Biogeochemical controls of surface ocean phosphate

Effects of nutrient ratios on a newly harmful dinoflagellate Heterocapsa bohaiensis: Evidence from growth, toxicity and transcriptome analyses

Heterocapsa bohaiensis is a newly identified dinoflagellate species that causes harmful blooms in coastal areas in China, Malaysian, and New Caledonian. These blooms have led to substantial economic losses for local aquaculture. Previous studies have mainly focused on understanding the toxicity of H. bohaiensis. However, the causes of H. bohaiensis blooms remain unknown. In this study, we aimed to ascertain nitrogen (N) and phosphorus (P) requirements for the growth and reproduction of H. bohaiensis. Additionally, we sought to understand the functional mechanisms by comparing the transcriptomes of H. bohaiensis under nutrient-limited conditions and control conditions. The results revealed a wide range of acceptable N:P ratios for H. bohainensis, attributed to a mechanism involving nutrient storage, which allowed H. bohainensis to sustain its growth even when either nitrate or phosphate was depleted. Higher N:P ratios (>27.5) were more conducive to the growth of H. bohainensis than f/2 medium or low ratios, which is related to the N:P ratios absorbed by H. bohainensis. The toxicity of H. bohainensis was significantly enhanced in N-limited or P-limited states. These findings underscore the significance of the physiological metabolism of H. bohainensis in adapting to environmental stresses induced by human activities and establishing the dominance of blooms.

Measurements and analysis of nitrogen and phosphorus in oceans: Practice, frontiers, and insights

Nitrogen and phosphorus concentrations in oceans have been extensively studied, and advancements in associated disciplines have rapidly progressed, enabling the exploration of novel and previously challenging questions. A keyword analysis was conducted using the Scopus database to examine chronological trends and hotspots, offering comprehensive insights into the evolution of marine nitrogen and phosphorus research. For this purpose, author keyword networks were developed for the periods before 1990, 1990 to 2000, 2001 to 2011, and 2012 to 2022. Furthermore, analytical techniques employed in the recent decade to determine nitrogen and phosphorus concentrations in seawater were assessed for their applicability and limitations through a critical review of more than 50 journal articles. Taxonomy and nitrogen biogeochemistry were the prominent research interests for the first two periods, respectively, while stable isotopic tracking of nitrogen and phosphorus processes emerged as the dominant research focus for the last two decades. The integration of macroeconomic factors in research development and the chronological rise of interdisciplinary research were identified. Conventional analytical techniques such as spectrophotometry, colorimetry, fluorometry, and elemental analysis were noted, along with emerging techniques like remote sensing and microfluidic sensors.

Spatial and temporal variation in surface nitrate and phosphate in the Northern Gulf of Mexico over 35 years

Dissolved inorganic nutrient concentrations in the surface waters (0 to 5 m) of the Northern Gulf of Mexico (NGoM) were analyzed from 1985 to 2019 (> 10,000 observations) to determine spatiotemporal trends and their connection to nutrients supplied from the Mississippi/Atchafalaya River (MAR). In the NGoM, annual mean dissolved inorganic P (DIP) concentrations increased significantly over time, while dissolved inorganic N (DIN) concentrations showed no temporal trend. With greater salinity, mean DIN:DIP decreased from above the Redfield ratio of 16 to below it, reflecting DIN losses and the more conservative behavior of DIP with salinity. Over the same time period, annual mean P (total dissolved P, DIP, dissolved organic P) loading from the MAR to the NGoM significantly increased, annual mean DIN and total dissolved N loading showed no temporal trend, and dissolved organic N loading significantly decreased. Though DIP increased in the MAR, MAR DIP alone was insufficient to explain the surface distribution of DIP with salinity. Therefore, increases in surface DIP in the NGoM are not simply a reflection of increasing MAR DIP, pointing to temporal changes in other DIP sources. The increase in NGoM DIP suggests greater N limitation for phytoplankton, with implications for N fixation and nutrient management.

Phosphorus forms and zinc concentrations affect the physiological ecology and sinking rate of Thalassiosira weissflogii

The combined effects of phosphorus (P) forms and zinc (Zn) concentrations on diatom silicification remain unclear. In this study, we investigate the effects of different Zn concentrations on the growth, cellular silicon content and sinking rate of Thalassiosira weissflogii under different P forms. The results showed that under the dissolved inorganic phosphorus (DIP) treatments, the specific growth rate of T. weissflogii in Zn limitation culture was significantly lower than that in Zn-replete culture. However, T. weissflogii cellular silicon content and sinking rate increased. Moreover, the reduced specific growth rate (7 %, p < 0.05), enhanced ALP activity (63 %, p < 0.05), and sinking rate (20 %, p < 0.05) for Zn-deplete T. weissflogii implied that the bioavailability of dissolved organic phosphorus (DOP) was depressed under Zn deplete medium. This study demonstrates that the physiological ecology and sinking rate of the diatom T. weissflogii were affected by both individual and combined changes in P forms and Zn concentrations.

