Effects of phosphorus starvation versus limitation on the marine cyanobacteriumProchlorococcus MED4 I: uptake physiology

Unveiling the responses of Alexandrium pacificum to phosphorus utilization by physiological and transcriptomic analysis

Phosphorus (P) is an essential macronutrient impacting bloom formation of marine dinoflagellates. The dinoflagellate Alexandrium pacificum is a cosmopolitan species known to frequently cause dense blooms in estuarine and coastal waters worldwide, while the physiological and molecular responses of A. pacificum to P utilization are still not well understood. Herein, the growth, P utilization, toxin production and transcriptomes of A. pacificum grown under P-deficient, inorganic P-replete, and organic P-replete conditions were compared. The results indicated that P-deficient adversely affected the growth of A. pacificum and significantly down-regulated the expression of genes related to P transport and material metabolism, but enhanced the production of toxin. On the other hand, no significant differences were observed in growth and toxin production between the organic and inorganic P-replete treatments. However, genes involved in P transport, utilization and TCA cycle were significantly changed in the organic P-replete compared with the inorganic P-replete group, and the mechanisms underlying the use of various organic P compounds were different. These findings suggested that A. pacificum evolved diverse organic P utilization strategies to adapt to low P conditions, which might be a crucial factor driving bloom formation in a low inorganic P environment.

Phosphorus storage and utilization strategies of two bloom-forming freshwater cyanobacteria

The inter-relationships between cellular phosphorus (P) storage, dissolved inorganic P (DIP) uptake affinity, alkaline phosphatase activity (APA) and dissolved inorganic nitrogen (DIN) concentrations were studied in two ubiquitous diazotrophic freshwater cyanobacteria, Raphidiopsis raciborskii (six strains) and Chrysosporum ovalisporum (two strains). DIP uptake kinetics were measured using rates of incorporation of the radio-isotope, 33P and APA as a proxy for DOP-ester utilization. The study showed that DIP uptake of individual strains followed Michaelis-Menten kinetics (modified in our study to incorporate cellular P quotas), but differed with DIN and P availability, and between growth stages. High-affinity DIP uptake and APA were activated below a P quota threshold of approximately 0.01 µg P µg-1 C across the species and strains. C. ovalisporum had significantly higher APA and P quotas (per unit C and cell) but lower uptake affinity than R. raciborskii. Demand for DIP by C. ovalisporum increased when N fixation occurred, but typically not for R. raciborskii. Our results indicate that cyanobacterial species and strains differ in their strategies to P limiting conditions, and highlight the interplay between N and P. Physiological adaptations like APA and diazotrophy of cyanobacteria adapting to low DIP and/or DIN conditions may occur simultaneously and drive species dominance in oligotrophic environments.

Biochemical and structural characterization of the cyanophage-encoded phosphate binding protein: implications for enhanced phosphate uptake of infected cyanobacteria

To acquire phosphorus, cyanobacteria use the typical bacterial ABC-type phosphate transporter, which is composed of a periplasmic high-affinity phosphate-binding protein PstS and a channel formed by two transmembrane proteins PstC and PstA. A putative pstS gene was identified in the genomes of cyanophages that infect the unicellular marine cyanobacteria Prochlorococcus and Synechococcus. However, it has not been determined whether the cyanophage PstS protein is functional during infection to enhance the phosphate uptake rate of host cells. Here we showed that the cyanophage P-SSM2 PstS protein was abundant in the infected Prochlorococcus NATL2A cells and the host phosphate uptake rate was enhanced after infection. This is consistent with our biochemical and structural analyses showing that the phage PstS protein is indeed a high-affinity phosphate-binding protein. We further modeled the complex structure of phage PstS with host PstCA and revealed three putative interfaces that may facilitate the formation of a chimeric ABC transporter. Our results provide insights into the molecular mechanism by which cyanophages enhance the phosphate uptake rate of cyanobacteria. Phosphate acquisition by infected bacteria can increase the phosphorus contents of released cellular debris and virus particles, which together constitute a significant proportion of the marine dissolved organic phosphorus pool. This article is protected by copyright. All rights reserved.

