Eddy covariance captures four-phase crassulacean acid metabolism (CAM) gas exchange signature in Agave

Bringing CAM photosynthesis to the table: Paving the way for resilient and productive agricultural systems in a changing climate

Modern agricultural systems are directly threatened by global climate change and the resulting freshwater crisis. A considerable challenge in the coming years will be to develop crops that can cope with the consequences of declining freshwater resources and changing temperatures. One approach to meeting this challenge may lie in our understanding of plant photosynthetic adaptations and water use efficiency. Plants from various taxa have evolved crassulacean acid metabolism (CAM), a water-conserving adaptation of photosynthetic carbon dioxide fixation that enables plants to thrive under semi-arid or seasonally drought-prone conditions. Although past research on CAM has led to a better understanding of the inner workings of plant resilience and adaptation to stress, successful introduction of this pathway into C3 or C4 plants has not been reported. The recent revolution in molecular, systems, and synthetic biology, as well as innovations in high-throughput data generation and mining, creates new opportunities to uncover the minimum genetic tool kit required to introduce CAM traits into drought-sensitive crops. Here, we propose four complementary research avenues to uncover this tool kit. First, genomes and computational methods should be used to improve understanding of the nature of variations that drive CAM evolution. Second, single-cell 'omics technologies offer the possibility for in-depth characterization of the mechanisms that trigger environmentally controlled CAM induction. Third, the rapid increase in new 'omics data enables a comprehensive, multimodal exploration of CAM. Finally, the expansion of functional genomics methods is paving the way for integration of CAM into farming systems.

Prospects and perspectives: inferring physiological and regulatory targets for CAM from molecular and modelling approaches

BACKGROUND AND SCOPE

This review summarizes recent advances in our understanding of Crassulacean Acid Metabolism (CAM) by integrating evolutionary, ecological, physiological, metabolic and molecular perspectives. A number of key control loops which moderate the expression of CAM phases, and their metabolic and molecular control, are explored. These include nocturnal stomatal opening, activation of phosphoenolpyruvate carboxylase by a specific protein kinase, interactions with circadian clock control, as well as daytime decarboxylation and activation of Rubisco. The vacuolar storage and release of malic acid and the interplay between the supply and demand for carbohydrate reserves are also key metabolic control points.

FUTURE OPPORTUNITIES

We identify open questions and opportunities, with experimentation informed by top-down molecular modelling approaches allied with bottom-up mechanistic modelling systems. For example, mining transcriptomic datasets using high-speed systems approaches will help to identify targets for future genetic manipulation experiments to define the regulation of CAM (whether circadian or metabolic control). We emphasize that inferences arising from computational approaches or advanced nuclear sequencing techniques can identify potential genes and transcription factors as regulatory targets. However, these outputs then require systematic evaluation, using genetic manipulation in key model organisms over a developmental progression, combining gene silencing and metabolic flux analysis and modelling to define functionality across the CAM day-night cycle. From an evolutionary perspective, the origins and function of CAM succulents and responses to water deficits are set against the mesophyll and hydraulic limitations imposed by cell and tissue succulence in contrasting morphological lineages. We highlight the interplay between traits across shoots (3D vein density, mesophyll conductance and cell shrinkage) and roots (xylem embolism and segmentation). Thus, molecular, biophysical and biochemical processes help to curtail water losses and exploit rapid rehydration during restorative rain events. In the face of a changing climate, we hope such approaches will stimulate opportunities for future research.

Rethinking the potential productivity of crassulacean acid metabolism by integrating metabolic dynamics with shoot architecture, using the example of Agave tequilana

Terrestrial CAM plants typically occur in hot semiarid regions, yet can show high crop productivity under favorable conditions. To achieve a more mechanistic understanding of CAM plant productivity, a biochemical model of diel metabolism was developed and integrated with 3-D shoot morphology to predict the energetics of light interception and photosynthetic carbon assimilation. Using Agave tequilana as an example, this biochemical model faithfully simulated the four diel phases of CO2 and metabolite dynamics during the CAM rhythm. After capturing the 3-D form over an 8-yr production cycle, a ray-tracing method allowed the prediction of the light microclimate across all photosynthetic surfaces. Integration with the biochemical model thereby enabled the simulation of plant and stand carbon uptake over daily and annual courses. The theoretical maximum energy conversion efficiency of Agave spp. is calculated at 0.045-0.049, up to 7% higher than for C3 photosynthesis. Actual light interception, and biochemical and anatomical limitations, reduced this to 0.0069, or 15.6 Mg ha-1  yr-1 dry mass annualized over an 8-yr cropping cycle, consistent with observation. This is comparable to the productivity of many C3 crops, demonstrating the potential of CAM plants in climates where little else may be grown while indicating strategies that could raise their productivity.

