Matthew P. Davey

Biodiesel from algae: challenges and prospects.

Microalgae offer great potential for exploitation, including the production of biodiesel, but the process is still some way from being carbon neutral or commercially viable. Part of the problem is that there is little established background knowledge in the area. We should look both to achieve incremental steps and to increase our fundamental understanding of algae to identify potential paradigm shifts. In doing this, integration of biology and engineering will be essential. In this review we present an overview of a potential algal biofuel pipeline, and focus on recent work that tackles optimization of algal biomass production and the content of fuel molecules within the algal cell.

Environmental metabolomics: a critical review and future perspectives

Environmental metabolomics is the application of metabolomics to characterise the interactions of organisms with their environment. This approach has many advantages for studying organism–environment interactions and for assessing organism function and health at the molecular level. As such, metabolomics is finding an increasing number of applications in the environmental sciences, ranging from understanding organismal responses to abiotic pressures, to investigating the responses of organisms to other biota. These interactions can be studied from individuals to populations, which can be related to the traditional fields of ecophysiology and ecology, and from instantaneous effects to those over evolutionary time scales, the latter enabling studies of genetic adaptation. This review provides a comprehensive and current overview of environmental metabolomics research. We begin with an overview of metabolomic studies into the effects of abiotic pressures on organisms. In the field of ecophysiology, studies on the metabolic responses to temperature, water, food availability, light and circadian rhythms, atmospheric gases and season are reviewed. A section on ecotoxicogenomics discusses research in aquatic and terrestrial ecotoxicology, assessing organismal responses to anthropogenic pollutants in both the laboratory and field. We then discuss environmental metabolomic studies of diseases and biotic–biotic interactions, in particular herbivory. Finally, we critically evaluate the contribution that metabolomics has made to the environmental sciences, and highlight and discuss recommendations to advance our understanding of the environment, ecology and evolution using a metabolomics approach.

Impacts of extreme winter warming events on plant physiology in a sub-Arctic heath community.

Insulation provided by snow cover and tolerance of freezing by physiological acclimation allows Arctic plants to survive cold winter temperatures. However, both the protection mechanisms may be lost with winter climate change, especially during extreme winter warming events where loss of snow cover from snow melt results in exposure of plants to warm temperatures and then returning extreme cold in the absence of insulating snow. These events cause considerable damage to Arctic plants, but physiological responses behind such damage remain unknown. Here, we report simulations of extreme winter warming events using infrared heating lamps and soil warming cables in a sub-Arctic heathland. During these events, we measured maximum quantum yield of photosystem II (PSII), photosynthesis, respiration, bud swelling and associated bud carbohydrate changes and lipid peroxidation to identify physiological responses during and after the winter warming events in three dwarf shrub species: Empetrum hermaphroditum, Vaccinium vitis-idaea and Vaccinium myrtillus. Winter warming increased maximum quantum yield of PSII, and photosynthesis was initiated for E. hermaphroditum and V. vitis-idaea. Bud swelling, bud carbohydrate decreases and lipid peroxidation were largest for E. hermaphroditum, whereas V. myrtillus and V. vitis-idaea showed no or less strong responses. Increased physiological activity and bud swelling suggest that sub-Arctic plants can initiate spring-like development in response to a short winter warming event. Lipid peroxidation suggests that plants experience increased winter stress. The observed differences between species in physiological responses are broadly consistent with interspecific differences in damage seen in previous studies, with E. hermaphroditum and V. myrtillus tending to be most sensitive. This suggests that initiation of spring-like development may be a major driver in the damage caused by winter warming events that are predicted to become more frequent in some regions of the Arctic and that may ultimately drive plant community shifts.

Standard reporting requirements for biological samples in metabolomics experiments: Environmental context

Metabolomic technologies are increasingly being applied to study biological questions in a range of different settings from clinical through to environmental. As with other high-throughput technologies, such as those used in transcriptomics and proteomics, metabolomics continues to generate large volumes of complex data that necessitates computational management. Making sense of this wealth of information also requires access to sufficiently detailed and well annotated meta-data. Here we provide standard reporting requirements for describing biological samples, taken from an environmental context and involved in metabolomic experiments. It is our intention that these reporting requirements should guide and support the standardised annotation, dissemination and interpretation of environmental metabolomics meta-data.

