Chemotaxis shapes the microscale organization of the ocean's microbiome.

The capacity of planktonic marine microorganisms to actively seek out and exploit microscale chemical hotspots has been widely theorized to affect ocean-basin scale biogeochemistry1-3, but has never been examined comprehensively in situ among natural microbial communities. Here, using a field-based microfluidic platform to quantify the behavioural responses of marine bacteria and archaea, we observed significant levels of chemotaxis towards microscale hotspots of phytoplankton-derived dissolved organic matter (DOM) at a coastal field site across multiple deployments, spanning several months. Microscale metagenomics revealed that a wide diversity of marine prokaryotes, spanning 27 bacterial and 2 archaeal phyla, displayed chemotaxis towards microscale patches of DOM derived from ten globally distributed phytoplankton species. The distinct DOM composition of each phytoplankton species attracted phylogenetically and functionally discrete populations of bacteria and archaea, with 54% of chemotactic prokaryotes displaying highly specific responses to the DOM derived from only one or two phytoplankton species. Prokaryotes exhibiting chemotaxis towards phytoplankton-derived compounds were significantly enriched in the capacity to transport and metabolize specific phytoplankton-derived chemicals, and displayed enrichment in functions conducive to symbiotic relationships, including genes involved in the production of siderophores, B vitamins and growth-promoting hormones. Our findings demonstrate that the swimming behaviour of natural prokaryotic assemblages is governed by specific chemical cues, which dictate important biogeochemical transformation processes and the establishment of ecological interactions that structure the base of the marine food web.

Environmental gradients predict the ratio of environmentally acquired carotenoids to self-synthesised pteridine pigments.

Carotenoids are important pigments producing integument colouration; however, their dietary availability may be limited in some environments. Many species produce yellow to red hues using a combination of carotenoids and self-synthesised pteridine pigments. A compelling hypothesis is that pteridines replace carotenoids in environments where carotenoid availability is limited. To test this hypothesis, we quantified concentrations of five carotenoid and six pteridine pigments in multiple skin colours and individuals from 27 species of agamid lizards. We show that environmental gradients predict the ratio of carotenoids to pteridines; carotenoid concentrations are lower and pteridine concentrations higher in arid environments with low vegetation productivity. Both carotenoid and pteridine pigments were present in all species, but only pteridine concentrations explained colour variation among species and there were no correlations between carotenoid and pteridine pigments with a similar hue. These results suggest that in arid environments, where carotenoids are likely limited, species may compensate by synthesising more pteridines but do not necessarily replace carotenoids with pteridines of similar hue.

Chemodiversity of Dissolved Organic Matter and Its Molecular Changes Driven by Rhizosphere Activities in Fe Ore Tailings Undergoing Eco-Engineered Pedogenesis.

Dissolved organic matter (DOM) plays an important role in soil structure and biogeochemical function development, which are fundamental for the eco-engineering of tailings-soil formation to underpin sustainable tailings rehabilitation. In the present study, we have characterized the DOM composition and its molecular changes in an alkaline Fe ore tailing primed with organic matter (OM) amendment and plant colonization. The results demonstrated that microbial OM decomposition dramatically increased DOM richness and average molecular weight, as well as its degree of unsaturation, aromaticity, and oxidation in the tailings. Plant colonization drove molecular shifts of DOM by depleting the unsaturated compounds with a high value of nominal oxidation state of carbon (NOSC), such as tannin-like and carboxyl-rich polycyclic-like compounds. This may be partially related to their sequestration by secondary Fe-Si minerals formed from rhizosphere-driven mineral weathering. Furthermore, the molecular shifts of DOM may have also resulted from plant-regulated microbial community changes, which further influenced DOM molecules through microbial-DOM interactions. These findings contribute to the understanding of DOM biogeochemistry and ecofunctionality in the tailings during early pedogenesis driven by OM input and pioneer plant/microbial colonization, providing an important basis for the development of strategies and technologies toward the eco-engineering of tailings-soil formation.

