Predicting photosynthetic pathway from anatomy using machine learning

Plants with Crassulacean acid metabolism (CAM) have long been associated with a specialized anatomy, including succulence and thick photosynthetic tissues. Firm, quantitative boundaries between non-CAM and CAM plants have yet to be established - if they indeed exist. Using novel computer vision software to measure anatomy, we combined new measurements with published data across flowering plants. We then used machine learning and phylogenetic comparative methods to investigate relationships between CAM and anatomy. We found significant differences in photosynthetic tissue anatomy between plants with differing CAM phenotypes. Machine learning-based classification was over 95% accurate in differentiating CAM from non-CAM anatomy, and had over 70% recall of distinct CAM phenotypes. Phylogenetic least squares regression and threshold analyses revealed that CAM evolution was significantly correlated with increased mesophyll cell size, thicker leaves, and decreased intercellular airspace. Our findings suggest that machine learning may be used to aid the discovery of new CAM species and that the evolutionary trajectory from non-CAM to strong, obligate CAM requires continual anatomical specialization.

Shifting photosynthesis between the fast and slow lane: Facultative CAM and water-deficit stress

Five decades ago, the first report of a shift from C3 to CAM (crassulacean acid metabolism) photosynthesis following the imposition of stress was published in this journal. The annual, Mesembryanthemum crystallinum (Aizoaceae), was shown to be a C3 plant when grown under non-saline conditions, and a CAM plant when exposed to high soil salinity. This observation of environmentally triggered CAM eventually led to the introduction of the term facultative CAM, which categorises CAM that is induced or upregulated in response to water-deficit stress and is lost or downregulated when the stress is removed. Reversibility of C3-to-CAM shifts distinguishes stress-driven facultative-CAM responses from purely ontogenetic increases of CAM activity. We briefly review how the understanding of facultative CAM has developed, evaluate the current state of knowledge, and highlight questions of continuing interest. We demonstrate that the long-lived leaves of a perennial facultative-CAM arborescent species, Clusia pratensis, can repeatedly switch between C3 and CAM in response to multiple wet-dry-wet cycles. Undoubtedly, this is a dedicated response to environment, independent of ontogeny. We highlight the potential for engineering facultative CAM into C3 crops to provide a flexible capacity for drought tolerance.

The CAM lineages of planet Earth

BACKGROUND AND SCOPE

The growth of experimental studies of crassulacean acid metabolism (CAM) in diverse plant clades, coupled with recent advances in molecular systematics, presents an opportunity to re-assess the phylogenetic distribution and diversity of species capable of CAM. It has been more than two decades since the last comprehensive lists of CAM taxa were published, and an updated survey of the occurrence and distribution of CAM taxa is needed to facilitate and guide future CAM research. We aimed to survey the phylogenetic distribution of these taxa, their diverse morphology, physiology and ecology, and the likely number of evolutionary origins of CAM based on currently known lineages.

RESULTS AND CONCLUSIONS

We found direct evidence (in the form of experimental or field observations of gas exchange, day-night fluctuations in organic acids, carbon isotope ratios and enzymatic activity) for CAM in 370 genera of vascular plants, representing 38 families. Further assumptions about the frequency of CAM species in CAM clades and the distribution of CAM in the Cactaceae and Crassulaceae bring the currently estimated number of CAM-capable species to nearly 7 % of all vascular plants. The phylogenetic distribution of these taxa suggests a minimum of 66 independent origins of CAM in vascular plants, possibly with dozens more. To achieve further insight into CAM origins, there is a need for more extensive and systematic surveys of previously unstudied lineages, particularly in living material to identify low-level CAM activity, and for denser sampling to increase phylogenetic resolution in CAM-evolving clades. This should allow further progress in understanding the functional significance of this pathway by integration with studies on the evolution and genomics of CAM in its many forms.

Klaus Winter - the indefatigable CAM experimentalist

BACKGROUND

In January 1972, Klaus Winter submitted his first paper on crassulacean acid metabolism (CAM) whilst still an undergraduate student in Darmstadt. During the subsequent half-century, he passed his Staatsexamensarbeit, obtained his Dr. rer. nat. summa cum laude and Dr. rer. nat. habil., won a Heinz Maier-Leibnitz Prize and a Heisenberg Fellowship, and has occupied positions in Germany, Australia, the USA and Panama. Now a doyen in CAM circles, and a Senior Staff Scientist at the Smithsonian Tropical Research Institute (STRI), he has published over 300 articles, of which about 44 % are about CAM.

