Molecular analysis of the phosphorus starvation response inTrichodesmiumspp

Deciphering the Impact of ZnO Nanoparticles and a Sunscreen Product Containing ZnO on Phosphorus Dynamics and Release in Chlorella pyrenoidosa in Aquatic Systems

Zinc oxide nanoparticles (ZnO NPs) expedite the conversion of organic phosphorus (OP) into PO4-P (Pi), facilitating phosphorus (P) absorption by algae. Our study explored the mechanisms of converting OP (2-aminoethylphosphonic acid (AEP) and β-glycerol phosphate (β-GP)) into Pi in Chlorella pyrenoidosa under P deficiency with sunscreen and ZnO NPs. Cell density followed the order of K2HPO4 > β-GP+ZnO > β-GP > AEP+ZnO > AEP > P-free. ZnO NPs promoted the conversion of β-GP, containing C-O-P bonds (0.028-0.041 mg/L), into Pi more efficiently than AEP, which possesses C-P bonds (0.022-0.037 mg/L). Transcriptomics revealed Pi transport/metabolism (phoB (3.99-12.01 fold), phoR (2.20-5.50 fold), ppa (4.49-10.40 fold), and ppk (2.50-5.40 fold)) and phospholipid metabolism (SQD1 (1.85-2.79 fold), SQD2 (2.60-6.53 fold), MGD (2.13-3.21 fold), and DGD (4.08-7.56 fold)) were up-regulated compared to K2HPO4. 31P nuclear magnetic resonance spectroscopy identified intracellular P as polyphosphate, orthophosphate, and pyrophosphate. Synchrotron radiation-based X-ray near-edge structure spectroscopy indicated that K2HPO4 and Zn3(PO4)2 in β-GP+ZnO were increased by 8.09% and 7.28% compared to AEP+ZnO, suggesting superior P storage in β-GP+ZnO. Overall, ZnO NPs improved photoinduced electron-hole pair separation and charge separation efficiency and amplified the ·OH and ·O2- levels, promoting OP photoconversion into Pi and algae growth.

Genomic and phenotypic characterization of 26 novel marine bacterial strains with relevant biogeochemical roles and widespread presence across the global ocean

Prokaryotes dominate global oceans and shape biogeochemical cycles, yet most taxa remain uncultured and uncharacterized as of today. Here we present the characterization of 26 novel marine bacterial strains from a large isolate collection obtained from Blanes Bay (NW Mediterranean) microcosm experiments made in the four seasons. Morphological, cultural, biochemical, physiological, nutritional, genomic, and phylogenomic analyses were used to characterize and phylogenetically place the novel isolates. The strains represent 23 novel bacterial species and six novel genera: three novel species pertaining to class Alphaproteobacteria (families Rhodobacteraceae and Sphingomonadaceae), six novel species and three new genera from class Gammaproteobacteria (families Algiphilaceae, Salinispheraceae, and Alteromonadaceae), 13 novel species and three novel genera from class Bacteroidia (family Flavobacteriaceae), and one new species from class Rhodothermia (family Rubricoccaceae). The bacteria described here have potentially relevant roles in the cycles of carbon (e.g., carbon fixation or energy production via proteorhodopsin), nitrogen (e.g., denitrification or use of urea), sulfur (oxidation of sulfur compounds), phosphorus (acquisition and use of different forms of phosphorus and remodeling of membrane phospholipids), and hydrogen (oxidation of hydrogen to obtain energy). We mapped the genomes of the presented strains to the Tara Oceans metagenomes to reveal that these strains were globally distributed, with those of the family Flavobacteriaceae being the most widespread and abundant, while Rhodothermia being the rarest and most localized. While molecular-only approaches are also important, our study stresses the importance of culturing as a powerful tool to further understand the functioning of marine bacterial communities.

Taxonomic distribution of metabolic functions in bacteria associated with Trichodesmium consortia

IMPORTANCE

Colonies of the cyanobacteria Trichodesmium act as a biological hotspot for the usage and recycling of key resources such as C, N, P, and Fe within an otherwise oligotrophic environment. While Trichodesmium colonies are known to interact and support a unique community of algae and particle-associated microbes, our understanding of the taxa that populate these colonies and the gene functions they encode is still limited. Characterizing the taxa and adaptive strategies that influence consortium physiology and its concomitant biogeochemistry is critical in a future ocean predicted to have increasingly resource-depleted regions.

Phosphorus conditions change the cellular responses of Microcystis aeruginosa to perfluorooctanoic acid

Perfluorooctanoic acid (PFOA), a widespread and emerging organic contaminant of aquatic environments, has high bioaccumulation potential and high toxicity. Consequently, major concerns have been raised worldwide regarding the management of this pollutant in aquatic ecosystems. To thoroughly understand PFOA's toxic effects on aquatic organisms, systematic investigations were conducted on the cellular responses of Microcystis aeruginosa to the environmental concentrations of PFOA under various concentrations as well as phosphorus (P) conditions (concentrations and forms). The results showed that P conditions remarkably affected cyanobacterial growth as well as photosynthetic pigment content, triggered oxidative stress to disrupt the function and structure of the cell membrane, and caused changes in the extracellular and intracellular contents of microcystin-LR (MC-LR). Furthermore, PFOA (100 μg/L) was absorbed by cyanobacterial cells through the stimulation of the secretion of extracellular polymeric substances (EPS) by M. aeruginosa. After entering the cyanobacterial cells, PFOA inhibited photosynthesis, reduced P absorption, induced oxidative damage, lead to a loss of cell integrity evident in scanning electron microscope images, and increased mcyA gene expression to promote MC-LR production. Moreover, the limited P concentration and forms conditions led to increased PFOA absorption by cyanobacterial cells, which further upregulated mcyA gene expression and increased the risk of MC-LR diffusion into the aquatic environment. Our present study provided a theoretical basis and new ideas for understanding and addressing safety issues related to the presence of PFOA in aquatic environments with varying nutritional statuses.

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.

Importance of mobile genetic element immunity in numerically abundant Trichodesmium clades

The colony-forming cyanobacteria Trichodesmium spp. are considered one of the most important nitrogen-fixing genera in the warm, low nutrient ocean. Despite this central biogeochemical role, many questions about their evolution, physiology, and trophic interactions remain unanswered. To address these questions, we describe Trichodesmium pangenomic potential via significantly improved genomic assemblies from two isolates and 15 new >50% complete Trichodesmium metagenome-assembled genomes from hand-picked, Trichodesmium colonies spanning the Atlantic Ocean. Phylogenomics identified ~four N2 fixing clades of Trichodesmium across the transect, with T. thiebautii dominating the colony-specific reads. Pangenomic analyses showed that all T. thiebautii MAGs are enriched in COG defense mechanisms and encode a vertically inherited Type III-B Clustered Regularly Interspaced Short Palindromic Repeats and associated protein-based immunity system (CRISPR-Cas). Surprisingly, this CRISPR-Cas system was absent in all T. erythraeum genomes, vertically inherited by T. thiebautii, and correlated with increased signatures of horizontal gene transfer. Additionally, the system was expressed in metaproteomic and transcriptomic datasets and CRISPR spacer sequences with 100% identical hits to field-assembled, putative phage genome fragments were identified. While the currently CO2-limited T. erythraeum is expected to be a 'winner' of anthropogenic climate change, their genomic dearth of known phage resistance mechanisms, compared to T. thiebautii, could put this outcome in question. Thus, the clear demarcation of T. thiebautii maintaining CRISPR-Cas systems, while T. erythraeum does not, identifies Trichodesmium as an ecologically important CRISPR-Cas model system, and highlights the need for more research on phage-Trichodesmium interactions.