Optimal nutrient exchange and immune responses operate in partner specificity in the cnidarian-dinoflagellate symbiosis.

The relationship between corals and dinoflagellates of the genus Symbiodinium is fundamental to the functioning of coral ecosystems. It has been suggested that reef corals may adapt to climate change by changing their dominant symbiont type to a more thermally tolerant one, although the capacity for such a shift is potentially hindered by the compatibility of different host-symbiont pairings. Here we combined transcriptomic and metabolomic analyses to characterize the molecular, cellular, and physiological processes that underlie this compatibility, with a particular focus on Symbiodinium trenchii, an opportunistic, thermally tolerant symbiont that flourishes in coral tissues after bleaching events. Symbiont-free individuals of the sea anemone Exaiptasia pallida (commonly referred to as Aiptasia), an established model system for the study of the cnidarian-dinoflagellate symbiosis, were colonized with the "normal" (homologous) symbiont Symbiodinium minutum and the heterologous S. trenchii Analysis of the host gene and metabolite expression profiles revealed that heterologous symbionts induced an expression pattern intermediate between the typical symbiotic state and the aposymbiotic state. Furthermore, integrated pathway analysis revealed that increased catabolism of fixed carbon stores, metabolic signaling, and immune processes occurred in response to the heterologous symbiont type. Our data suggest that both nutritional provisioning and the immune response induced by the foreign "invader" are important factors in determining the capacity of corals to adapt to climate change through the establishment of novel symbioses.

Identification of a gene cluster for the synthesis of the plant hormone abscisic acid in the plant pathogen Leptosphaeria maculans.

Leptosphaeria maculans is an ascomycetous fungus that causes the disease blackleg on Brassica napus (canola). In spite of the importance of the disease worldwide, the mechanisms of disease development are poorly understood. Secondary metabolites, which are one of the common virulence factors of pathogenic fungi, have not been extensively explored from this fungus. An RNA-seq dataset was examined to find genes responsible for secondary metabolite synthesis by this fungus during infection. One polyketide synthase gene, pks5, was found to be upregulated during the early biotrophic stage of development. In addition to pks5, six other genes adjacent to the pks5 gene, including one encoding a Zn(II)2Cys6 transcription factor abscisic acid-like 7 gene (abl7), were also upregulated during that time. A striking feature of the L. maculans genome is that it contains large AT-rich regions that are gene-poor and large GC-rich regions that are gene rich. This set of seven co-regulated genes is embedded within and separated by two such AT-rich regions. Three of the genes in the cluster have similarities to those known to be involved in the synthesis of abscisic acid (ABA) in other fungi. When L. maculans is grown in axenic culture the genes in this cluster are not expressed and ABA is not produced. Overexpressing abl7, encoding the putative transcription factor, resulted in the transcription of the six adjacent genes in axenic culture and in the production of ABA, as detected by liquid chromatography quadrupole-time-of-flight mass spectrometry analysis. Mutation of two genes of the cluster using CRISPR/Cas9 did not affect pathogenicity on canola cotyledons. The characterization of the ABA gene cluster has led to the discovery of the co-regulation of genes within an AT-rich region by a transcription factor, and the first report of the plant hormone abscisic acid being produced by L. maculans.

Red carotenoids and associated gene expression explain colour variation in frillneck lizards.

A long-standing hypothesis in evolutionary ecology is that red-orange ornamental colours reliably signal individual quality owing to limited dietary availability of carotenoids and metabolic costs associated with their production, such as the bioconversion of dietary yellow carotenoids to red ketocarotenoids. However, in ectothermic vertebrates, these colours can also be produced by self-synthesized pteridine pigments. As a consequence, the relative ratio of pigment types and their biochemical and genetic basis have implications for the costs and information content of colour signals; yet they remain poorly known in most taxonomic groups. We tested whether red- and yellow-frilled populations of the frillneck lizard, Chlamydosaurus kingii, differ in the ratio of different biochemical classes of carotenoid and pteridine pigments, and examined associated differences in gene expression. We found that, unlike other squamate reptiles, red hues derive from a higher proportion of ketocarotenoids relative to both dietary yellow carotenoids and to pteridines. Whereas red frill skin showed higher expression of several genes associated with carotenoid metabolism, yellow frill skin showed higher expression of genes associated with steroid hormones. Based on the different mechanisms underlying red and yellow signals, we hypothesize that frill colour conveys different information in the two populations. More generally, the data expand our knowledge of the genetic and biochemical basis of colour signals in vertebrates.