The effect of conventional and sustainable agricultural management practices on carbon and water fluxes in a Mexican semi-arid region

Background

Agriculture is essential for food security. However, conventional agriculture alters the water and carbon cycle and soil properties. We investigated the effect of conventional management (CM) and sustainable management (SM) on the carbon and water cycle in crops of nopal (Np) and wheat (Wh).

Methods

A micrometeorological eddy covariance tower was installed to measure water use through evapotranspiration (ET) and the net exchange of CO₂ during the crop's development. Gross primary productivity (GPP), water use efficiency (WUE), and soil properties were obtained.

Results

The results showed that both agricultural managements influenced the carbon flux of the ecosystem, with a lower GPP and Reco in the nopal field (1.85 and 0.99 mmol C m^-2 s^-1, respectively), compared to the wheat field (6.34 and 1.8 mmol C m^-2 s^-1, respectively). It was mainly attributed to the metabolic plant differences, phenological stages, and wheat biomass developed during the winter. On the other hand, the accumulated ET in the SM-Wh plots was lower than SM-Np. Therefore, the crops subjected to sustainable practices use water more efficiently with 1.42 and 1.03 g C m^-3 H₂O for nopal and wheat, respectively. In regard to soil properties, it was observed that tillage alters microbial activity affecting organic matter and carbon. It can be concluded that the differences in agricultural management for both crops altered the carbon and water cycle and soil quality. In addition, implementing good agricultural practices allows more efficient use of water by the plant, higher retention of water in the soil, and less ET.

Understanding interactive processes: a review of CO2 flux, evapotranspiration, and energy partitioning under stressful conditions in dry forest and agricultural environments

Arid and semiarid environments are characterized by low water availability (e.g., in soil and atmosphere), high air temperature, and irregularity in the spatio-temporal distribution of rainfall. In addition to the economic and environmental consequences, drought also causes physiological damage to crops and compromises their survival in ecosystems. The removal of vegetation is responsible for altering the energy exchange of heat and water in natural ecosystems and agricultural areas. The fluxes of CO₂ are also changed, and environments with characteristics of sinks, which can be sources of CO₂ after anthropic disturbances. These changes can be measured through methods such as sap flow, eddy covariance, remote sensing, and energy balance. Despite the relevance of each method mentioned above, there are limitations in their applications that must be respected. Thus, this review aims to quantify the processes and changes of energy fluxes, CO₂, and their interactions with the surfaces of terrestrial ecosystems in dry environments. Studies report that the use of methods that integrate data from climate monitoring towers and remote sensing products helps to improve the accuracy of the determination of energy fluxes on a global scale, also helping to reduce the dissimilarity of results obtained individually. Through the collection of works in the literature, it is reported that several areas of the Brazilian Caatinga biome, which is a Seasonally Dry Tropical Forest have been suffering from changes in land use and land cover. Similar fluxes of sensible heat in areas with cacti and Caatinga can be observed in studies. On the other hand, one of the variables influenced mainly by air temperature is net radiation. In dry forest areas, woody species can store large amounts of carbon in their biomass above and belowground. The use of cacti can modify the local carbon budget when using tree crops together. Therefore, the study highlights the complexity and severity of land degradation and changes in CO₂, water, and energy fluxes in dry environments with areas of forest, grassland, and cacti. Vegetation energy balance is also a critical factor, as these simulations are helpful for use in forecasting weather or climate change. We also highlight the need for more studies that address environmental conservation techniques and cactus in the conservation of degraded areas.

Diversity of CAM plant photosynthesis (crassulacean acid metabolism): a tribute to Barry Osmond

This special issue is a tribute to the Australian plant biologist Professor Charles Barry Osmond - Fellow of the Australian Academy of Sciences, the Royal Society of London, and Leopoldina, the German National Academy of Sciences - and his many contributions to our understanding of the biochemistry and physiological ecology of CAM (crassulacean acid metabolism) photosynthesis. This water-conserving photosynthetic pathway is characterised by nocturnal uptake of atmospheric CO2 and typically enables succulent plants to perform and survive in warm semiarid terrestrial and epiphytic habitats. The idea for this issue is to mark the occasion of Barry's 80th birthday in 2019. The foreword highlights some of his outstanding contributions and introduces the research papers of the special issue.