Low Specific Phosphorus Uptake Affinity of Epilithon in Three Oligo- to Mesotrophic Post-mining Lakes

Epilithon contributes to phosphorus (P) cycling in lakes, but its P uptake traits have been rarely studied. We measured the chemical composition of epilithon and its inorganic P uptake kinetics using isotope ³³P in three deep oligo- to mesotrophic post-mining lakes in April, July, and October 2019. Over the sampling period, epilithon biomass doubled, while the P content in biomass dropped to 60% of the April values, and the seasonal changes in P content expressed per epilithon area were only marginal and statistically not significant. High epilithic C:P molar ratios (677 on average) suggested strong P deficiency in all investigated lakes. Regarding the kinetic parameters of phosphorus uptake, maximum uptake velocity (V_max, seasonal range 1.9–129 mg P g OM^–1 h^–1) decreased by an order of magnitude from April to October, while half-saturation constant (K_S, seasonal range 3.9–135 mg P L^–1) did not show any consistent temporal trend. Values of epilithic specific P uptake affinity (SPUA_E, seasonal range 0.08–3.1 L g OM^–1 h^–1) decreased from spring to autumn and were two to four orders of magnitude lower than the corresponding values for seston (SPUA_sest), which showed an opposite trend. Considering our results, we suggest a possible mechanism underlying a stable coexistence of planktonic and epilithic microorganisms, with plankton prospering mostly in summer and autumn and epilithon in winter and spring season. Additionally, a phenomenon of reversible abiotic P adsorption on epilithon was observed.

Phosphorus Release and Regeneration Following Laboratory Lysis of Bacterial Cells

The availability of phosphorus limits primary production in large regions of the oceans, and marine microbes use a variety of strategies to overcome this limitation. One strategy is the production of alkaline phosphatase (APase), which allows hydrolysis of larger dissolved organic phosphorus (DOP) compounds in the periplasm or at the cell surface for transport of orthophosphate into the cell. Cell lysis, driven by grazing and viral infection, releases phosphorus-containing cell components, along with active enzymes that could persist after lysis. The importance of this continued enzymatic activity for orthophosphate regeneration is unknown. We used three model bacteria – Escherichia coli K-12 MG1655, Synechococcus sp. WH7803, and Prochlorococcus sp. MED4 – to assess the impact of continued APase activity after cell lysis, via lysozyme treatment, on orthophosphate regeneration. Direct release of orthophosphate scaled with cell size and was reduced under phosphate-starved conditions where APase activity continued for days after lysis. All lysate incubations showed post-lysis orthophosphate generation suggesting phosphatases other than APase maintain activity. Rates of DOP hydrolysis and orthophosphate remineralization varied post-lysis among strains. Escherichia coli K-12 MG1655 rates of remineralization were 0.6 and 1.2 amol cell^–1hr^–1 under deplete and replete conditions; Synechococcus WH7803 lysates ranged from 0.04 up to 0.3 amol cell^–1hr^–1 during phosphorus deplete and replete conditions, respectively, while in Prochlorococcus MED4 lysates, rates were stable at 0.001 amol cell^–1hr^–1 in both conditions. The range of rates of hydrolysis and regeneration underscores the taxonomic and biochemical variability in the process of nutrient regeneration and further highlights the complexity of quantitatively resolving the major fluxes within the microbial loop.

Dynamic Allocation of Carbon Storage and Nutrient-Dependent Exudation in a Revised Genome-Scale Model of Prochlorococcus

Microbial life in the oceans impacts the entire marine ecosystem, global biogeochemistry and climate. The marine cyanobacterium Prochlorococcus, an abundant component of this ecosystem, releases a significant fraction of the carbon fixed through photosynthesis, but the amount, timing and molecular composition of released carbon are still poorly understood. These depend on several factors, including nutrient availability, light intensity and glycogen storage. Here we combine multiple computational approaches to provide insight into carbon storage and exudation in Prochlorococcus. First, with the aid of a new algorithm for recursive filling of metabolic gaps (ReFill), and through substantial manual curation, we extended an existing genome-scale metabolic model of Prochlorococcus MED4. In this revised model (iSO595), we decoupled glycogen biosynthesis/degradation from growth, thus enabling dynamic allocation of carbon storage. In contrast to standard implementations of flux balance modeling, we made use of forced influx of carbon and light into the cell, to recapitulate overflow metabolism due to the decoupling of photosynthesis and carbon fixation from growth during nutrient limitation. By using random sampling in the ensuing flux space, we found that storage of glycogen or exudation of organic acids are favored when the growth is nitrogen limited, while exudation of amino acids becomes more likely when phosphate is the limiting resource. We next used COMETS to simulate day-night cycles and found that the model displays dynamic glycogen allocation and exudation of organic acids. The switch from photosynthesis and glycogen storage to glycogen depletion is associated with a redistribution of fluxes from the Entner–Doudoroff to the Pentose Phosphate pathway. Finally, we show that specific gene knockouts in iSO595 exhibit dynamic anomalies compatible with experimental observations, further demonstrating the value of this model as a tool to probe the metabolic dynamic of Prochlorococcus.