Resolving coral photoacclimation dynamics through coupled photophysiological and metabolomic profiling.

Corals continuously adjust to short-term variation in light availability on shallow reefs. Long-term light alterations can also occur as a result of natural and anthropogenic stressors, as well as management interventions such as coral transplantation. Although short-term photophysiological responses are relatively well understood in corals, little information is available regarding photoacclimation dynamics over weeks of altered light availability. We coupled photophysiology and metabolomic profiling to explore changes that accompany longer-term photoacclimation in a key Great Barrier Reef coral species, Acropora muricata High light (HL)- and low light (LL)-acclimated corals were collected from the reef and reciprocally exposed to high and low light ex situ Rapid light curves using pulse-amplitude modulation (PAM) fluorometry revealed photophysiological acclimation of LL corals to HL and HL corals to LL within 21 days. A subset of colonies sampled at 7 and 21 days for untargeted LC-MS and GC-MS metabolomic profiling revealed metabolic reorganization before acclimation was detected using PAM fluorometry. Metabolomic shifts were more pronounced for LL to HL corals than for their HL to LL counterparts. Compounds driving metabolomic separation between HL-exposed and LL control colonies included amino acids, organic acids, fatty acids and sterols. Reduced glycerol and campesterol suggest decreased translocation of photosynthetic products from symbiont to host in LL to HL corals, with concurrent increases in fatty acid abundance indicating reliance on stored lipids for energy. We discuss how these data provide novel insight into environmental regulation of metabolism and implications for management strategies that drive rapid changes in light availability.

DMSP biosynthesis by an animal and its role in coral thermal stress response.

Globally, reef-building corals are the most prolific producers of dimethylsulphoniopropionate (DMSP), a central molecule in the marine sulphur cycle and precursor of the climate-active gas dimethylsulphide. At present, DMSP production by corals is attributed entirely to their algal endosymbiont, Symbiodinium. Combining chemical, genomic and molecular approaches, we show that coral juveniles produce DMSP in the absence of algal symbionts. DMSP levels increased up to 54% over time in newly settled coral juveniles lacking algal endosymbionts, and further increases, up to 76%, were recorded when juveniles were subjected to thermal stress. We uncovered coral orthologues of two algal genes recently identified in DMSP biosynthesis, strongly indicating that corals possess the enzymatic machinery necessary for DMSP production. Our results overturn the paradigm that photosynthetic organisms are the sole biological source of DMSP, and highlight the double jeopardy represented by worldwide declining coral cover, as the potential to alleviate thermal stress through coral-produced DMSP declines correspondingly.

Revealing the Biochemical and Genetic Basis of Color Variation in a Polymorphic Lizard.

Determining the mechanistic and genetic basis of animal coloration is essential to understand the costs and constraints on color production, and the evolution and maintenance of phenotypic variation. However, genes underlying structural color and widespread pigment classes apart from melanin remain largely uncharacterized, in part due to restricted taxonomic focus. We combined liquid chromatography-mass spectrometry and RNA-seq gene expression analyses to characterize the pigments and genes associated with skin color in the polymorphic lizard, Ctenophorus decresii. Throat coloration in male C. decresii may be a combination of orange, yellow, grey, or ultra-violet blue. We confirmed the presence of two biochemically different pigment classes, pteridines (self-synthesized) and carotenoids (acquired through the diet), in all skin colors. Orange skin had the highest levels of pteridine pigments while yellow skin tended to have higher levels of carotenoids, of which the vitamin A precursors ß-carotene and ß-cryptoxanthin have not been previously confirmed in reptiles. These results were confirmed by gene expression analyses, which detected 489 genes differentially expressed between the skin colors, including genes associated with pteridine production, provitamin A carotenoid metabolism, iridophore-specific synthesis, melanin synthesis, and steroid hormone pathways. For the majority of these 489 genes, however, our study reveals a new association with color production in vertebrates. These data represent a significant contribution to understanding the genetic basis of color variation in vertebrates and a rich resource for further studies.