Molecular mechanisms underlying iron and phosphorus co-limitation responses in the nitrogen-fixing cyanobacterium Crocosphaera

In the nitrogen-limited subtropical gyres, diazotrophic cyanobacteria, including Crocosphaera, provide an essential ecosystem service by converting dinitrogen (N2) gas into ammonia to support primary production in these oligotrophic regimes. Natural gradients of phosphorus (P) and iron (Fe) availability in the low-latitude oceans constrain the biogeography and activity of diazotrophs with important implications for marine biogeochemical cycling. Much remains unknown regarding Crocosphaera's physiological and molecular responses to multiple nutrient limitations. We cultured C. watsonii under Fe, P, and Fe/P (co)-limiting scenarios to link cellular physiology with diel gene expression and observed unique physiological and transcriptional profiles for each treatment. Counterintuitively, reduced growth and N2 fixation resource use efficiencies (RUEs) for Fe or P under P limitation were alleviated under Fe/P co-limitation. Differential gene expression analyses show that Fe/P co-limited cells employ the same responses as single-nutrient limited cells that reduce cellular nutrient requirements and increase responsiveness to environmental change including smaller cell size, protein turnover (Fe-limited), and upregulation of environmental sense-and-respond systems (P-limited). Combined, these mechanisms enhance growth and RUEs in Fe/P co-limited cells. These findings are important to our understanding of nutrient controls on N2 fixation and the implications for primary productivity and microbial dynamics in a changing ocean.

Phosphate limitation intensifies negative effects of ocean acidification on globally important nitrogen fixing cyanobacterium

Growth of the prominent nitrogen-fixing cyanobacterium Trichodesmium is often limited by phosphorus availability in the ocean. How nitrogen fixation by phosphorus-limited Trichodesmium may respond to ocean acidification remains poorly understood. Here, we use phosphate-limited chemostat experiments to show that acidification enhanced phosphorus demands and decreased phosphorus-specific nitrogen fixation rates in Trichodesmium. The increased phosphorus requirements were attributed primarily to elevated cellular polyphosphate contents, likely for maintaining cytosolic pH homeostasis in response to acidification. Alongside the accumulation of polyphosphate, decreased NADP(H):NAD(H) ratios and impaired chlorophyll synthesis and energy production were observed under acidified conditions. Consequently, the negative effects of acidification were amplified compared to those demonstrated previously under phosphorus sufficiency. Estimating the potential implications of this finding, using outputs from the Community Earth System Model, predicts that acidification and dissolved inorganic and organic phosphorus stress could synergistically cause an appreciable decrease in global Trichodesmium nitrogen fixation by 2100.

Schindler's legacy: from eutrophic lakes to the phosphorus utilization strategies of cyanobacteria

David Schindler and his colleagues pioneered studies in the 1970s on the role of phosphorus in stimulating cyanobacterial blooms in North American lakes. Our understanding of the nuances of phosphorus utilization by cyanobacteria has evolved since that time. We review the phosphorus utilization strategies used by cyanobacteria, such as use of organic forms, alternation between passive and active uptake, and luxury storage. While many aspects of physiological responses to phosphorus of cyanobacteria have been measured, our understanding of the critical processes that drive species diversity, adaptation and competition remains limited. We identify persistent critical knowledge gaps, particularly on the adaptation of cyanobacteria to low nutrient concentrations. We propose that traditional discipline-specific studies be adapted and expanded to encompass innovative new methodologies and take advantage of interdisciplinary opportunities among physiologists, molecular biologists, and modellers, to advance our understanding and prediction of toxic cyanobacteria, and ultimately to mitigate the occurrence of blooms.

Nitrogen Fixation Influenced by Phosphorus and Nitrogen Availability in the Benthic Bloom-forming Cyanobacterium Hydrocoleum sp. Identified in a Temperate Marine Lagoon

The nitrogen-fixing, non-heterocystous cyanobacterium Hydrocoleum sp. (Oscillatoriales) is a common epiphytic and benthic bloom-former in tropical and subtropical shallow water systems but shares high phylogenetic similarity with the planktonic, globally important diazotroph Trichodesmium. Multiphasic observations in this study resulted in unexpected identification of Hydrocoleum sp. in mass accumulations in a coastal lagoon in the Western temperate North Atlantic Ocean. Hydrocoleum physiology was examined in situ through measurements of N₂ and CO₂ fixation rates and expression of genes involved with N₂ fixation, CO₂ fixation, and phosphorus (P) stress. Bulk N₂ fixation rates and Hydrocoleum nifH expression peaked at night and were strongly suppressed by dissolved inorganic nitrogen (DIN). The expression of high affinity phosphate transporter (pstS) and alkaline phosphatase (phoA) genes of Hydrocoleum was elevated during the night and negatively responded to phosphate amendments, as evidence that these mechanisms contribute to P acquisition during diazotrophic growth of Hydrocoleum in situ. This discovery at the edge of the previously known Hydrocoleum habitat range in the warming oceans raises intriguing questions about diazotrophic cyanobacterial adaptations and transitions on the benthic-pelagic continuum.

Organic Phosphorus Scavenging Supports Efficient Growth of Diazotrophic Cyanobacteria Under Phosphate Depletion

Considering the reported significant diazotrophic activities in open-ocean regions where primary production is strongly limited by phosphate, we explored the ability of diazotrophs to use other sources of phosphorus to alleviate the phosphate depletion. We tested the actual efficiency of the open-ocean, N₂-fixer Crocosphaera watsonii to grow on organic phosphorus as the sole P source, and observed how the P source affects the cellular C, N, and P composition. We obtained equivalent growth efficiencies on AMP and DL-α-glycerophosphate as compared with identical cultures grown on phosphate, and survival of the population on phytic acid. Our results show that Crocosphaera cannot use all phosphomonoesters with the same efficiency, but it can grow without phosphate, provided that usable DOP and sufficient light energy are available. Also, results point out that organic phosphorus uptake is not proportional to alkaline phosphatase activity, demonstrating that the latter is not a suitable proxy to estimate DOP-based growth yields of organisms, whether in culture experiments or in the natural environment. The growth parameters obtained, as a function of the P source, will be critical to improve and calibrate mathematical models of diazotrophic growth and the distribution of nitrogen fixation in the global ocean.

Transcriptional responses of Trichodesmium to natural inverse gradients of Fe and P availability

The filamentous diazotrophic cyanobacterium Trichodesmium is responsible for a significant fraction of marine di-nitrogen (N₂) fixation. Growth and distribution of Trichodesmium and other diazotrophs in the vast oligotrophic subtropical gyres is influenced by iron (Fe) and phosphorus (P) availability, while reciprocally influencing the biogeochemistry of these nutrients. Here we use observations across natural inverse gradients in Fe and P in the North Atlantic subtropical gyre (NASG) to demonstrate how Trichodesmium acclimates in situ to resource availability. Transcriptomic analysis identified progressive upregulation of known iron-stress biomarker genes with decreasing Fe availability, and progressive upregulation of genes involved in the acquisition of diverse P sources with decreasing P availability, while genes involved in N₂ fixation were upregulated at the intersection under moderate Fe and P availability. Enhanced N₂ fixation within the Fe and P co-stressed transition region was also associated with a distinct, consistent metabolic profile, including the expression of alternative photosynthetic pathways that potentially facilitate ATP generation required for N₂ fixation with reduced net oxygen production. The observed response of Trichodesmium to availability of both Fe and P supports suggestions that these biogeochemically significant organisms employ unique molecular, and thus physiological responses as adaptations to specifically exploit the Fe and P co-limited niche they construct.