Prochlorococcus Cells Rely on Microbial Interactions Rather than on Chlorotic Resting Stages To Survive Long-Term Nutrient Starvation

The ability of microorganisms to withstand long periods of nutrient starvation is key to their survival and success under highly fluctuating conditions that are common in nature. Therefore, one would expect this trait to be prevalent among organisms in the nutrient-poor open ocean. Here, we show that this is not the case for Prochlorococcus, a globally abundant and ecologically important marine cyanobacterium. Instead, Prochlorococcus relies on co-occurring heterotrophic bacteria to survive extended phases of nutrient and light starvation. Our results highlight the power of microbial interactions to drive major biogeochemical cycles in the ocean and elsewhere with consequences at the global scale.

Many microorganisms produce resting cells with very low metabolic activity that allow them to survive phases of prolonged nutrient or energy stress. In cyanobacteria and some eukaryotic phytoplankton, the production of resting stages is accompanied by a loss of photosynthetic pigments, a process termed chlorosis. Here, we show that a chlorosis-like process occurs under multiple stress conditions in axenic laboratory cultures of Prochlorococcus, the dominant phytoplankton linage in large regions of the oligotrophic ocean and a global key player in ocean biogeochemical cycles. In Prochlorococcus strain MIT9313, chlorotic cells show reduced metabolic activity, measured as C and N uptake by Nanoscale secondary ion mass spectrometry (NanoSIMS). However, unlike many other cyanobacteria, chlorotic Prochlorococcus cells are not viable and do not regrow under axenic conditions when transferred to new media. Nevertheless, cocultures with a heterotrophic bacterium, Alteromonas macleodii HOT1A3, allowed Prochlorococcus to survive nutrient starvation for months. We propose that reliance on co-occurring heterotrophic bacteria, rather than the ability to survive extended starvation as resting cells, underlies the ecological success of Prochlorococcus.

Nutrient ratios in marine particulate organic matter are predicted by the population structure of well-adapted phytoplankton

A common assumption of a constant nitrogen-to-phosphorus ratio (N:P) of 16:1 in marine particulate organic matter (POM) appears to be invalidated by observations of major spatial variations in N:P. Two main explanations have been proposed. The first attributes the N:P variability to changes in the community composition of well-adapted phytoplankton. The second proposes that variability arises from physiological acclimation involving intracellular adjustments of nutrient allocation under nutrient deficiency. Using a model of phytoplankton physiology, observational datasets, and a review of laboratory culture results, we assess the mechanistic basis of N:P variability. We find that the taxonomic composition of well-adapted phytoplankton best explains observed variations in POM N:P. Furthermore, we show that acclimation to nutrient deficiency may be safely neglected when considering the effects of ecology on POM N:P. These findings provide insight into the controls on global variability in POM composition and average phytoplankton physiological performance in the oceans.

Mixotrophy in marine picocyanobacteria: use of organic compounds by Prochlorococcus and Synechococcus

Marine picocyanobacteria of the Prochlorococcus and Synechococcus genera have been longtime considered as autotrophic organisms. However, compelling evidence published over the last 15 years shows that these organisms can use different organic compounds containing key elements to survive in oligotrophic oceans, such as N (amino acids, amino sugars), S (dimethylsulfoniopropionate, DMSP), or P (ATP). Furthermore, marine picocyanobacteria can also take up glucose and use it as a source of carbon and energy, despite the fact that this compound is devoid of limiting elements and can also be synthesized by using standard metabolic pathways. This review will outline the main findings suggesting mixotrophy in the marine picocyanobacteria Prochlorococcus and Synechococcus, and its ecological relevance for these important primary producers.

Transcriptomic and physiological responses of Skeletonema costatum to ATP utilization

The capacity of phytoplankton to utilize dissolved organic phosphorus (DOP) plays an important role in their competition for resources when the availability of dissolved inorganic phosphorus (DIP) is low in the aquatic systems. Here, we explored the physiological and molecular responses of a globally distributed marine diatom, Skeletonema costatum, in utilizing adenosine-5'-triphosphate (ATP) based on incubation experiments under ATP, DIP-replete, and DIP-depleted conditions. The results show that ATP supports the growth of S. costatum as efficiently as DIP. The pathway of S. costatum involved in utilizing ATP is not related to alkaline phosphatase (AP), an important DOP hydrolase, although extracellular hydrolysis is involved. The transcriptome analysis revealed several transcripts related to the hydrolase activity (e.g. NAD+ diphosphatase), which were significantly upregulated in the ATP culture group, indicating their possible involvement in ATP hydrolysis. Meanwhile, ATP-grown S. costatum exhibited downregulation of the genes related to a series of metabolic activities (e.g. purine metabolism), apparently to adapt to ATP condition.