Partner switching and metabolic flux in a model cnidarian-dinoflagellate symbiosis.

Metabolite exchange is fundamental to the viability of the cnidarian-Symbiodiniaceae symbiosis and survival of coral reefs. Coral holobiont tolerance to environmental change might be achieved through changes in Symbiodiniaceae species composition, but differences in the metabolites supplied by different Symbiodiniaceae species could influence holobiont fitness. Using 13C stable-isotope labelling coupled to gas chromatography-mass spectrometry, we characterized newly fixed carbon fate in the model cnidarian Exaiptasia pallida (Aiptasia) when experimentally colonized with either native Breviolum minutum or non-native Durusdinium trenchii Relative to anemones containing B. minutum, D. trenchii-colonized hosts exhibited a 4.5-fold reduction in 13C-labelled glucose and reduced abundance and diversity of 13C-labelled carbohydrates and lipogenesis precursors, indicating symbiont species-specific modifications to carbohydrate availability and lipid storage. Mapping carbon fate also revealed significant alterations to host molecular signalling pathways. In particular, D. trenchii-colonized hosts exhibited a 40-fold reduction in 13C-labelled scyllo-inositol, a potential interpartner signalling molecule in symbiosis specificity. 13C-labelling also highlighted differential antioxidant- and ammonium-producing pathway activities, suggesting physiological responses to different symbiont species. Such differences in symbiont metabolite contribution and host utilization may limit the proliferation of stress-driven symbioses; this contributes valuable information towards future scenarios that select in favour of less-competent symbionts in response to environmental change.

Mapping carbon fate during bleaching in a model cnidarian symbiosis: the application of 13 C metabolomics.

Coral bleaching is a major threat to the persistence of coral reefs. Yet we lack detailed knowledge of the metabolic interactions that determine symbiosis function and bleaching-induced change. We mapped autotrophic carbon fate within the free metabolite pools of both partners of a model cnidarian-dinoflagellate symbiosis (Aiptasia-Symbiodinium) during exposure to thermal stress via the stable isotope tracer (13 C bicarbonate), coupled to GC-MS. Symbiont photodamage and pronounced bleaching coincided with substantial increases in the turnover of non13 C-labelled pools in the dinoflagellate (lipid and starch store catabolism). However, 13 C enrichment of multiple compounds associated with ongoing carbon fixation and de novo biosynthesis pathways was maintained (glucose, fatty acid and lipogenesis intermediates). Minimal change was also observed in host pools of 13 C-enriched glucose (a major symbiont-derived mobile product). However, host pathways downstream showed altered carbon fate and/or pool composition, with accumulation of compatible solutes and nonenzymic antioxidant precursors. In hospite symbionts continue to provide mobile products to the host, but at a significant cost to themselves, necessitating the mobilization of energy stores. These data highlight the need to further elucidate the role of metabolic interactions between symbiotic partners, during the process of thermal acclimation and coral bleaching.

Epidermal bladder cells confer salinity stress tolerance in the halophyte quinoa and Atriplex species.