Colonies of the marine cyanobacterium Trichodesmium optimize dust utilization by selective collection and retention of nutrient-rich particles

Trichodesmium, a globally important, N₂-fixing, and colony-forming cyanobacterium, employs multiple pathways for acquiring nutrients from air-borne dust, including active dust collection. Once concentrated within the colony core, dust can supply Trichodesmium with nutrients. Recently, we reported a selectivity in particle collection enabling Trichodesmium to center iron-rich minerals and optimize its nutrient utilization. In this follow-up study we examined if colonies select Phosphorus (P) minerals. We incubated 1,200 Trichodesmium colonies from the Red Sea with P-free CaCO₃, P-coated CaCO₃, and dust, over an entire bloom season. These colonies preferably interacted, centered, and retained P-coated CaCO₃ compared with P-free CaCO₃. In both studies, Trichodesmium clearly favored dust over all other particles tested, whereas nutrient-free particles were barely collected or retained, indicating that the colonies sense the particle composition and preferably collect nutrient-rich particles. This unique ability contributes to Trichodesmium's current ecological success and may assist it to flourish in future warmer oceans.

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Natural Trichodesmium colonies collect and maintain dust within their colony core

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Using synthetic particles we tested if colonies select the particles they collect

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Colonies selectively collect and retain nutrient-rich over nutrient-free particles

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Selective collection of particles optimizes their nutrient acquisition from dust

Transcriptomic responses to phosphorus in an invasive cyanobacterium, Raphidiopsis raciborskii: Implications for nutrient management

Phosphorus (P) is a vital macronutrient associated with the growth and proliferation of Raphidiopsis raciborskii, an invasive and notorious bloom-forming cyanobacterium. However, the molecular mechanisms involved in P acclimation remain largely unexplored for Raphidiopsis raciborskii. Here, transcriptome sequencing of Raphidiopsis raciborskii was conducted to reveal multifaceted mechanisms involved in mimicking dipotassium phosphate (DIP), β-glycerol phosphate (Gly), 2-aminoethylphosphonic acid (AEP), and P-free conditions (NP). Chlorophyll a fluorescence parameters showed significant differences in the NP and AEP groups compared with the DIP and Gly-groups. Expression levels of genes related to phosphate transportation and uptake, organic P utilization, nitrogen metabolism, urea cycling, carbon fixation, amino acid metabolism, environmental information, the ATP-synthesis process in glycolysis, the tricarboxylic acid (TCA) cycle, and the pentose phosphate pathway were remarkably upregulated, while those related to photosynthesis, phycobiliproteins, respiration, oxidative phosphorylation, sulfur metabolism, and genetic information were markedly downregulated in the NP group relative to the DIP group. However, the expression of genes involved in organic P utilization, the urea cycle, and genetic information in the Gly-group, and carbon-phosphorus lyase, genetic information and environmental information in the AEP group were significantly increased compared to the DIP group. Together, these results indicate that Raphidiopsis raciborskii exhibits the evolution of coordination of multiple metabolic pathways and certain key genes to adapt to ambient P changes, which implies that if P is reduced to control Raphidiopsis raciborskii bloom, there is a risk that external nutrients (such as nitrogen, amino acids, and urea) will stimulate the growth or metabolism of Raphidiopsis.

Why Environmental Biomarkers Work: Transcriptome-Proteome Correlations and Modeling of Multistressor Experiments in the Marine Bacterium Trichodesmium

Ocean microbial communities are important contributors to the global biogeochemical reactions that sustain life on Earth. The factors controlling these communities are being increasingly explored using metatranscriptomic and metaproteomic environmental biomarkers. Using published proteomes and transcriptomes from the abundant colony-forming cyanobacterium Trichodesmium (strain IMS101) grown under varying Fe and/or P limitation in low and high CO₂, we observed robust correlations of stress-induced proteins and RNAs (i.e., involved in transport and homeostasis) that yield useful information on the nutrient status under low and/or high CO₂. Conversely, transcriptional and translational correlations of many other central metabolism pathways exhibit broad discordance. A cellular RNA and protein production/degradation model demonstrates how biomolecules with small initial inventories, such as environmentally responsive proteins, achieve large increases in fold-change units as opposed to those with a higher basal expression and inventory such as metabolic systems. Microbial cells, due to their immersion in the environment, tend to show large adaptive responses in both RNA and protein that result in transcript-protein correlations. These observations and model results demonstrate multi-omic coherence for environmental biomarkers and provide the underlying mechanism for those observations, supporting the promise for global application in detecting responses to environmental stimuli in a changing ocean.

Molecular responses to inorganic and organic phosphorus sources in the growth and toxin formation of Microcystis aeruginosa

Toxic cyanobacteria bloom is a ubiquitous phenomenon worldwide in eutrophic lakes or reservoirs. Microcystis, is a cosmopolitan genus in cyanobacteria and exists in many different forms. Microcystis aeruginosa (M. aeruginosa) can produce microcystins (MCs) with strong liver toxicity during its growth and decomposition. Phosphorus (P) is a typical growth limiting factor of M. aeruginosa. Though different forms and concentrations of P are common in natural water, the molecular responses in the growth and MCs formation of M. aeruginosa remain unclear. In this study, laboratory experiments were conducted to determine the uptake of P, cell activity, MCs release, and related gene expression under different concentrations of dissolved inorganic phosphorus (DIP) and dissolved organic phosphorus (DOP). We found that the growth of M. aeruginosa was promoted by increasing DIP concentration but coerced under high concentration (0.6 and 1.0 mg P/L) of DOP after P starvation. The growth stress was not related to the alkaline phosphatase activity (APA). Although alkaline phosphatase (AP) could convert DOP into algae absorbable DIP, the growth status of M. aeruginosa mainly depended on the response mechanism of phosphate transporter expression to the extracellular P concentration. High-concentration DIP promoted MCs production in M. aeruginosa, while high-concentration DOP triggered the release of intracellular MCs rather than affecting MCs production. Our study revealed the molecular responses of algal growth and toxin formation under different P sources, and provided a theoretical basis and novel idea for risk management of eutrophic lakes and reservoirs.

Identification and characterization of alkaline phosphatase gene phoX in Microcystis aeruginosa PCC7806

PhoX is an extracellular alkaline phosphatase that is widely found in cyanobacteria and plays an important role in the conversion of extracellular organophosphorus into soluble inorganic phosphorus. However, the phoX gene has not yet been experimentally confirmed to exist in bloom-forming Microcystis species. In this study, we identified a putative phoX gene (GenBank accession no. ARI79942.1) in M. aeruginosa PCC7806 and overexpressed it in Escherichia coli 21 (DE3). The expressed PhoX protein displayed phosphodiesterase and phosphomonoesterase activities. In contrast to other bacterial PhoX proteins, which are activated mainly by Ca²⁺, Microcysits PhoX was most strongly activated by Mg²⁺, followed by Co²⁺, Ca²⁺, Zn²⁺ and Mn²⁺, but it was inhibited by Ni²⁺. Sequence analysis showed that phoX was highly conserved in the Microcystis genus (DNA similarity > 96% between species). phoX expression responded significantly to different environmental phosphorus levels. When PCC7806 cells were cultured in phosphorus-deficient medium (BG11-P), phoX expression reached its highest level at 2 h and then decreased to a low level at 4 h. Organophosphate induced the expression of phoX; its expression reached the highest level at 4 h and was maintained at a high level at 6 h. Our results confirmed a putative phoX gene and demonstrated that the phoX gene of Microcystis is conserved.