Temporal phosphate gradients reveal diverse acclimation responses in phytoplankton phosphate uptake

Phytoplankton face environmental nutrient variations that occur in the dynamic upper layers of the ocean. Phytoplankton cells are able to rapidly acclimate to nutrient fluctuations by adjusting their nutrient-uptake system and metabolism. Disentangling these acclimation responses is a critical step in bridging the gap between phytoplankton cellular physiology and community ecology. Here, we analyzed the dynamics of phosphate (P) uptake acclimation responses along different P temporal gradients by using batch cultures of the diatom Phaeodactylum tricornutum. We employed a multidisciplinary approach that combined nutrient-uptake bioassays, transcriptomic analysis, and mathematical models. Our results indicated that cells increase their maximum nutrient-uptake rate (V_max) both in response to P pulses and strong phosphorus limitation. The upregulation of three genes coding for different P transporters in cells experiencing low intracellular phosphorus levels supported some of the observed V_max variations. In addition, our mathematical model reproduced the empirical V_max patterns by including two types of P transporters upregulated at medium-high environmental and low intracellular phosphorus levels, respectively. Our results highlight the existence of a sequence of acclimation stages along the phosphate continuum that can be understood as a succession of acclimation responses. We provide a novel conceptual framework that can contribute to integrating and understanding the dynamics and wide diversity of acclimation responses developed by phytoplankton.

Methylphosphonate Oxidation in Prochlorococcus Strain MIT9301 Supports Phosphate Acquisition, Formate Excretion, and Carbon Assimilation into Purines

Until recently, MPn was only known to be degraded in the environment by the bacterial carbon-phosphorus (CP) lyase pathway, a reaction that releases the greenhouse gas methane. The identification of a formate-yielding MPn oxidative pathway in the marine planctomycete Gimesia maris (S. R. Gama, M. Vogt, T. Kalina, K. Hupp, et al., ACS Chem Biol 14:735–741, 2019, https://doi.org/10.1021/acschembio.9b00024) and the presence of this pathway in Prochlorococcus indicate that this compound can follow an alternative fate in the environment while providing a valuable source of P to organisms. In the ocean, where MPn is a major component of dissolved organic matter, the oxidation of MPn to formate by Prochlorococcus may direct the flow of this one-carbon compound to carbon dioxide or assimilation into biomass, thus limiting the production of methane.

The marine unicellular cyanobacterium Prochlorococcus is an abundant primary producer and widespread inhabitant of the photic layer in tropical and subtropical marine ecosystems, where the inorganic nutrients required for growth are limiting. In this study, we demonstrate that Prochlorococcus high-light strain MIT9301, an isolate from the phosphate-depleted subtropical North Atlantic Ocean, can oxidize methylphosphonate (MPn) and hydroxymethylphosphonate (HMPn), two phosphonate compounds present in marine dissolved organic matter, to obtain phosphorus. The oxidation of these phosphonates releases the methyl group as formate, which is both excreted and assimilated into purines in RNA and DNA. Genes encoding the predicted phosphonate oxidative pathway of MIT9301 were predominantly present in Prochlorococcus genomes from parts of the North Atlantic Ocean where phosphate availability is typically low, suggesting that phosphonate oxidation is an ecosystem-specific adaptation of some Prochlorococcus populations to cope with phosphate scarcity.

IMPORTANCE Until recently, MPn was only known to be degraded in the environment by the bacterial carbon-phosphorus (CP) lyase pathway, a reaction that releases the greenhouse gas methane. The identification of a formate-yielding MPn oxidative pathway in the marine planctomycete Gimesia maris (S. R. Gama, M. Vogt, T. Kalina, K. Hupp, et al., ACS Chem Biol 14:735–741, 2019, https://doi.org/10.1021/acschembio.9b00024) and the presence of this pathway in Prochlorococcus indicate that this compound can follow an alternative fate in the environment while providing a valuable source of P to organisms. In the ocean, where MPn is a major component of dissolved organic matter, the oxidation of MPn to formate by Prochlorococcus may direct the flow of this one-carbon compound to carbon dioxide or assimilation into biomass, thus limiting the production of methane.