Epidermal bladder cells (EBCs) have been postulated to assist halophytes in coping with saline environments. However, little direct supporting evidence is available. Here, Chenopodium quinoa plants were grown under saline conditions for 5 weeks. One day prior to salinity treatment, EBCs from all leaves and petioles were gently removed by using a soft cosmetic brush and physiological, ionic and metabolic changes in brushed and non-brushed leaves were compared. Gentle removal of EBC neither initiated wound metabolism nor affected the physiology and biochemistry of control-grown plants but did have a pronounced effect on salt-grown plants, resulting in a salt-sensitive phenotype. Of 91 detected metabolites, more than half were significantly affected by salinity. Removal of EBC dramatically modified these metabolic changes, with the biggest differences reported for gamma-aminobutyric acid (GABA), proline, sucrose and inositol, affecting ion transport across cellular membranes (as shown in electrophysiological experiments). This work provides the first direct evidence for a role of EBC in salt tolerance in halophytes and attributes this to (1) a key role of EBC as a salt dump for external sequestration of sodium; (2) improved K+ retention in leaf mesophyll and (3) EBC as a storage space for several metabolites known to modulate plant ionic relations.

13C metabolomics reveals widespread change in carbon fate during coral bleaching.

INTRODUCTION: Rising seawater temperatures are threatening the persistence of coral reefs; where above critical thresholds, thermal stress results in a breakdown of the coral-dinoflagellate symbiosis and the loss of algal symbionts (coral bleaching). As symbiont-derived organic products typically form a major portion of host energy budgets, this has major implications for the fitness and persistence of symbiotic corals. OBJECTIVES: We aimed to determine change in autotrophic carbon fate within individual compounds and downstream metabolic pathways in a coral symbiosis exposed to varying degrees of thermal stress and bleaching. METHODS: We applied gas chromatography-mass spectrometry coupled to a stable isotope tracer (13C), to track change in autotrophic carbon fate, in symbiont and host individually, following exposure to elevated water temperature. RESULTS: Thermal stress resulted in partner-specific changes in carbon fate, which progressed with heat stress duration. We detected modifications to carbohydrate and fatty acid metabolism, lipogenesis, and homeostatic responses to thermal, oxidative and osmotic stress. Despite pronounced photodamage, remaining in hospite symbionts continued to produce organic products de novo and translocate to the coral host. However as bleaching progressed, we observed minimal 13C enrichment of symbiont long-chain fatty acids, also reflected in 13C enrichment of host fatty acid pools. CONCLUSION: These data have major implications for our understanding of coral symbiosis function during bleaching. Our findings suggest that during early stage bleaching, remaining symbionts continue to effectively translocate a variety of organic products to the host, however under prolonged thermal stress there is likely a reduction in the quality of these products.

AI Denoising Significantly Enhances Image Quality and Diagnostic Confidence in Interventional Cone-Beam Computed Tomography.

(1) To investigate whether interventional cone-beam computed tomography (cbCT) could benefit from AI denoising, particularly with respect to patient body mass index (BMI); (2) From 1 January 2016 to 1 January 2022, 100 patients with liver-directed interventions and peri-procedural cbCT were included. The unenhanced mask run and the contrast-enhanced fill run of the cbCT were reconstructed using weighted filtered back projection. Additionally, each dataset was post-processed using a novel denoising software solution. Place-consistent regions of interest measured signal-to-noise ratio (SNR) per dataset. Corrected mixed-effects analysis with BMI subgroup analyses compared objective image quality. Multiple linear regression measured the contribution of "Radiation Dose", "Body-Mass-Index", and "Mode" to SNR. Two radiologists independently rated diagnostic confidence. Inter-rater agreement was measured using Spearman correlation (r); (3) SNR was significantly higher in the denoised datasets than in the regular datasets (p < 0.001). Furthermore, BMI subgroup analysis showed significant SNR deteriorations in the regular datasets for higher patient BMI (p < 0.001), but stable results for denoising (p > 0.999). In regression, only denoising contributed positively towards SNR (0.6191; 95%CI 0.6096 to 0.6286; p < 0.001). The denoised datasets received overall significantly higher diagnostic confidence grades (p = 0.010), with good inter-rater agreement (r ≥ 0.795, p < 0.001). In a subgroup analysis, diagnostic confidence deteriorated significantly for higher patient BMI (p < 0.001) in the regular datasets but was stable in the denoised datasets (p ≥ 0.103).; (4) AI denoising can significantly enhance image quality in interventional cone-beam CT and effectively mitigate diagnostic confidence deterioration for rising patient BMI.