Modelling nonlinear dynamics of Crassulacean acid metabolism productivity and water use for global predictions

Crassulacean acid metabolism (CAM) crops are important agricultural commodities in water-limited environments across the globe, yet modelling of CAM productivity lacks the sophistication of widely used C3 and C4 crop models, in part due to the complex responses of the CAM cycle to environmental conditions. This work builds on recent advances in CAM modelling to provide a framework for estimating CAM biomass yield and water use efficiency from basic principles. These advances, which integrate the CAM circadian rhythm with established models of carbon fixation, stomatal conductance and the soil-plant-atmosphere continuum, are coupled to models of light attenuation, plant respiration and biomass partitioning. Resulting biomass yield and transpiration for Opuntia ficus-indica and Agave tequilana are validated against field data and compared with predictions of CAM productivity obtained using the empirically based environmental productivity index. By representing regulation of the circadian state as a nonlinear oscillator, the modelling approach captures the diurnal dynamics of CAM stomatal conductance, allowing the prediction of CAM transpiration and water use efficiency for the first time at the plot scale. This approach may improve estimates of CAM productivity under light-limiting conditions when compared with previous methods.

Model approaches to advance crassulacean acid metabolism system integration

This review summarises recent progress in understanding crassulacean acid metabolism (CAM) systems and the integration of internal and external stimuli to maximise water-use efficiency. Complex CAM traits have been reduced to their minimum and captured as computational models, which can now be refined using recently available data from transgenic manipulations and large-scale omics studies. We identify three key areas in which an appropriate choice of modelling tool could help capture relevant comparative molecular data to address the evolutionary drivers and plasticity of CAM. One focus is to identify the environmental and internal signals that drive inverse stomatal opening at night. Secondly, it is important to identify the regulatory processes required to orchestrate the diel pattern of carbon fluxes within mesophyll layers. Finally, the limitations imposed by contrasting succulent systems and associated hydraulic conductance components should be compared in the context of water-use and evolutionary strategies. While network analysis of transcriptomic data can provide insights via co-expression modules and hubs, alternative forms of computational modelling should be used iteratively to define the physiological significance of key components and informing targeted functional gene manipulation studies. We conclude that the resultant improvements of bottom-up, mechanistic modelling systems can enhance progress towards capturing the physiological controls for phylogenetically diverse CAM systems in the face of the recent surge of information in this omics era.

A model of environmental limitations on production of Agave americana L. grown as a biofuel crop in semi-arid regions

Plants that use crassulacean acid metabolism (CAM) have the potential to meet growing agricultural resource demands using land that is considered unsuitable for many common crop species. Agave americana L., an obligate CAM plant, has potential as an advanced biofuel crop in water-limited regions, and has greater cold tolerance than other high-yielding CAM species, but physiological tolerances have not been completely resolved. We developed a model to estimate the growth responses of A. americana to water input, temperature, and photosynthetically active radiation (PAR). The photosynthetic response to PAR was determined experimentally by measuring the integrated leaf gas exchange over 24 h after acclimation to six light levels. Maximum CO2 fixation rates were observed at a PAR intensity of 1250 µmol photons m-2 s-1. Growth responses of A. americana to water and temperature were also determined, and a monthly environmental productivity index (EPI) was derived that can be used to predict biomass growth. The EPI was calculated as the product of water, temperature, and light indices estimated for conditions at a site in Maricopa (Arizona), and compared with measured biomass at the same site (where the first field trial of A. americana as a crop was completed). The monthly EPI summed over the lifetime of multi-year crops was highly correlated with the average measured biomass of healthy 2- and 3-year-old plants grown in the field. The resulting relationship between EPI and biomass provides a simple model for estimating the production of A. americana at a monthly time step according to light, temperature, and precipitation inputs, and is a useful tool for projecting the potential geographic range of this obligate CAM species in future climatic conditions.