Transcriptomic and physiological analyses of the dinoflagellate Karenia mikimotoi reveal non-alkaline phosphatase-based molecular machinery of ATP utilisation

The ability to utilize dissolved organic phosphorus (DOP) is important for phytoplankton to survive the scarcity of dissolved inorganic phosphorus (DIP), and alkaline phosphatase (AP) has been the major research focus as a facilitating mechanism. Here, we employed a unique molecular ecological approach and conducted a broader search for underpinning molecular mechanisms of adenosine triphosphate (ATP) utilisation. Cultures of the dinoflagellate Karenia mikimotoi were set up in L1 medium (+P), DIP-depleted L1 medium (-P) and ATP-replacing-DIP medium (ATP). Differential gene expression was profiled for ATP and +P cultures using suppression subtractive hybridisation (SSH) followed by 454 pyrosequencing, and RT-qPCR methods. We found that ATP supported a similar growth rate and cell yield as L1 medium and observed DIP release from ATP into the medium, suggesting that K. mikimotoi cells were expressing extracellular hydrolases to hydrolyse ATP. However, our SSH, qPCR and enzymatic activity assays indicated that 5'-nucleotidase (5NT), rather than AP, was responsible for ATP hydrolysis. Further gene expression analyses uncovered that intercellular purine metabolism was significantly changed following the utilisation of ATP. Our findings reveal a multi-faceted machinery regulating ATP utilisation and P metabolism in K. mikimotoi, and underscore AP activity is not the exclusive indicator of DOP utilisation.

Aspects of phosphorus physiology associated with phosphate-induced polar lipid remodelling in marine microalgae

Marine microalgae exhibit a diversified phosphorus physiology and have also been recently found to show high inter-taxa variability in their phosphate induced-polar lipids' remodelling. Identification of phosphorus physiology aspects that are more related to lipid remodelling can contribute to better understanding of such intricate phytoplankton lipid metabolism. Therefore, some aspects of phosphorus physiology related to its uptake, storage and use were evaluated in a taxonomically diversified group of nine marine microalgae that was arranged into three subgroups, each of them including species showing similar polar lipid responses to phosphate. Luxury phosphate uptake (PU) was the physiological aspect best associated to microalgal polar lipid metabolism as it was maximal in species (Picochlorum atomus, Tetraselmis suecica and Nannochloropsis gaditana) that were able to counterbalance between phospholipids (PL) and betaine lipids (BL). Cryptophytes (Rhodomonas baltica, Chroomonas placoidea), characterized by their constitutive BL and flexible PL contents in response to phosphate, had almost no luxury PU and showed higher phosphorus cell quota (Q_P) under phosphate deprivation. Haptophyes (Isochrysis galbana, Diacronema vlkianum), with constitutive BL contents and permanently minimal PL contents, showed the lowest Q_P when deprived of phosphate while their luxury PU was below that for green microalgae. Induction of alkaline phosphatase activity following phosphate depletion was maximal in diatoms (Phaeodactylum tricornutum, Chaetoceros gracilis) and I. galbana but it was unrelated to lipid remodelling. Despite strong influence of taxonomy, polar lipid remodelling accounted for 38.8% of total variation when microalgae were ordinated using their physiological responses to phosphorus as descriptive variables.

Adaptive Evolution of Phosphorus Metabolism in Prochlorococcus

Microbes are known to employ three basic strategies to compete for limiting elemental resources: (i) cell quotas may be adjusted by alterations to cell physiology or by substitution of a more plentiful resource, (ii) stressed cells may synthesize high-affinity transporters, and (iii) cells may access more costly sources from internal stores, by degradation, or by petitioning other microbes. In the case of phosphorus, a limiting resource in vast oceanic regions, the cosmopolitan cyanobacterium Prochlorococcus marinus thrives by adopting all three strategies and a fourth, previously unknown strategy. By generating a detailed model of its metabolism, we found that strain MED4 has evolved a way to reduce its dependence on phosphate by minimizing the number of enzymes involved in phosphate transformations, despite the stringency of nearly half of its metabolic genes being essential for survival. Relieving phosphorus limitation, both physiologically and throughout intermediate metabolism, substantially improves phosphorus-specific growth rates.