Proteome metabolome and transcriptome data for three Symbiodiniaceae under ambient and heat stress conditions.

The Symbiodiniaceae are a taxonomically and functionally diverse family of marine dinoflagellates. Their symbiotic relationship with invertebrates such as scleractinian corals has made them the focus of decades of research to resolve the underlying biology regulating their sensitivity to stressors, particularly thermal stress. Research to-date suggests that Symbiodiniaceae stress sensitivity is governed by a complex interplay between phylogenetic dependent and independent traits (diversity of characteristics of a species). Consequently, there is a need for datasets that simultaneously broadly resolve molecular and physiological processes under stressed and non-stressed conditions. Therefore, we provide a dataset simultaneously generating transcriptome, metabolome, and proteome data for three ecologically important Symbiodiniaceae isolates under nutrient replete growth conditions and two temperature treatments (ca. 26 °C and 32 °C). Elevated sea surface temperature is primarily responsible for coral bleaching events that occur when the coral-Symbiodiniaceae relationship has been disrupted. Symbiodiniaceae can strongly influence their host's response to thermal stress and consequently it is necessary to resolve drivers of Symbiodiniaceae heat stress tolerance. We anticipate these datasets to expand our understanding on the key genotypic and functional properties that influence the sensitivities of Symbiodiniaceae to thermal stress.

Production of metabolites of the anti-cancer drug noscapine using a P450BM3 mutant library.

Cytochrome P450 enzymes are a promising tool for the late-stage diversification of lead drug candidates and can provide an alternative route to structural modifications that are difficult to achieve with synthetic chemistry. In this study, a library of P450BM3 mutants was produced using site-directed mutagenesis and the enzymes screened for metabolism of the opium poppy alkaloid noscapine, a drug with anticancer activity. Of the 18 enzyme mutants screened, 12 showed an ability to metabolise noscapine that was not present in the wild-type enzyme. Five noscapine metabolites were detected by LC-MS/MS, with the major metabolite for all mutants being N-demethylated noscapine. The highest observed regioselectivity for N-demethylation was 88%. Two hydroxylated metabolites, a catechol and two C-C cleavage products were also detected. P450-mediated production of hydroxylated and N-demethylated noscapine structures may be useful for the development of noscapine analogues with improved biological activity. The variation in substrate turnover, coupling efficiency and product distribution between the active mutants was considered alongside in silico docking experiments to gain insight into structural and functional effects of the introduced mutations. Selected mutants were identified as targets for further mutagenesis to improve activity and when coupled with an optimised process may provide a route for the preparative-scale production of noscapine metabolites.

Structural and functional measures of marine microbial communities: An experiment to assess implications for oil spill management.

Microbial communities are ecologically important in aquatic environments and impacts on microbes have the potential to affect a number of functional processes. We have amended seawater with a crude oil and assessed changes in species composition as well as a measure of functional diversity (the ability of the community to utilise different carbon sources) and the community level metabolic signature. We found that there was a degree of functional redundancy in the community we tested. Oiled assemblages became less diverse and more dominated by specialist hydrocarbon degraders, carbon source utilisation increased initially but there was no change in metabolic signature in this small scale laboratory experiment. This study supports the decision framework around management of oil spills. This package of methods has the potential to be used in the testing and selection of new dispersants for use in oil spill response.

Statistical modelling coupled with LC-MS analysis to predict human upper intestinal absorption of phytochemical mixtures.

