Climate change scenarios predict a doubling of the atmospheric CO(2) concentration by the end of this century. Yet, how rising CO(2) will affect the species composition of aquatic microbial communities is still largely an open question. In this study, we develop a resource competition model to investigate competition for dissolved inorganic carbon in dense algal blooms. The model predicts how dynamic changes in carbon chemistry, pH and light conditions during bloom development feed back on competing phytoplankton species. We test the model predictions in chemostat experiments with monocultures and mixtures of a toxic and non-toxic strain of the freshwater cyanobacterium Microcystis aeruginosa. The toxic strain was able to reduce dissolved CO(2) to lower concentrations than the non-toxic strain, and became dominant in competition at low CO(2) levels. Conversely, the non-toxic strain could grow at lower light levels, and became dominant in competition at high CO(2) levels but low light availability. The model captured the observed reversal in competitive dominance, and was quantitatively in good agreement with the results of the competition experiments. To assess whether microcystins might have a role in this reversal of competitive dominance, we performed further competition experiments with the wild-type strain M. aeruginosa PCC 7806 and its mcyB mutant impaired in microcystin production. The microcystin-producing wild type had a strong selective advantage at low CO(2) levels but not at high CO(2) levels. Our results thus demonstrate both in theory and experiment that rising CO(2) levels can alter the community composition and toxicity of harmful algal blooms.

Inorganic carbon acquisition by eukaryotic algae: four current questions

The phylogenetically and morphologically diverse eukaryotic algae are typically oxygenic photolithotrophs. They have a diversity of incompletely understood mechanisms of inorganic carbon acquisition: this article reviews four areas where investigations continue. The first topic is diffusive CO(2) entry. Most eukaryotic algae, like all cyanobacteria, have inorganic carbon concentrating mechanisms (CCMs). The ancestral condition was presumably the absence of a CCM, i.e. diffusive CO(2) entry, as found in a small minority of eukaryotic algae today; however, it is likely that, as is found in several cases, this condition is due to a loss of a CCM. There are a number of algae which are in various respects intermediate between diffusive CO(2) entry and occurrence of a CCM: further study is needed on this aspect. A second topic is the nature of cyanelles and their role in inorganic carbon assimilation. The cyanelles (plastids) of the euglyphid amoeba Paulinella have been acquired relatively recently by endosymbiosis with genetic integration of an α-cyanobacterium with a Form 1A Rubisco. The α-carboxysomes in the cyanelles are presumably involved in a CCM, but further investigation is needed.Also called cyanelles are the plastids of glaucocystophycean algae, but is it now clear that these were derived from the β-cyanobacterial ancestor of all plastids other than that of Paulinella. The resemblances of the central body of the cyanelles of glaucocystophycean algae to carboxysomes may not reflect derivation from cyanobacterial β-carboxysomes; although it is clear that these algae have CCMs but these are now well characterized. The other two topics concern CCMs in other eukaryotic algae; these CCMs arose polyphyletically and independently of the cyanobacterial CCMs. It is generally believed that eukaryotic algal, like cyanobacterial, CCMs are based on active transport of an inorganic carbon species and/or protons, and they have C(3) biochemistry. This is the case for the organism considered as the third topic, i.e. Chlamydomonas reinhardtii, the eukaryotic alga with the best understood CCM. This CCM involves HCO(3)(-) conversion to CO(2) in the thylakoid lumen so the external inorganic carbon must cross four membranes in series with a final CO(2) effux from the thylakoid. More remains to be investigated about this CCM. The final topic is that of the occurrence of C(4)-like metabolism in the CCMs of marine diatoms. Different conclusions have been reached depending on the organism investigated and the techniques used, and several aspects require further study.