Inorganic phosphorus is scarce in the eastern Mediterranean Sea, where the high-light-adapted ecotype HLI of the marine picocyanobacterium Prochlorococcus marinus thrives. Physiological and regulatory control of phosphorus acquisition and partitioning has been observed in HLI both in culture and in the field; however, the optimization of phosphorus metabolism and associated gains for its phosphorus-limited-growth (PLG) phenotype have not been studied. Here, we reconstructed a genome-scale metabolic network of the HLI axenic strain MED4 (iJC568), consisting of 568 metabolic genes in relation to 794 reactions involving 680 metabolites distributed in 6 subcellular locations. iJC568 was used to quantify metabolic fluxes under PLG conditions, and we observed a close correspondence between experimental and computed fluxes. We found that MED4 has minimized its dependence on intracellular phosphate, not only through drastic depletion of phosphorus-containing biomass components but also through network-wide reductions in phosphate-reaction participation and the loss of a key enzyme, succinate dehydrogenase. These alterations occur despite the stringency of having relatively few pathway redundancies and an extremely high proportion of essential metabolic genes (47%; defined as the percentage of lethal in silico gene knockouts). These strategies are examples of nutrient-controlled adaptive evolution and confer a dramatic growth rate advantage to MED4 in phosphorus-limited regions.

IMPORTANCE Microbes are known to employ three basic strategies to compete for limiting elemental resources: (i) cell quotas may be adjusted by alterations to cell physiology or by substitution of a more plentiful resource, (ii) stressed cells may synthesize high-affinity transporters, and (iii) cells may access more costly sources from internal stores, by degradation, or by petitioning other microbes. In the case of phosphorus, a limiting resource in vast oceanic regions, the cosmopolitan cyanobacterium Prochlorococcus marinus thrives by adopting all three strategies and a fourth, previously unknown strategy. By generating a detailed model of its metabolism, we found that strain MED4 has evolved a way to reduce its dependence on phosphate by minimizing the number of enzymes involved in phosphate transformations, despite the stringency of nearly half of its metabolic genes being essential for survival. Relieving phosphorus limitation, both physiologically and throughout intermediate metabolism, substantially improves phosphorus-specific growth rates.

Dominant oceanic bacteria secure phosphate using a large extracellular buffer

The ubiquitous SAR11 and Prochlorococcus bacteria manage to maintain a sufficient supply of phosphate in phosphate-poor surface waters of the North Atlantic subtropical gyre. Furthermore, it seems that their phosphate uptake may counter-intuitively be lower in more productive tropical waters, as if their cellular demand for phosphate decreases there. By flow sorting ³³P-phosphate-pulsed ³²P-phosphate-chased cells, we demonstrate that both Prochlorococcus and SAR11 cells exploit an extracellular buffer of labile phosphate up to 5–40 times larger than the amount of phosphate required to replicate their chromosomes. Mathematical modelling is shown to support this conclusion. The fuller the buffer the slower the cellular uptake of phosphate, to the point that in phosphate-replete tropical waters, cells can saturate their buffer and their phosphate uptake becomes marginal. Hence, buffer stocking is a generic, growth-securing adaptation for SAR11 and Prochlorococcus bacteria, which lack internal reserves to reduce their dependency on bioavailable ambient phosphate.

Oceanic SAR11 Alphaproteobacteria and Prochlorococcus cyanobacteria are abundant in phosphate-poor regions, despite it being vital for growth. Here, Zubkov et al. show these bacterioplankton exploit an extracellular buffer of labile phosphate to reduce their dependency on bioavailable ambient phosphate.

Genomic potential for arsenic efflux and methylation varies among global Prochlorococcus populations

The globally significant picocyanobacterium Prochlorococcus is the main primary producer in oligotrophic subtropical gyres. When phosphate concentrations are very low in the marine environment, the mol:mol availability of phosphate relative to the chemically similar arsenate molecule is reduced, potentially resulting in increased cellular arsenic exposure. To mediate accidental arsenate uptake, some Prochlorococcus isolates contain genes encoding a full or partial efflux detoxification pathway, consisting of an arsenate reductase (arsC), an arsenite-specific efflux pump (acr3) and an arsenic-related repressive regulator (arsR). This efflux pathway was the only previously known arsenic detox pathway in Prochlorococcus. We have identified an additional putative arsenic mediation strategy in Prochlorococcus driven by the enzyme arsenite S-adenosylmethionine methyltransferase (ArsM) which can convert inorganic arsenic into more innocuous organic forms and appears to be a more widespread mode of detoxification. We used a phylogenetically informed approach to identify Prochlorococcus linked arsenic genes from both pathways in the Global Ocean Sampling survey. The putative arsenic methylation pathway is nearly ubiquitously present in global Prochlorococcus populations. In contrast, the complete efflux pathway is only maintained in populations which experience extremely low PO4:AsO4, such as regions in the tropical and subtropical Atlantic. Thus, environmental exposure to arsenic appears to select for maintenance of the efflux detoxification pathway in Prochlorococcus. The differential distribution of these two pathways has implications for global arsenic cycling, as their associated end products, arsenite or organoarsenicals, have differing biochemical activities and residence times.