SCOPE

I document Winter's career, attempting to place his CAM-related scientific output and evolution in the context of factors that have influenced him as he and his science progressed from the 1970s to the 2020s.

The diverse diaspora of CAM: a pole-to-pole sketch

BACKGROUND

Crassulacean acid metabolism (CAM) photosynthesis is a successful adaptation that has evolved often in angiosperms, gymnosperms, ferns and lycophytes. Present in ~5 % of vascular plants, the CAM diaspora includes all continents apart from Antarctica. Species with CAM inhabit most landscapes colonized by vascular plants, from the Arctic Circle to Tierra del Fuego, from below sea level to 4800 m a.s.l., from rainforests to deserts. They have colonized terrestrial, epiphytic, lithophytic, palustrine and aquatic systems, developing perennial, annual or geophyte strategies that can be structurally arborescent, shrub, forb, cladode, epiphyte, vine or leafless with photosynthetic roots. CAM can enhance survival by conserving water, trapping carbon, reducing carbon loss and/or via photoprotection.

SCOPE

This review assesses the phylogenetic diversity and historical biogeography of selected lineages with CAM, i.e. ferns, gymnosperms and eumagnoliids, Orchidaceae, Bromeliaceae, Crassulaceae, Euphorbiaceae, Aizoaceae, Portulacineae (Montiaceae, Basellaceae, Halophytaceae, Didiereaceae, Talinaceae, Portulacaceae, Anacampserotaceae and Cactaceae) and aquatics.

CONCLUSIONS

Most extant CAM lineages diversified after the Oligocene/Miocene, as the planet dried and CO2 concentrations dropped. Radiations exploited changing ecological landscapes, including Andean emergence, Panamanian Isthmus closure, Sundaland emergence and submergence, changing climates and desertification. Evidence remains sparse for or against theories that CAM biochemistry tends to evolve before pronounced changes in anatomy and that CAM tends to be a culminating xerophytic trait. In perennial taxa, any form of CAM can occur depending upon the lineage and the habitat, although facultative CAM appears uncommon in epiphytes. CAM annuals lack strong CAM. In CAM annuals, C3 + CAM predominates, and inducible or facultative CAM is common.

CAM photosynthesis in Bulnesia retama (Zygophyllaceae), a non-succulent desert shrub from South America

BACKGROUND AND AIMS

Bulnesia retama is a drought-deciduous, xerophytic shrub from arid landscapes of South America. In a survey of carbon isotope ratios (δ13C) in specimens from the field, B. retama exhibited less negative values, indicative of CAM or C4 photosynthesis. Here, we investigate whether B. retama is a C4 or CAM plant.

METHODS

Gas-exchange responses to intercellular CO2, diurnal gas-exchange profiles, δ13C and dawn vs. afternoon titratable acidity were measured on leaves and stems of watered and droughted B. retama plants. Leaf and stem cross-sections were imaged to determine whether the tissues exhibited succulent CAM or C4 Kranz anatomy.

KEY RESULTS

Field-collected stems and fruits of B. retama exhibited δ13C between -16 and -19 ‰. Plants grown in a glasshouse from field-collected seeds had leaf δ13C values near -31 ‰ and stem δ13C values near -28 ‰. The CO2 response of photosynthesis showed that leaves and stems used C3 photosynthesis during the day, while curvature in the nocturnal response of net CO2 assimilation rate (A) in all stems, coupled with slightly positive rates of A at night, indicated modest CAM function. C4 photosynthesis was absent. Succulence was absent in all tissues, although stems exhibited tight packing of the cortical chlorenchyma in a CAM-like manner. Tissue titratable acidity increased at night in droughted stems.

CONCLUSIONS

Bulnesia retama is a weak to modest C3 + CAM plant. This is the first report of CAM in the Zygophyllaceae and the first showing that non-succulent, xerophytic shrubs use CAM. CAM alone in B. retama was too limited to explain less negative δ13C in field-collected plants, but combined with effects of low stomatal and mesophyll conductance it could raise δ13C to observed values between -16 and -19 ‰. Modest CAM activity, particularly during severe drought, could enable B. retama to persist in arid habitats of South America.