Ecophysiology of constitutive and facultative CAM photosynthesis

In plants exhibiting crassulacean acid metabolism (CAM), CAM photosynthesis almost always occurs together with C3 photosynthesis, and occasionally with C4 photosynthesis. Depending on species, ontogeny, and environment, CAM input to total carbon gain can vary from values of <1% to 100%. The wide range of CAM phenotypes between and within species is a fascinating example of functional diversity and plasticity, but poses a significant challenge when attempting to define CAM. CO2 gas exchange experiments designed for this review illustrate key patterns of CAM expression and highlight distinguishing features of constitutive and facultative CAM. Furthermore, they help to address frequently recurring questions on CAM terminology. The functional and evolutionary significance of contrasting CAM phenotypes and of intermediate states between extremes is discussed. Results from a study on nocturnal malate accumulation in 50 species of Aizoaceae exposed to drought and salinity stress suggest that facultative CAM is more widespread amongst vascular plants than previously thought.

RNA-seq transcriptomic profiling of crassulacean acid metabolism pathway in Dendrobium catenatum

The regulation of crassulacean acid metabolism (CAM) pathway has recently become a topic of intensive research and has been explored in terms of several aspects, including phylogenetics, genomics, and transcriptomics. Orchidaceae, which contains approximately 9,000 CAM species, is one of the largest lineages using this special photosynthetic pathway. However, no comprehensive transcriptomic profiling focused on CAM regulation in orchid species had previously been performed. In this report, we present two Illumina RNA-seq datasets, including a total of 24 mature leaf samples with 844.4 million reads, from Dendrobium catenatum (Orchidaceae), a facultative CAM species. The first dataset was generated from a time-course experiment based on the typical CAM phases in a diel. The second was derived from an experiment on drought stress and stress removal. A series of quality assessments were conducted to verify the reliability of the datasets. These transcriptomic profiling datasets will be useful to explore and understand the essence of CAM regulation.

Shifts in gene expression profiles are associated with weak and strong Crassulacean acid metabolism

PREMISE OF THE STUDY

The relative ease of high throughput sequencing is facilitating comprehensive phylogenomic and gene expression studies, even for nonmodel groups. To date, however, these two approaches have not been merged; while phylogenomic methods might use transcriptome sequences to resolve relationships, assessment of gene expression patterns in a phylogenetic context is less common. Here we analyzed both carbon assimilation and gene expression patterns of closely related species within the Agavoideae (Asparagaceae) to elucidate changes in gene expression across weak and strong phenotypes for Crassulacean acid metabolism (CAM).

METHODS

Gene expression patterns were compared across four genera: Agave (CAM), which is paraphyletic with Polianthes (weak CAM) and Manfreda (CAM), and Beschorneria (weak CAM). RNA-sequencing was paired with measures of gas exchange and titratable acidity. Climate niche space was compared across the four lineages to examine abiotic factors and their correlation to CAM.

KEY RESULTS

Expression of homologous genes showed both shared and variable patterns in weak and strong CAM species. Network analysis highlights that despite shared expression patterns, highly connected genes differ between weak and strong CAM, implicating shifts in regulatory gene function as key for the evolution of CAM. Variation in carbohydrate metabolism between weak and strong CAM supports the importance of sugar turnovers for CAM physiology.

CONCLUSIONS

Integration of phylogenetics and RNA-sequencing provides a powerful tool to study the evolution of CAM photosynthesis across closely related but photosynthetically variable species. Our findings regarding shared or shifted gene expression and regulation of CAM via carbohydrate metabolism have important implications for efforts to engineer the CAM pathway into C₃ food and biofuel crops.

Secrets of succulence

Succulent plants are iconic components of the florae of many terrestrial ecosystems, but despite having caused fascination and prompted investigation for centuries, they still harbour many secrets in terms of physiological function and evolution. Tackling these mysteries is important, as this will not only provide insights into the dynamics and details of the convergent evolution of a major adaptive syndrome, but also inform efforts to conserve endangered biodiversity and utilize the unique physiological characteristics of succulents for biofuel and biomass production. Here I review advances in the phylogeny and organismal biology of succulent plants, and discuss how insights from recent work in the wider fields of plant hydraulics and photosynthetic physiology may relate to succulents. The potential for the exploration of mechanistic relationships between anatomical structure and physiological function to improve our understanding of the constraints that have shaped the evolution of succulence is highlighted. Finally, attention is drawn to how new methodologies and technologies provide exciting opportunities to address the wide range of outstanding questions in succulent plant biology.