Nitrogen availability facilitates phosphorus acquisition by bloom-forming cyanobacteria

Cyanobacterial blooms are threatening freshwater ecosystems. The physiological basis involved in the onset of cyanobacterial bloom is fundamental to advance in bloom predictions. Generally, cyanobacteria grow until the availability of nitrogen (N), phosphorus (P) or both nutrients becomes limited. Population survival may depend on physiological adjustments to nutrient deficiency as well as on the efficient use of episodic N and P inputs. This study investigated the effect of N inputs on phosphate uptake affinity and activity of N-deficient bloom-forming cyanobacteria. Lake samples dominated by filamentous cyanobacteria were preincubated with and without nitrate addition, and the uptake of [32P] phosphate pulses was measured in the following days. Phosphate uptake kinetics were analyzed with a flow-force model that provides the threshold concentration, reflecting phosphate uptake affinity, and the membrane conductivity coefficient that corresponds to the activity of uptake systems. After 24 h of nitrate preincubation, phosphate uptake kinetics showed a progressive increase in affinity (nanomolar [Pe]A) and activity (25-fold) concomitant with cyanobacterial growth. It was demonstrated that the alleviation of N-deficiency by N inputs boosts the activation of phosphate uptake systems of non-N2-fixing cyanobacteria to sustain growth. Therefore, reduction of dissolved inorganic N levels in lakes is also mandatory to limit cyanobacterial phosphate uptake affinity and activity capabilities.

Differential strain response in alkaline phosphatase activity to available phosphorus in Microcoleus autumnalis

Toxic, benthic cyanobacterial proliferations have increased in frequency and severity globally and can have negative impacts on aquatic ecosystems, recreation and human health. Microcoleus autumnalis has been associated with numerous animal fatalities and is causing increasing concern. It tends to grow in systems with moderate dissolved inorganic nitrogen and very low dissolved reactive phosphorus. Acquisition of nutrients, particularly phosphorus, from organic sources may explain how M. autumnalis can reach the high biomass in these relatively nutrient deplete environments. In the present study the effect of phosphorus concentration and source on alkaline phosphatase activity was investigated in toxic and non-toxic M. autumnalis strains. Toxic strains exhibited significantly higher alkaline phosphatase activity than non-toxic strains (p <  0.05), and alkaline phosphatase activity increased in all strains under phosphorus-depleted conditions (p <  0.05). Alkaline phosphatase activity was also present in environmental M. autumnalis mats, though at lower levels than in laboratory experiments. The presence of alkaline phosphatase activity indicates that the acquisition of phosphorus from organic phosphorus sources may contribute to the ability of M. autumnalis to grow in systems with low dissolved reactive phosphorus.

Use of the high-affinity phosphate transporter gene, pstS, as an indicator for phosphorus stress in the marine diazotroph Crocosphaera watsonii (Chroococcales, Cyanobacteria)

The marine diazotroph Crocosphaera watsonii provides fixed carbon (C) and nitrogen (N) to open-ocean regimes, where nutrient deficiency controls productivity. The growth of Crocosphaera can be limited by low phosphorus (P) concentrations in these oligotrophic environments. Biomarkers such as the high-affinity ABC transporter phosphate-binding gene, pstS, are commonly used to monitor when such organisms are under P stress; however, transcriptional regulation of these markers is often complex and not well-understood. In this study, we interrogated changes in pstS transcript levels in C. watsonii cells under P starvation, and in response to added dissolved inorganic phosphorus (DIP), dissolved organic phosphorus (DOP), and changing light levels. We observed elevated relative pstS transcript levels in C. watsonii WH8501 at DIP concentrations below 60 and above 20 nmol · L^-1 . Transcript levels were suppressed by both inorganic and bioavailable organic phosphorus; however, the P stress response was more sensitive to DIP than DOP sources. Increasing light intensity resulted in increased relative pstS transcript abundances independently of low external P, and seemed to exacerbate the physiological effects of P stress. The variable response to different P compounds and rapid and transient influence of high light on pstS transcript abundances suggests that pstS is an indicator of internal P status in Crocosphaera.

Distinct Responses of the Nitrogen-Fixing Marine Cyanobacterium Trichodesmium to a Thermally Variable Environment as a Function of Phosphorus Availability

Surface temperature in the ocean is projected to be elevated and more variable in the future, which will interact with other environmental changes like reduced nutrient supplies. To explore these multiple stressor relationships, we tested the influence of thermal variation on the key marine diazotrophic cyanobacterium Trichodesmium erythraeum GBRTRLI101 as a function of the limiting nutrient phosphorus (P). Two constant temperature treatments represented current winter (22°C) and summer (30°C) mean values. Three variable temperature treatments fluctuated around the constant control values: Mean 22°C, either ± 2°C or ± 4°C; and mean 30°C ± 2°C. Each thermal treatment was grown under both P-replete (10 μmol/L) and P-limiting conditions (0.2 μmol/L). Effects of thermal variability on Trichodesmium were mainly found in the two winter variable temperature treatments (22°C ± 2°C or ± 4°C). P availability affected growth and physiology in all treatments and had significant interactions with temperature. P-replete cultures had higher growth and nitrogen and carbon fixation rates in the 22°C constant control, than in the corresponding variable treatments. However, physiological rates were not different in the P-replete constant and variable treatments at 30°C. In contrast, in P-limited cultures an advantage of constant temperature over variable temperature was not apparent. Phosphorus use efficiencies (PUE, mol N or C fixed h-1 mol cellular P-1) for nitrogen and carbon fixation were significantly elevated under P-limited conditions, and increased with temperature from 22 to 30°C, implying a potential advantage in a future warmer, P-limited environment. Taken together, these results imply that future increasing temperature and greater thermal variability could have significant feedback interactions with the projected intensification of P-limitation of marine N2-fixing cyanobacteria.

The Composition of Nitrogen-Fixing Microorganisms Correlates With Soil Nitrogen Content During Reforestation: A Comparison Between Legume and Non-legume Plantations

Numerous reforestation projects have been conducted to improve soil fertility in degraded forests, often causing alterations to the soil microbial communities. However, it remains unclear whether microbial functional groups are affected and how these groups correlate with an increase in the nutrient contents during reforestation. We investigated the abundance and composition of free-living nitrogen-fixing microorganisms (diazotrophs) by quantifying and sequencing the marker gene nifH in bulk soils from five reforestation approaches, including legumes and non-legumes, in subtropical China. The relationships between diazotrophic community attributes and soil nitrogen (N) content [NO3 -, NH4 +, and microbial biomass N (MBN)] were examined under various approaches. Abundance of diazotrophs was highest in the native tree plantation (Schima spp. and Michelia macclurei) and Acacia mangium monoculture (AM), and lowest in the Pinus massoniana monoculture. The diazotrophic abundance correlated positively with soil organic matter and water content while there was a negative correlation to pH. The composition of diazotrophic community differed significantly among the five reforestation approaches examined and was closely correlated with variations in soil pH, NH4 + and water content. Diazotrophic community composition was closely related to soil NH4 + content, whereas abundance was not. The AM contained higher NH4 +, NO3 - and MBN contents than the other reforestation approaches, which may be associated with the indicator species of diazotrophs (Actinobacteria, Proteobacteria, and Firmicutes). However, there were more indicator species of Proteobacteria in the mixed Acacia plantation (Acacia mangium and Acacia crassicarpa) than in AM, which might have contributed to the remarkedly lower N content compared to AM. Overall, the soil N content under reforestation appeared to be more related to the composition of diazotroph community than to the abundance of diazotrophs.