Genomic potential for arsenic efflux and methylation varies among global Prochlorococcus populations

The globally significant picocyanobacterium Prochlorococcus is the main primary producer in oligotrophic subtropical gyres. When phosphate concentrations are very low in the marine environment, the mol:mol availability of phosphate relative to the chemically similar arsenate molecule is reduced, potentially resulting in increased cellular arsenic exposure. To mediate accidental arsenate uptake, some Prochlorococcus isolates contain genes encoding a full or partial efflux detoxification pathway, consisting of an arsenate reductase (arsC), an arsenite-specific efflux pump (acr3) and an arsenic-related repressive regulator (arsR). This efflux pathway was the only previously known arsenic detox pathway in Prochlorococcus. We have identified an additional putative arsenic mediation strategy in Prochlorococcus driven by the enzyme arsenite S-adenosylmethionine methyltransferase (ArsM) which can convert inorganic arsenic into more innocuous organic forms and appears to be a more widespread mode of detoxification. We used a phylogenetically informed approach to identify Prochlorococcus linked arsenic genes from both pathways in the Global Ocean Sampling survey. The putative arsenic methylation pathway is nearly ubiquitously present in global Prochlorococcus populations. In contrast, the complete efflux pathway is only maintained in populations which experience extremely low PO4:AsO4, such as regions in the tropical and subtropical Atlantic. Thus, environmental exposure to arsenic appears to select for maintenance of the efflux detoxification pathway in Prochlorococcus. The differential distribution of these two pathways has implications for global arsenic cycling, as their associated end products, arsenite or organoarsenicals, have differing biochemical activities and residence times.

SAR11 lipid renovation in response to phosphate starvation

Phytoplankton inhabiting oligotrophic ocean gyres actively reduce their phosphorus demand by replacing polar membrane phospholipids with those lacking phosphorus. Although the synthesis of nonphosphorus lipids is well documented in some heterotrophic bacterial lineages, phosphorus-free lipid synthesis in oligotrophic marine chemoheterotrophs has not been directly demonstrated, implying they are disadvantaged in phosphate-deplete ecosystems, relative to phytoplankton. Here, we show the SAR11 clade chemoheterotroph Pelagibacter sp. str. HTCC7211 renovates membrane lipids when phosphate starved by replacing a portion of its phospholipids with monoglucosyl- and glucuronosyl-diacylglycerols and by synthesizing new ornithine lipids. Lipid profiles of cells grown with excess phosphate consisted entirely of phospholipids. Conversely, up to 40% of the total lipids were converted to nonphosphorus lipids when cells were starved for phosphate, or when growing on methylphosphonate. Cells sequentially limited by phosphate and methylphosphonate transformed >75% of their lipids to phosphorus-free analogs. During phosphate starvation, a four-gene cluster was significantly up-regulated that likely encodes the enzymes responsible for lipid renovation. These genes were found in Pelagibacterales strains isolated from a phosphate-deficient ocean gyre, but not in other strains from coastal environments, suggesting alternate lipid synthesis is a specific adaptation to phosphate scarcity. Similar gene clusters are found in the genomes of other marine α-proteobacteria, implying lipid renovation is a common strategy used by heterotrophic cells to reduce their requirement for phosphorus in oligotrophic habitats.

The unique chemistry of Eastern Mediterranean water masses selects for distinct microbial communities by depth

The waters of the Eastern Mediterranean are characterized by unique physical and chemical properties within separate water masses occupying different depths. Distinct water masses are present throughout the oceans, which drive thermohaline circulation. These water masses may contain specific microbial assemblages. The goal of this study was to examine the effect of physical and geological phenomena on the microbial community of the Eastern Mediterranean water column. Chemical measurements were combined with phospholipid fatty acid (PLFA) analysis and high-throughput 16S rRNA sequencing to characterize the microbial community in the water column at five sites. We demonstrate that the chemistry and microbial community of the water column were stratified into three distinct water masses. The salinity and nutrient concentrations vary between these water masses. Nutrient concentrations increased with depth, and salinity was highest in the intermediate water mass. Our PLFA analysis indicated different lipid classes were abundant in each water mass, suggesting that distinct groups of microbes inhabit these water masses. 16S rRNA gene sequencing confirmed the presence of distinct microbial communities in each water mass. Taxa involved in autotrophic nitrogen cycling were enriched in the intermediate water mass suggesting that microbes in this water mass may be important to the nitrogen cycle of the Eastern Mediterranean. The Eastern Mediterranean also contains numerous active hydrocarbon seeps. We sampled above the North Alex Mud Volcano, in order to test the effect of these geological features on the microbial community in the adjacent water column. The community in the waters overlaying the mud volcano was distinct from other communities collected at similar depths and was enriched in known hydrocarbon degrading taxa. Our results demonstrate that physical phenomena such stratification as well as geological phenomena such as mud volcanoes strongly affect microbial community structure in the Eastern Mediterranean water column.