A diet rich in phytochemicals confers benefits for health by reducing the risk of chronic diseases via regulation of oxidative stress and inflammation (OSI). For optimal protective bio-efficacy, the time required for phytochemicals and their metabolites to reach maximal plasma concentrations (Tmax) should be synchronised with the time of increased OSI. A statistical model has been reported to predict Tmax of individual phytochemicals based on molecular mass and lipophilicity. We report the application of the model for predicting the absorption profile of an uncharacterised phytochemical mixture, herein referred to as the 'functional fingerprint'. First, chemical profiles of phytochemical extracts were acquired using liquid chromatography mass spectrometry (LC-MS), then the molecular features for respective components were used to predict their plasma absorption maximum, based on molecular mass and lipophilicity. This method of 'functional fingerprinting' of plant extracts represents a novel tool for understanding and optimising the health efficacy of plant extracts.

Diurnal Changes in Transcript and Metabolite Levels during the Iron Deficiency Response of Rice.

BACKGROUND: Rice (Oryza sativa L.) is highly susceptible to iron (Fe) deficiency due to low secretion levels of the mugineic acid (MA) family phytosiderophore (PS) 2'-deoxymugineic acid (DMA) into the rhizosphere. The low levels of DMA secreted by rice have proved challenging to measure and, therefore, the pattern of DMA secretion under Fe deficiency has been less extensively studied relative to other graminaceous monocot species that secrete high levels of PS, such as barley (Hordeum vulgare L.). RESULTS: Gene expression and metabolite analyses were used to characterise diurnal changes occurring during the Fe deficiency response of rice. Iron deficiency inducible genes involved in root DMA biosynthesis and secretion followed a diurnal pattern with peak induction occurring 3-5 h after the onset of light; a result consistent with that of other Strategy II plant species such as barley and wheat. Furthermore, triple quadrupole mass spectrometry identified 3-5 h after the onset of light as peak time of DMA secretion from Fe-deficient rice roots. Metabolite profiling identified accumulation of amines associated with metal chelation, metal translocation and plant oxidative stress responses occurring with peak induction 10-12 h after the onset of light. CONCLUSION: The results of this study confirmed that rice shares a similar peak time of Fe deficiency associated induction of DMA secretion compared to other Strategy II plant species but has less prominent daily fluctuations of DMA secretion. It also revealed metabolic changes associated with the remediation of Fe deficiency and mitigation of damage from resulting stress in rice roots. This study complements previous studies on the genetic changes in response to Fe deficiency in rice and constitutes an important advance towards our understanding of the molecular mechanisms underlying the rice Fe deficiency response.

In situ metabolomic- and transcriptomic-profiling of the host-associated cyanobacteria Prochloron and Acaryochloris marina.

The tropical ascidian Lissoclinum patella hosts two enigmatic cyanobacteria: (1) the photoendosymbiont Prochloron spp., a producer of valuable bioactive compounds and (2) the chlorophyll-d containing Acaryochloris spp., residing in the near-infrared enriched underside of the animal. Despite numerous efforts, Prochloron remains uncultivable, restricting the investigation of its biochemical potential to cultivation-independent techniques. Likewise, in both cyanobacteria, universally important parameters on light-niche adaptation and in situ photosynthetic regulation are unknown. Here we used genome sequencing, transcriptomics and metabolomics to investigate the symbiotic linkage between host and photoendosymbiont and simultaneously probed the transcriptional response of Acaryochloris in situ. During high light, both cyanobacteria downregulate CO2 fixing pathways, likely a result of O2 photorespiration on the functioning of RuBisCO, and employ a variety of stress-quenching mechanisms, even under less stressful far-red light (Acaryochloris). Metabolomics reveals a distinct biochemical modulation between Prochloron and L. patella, including noon/midnight-dependent signatures of amino acids, nitrogenous waste products and primary photosynthates. Surprisingly, Prochloron constitutively expressed genes coding for patellamides, that is, cyclic peptides of great pharmaceutical value, with yet unknown ecological significance. Together these findings shed further light on far-red-driven photosynthesis in natural consortia, the interplay of Prochloron and its ascidian partner in a model chordate photosymbiosis and the uncultivability of Prochloron.The ISME Journal advance online publication, 31 October 2017; doi:10.1038/ismej.2017.192.