Transcriptional and Proteomic Choreography Under Phosphorus Deficiency and Re-supply in the N2 Fixing Cyanobacterium Trichodesmium erythraeum

The N₂ fixing cyanobacterium Trichodesmium is a critically important organism in oligotrophic marine ecosystems, supplying “new” nitrogen (N) to the otherwise N-poor tropical and subtropical regions where it occurs. Low concentrations of phosphorus (P) in these regions can constrain Trichodesmium distribution and N₂ fixation rates. Physiological characterization of a single species in a mixed community can be challenging, and ‘omic approaches are increasingly important tools for tracking nutritional physiology in a taxon-specific manner. As such, studies examining the dynamics of gene and protein markers of physiology (e.g., nutrient stress) are critical for the application and interpretation of such ‘omic data in situ. Here we leveraged combined transcriptomics, proteomics, and enzyme activity assays to track the physiological response of Trichodesmium erythraeum IMS101 to P deficiency and subsequent P re-supply over 72 h of sampling. P deficiency resulted in differential gene expression, protein abundance, and enzyme activity that highlighted a synchronous shift in P physiology with increases in the transcripts and corresponding proteins for hydrolyzing organic phosphorus, taking up phosphate with higher affinity, and modulating intracellular P demand. After P deficiency was alleviated, gene expression of these biomarkers was reduced to replete levels within 4 h of P amendment. A number of these gene biomarkers were adjacent to putative pho boxes and their expression patterns were similar to a sphR response regulator. Protein products of the P deficiency biomarkers were slow to decline, with 84% of the original P deficient protein set still significantly differentially expressed after 72 h. Alkaline phosphatase activity tracked with proteins for this enzyme. With the rapid turnover time of transcripts, they appear to be good biomarkers of a P stress phenotype, whereas proteins, with a slower turnover time, may better reflect cellular activities. These results highlight the importance of validating and pairing transcriptome and proteome data that can be applied to physiological studies of key species in situ.

Unique Patterns and Biogeochemical Relevance of Two-Component Sensing in Marine Bacteria

Marine microbes must manage variation in their chemical, physical, and biological surroundings. Because they directly link bacterial physiology to environmental changes, TCS systems are crucial to the bacterial cell. This study surveyed TCS systems in a large number of marine bacteria and identified key phylogenetic and lifestyle patterns in environmental sensing. We found evidence that, in comparison with bacteria as a whole, marine organisms have irregular TCS system constructs which might represent an adaptation specific to the marine environment. Additionally, we demonstrate the biogeochemical relevance of TCS systems by correlating the presence of the PMT9312_0717 response regulator protein to phosphate concentrations in the South Pacific. We highlight that despite their potential ecological and biogeochemical relevance, TCS systems have been understudied in the marine ecosystem. This report expands our understanding of the breadth of bacterial TCS systems and how marine bacteria have adapted to survive in their unique environment.

Two-component sensory (TCS) systems link microbial physiology to the environment and thus may play key roles in biogeochemical cycles. In this study, we surveyed the TCS systems of 328 diverse marine bacterial species. We identified lifestyle traits such as copiotrophy and diazotrophy that are associated with larger numbers of TCS system genes within the genome. We compared marine bacterial species with 1,152 reference bacterial species from a variety of habitats and found evidence of extra response regulators in marine genomes. Examining the location of TCS genes along the circular bacterial genome, we also found that marine bacteria have a large number of “orphan” genes, as well as many hybrid histidine kinases. The prevalence of “extra” response regulators, orphan genes, and hybrid TCS systems suggests that marine bacteria break with traditional understanding of how TCS systems operate. These trends suggest prevalent regulatory networking, which may allow coordinated physiological responses to multiple environmental signals and may represent a specific adaptation to the marine environment. We examine phylogenetic and lifestyle traits that influence the number and structure of two-component systems in the genome, finding, for example, that a lack of two-component systems is a hallmark of oligotrophy. Finally, in an effort to demonstrate the importance of TCS systems to marine biogeochemistry, we examined the distribution of Prochlorococcus/Synechococcus response regulator PMT9312_0717 in metaproteomes of the tropical South Pacific. We found that this protein’s abundance is related to phosphate concentrations, consistent with a putative role in phosphate regulation.

IMPORTANCE Marine microbes must manage variation in their chemical, physical, and biological surroundings. Because they directly link bacterial physiology to environmental changes, TCS systems are crucial to the bacterial cell. This study surveyed TCS systems in a large number of marine bacteria and identified key phylogenetic and lifestyle patterns in environmental sensing. We found evidence that, in comparison with bacteria as a whole, marine organisms have irregular TCS system constructs which might represent an adaptation specific to the marine environment. Additionally, we demonstrate the biogeochemical relevance of TCS systems by correlating the presence of the PMT9312_0717 response regulator protein to phosphate concentrations in the South Pacific. We highlight that despite their potential ecological and biogeochemical relevance, TCS systems have been understudied in the marine ecosystem. This report expands our understanding of the breadth of bacterial TCS systems and how marine bacteria have adapted to survive in their unique environment.

Differential expression of phosphorus acquisition genes in response to phosphorus stress in two Raphidiopsis raciborskii strains

The cyanobacterium Raphidiopsis raciborskii is a nuisance in freshwater ecosystems. Strains vary in their physiological responses to environmental drivers, thus a greater understanding of the magnitude of strain variation is required to characterize the species. In this study, two strains of R. raciborskii isolated from a tropical Australian water reservoir were grown with and without phosphorus (P) to determine any relative response to P stress. The strains had the same growth rates and under P free conditions, cells grew at the same rate as P replete conditions until day 9 when cell growth ceased. There was no difference in the alkaline phosphatase activity per cell for the P replete and P free conditions, but the level of activity per cell was greater in CS-505 than CS-506. P acquisition genes were identified from the sequenced genomes; both strains contained the same genes, but with differences in copy number of phoA (7 and 6), phnK (3 and 1) and phnH (2 and 1) between CS-505 and CS-506 (respectively). The expression of P acquisition genes under P stress was measured throughout the experiment and shown to vary in magnitude and timing across strains, and in P replete versus P free cultures. In strain CS-505, upregulation of the pstS1 and phoA genes occurred late in the growth phase and into senescence. These genes are involved in phosphate uptake and use of various forms of organic P. For strain CS-506, there was upregulation of the phosphate uptake gene, pit, and organic P utilization genes, phoA, phoU, phnD and phnK, commencing late in the growth phase. Our study shows that despite the fact that these two strains were isolated from the same waterbody, they differed markedly in their gene expression response to P free conditions. This capacity of R. raciborskii to vary in strain responses to P conditions gives the organism flexibility in responding to environmental change, particularly P stress conditions.

Transcriptional responses of the marine green alga Micromonas pusilla and an infecting prasinovirus under different phosphate conditions

Prasinophytes are widespread marine algae for which responses to nutrient limitation and viral infection are not well understood. We studied the picoprasinophyte, Micromonas pusilla, grown under phosphate-replete (0.65 ± 0.07 d^-1 ) and 10-fold lower (low)-phosphate (0.11 ± 0.04 d^-1 ) conditions, and infected by the phycodnavirus MpV-SP1. Expression of 17% of Micromonas genes in uninfected cells differed by >1.5-fold (q < 0.01) between nutrient conditions, with genes for P-metabolism and the uniquely-enriched Sel1-like repeat (SLR) family having higher relative transcript abundances, while phospholipid-synthesis genes were lower in low-P than P-replete. Approximately 70% (P-replete) and 30% (low-P) of cells were lysed 24 h post-infection, and expression of ≤5.8% of host genes changed relative to uninfected treatments. Host genes for CAZymes and glycolysis were activated by infection, supporting importance in viral production, which was significantly lower in slower growing (low-P) hosts. All MpV-SP1 genes were expressed, and our analyses suggest responses to differing host-phosphate backgrounds involve few viral genes, while the temporal program of infection involves many more, and is largely independent of host-phosphate background. Our study (i) identifies genes previously unassociated with nutrient acclimation or viral infection, (ii) provides insights into the temporal program of prasinovirus gene expression by hosts and (iii) establishes cell biological aspects of an ecologically important host-prasinovirus system that differ from other marine algal-virus systems.