Reconciling continuous and discrete models of C4 and CAM evolution

BACKGROUND

A current argument in the CAM biology literature has focused on the nature of the CAM evolutionary trajectory: whether there is a smooth continuum of phenotypes between plants with C3 and CAM photosynthesis or whether there are discrete steps of phenotypic evolutionary change such as has been modelled for the evolution of C4 photosynthesis. A further implication is that a smooth continuum would increase the evolvability of CAM, whereas discrete changes would make the evolutionary transition from C3 to CAM more difficult.

SCOPE

In this essay, I attempt to reconcile these two viewpoints, because I think in many ways this is a false dichotomy that is constraining progress in understanding how both CAM and C4 evolved. In reality, the phenotypic space connecting C3 species and strong CAM/C4 species is both a continuum of variably expressed quantitative traits and yet also contains certain combinations of traits that we are able to identify as discrete, recognizable phenotypes. In this sense, the evolutionary mechanics of CAM origination are no different from those of C4 photosynthesis, nor from the evolution of any other complex trait assemblage.

CONCLUSIONS

To make progress, we must embrace the concept of discrete phenotypic phases of CAM evolution, because their delineation will force us to articulate what aspects of phenotypic variation we think are significant. There are some current phenotypic gaps that are limiting our ability to build a complete CAM evolutionary model: the first is how a rudimentary CAM biochemical cycle becomes established, and the second is how the 'accessory' CAM cycle in C3+CAM plants is recruited into a primary metabolism. The connections to the C3 phenotype we are looking for are potentially found in the behaviour of C3 plants when undergoing physiological stress - behaviour that, strangely enough, remains essentially unexplored in this context.

The climate changes promoted the chloroplast genomic evolution of Dendrobium orchids among multiple photosynthetic pathways

Dendrobium orchids have multiple photosynthetic pathways, which can be used as a model system for studying the evolution of crassulacean acid metabolism (CAM). In this study, based on the results of the net photosynthetic rates (P_n), we classified Dendrobium species into three photosynthetic pathways, then employed and compared their chloroplast genomes. The Dendrobium chloroplast genomes have typical quartile structures, ranging from 150,841-153,038 bp. The apparent differences in GC content, sequence variability, and IR junctions of SSC/IR_B junctions (J_SBs) were measured within chloroplast genomes among different photosynthetic pathways. The phylogenetic analysis has revealed multiple independent CAM origins among the selected Dendrobium species. After counting insertions and deletions (InDels), we found that the occurrence rates and distribution densities among different photosynthetic pathways were inconsistent. Moreover, the evolution patterns of chloroplast genes in Dendrobium among three photosynthetic pathways were also diversified. Considering the diversified genome structure variations and the evolution patterns of protein-coding genes among Dendrobium species, we proposed that the evolution of the chloroplast genomes was disproportional among different photosynthetic pathways. Furthermore, climatic correlation revealed that temperature and precipitation have influenced the distribution among different photosynthetic pathways and promoted the foundation of CAM pathway in Dendrobium orchids. Based on our study, we provided not only new insights into the CAM evolution of Dendrobium but also provided beneficial genetic data resources for the further systematical study of Dendrobium.

CAM photosynthesis: the acid test

There is currently considerable interest in the prospects for bioengineering crassulacean acid metabolism (CAM) photosynthesis - or key elements associated with it, such as increased water-use efficiency - into C₃ plants. Resolving how CAM photosynthesis evolved from the ancestral C₃ pathway could provide valuable insights into the targets for such bioengineering efforts. It has been proposed that the ability to accumulate organic acids at night may be common among C₃ plants, and that the transition to CAM might simply require enhancement of pre-existing fluxes, without the need for changes in circadian or diurnal regulation. We show, in a survey encompassing 40 families of vascular plants, that nocturnal acidification is a feature entirely restricted to CAM species. Although many C₃ species can synthesize malate during the light period, we argue that the switch to night-time malic acid accumulation requires a fundamental metabolic reprogramming that couples glycolytic breakdown of storage carbohydrate to the process of net dark CO₂ fixation. This central element of the CAM pathway, even when expressed at a low level, represents a biochemical capability not seen in C₃ plants, and so is better regarded as a discrete evolutionary innovation than as part of a metabolic continuum between C₃ and CAM.