Metabolomic and physiological responses reveal multi-phasic acclimation of Arabidopsis thaliana to chronic UV radiation.

Biochemical changes in vivo and pathway interactions were investigated using integrated physiological and metabolic responses of Arabidopsis thaliana L. to ultraviolet (UV) radiation (280-400 nm) at 9.96 kJ m(-2) d(-1) over the entire life cycle from seed to seed (8 weeks). Columbia-0 (Col-0) and a UV-B sensitive accession (fah-1) showed significant (P < 0.001) reductions in leaf growth after 6 weeks. Col-0 recovered growth after 8 weeks, with recovery corresponding to a switch from production of phenylpropanoids to flavonoids. fah-1 failed to recover, indicating that sinapate production is an essential component of recovery. Epidermal features show that UV radiation caused significant (P < 0.001) increases in trichome density, which may act as a structural defence response. Stomatal indices showed a significant (P < 0.0001) reduction in Col-0 and a significant (P < 0.001) increase in fah-1. Epidermal cell density was significantly increased under UV radiation on the abaxial leaf surface, suggesting that that a fully functioning phenylpropanoid pathway is a requirement for cell expansion and leaf development. Despite wild-type acclimation, the costs of adaptation lead to reduced plant fitness by decreasing flower numbers and total seed biomass. A multi-phasic acclimation to UV radiation and the induction of specific metabolites link stress-induced biochemical responses to enhanced acclimation.

Variation at range margins across multiple spatial scales: environmental temperature, population genetics and metabolomic phenotype

Range margins are spatially complex, with environmental, genetic and phenotypic variations occurring across a range of spatial scales. We examine variation in temperature, genes and metabolomic profiles within and between populations of the subalpine perennial plant Arabidopsis lyrata ssp. petraea from across its northwest European range. Our surveys cover a gradient of fragmentation from largely continuous populations in Iceland, through more fragmented Scandinavian populations, to increasingly widely scattered populations at the range margin in Scotland, Wales and Ireland. Temperature regimes vary substantially within some populations, but within-population variation represents a larger fraction of genetic and especially metabolomic variances. Both physical distance and temperature differences between sites are found to be associated with genetic profiles, but not metabolomic profiles, and no relationship was found between genetic and metabolomic population structures in any region. Genetic similarity between plants within populations is the highest in the fragmented populations at the range margin, but differentiation across space is the highest there as well, suggesting that regional patterns of genetic diversity may be scale dependent.

Kinetic modelling of growth and storage molecule production in microalgae under mixotrophic and autotrophic conditions

In order to improve algal biofuel production on a commercial-scale, an understanding of algal growth and fuel molecule accumulation is essential. A mathematical model is presented that describes biomass growth and storage molecule (TAG lipid and starch) accumulation in the freshwater microalga Chlorella vulgaris, under mixotrophic and autotrophic conditions. Biomass growth was formulated based on the Droop model, while the storage molecule production was calculated based on the carbon balance within the algal cells incorporating carbon fixation via photosynthesis, organic carbon uptake and functional biomass growth. The model was validated with experimental growth data of C. vulgaris and was found to fit the data well. Sensitivity analysis showed that the model performance was highly sensitive to variations in parameters associated with nutrient factors, photosynthesis and light intensity. The maximum productivity and biomass concentration were achieved under mixotrophic nitrogen sufficient conditions, while the maximum storage content was obtained under mixotrophic nitrogen deficient conditions.

The UV-B photoreceptor UVR8 promotes photosynthetic efficiency in Arabidopsis thaliana exposed to elevated levels of UV-B

The UV-B photoreceptor UVR8 regulates expression of genes in response to UV-B, some encoding chloroplast proteins, but the importance of UVR8 in maintaining photosynthetic competence is unknown. The maximum quantum yield of PSII (Fv/Fm) and the operating efficiency of PSII (ΦPSII) were measured in wild-type and uvr8 mutant Arabidopsis thaliana. The importance of specific UVR8-regulated genes in maintaining photosynthetic competence was examined using mutants. Both Fv/Fm and ΦPSII decreased when plants were exposed to elevated UV-B, in general more so in uvr8 mutant plants than wild-type. UV-B increased the level of psbD-BLRP (blue light responsive promoter) transcripts, encoding the PSII D2 protein. This increase was mediated by the UVR8-regulated chloroplast RNA polymerase sigma factor SIG5, but SIG5 was not required to maintain photosynthetic efficiency at elevated UV-B. Levels of the D1 protein of PSII decreased markedly when plants were exposed to elevated UV-B, but there was no significant difference between wild-type and uvr8 under conditions where the mutant showed increased photoinhibition. The results show that UVR8 promotes photosynthetic efficiency at elevated levels of UV-B. Loss of the DI polypeptide is probably important in causing photoinhibition, but does not entirely explain the reduced photosynthetic efficiency of the uvr8 mutant compared to wild-type.