Metagenomic Evidence of Microbial Community Responsiveness to Phosphorus and Salinity Gradients in Seagrass Sediments

Sediment microorganisms can have profound influence on productivity and functioning of marine ecosystems through their critical roles in regulating biogeochemical processes. However, the identity of sediment microorganisms that mediate organic matter turnover and nutrient cycling in seagrass sediments is only poorly understood. Here, we used metagenomic sequencing to investigate shifts in the structure and functioning of the microbial community of seagrass sediments across a salinity and phosphorus (P) availability gradient in Shark Bay, WA, Australia. This iconic ecosystem is oligotrophic and hypersaline with abundant seagrass meadows that directly contribute Shark Bay's status as a World Heritage Site. We show that sediment phosphonate metabolism genes as well as enzyme activities increase in hypersaline conditions with lower soluble reactive phosphate in the water column. Given that sediment organic P content is also highest where P concentrations in the water column are low, we suggest that microbial processing of organic P can contribute to the P requirements of seagrasses at particularly oligotrophic sites. Seagrass meadows are often highly productive in oligotrophic waters, and our findings suggest that an increase in the functional capacity of microbial communities in seagrass sediments to break down organic P may contribute to the high productivity of seagrass meadows under oligotrophic conditions. When compared to soil and sediment metagenomes from other aquatic and terrestrial ecosystems, we also show microbial communities in seagrass sediments have a disproportionately high abundance of putative phosphorus and sulfur metabolism genes, which may have played an important evolutionary role in allowing these angiosperms to recolonize the marine environment and prosper under oligotrophic conditions.

Mutual Dependence of Nitrogen and Phosphorus as Key Nutrient Elements: One Facilitates Dolichospermum flos-aquae to Overcome the Limitations of the Other

Dolichospermum flos-aquae (formerly Anabaena flos-aquae) is a diazotrophic cyanobacterium causing harmful blooms worldwide, which is partly attributed to its capacity to compete for nitrogen (N) and phosphorus (P). Preventing the blooms by reducing P alone or both N and P has caused debate. To test the effects alone and together on the growth of cyanobacteria, we performed culture experiments in different eutrophication scenarios. N₂ fixation in terms of heterocyst density, nitrogenase activity and nifH expression increased significantly in P-replete cultures, suggesting that P enrichment facilitates N₂ fixation. Correspondingly, the expression of genes involved in P uptake, e.g., those involved in P-transport ( pstS) and the hydrolysis of phosphomonoesters ( phoD), was upregulated in P-deficient cultures. Interestingly, N addition enhanced not only the expression of these genes but also polyphosphate formation and alkaline phosphatase activity in P-deficient cultures relative to the P-replete cultures, as evidenced by qualitative (enzyme-labeled fluorescence) and quantitative (fluorogenic spectrophotometry) measurements. Furthermore, after N addition, cell activity and growth increased in the P-deficient cultures, underscoring the risk of N enrichment in P-limited systems. The eco-physiological responses shown here help further our understanding of the mechanism of N and P colimitation and underscore the importance of dual N and P reduction in controlling cyanobacterial blooms.

Transcriptional patterns identify resource controls on the diazotroph Trichodesmium in the Atlantic and Pacific oceans

The N₂-fixing cyanobacterium Trichodesmium is intensely studied because of the control this organism exerts over the cycling of carbon and nitrogen in the low nutrient ocean gyres. Although iron (Fe) and phosphorus (P) bioavailability are thought to be major drivers of Trichodesmium distributions and activities, identifying resource controls on Trichodesmium is challenging, as Fe and P are often organically complexed and their bioavailability to a single species in a mixed community is difficult to constrain. Further, Fe and P geochemistries are linked through the activities of metalloenzymes, such as the alkaline phosphatases (APs) PhoX and PhoA, which are used by microbes to access dissolved organic P (DOP). Here we identified significant correlations between Trichodesmium-specific transcriptional patterns in the North Atlantic (NASG) and North Pacific Subtropical Gyres (NPSG) and patterns in Fe and P biogeochemistry, with the relative enrichment of Fe stress markers in the NPSG, and P stress markers in the NASG. We also observed the differential enrichment of Fe-requiring PhoX transcripts in the NASG and Fe-insensitive PhoA transcripts in the NPSG, suggesting that metalloenzyme switching may be used to mitigate Fe limitation of DOP metabolism in Trichodesmium. This trait may underpin Trichodesmium success across disparate ecosystems.

Iron and phosphorus deprivation induce sociality in the marine bloom-forming cyanobacterium Trichodesmium

Trichodesmium spp. are diazotrophic cyanobacteria that exist as single filaments (trichomes) and as macroscopic colonies of varying shapes formed by aggregating trichomes. The causes and dynamics of colony formation and disassociation are not yet elucidated. we demonstrate that limited availability of dissolved phosphorus (P) or iron (Fe) stimulated trichome mobility and induced colony formation in Trichodesmium erythraeum IMS101 cultures. The specific nutrient limitation differentially affected the rate of colony formation and morphology of the colonies. Fe starvation promoted rapid colony formation (10-48 h from depletion) while 5-7 days were required for colonies to form in P-depleted cultures. Video analyses confirmed that the probability of trichomes to cluster increased from 12 to 35% when transferred from nutrient replete to Fe-depleted conditions. Moreover, the probability for Fe-depleted aggregates to remain colonial increased to 50% from only 10% in nutrient replete cultures. These colonies were also characterized by stronger attachment forces between the trichomes. Enrichment of nutrient-depleted cultures with the limited nutrient-stimulated colony dissociation into single trichomes. We postulate that limited P and Fe availability enhance colony formation of Trichodesmium and primarily control the abundance and distribution of its different morphologies in the nutrient-limited surface ocean.

Epibionts dominate metabolic functional potential of Trichodesmium colonies from the oligotrophic ocean

Trichodesmium is a genus of marine diazotrophic colonial cyanobacteria that exerts a profound influence on global biogeochemistry, by injecting 'new' nitrogen into the low nutrient systems where it occurs. Colonies of Trichodesmium ubiquitously contain a diverse assemblage of epibiotic microorganisms, constituting a microbiome on the Trichodesmium host. Metagenome sequences from Trichodesmium colonies were analyzed along a resource gradient in the western North Atlantic to examine microbiome community structure, functional diversity and metabolic contributions to the holobiont. Here we demonstrate the presence of a core Trichodesmium microbiome that is modulated to suit different ocean regions, and contributes over 10 times the metabolic potential of Trichodesmium to the holobiont. Given the ubiquitous nature of epibionts on colonies, the substantial functional diversity within the microbiome is likely an integral facet of Trichodesmium physiological ecology across the oligotrophic oceans where this biogeochemically significant diazotroph thrives.

Conserved Transcriptional Responses to Nutrient Stress in Bloom-Forming Algae

The concentration and composition of bioavailable nitrogen (N) and phosphorus (P) in the upper ocean shape eukaryotic phytoplankton communities and influence their physiological responses. Phytoplankton are known to exhibit similar physiological responses to limiting N and P conditions such as decreased growth rates, chlorosis, and increased assimilation of N and P. Are these responses similar at the molecular level across multiple species? To interrogate this question, five species from biogeochemically important, bloom-forming taxa (Bacillariophyta, Dinophyta, and Haptophyta) were grown under similar low N, low P, and replete nutrient conditions to identify transcriptional patterns and associated changes in biochemical pools related to N and P stress. Metabolic profiles, revealed through the transcriptomes of these taxa, clustered together based on species rather than nutrient stressor, suggesting that the global metabolic response to nutrient stresses was largely, but not exclusively, species-specific. Nutrient stress led to few transcriptional changes in the two dinoflagellates, consistent with other research. An orthologous group analysis examined functionally conserved (i.e., similarly changed) responses to nutrient stress and therefore focused on the diatom and haptophytes. Most conserved ortholog changes were specific to a single nutrient treatment, but a small number of orthologs were similarly changed under both N and P stress in 2 or more species. Many of these orthologs were related to photosynthesis and may represent generalized stress responses. A greater number of orthologs were conserved across more than one species under low P compared to low N. Screening the conserved orthologs for functions related to N and P metabolism revealed increased relative abundance of orthologs for nitrate, nitrite, ammonium, and amino acid transporters under N stress, and increased relative abundance of orthologs related to acquisition of inorganic and organic P substrates under P stress. Although the global transcriptional responses were dominated by species-specific changes, the analysis of conserved responses revealed functional similarities in resource acquisition pathways among different phytoplankton taxa. This overlap in nutrient stress responses observed among species may be useful for tracking the physiological ecology of phytoplankton field populations.