Does the C4 plant Trianthema portulacastrum (Aizoaceae) exhibit weakly expressed crassulacean acid metabolism (CAM)?

We examined whether crassulacean acid metabolism (CAM) is present in Trianthema portulacastrum L. (Aizoaceae), a pantropical, salt-tolerant C4 annual herb with atriplicoid-type Kranz anatomy in leaves but not in stems. The leaves of T. portulacastrum are slightly succulent and the stems are fleshy, similar to some species of Portulaca, the only genus known in which C4 and CAM co-occur. Low- level nocturnal acidification typical of weakly expressed, predominantly constitutive CAM was measured in plants grown for their entire life-cycle in an outdoor raised garden box. Acidification was greater in stems than in leaves. Plants showed net CO2 uptake only during the light irrespective of soil water availability. However, nocturnal traces of CO2 exchange exhibited curved kinetics of reduced CO2 loss during the middle of the night consistent with low-level CAM. Trianthema becomes the second genus of vascular land plants in which C4 and features of CAM have been demonstrated to co-occur in the same plant and the first C4 plant with CAM-type acidification described for the Aizoaceae. Traditionally the stems of herbs are not sampled in screening studies. Small herbs with mildly succulent leaves and fleshy stems might be a numerically significant component of CAM biodiversity.

CAM photosynthesis in desert blooming Cistanthe of the Atacama, Chile

When plants of the Atacama desert undergo episodic blooms, among the most prominent are succulent-leaved Cistanthe (Montiaceae). We demonstrate that two Cistanthe species, the perennial Cistanthe sp. aff. crassifolia and the annual/biannual Cistanthe sp. aff. longiscapa, can exhibit net CO2 uptake and leaf acidification patterns typical of crassulacean acid metabolism (CAM). In C. sp. aff. crassifolia leaves, CAM expression was facultative. CAM-type nocturnal net CO2 uptake and acid accumulation occurred in drought-stressed but not in well-watered plants. By contrast, CAM expression in C. sp. aff. longiscapa was largely constitutive. Nocturnal acid accumulation was present in leaves of well-watered and in droughted plants. Following water-deficit stress, net nocturnal CO2 uptake was induced and the level of acid accumulated increased. Neither nocturnal CO2 uptake nor acid accumulation was reduced when the plants were re-watered. δ13C values of a further nine field-collected Cistanthe species are consistent with a contribution of CAM to their carbon pools. In the Portulacinae, a suborder with eight CAM-containing families, Cistanthe becomes the sixth genus with CAM within the family Montiaceae, and it is likely that the ancestor of all Portulacineae also possessed CAM photosynthesis. In the stochastic rainfall landscape of the Atacama, carbon uptake in the dark is a water-use efficient mechanism that increases the carbon pool available for seed production or dormancy. The next rain event may be years away.

The eco-evolutionary significance of rainfall constancy for facultative CAM photosynthesis

A flexible use of the crassulacean acid metabolism (CAM) has been hypothesised to represent an intermediate stage along a C₃ to full CAM evolutionary continuum, when relative contributions of C₃ vs CAM metabolism are co-determined by evolutionary history and prevailing environmental constraints. However, evidence for such eco-evolutionary interdependencies is lacking. We studied these interdependencies for the leaf-succulent genus Drosanthemum (Aizoaceae, Southern African Succulent Karoo) by testing for relationships between leaf δ¹³ C diagnostic for CAM dependence (i.e. contribution of C₃ and CAM to net carbon gain), and climatic variables related to temperature and precipitation and their temporal variation. We further quantified the effects of shared phylogenetic ancestry on CAM dependence and its relation to climate. CAM dependence is predicted by rainfall and its temporal variation, with high predictive power of rainfall constancy (temporal entropy). The predictive power of rainfall seasonality and temperature-related variables was negligible. Evolutionary history of the tested clades significantly affected the relationship between rainfall constancy and CAM dependence. We argue that higher CAM dependence might provide an adaptive advantage in increasingly unpredictable rainfall environments when the anatomic exaptation (succulence) is already present. These observations might shed light on the evolution of full CAM.