Contribution of cyanobacterial alkane production to the ocean hydrocarbon cycle

Significance A number of organisms synthesize hydrocarbons, but the scale at which this occurs in the environment is unknown. Here, we provide the first global estimates of hydrocarbon production by the two most abundant cyanobacteria on Earth, Prochlorococcus and Synechococcus. We suggest that these organisms represent a significant and widespread source of hydrocarbons to the world’s oceans, which in turn may sustain populations of obligate hydrocarbon-degrading bacteria known to be important in consuming anthropogenic oil spills. Our study demonstrates the role cyanobacteria play in the ocean ‟hydrocarbon cycle” and reveals the massive scale of this process. The widespread distribution of cyanobacteria and hydrocarbon-degrading bacteria in freshwater, marine, and terrestrial environments suggests the hydrocarbon cycle is pervasive in many natural ecosystems. Hydrocarbons are ubiquitous in the ocean, where alkanes such as pentadecane and heptadecane can be found even in waters minimally polluted with crude oil. Populations of hydrocarbon-degrading bacteria, which are responsible for the turnover of these compounds, are also found throughout marine systems, including in unpolluted waters. These observations suggest the existence of an unknown and widespread source of hydrocarbons in the oceans. Here, we report that strains of the two most abundant marine cyanobacteria, Prochlorococcus and Synechococcus, produce and accumulate hydrocarbons, predominantly C15 and C17 alkanes, between 0.022 and 0.368% of dry cell weight. Based on global population sizes and turnover rates, we estimate that these species have the capacity to produce 2–540 pg alkanes per mL per day, which translates into a global ocean yield of ∼308–771 million tons of hydrocarbons annually. We also demonstrate that both obligate and facultative marine hydrocarbon-degrading bacteria can consume cyanobacterial alkanes, which likely prevents these hydrocarbons from accumulating in the environment. Our findings implicate cyanobacteria and hydrocarbon degraders as key players in a notable internal hydrocarbon cycle within the upper ocean, where alkanes are continually produced and subsequently consumed within days. Furthermore we show that cyanobacterial alkane production is likely sufficient to sustain populations of hydrocarbon-degrading bacteria, whose abundances can rapidly expand upon localized release of crude oil from natural seepage and human activities.

Triacylglyceride Production and Autophagous Responses in Chlamydomonas reinhardtii Depend on Resource Allocation and Carbon Source

ABSTRACT To improve the economic viability of microalgal biodiesel, it will be essential to optimize the productivity of fuel molecules such as triacylglyceride (TAG) within the microalgal cell. To understand some of the triggers required for the metabolic switch to TAG production, we studied the effect of the carbon supply (acetate or CO2) in Chlamydomonas reinhardtii (wild type and the starchless sta6 mutant) grown under low N availability. As expected, initial rates of TAG production were much higher when acetate was present than under strictly photosynthetic conditions, particularly for the sta6 mutant, which cannot allocate resources to starch. However, in both strains, TAG production plateaued after a few days in mixotrophic cultures, whereas under autotrophic conditions, TAG levels continued to rise. Moreover, the reduced growth of the sta6 mutant meant that the greatest productivity (measured as mg TAG liter−1 day−1) was found in the wild type growing autotrophically. Wild-type cells responded to low N by autophagy, as shown by degradation of polar (membrane) lipids and loss of photosynthetic pigments, and this was less in cells supplied with acetate. In contrast, little or no autophagy was observed in sta6 mutant cells, regardless of the carbon supply. Instead, very high levels of free fatty acids were observed in the sta6 mutant, suggesting considerable alteration in metabolism. These measurements show the importance of carbon supply and strain selection for lipid productivity. Our findings will be of use for industrial cultivation, where it will be preferable to use fast-growing wild-type strains supplied with gaseous CO2 under autotrophic conditions rather than require an exogenous supply of organic carbon.