Molecular mechanism of glucose-6-phosphate utilization in the dinoflagellate Karenia mikimotoi

Phosphorus (P) is an essential nutrient for marine phytoplankton as for other living organisms, and the preferred form, dissolved inorganic phosphate (DIP), is often quickly depleted in the sunlit layer of the ocean. Phytoplankton have developed mechanisms to utilize organic forms of P (DOP). Hydrolysis of DOP to release DIP by alkaline phosphatase is believed to be the most common mechanism of DOP utilization. Little effort has been made, however, to understand other potential molecular mechanisms of utilizing different types of DOP. This study investigated the bioavailability of glucose-6-phosphate (G6P) and its underlying molecular mechanism in the dinoflagellate Karenia mikimotoi. Suppression Subtraction Hybridization (SSH) was used to identify genes up- and down-regulated during G6P utilization compared to DIP condition. The results showed that G6P supported the growth and yield of K. mikimotoi as efficiently as DIP. Neither DIP release nor AP activity was detected in the cultures grown in G6P medium, however, suggesting direct uptake of G6P. SSH analysis and RT-qPCR results showed evidence of metabolic modifications, particularly that mitochondrial ATP synthase f1gamma subunit and thioredoxin reductase were up-regulated while diphosphatase and pyrophosphatase were down-regulated in the G6P cultures. All the results indicate that K. mikimotoi has developed a mechanism other than alkaline phosphatase to utilize G6P.

Iron limitation of microbial phosphorus acquisition in the tropical North Atlantic

In certain regions of the predominantly nitrogen limited ocean, microbes can become co-limited by phosphorus. Within such regions, a proportion of the dissolved organic phosphorus pool can be accessed by microbes employing a variety of alkaline phosphatase (APase) enzymes. In contrast to the PhoA family of APases that utilize zinc as a cofactor, the recent discovery of iron as a cofactor in the more widespread PhoX and PhoD implies the potential for a biochemically dependant interplay between oceanic zinc, iron and phosphorus cycles. Here we demonstrate enhanced natural community APase activity following iron amendment within the low zinc and moderately low iron Western North Atlantic. In contrast we find no evidence for trace metal limitation of APase activity beneath the Saharan dust plume in the Eastern Atlantic. Such intermittent iron limitation of microbial phosphorus acquisition provides an additional facet in the argument for iron controlling the coupling between oceanic nitrogen and phosphorus cycles.

Comparative Transcriptomic Analysis Reveals Novel Insights into the Adaptive Response of Skeletonema costatum to Changing Ambient Phosphorus

Phosphorus (P) is a limiting macronutrient for diatom growth and productivity in the ocean. Much effort has been devoted to the physiological response of marine diatoms to ambient P change, however, the whole-genome molecular mechanisms are poorly understood. Here, we utilized RNA-Seq to compare the global gene expression patterns of a marine diatom Skeletonema costatum grown in inorganic P-replete, P-deficient, and inorganic- and organic-P resupplied conditions. In total 34,942 unique genes were assembled and 20.8% of them altered significantly in abundance under different P conditions. Genes encoding key enzymes/proteins involved in P utilization, nucleotide metabolism, photosynthesis, glycolysis, and cell cycle regulation were significantly up-regulated in P-deficient cells. Genes participating in circadian rhythm regulation, such as circadian clock associated 1, were also up-regulated in P-deficient cells. The response of S. costatum to ambient P deficiency shows several similarities to the well-described responses of other marine diatom species, but also has its unique features. S. costatum has evolved the ability to re-program its circadian clock and intracellular biological processes in response to ambient P deficiency. This study provides new insights into the adaptive mechanisms to ambient P deficiency in marine diatoms.

Phosphorus Deficiency Inhibits Cell Division But Not Growth in the Dinoflagellate Amphidinium carterae

Phosphorus (P) is an essential nutrient element for the growth of phytoplankton. How P deficiency affects population growth and the cell division cycle in dinoflagellates has only been studied in some species, and how it affects photosynthesis and cell growth remains poorly understood. In the present study, we investigated the impact of P deficiency on the cell division cycle, the abundance of the carbon-fixing enzyme Rubisco, and other cellular characteristics in the Gymnodiniales peridinin-plastid species Amphidinium carterae. We found that under P-replete condition, the cell cycle actively progressed in the culture in a 24-h diel cycle with daily growth rates markedly higher than the P-deficient cultures, in which cells were arrested in the G1 phase and cell size significantly enlarged. The results suggest that, as in previously studied dinoflagellates, P deficiency likely disenables A. carterae to complete DNA duplication or check-point protein phosphorylation. We further found that under P-deficient condition, overall photosystem II quantum efficiency (Fv/Fm ratio) and Rubisco abundance decreased but not significantly, while cellular contents of carbon, nitrogen, and proteins increased significantly. These observations indicated that under P-deficiency, this dinoflagellate was able to continue photosynthesis and carbon fixation, such that proteins and photosynthetically fixed carbon could accumulate resulting in continued cell growth in the absence of division. This is likely an adaptive strategy thereby P-limited cells can be ready to resume the cell division cycle upon resupply of phosphorus.

Molecular markers define progressing stages of phosphorus limitation in the nitrogen-fixing cyanobacterium, Crocosphaera

Crocosphaera watsonii is a marine cyanobacterium that frequently inhabits low phosphate environments in oligotrophic oceans. While C. watsonii has the ability to fix atmospheric nitrogen, its growth may be limited by availability of phosphorus. Biomarkers that indicate cellular phosphorus status give insight into how P-limitation can affect the distribution of nitrogen-fixing cyanobacterial populations. However, adaptation to phosphorus stress is complex and one marker may not be sufficient to determine when an organism is P-limited. In this study, we characterized the transcription of key genes, activated during phosphorus stress in C. watsonii WH8501, to determine how transcription changed during the phosphorus stress response. Transcription of pstS, which encodes a high-affinity phosphate binding protein, was discovered to be quickly up-regulated in phosphorus-depleted cells as an immediate stress response; however, its transcription declined after a period of phosphorus starvation. In addition, diel regulation of pstS in C. watsonii WH8501 complicates the interpretation of this marker in field applications. Transcription of the gene coding for the arsenite efflux protein, arsB, was upregulated after pstS in phosphorus limited cells, but it remained upregulated at later stages of phosphorus limitation. These results demonstrate that a single molecular marker does not adequately represent the entire phosphorus stress response in C. watsonii WH8501. Using both markers, the variations in transcriptional response over a range of degrees of phosphorus limitation may be a better approach for defining cellular phosphorus status.

Phosphorus physiological ecology and molecular mechanisms in marine phytoplankton

Phosphorus (P) is an essential nutrient for marine phytoplankton and indeed all life forms. Current data show that P availability is growth-limiting in certain marine systems and can impact algal species composition. Available P occurs in marine waters as dissolved inorganic phosphate (primarily orthophosphate [Pi]) or as a myriad of dissolved organic phosphorus (DOP) compounds. Despite numerous studies on P physiology and ecology and increasing research on genomics in marine phytoplankton, there have been few attempts to synthesize information from these different disciplines. This paper is aimed to integrate the physiological and molecular information on the acquisition, utilization, and storage of P in marine phytoplankton and the strategies used by these organisms to acclimate and adapt to variations in P availability. Where applicable, we attempt to identify gaps in our current knowledge that warrant further research and examine possible metabolic pathways that might occur in phytoplankton from well-studied bacterial models. Physical and chemical limitations governing cellular P uptake are explored along with physiological and molecular mechanisms to adapt and acclimate to temporally and spatially varying P nutrient regimes. Topics covered include cellular Pi uptake and feedback regulation of uptake systems, enzymatic utilization of DOP, P acquisition by phagotrophy, P-limitation of phytoplankton growth in oceanic and coastal waters, and the role of P-limitation in regulating cell size and toxin levels in phytoplankton. Finally, we examine the role of P and other nutrients in the transition of phytoplankton communities from early succession species (diatoms) to late succession ones (e.g., dinoflagellates and haptophytes).