The photosynthetic pathways of plant species surveyed in Australia's national terrestrial monitoring network

The photosynthetic pathway of plants is a fundamental trait that influences terrestrial environments from the local to global level. The distribution of different photosynthetic pathways in Australia is expected to undergo a substantial shift due to climate change and rising atmospheric CO2; however, tracking change is hindered by a lack of data on the pathways of species, as well as their distribution and relative cover within plant communities. Here we present the photosynthetic pathways for 2428 species recorded across 541 plots surveyed by Australia's Terrestrial Ecosystem Research Network (TERN) between 2011 and 2017. This dataset was created to facilitate research exploring trends in vegetation change across Australia. Species were assigned a photosynthetic pathway using published literature and stable carbon isotope analysis of bulk tissue. The photosynthetic pathway of species can be extracted from the dataset individually, or used in conjunction with vegetation surveys to study the occurrence and abundance of pathways across the continent. This dataset will be updated as TERN's plot network expands and new information becomes available.

Comparison of CAM expression, photochemistry and antioxidant responses in Sedum album and Portulaca oleracea under combined stress

Previous studies of crassulacean acid metabolism (CAM) pathway during stress have been directed at individual drought and salinity stress, here, we studied the effects of a combination of drought and salt on CAM expression, chlorophyll fluorescence and antioxidant parameters in the C₃ -CAM facultative Sedum album and C₄ -CAM facultative Portulaca oleracea plants. While salinity alone was not able to induce functional CAM expression in P. oleracea leaves, we showed that salinity induced low level of nocturnal acid accumulation in S. album species. After 20 d of exposure to the combination of simultaneous salt and drought stress, P. oleracea plants exhibited more resistance to photoinhibition as compared to S. album plants. The decrease of maximum quantum yield (F_v /F_m ) in S. album leaves under combined stress was in parallel with the largest suppression of CAM expression of >50%, probably displaying the withdrawal of functional CAM back to C₃ pathway. However, under drought treatment alone, S. album plants exhibited higher photosynthetic flexibility, which was associated with the up-regulation of antioxidant enzymes activities and maintenance of glutathione (GSH) pool, and consequently higher photochemical functioning. The levels of nitric oxide (NO) correlated well with CAM expression, which was observed only in S. album, suggesting that NO acts in a different way in C₃ and C₄ species during CAM induction. Additionally, in both species, over the course of CAM induction, the changes in CAM expression parameters exhibited a similar pattern to that of antioxidant capacity and photochemical functioning parameters.

Celebrating a New Division of Botany at SICB: An Introduction to the Integrative Plant Biology Symposium

The Society for Integrative and Comparative Biology (SICB) should, in theory, be a home for scientists working across the entire Tree of Life. In practice, SICB has remained principally a society that supports integrative zoological research. Here we highlight a broad collection of what we consider to the best in integrative and comparative plant biology, gathered together for a special symposium at the 2019 SICB meeting. This symposium and special issue mark the initiation of a new Division of Botany within SICB, which we hope will usher in a new era of SICB where botanists and zoologists engage, collaborate, and celebrate together in this especially creative period of integrative and comparative biology.

Evolutionary trajectories, accessibility and other metaphors: the case of C4 and CAM photosynthesis

Are evolutionary outcomes predictable? Adaptations that show repeated evolutionary convergence across the Tree of Life provide a special opportunity to dissect the context surrounding their origins, and identify any commonalities that may predict why certain traits evolved many times in particular clades and yet never evolved in others. The remarkable convergence of C₄ and Crassulacean Acid Metabolism (CAM) photosynthesis in vascular plants makes them exceptional model systems for understanding the repeated evolution of complex phenotypes. This review highlights what we have learned about the recurring assembly of C₄ and CAM, focusing on the increasingly predictable stepwise evolutionary integration of anatomy and biochemistry. With the caveat that we currently understand C₄ evolution better than we do CAM, I propose a general model that explains and unites C₄ and CAM evolutionary trajectories. Available data suggest that anatomical modifications are the 'rate-limiting step' in each trajectory, which in large part determines the evolutionary accessibility of both syndromes. The idea that organismal structure exerts a primary influence on innovation is discussed in the context of other systems. Whether the rate-limiting step occurs early or late in the evolutionary assembly of a new phenotype may have profound implications for its distribution across the Tree of Life.