Influence of growth rate on the physiological response of marine Synechococcus to phosphate limitation

Phosphate (P) is an important nutrient potentially limiting for primary productivity, yet, we currently know little about the relationship between growth rate and physiological response to P limitation in abundant marine Cyanobacteria. Thus, the aim of this research was to determine how variation in growth rate affected the physiology of marine Synechococcus WH8102 and CC9311 when growing under high N:P conditions. Experiments were carried out in chemostats with a media input N:P of 441 and we estimated the half saturation concentration for growth under P limiting conditions (K s,p ) and cellular C:N:P ratios. The K s,p values were the lowest measured for any phytoplankton and on par with ambient P concentrations in oligotrophic regions. We also observed that both strains were able draw down P below 3 nM. Both K s,p and drawdown concentration were lower for the open ocean vs. coastal Synechococcus strain, which may be linked to differences in P acquisition genes in these strains. Cellular C:P and N:P ratios were significantly higher in relation to the Redfield ratio for both Synechococcus strains but we saw no difference in these ratios among growth rates or strains. These results demonstrate that Synechococcus can proliferate under very low P conditions and also that genetically different strains have unique physiological responses to P limitation.

Physiological regulation of isocitrate dehydrogenase and the role of 2-oxoglutarate in Prochlorococcus sp. strain PCC 9511

The enzyme isocitrate dehydrogenase (ICDH; EC 1.1.1.42) catalyzes the oxidative decarboxylation of isocitrate, to produce 2-oxoglutarate. The incompleteness of the tricarboxylic acids cycle in marine cyanobacteria confers a special importance to isocitrate dehydrogenase in the C/N balance, since 2-oxoglutarate can only be metabolized through the glutamine synthetase/glutamate synthase pathway. The physiological regulation of isocitrate dehydrogenase was studied in cultures of Prochlorococcus sp. strain PCC 9511, by measuring enzyme activity and concentration using the NADPH production assay and Western blotting, respectively. The enzyme activity showed little changes under nitrogen or phosphorus starvation, or upon addition of the inhibitors DCMU, DBMIB and MSX. Azaserine, an inhibitor of glutamate synthase, induced clear increases in the isocitrate dehydrogenase activity and icd gene expression after 24 h, and also in the 2-oxoglutarate concentration. Iron starvation had the most significant effect, inducing a complete loss of isocitrate dehydrogenase activity, possibly mediated by a process of oxidative inactivation, while its concentration was unaffected. Our results suggest that isocitrate dehydrogenase responds to changes in the intracellular concentration of 2-oxoglutarate and to the redox status of the cells in Prochlorococcus.

Effects of phosphorus starvation versus limitation on the marine cyanobacterium Prochlorococcus MED4 II: gene expression

Phosphorus (P) availability drives niche differentiation in the most abundant phytoplankter in the oceans, the marine cyanobacterium Prochlorococcus. We compared the molecular response of Prochlorococcus strain MED4 to P starvation in batch culture to P-limited growth in chemostat culture. We also identified an outer membrane porin, PMM0709, which may allow transport of organic phosphorous compounds, rather than phosphate as previously suggested. The expression of three P uptake genes, pstS, the high-affinity phosphate-binding component of the phosphate transporter, phoA, an alkaline phosphatase, and porin PMM0709, were strongly upregulated (between 10- and 700-fold) under both P starvation and limitation. pstS exhibits high basal expression under P-replete conditions and is likely necessary for P uptake regardless of P availability. A P-stress regulatory gene, ptrA, was upregulated in response to both P starvation and limitation although a second regulatory gene, phoB, was not. Elevated expression levels (> 10-fold) of phoR, a P-sensing histidine kinase, were only observed under conditions of P limitation. We suggest Prochlorococcus in P-limited systems are physiologically distinct from cells subjected to abrupt P depletion. Detection of expression of both pstS and phoR in field populations will enable discernment of the present P status of Prochlorococcus in the oligotrophic oceans.