Phosphite utilization by the globally important marine diazotroph Trichodesmium

Species belonging to the filamentous cyanobacterial genus Trichodesmium are responsible for a significant fraction of oceanic nitrogen fixation. The availability of phosphorus (P) likely constrains the growth of Trichodesmium in certain regions of the ocean. Moreover, Trichodesmium species have recently been shown to play a role in an emerging oceanic phosphorus redox cycle, further highlighting the key role these microbes play in many biogeochemical processes in the contemporary ocean. Here, we show that Trichodesmium erythraeum IMS101 can grow on the reduced inorganic compound phosphite as its sole source of P. The components responsible for phosphite utilization are identified through heterologous expression of the T. erythraeum IMS101 Tery_0365-0368 genes, encoding a putative adenosine triphosphate (ATP)-binding cassette transporter and nicotinamide adenine dinucleotide (NAD)-dependent dehydrogenase, in the model cyanobacteria Synechocystis sp. PCC6803. We demonstrate that only combined expression of both the transporter and the dehydrogenase enables Synechocystis to utilize phosphite, confirming the function of Tery_0365-0367 as a phosphite uptake system (PtxABC) and Tery_0368 as a phosphite dehydrogenase (PtxD). Our findings suggest that reported uptake of phosphite by Trichodesmium consortia in the field likely reflects an active biological process by Trichodesmium. These results highlight the diversity of phosphorus sources available to Trichodesmium in a resource-limited ocean.

Rapidly diverging evolution of an atypical alkaline phosphatase (PhoA(aty)) in marine phytoplankton: insights from dinoflagellate alkaline phosphatases

Alkaline phosphatase (AP) is a key enzyme that enables marine phytoplankton to scavenge phosphorus (P) from dissolved organic phosphorus (DOP) when inorganic phosphate is scarce in the ocean. Yet how the AP gene has evolved in phytoplankton, particularly dinoflagellates, is poorly understood. We sequenced full-length AP genes and corresponding complementary DNA (cDNA) from 15 strains (10 species), representing four classes of the core dinoflagellate lineage, Gymnodiniales, Prorocentrales, Suessiales, and Gonyaulacales. Dinoflagellate AP gene sequences exhibited high variability, containing variable introns, pseudogenes, single nucleotide polymorphisms and consequent variations in amino acid sequence, indicative of gene duplication events and consistent with the “birth-and-death” model of gene evolution. Further sequence comparison showed that dinoflagellate APs likely belong to an atypical type AP (PhoA^aty), which shares conserved motifs with counterparts in marine bacteria, cyanobacteria, green algae, haptophytes, and stramenopiles. Phylogenetic analysis suggested that PhoA^aty probably originated from an ancestral gene in bacteria and evolved divergently in marine phytoplankton. Because variations in AP amino acid sequences may lead to differential subcellular localization and potentially different metal ion requirements, the multiple types of APs in algae may have resulted from selection for diversifying strategies to utilize DOP in the P variable marine environment.

Mesoscale eddies and Trichodesmium spp. distributions in the southwestern North Atlantic

Trichodesmium abundance was elevated in certain cyclonic and anticyclonic eddiesEnhancement in cyclonic eddies could be driven by Ekman convergenceAnticyclonic eddies with elevated abundance were anomalously fresh.

Transcriptomic and Proteomic Profiling of Anabaena sp. Strain 90 under Inorganic Phosphorus Stress

Inorganic phosphorus (Pi) is one of the main growth-limiting factors of diazotrophic cyanobacteria. Due to human activity, the availability of Pi has increased in water bodies, resulting in eutrophication and the formation of massive cyanobacterial blooms. In this study, we examined the molecular responses of the cyanobacterium Anabaena sp. strain 90 to phosphorus deprivation, aiming at the identification of candidate genes to monitor the Pi status in cyanobacteria. Furthermore, this study increased the basic understanding of how phosphorus affects diazotrophic and bloom-forming cyanobacteria as a major growth-limiting factor. Based on RNA sequencing data, we identified 246 differentially expressed genes after phosphorus starvation and 823 differentially expressed genes after prolonged Pi limitation, most of them related to central metabolism and cellular growth. The transcripts of the genes related to phosphorus transport and assimilation (pho regulon) were most upregulated during phosphorus depletion. One of the most increased transcripts encodes a giant protein of 1,869 amino acid residues, which contains, among others, a phytase-like domain. Our findings predict its crucial role in phosphorus starvation, but future studies are still needed. Using two-dimensional difference in gel electrophoresis (2D-DIGE) and liquid chromatography-tandem mass spectrometry (LC-MS/MS), we found 43 proteins that were differentially expressed after prolonged phosphorus stress. However, correlation analysis unraveled an association only to some extent between the transcriptomic and proteomic abundances. Based on the present results, we suggest that the method used for monitoring the Pi status in cyanobacterial bloom should contain wider combinations of pho regulon genes (e.g., PstABCS transport systems) in addition to the commonly used alkaline phosphatase gene alone.

A complex iron-calcium cofactor catalyzing phosphotransfer chemistry

Alkaline phosphatases play a crucial role in phosphate acquisition by microorganisms. To expand our understanding of catalysis by this class of enzymes, we have determined the structure of the widely occurring microbial alkaline phosphatase PhoX. The enzyme contains a complex active-site cofactor comprising two antiferromagnetically coupled ferric iron ions (Fe(3+)), three calcium ions (Ca(2+)), and an oxo group bridging three of the metal ions. Notably, the main part of the cofactor resembles synthetic oxide-centered triangular metal complexes. Structures of PhoX-ligand complexes reveal how the active-site metal ions bind substrate and implicate the cofactor oxo group in the catalytic mechanism. The presence of iron in PhoX raises the possibility that iron bioavailability limits microbial phosphate acquisition.

Expression of a xanthine permease and phosphate transporter in cultures and field populations of the harmful alga Aureococcus anophagefferens: tracking nutritional deficiency during brown tides

Targeted gene expression using quantitative reverse transcription polymerase chain reaction (qRT-PCR) was employed to track patterns in the expression of genes indicative of nitrogen or phosphorus deficiency in the brown tide-forming alga Aureococcus anophagefferens. During culture experiments, a xanthine/uracil/vitamin C permease (XUV) was upregulated ∼20-fold under nitrogen-deficient conditions relative to a nitrogen-replete control and rapidly returned to nitrogen-replete levels after nitrogen-deficient cells were resupplied with nitrate or ammonium. It was not responsive to phosphorus deficiency. Expression of an inorganic phosphate transporter (PTA3) was enriched ∼10-fold under phosphorus-deficient conditions relative to a phosphorus-replete control, and this signal was rapidly lost upon phosphate resupply. PTA3 was not upregulated by nitrogen deficiency. Natural A. anophagefferens populations from a dense brown tide that occurred in Long Island, NY, in 2009 were assayed for XUV and PTA3 expression and compared with nutrient concentrations over the peak of a bloom. Patterns in XUV expression were consistent with nitrogen-replete growth, never reaching the values observed in N-deficient cultures. PTA3 expression was highest prior to peak bloom stages, reaching expression levels within the range of P-deficient cultures. These data highlight the value of molecular-level assessments of nutrient deficiency and suggest that phosphorus deficiency could play a role in the dynamics of destructive A. anophagefferens blooms.