Environment-specific virocell metabolic reprogramming

Viruses impact microbial systems through killing hosts, horizontal gene transfer, and altering cellular metabolism, consequently impacting nutrient cycles. A virus-infected cell, a "virocell," is distinct from its uninfected sister cell as the virus commandeers cellular machinery to produce viruses rather than replicate cells. Problematically, virocell responses to the nutrient-limited conditions that abound in nature are poorly understood. Here we used a systems biology approach to investigate virocell metabolic reprogramming under nutrient limitation. Using transcriptomics, proteomics, lipidomics, and endo- and exo-metabolomics, we assessed how low phosphate (low-P) conditions impacted virocells of a marine Pseudoalteromonas host when independently infected by two unrelated phages (HP1 and HS2). With the combined stresses of infection and nutrient limitation, a set of nested responses were observed. First, low-P imposed common cellular responses on all cells (virocells and uninfected cells), including activating the canonical P-stress response, and decreasing transcription, translation, and extracellular organic matter consumption. Second, low-P imposed infection-specific responses (for both virocells), including enhancing nitrogen assimilation and fatty acid degradation, and decreasing extracellular lipid relative abundance. Third, low-P suggested virocell-specific strategies. Specifically, HS2-virocells regulated gene expression by increasing transcription and ribosomal protein production, whereas HP1-virocells accumulated host proteins, decreased extracellular peptide relative abundance, and invested in broader energy and resource acquisition. These results suggest that although environmental conditions shape metabolism in common ways regardless of infection, virocell-specific strategies exist to support viral replication during nutrient limitation, and a framework now exists for identifying metabolic strategies of nutrient-limited virocells in nature.

Methylphosphonate-driven methane formation and its link to primary production in the oligotrophic North Atlantic

Methylphosphonate is an organic phosphorus compound used by microorganisms when phosphate, a key nutrient limiting growth in most marine surface waters, becomes unavailable. Microbial methylphosphonate use can result in the formation of methane, a potent greenhouse gas, in oxic waters where methane production is traditionally unexpected. The extent and controlling factors of such aerobic methane formation remain underexplored. Here, we show high potential net rates of methylphosphonate-driven methane formation (median 0.4 nmol methane L-1 d-1) in the upper water column of the western tropical North Atlantic. The rates are repressed but still quantifiable in the presence of in-situ or added phosphate, suggesting that some methylphosphonate-driven methane formation persists in phosphate-replete waters. The genetic potential for methylphosphonate utilisation is present in and transcribed by key photo- and heterotrophic microbial taxa, such as Pelagibacterales, SAR116, and Trichodesmium. While the large cyanobacterial nitrogen-fixers dominate in the surface layer, phosphonate utilisation by Alphaproteobacteria appears to become more important in deeper depths. We estimate that at our study site, a substantial part (median 11%) of the measured surface carbon fixation can be sustained by phosphorus liberated from phosphonate utilisation, highlighting the ecological importance of phosphonates in the carbon cycle of the oligotrophic ocean.

Holistic view of the seascape dynamics and environment impact on macro-scale genetic connectivity of marine plankton populations

BACKGROUND

Plankton seascape genomics studies have revealed different trends from large-scale weak differentiation to microscale structures. Previous studies have underlined the influence of the environment and seascape on species differentiation and adaptation. However, these studies have generally focused on a few single species, sparse molecular markers, or local scales. Here, we investigated the genomic differentiation of plankton at the macro-scale in a holistic approach using Tara Oceans metagenomic data together with a reference-free computational method.

RESULTS

We reconstructed the FST-based genomic differentiation of 113 marine planktonic taxa occurring in the North and South Atlantic Oceans, Southern Ocean, and Mediterranean Sea. These taxa belong to various taxonomic clades spanning Metazoa, Chromista, Chlorophyta, Bacteria, and viruses. Globally, population genetic connectivity was significantly higher within oceanic basins and lower in bacteria and unicellular eukaryotes than in zooplankton. Using mixed linear models, we tested six abiotic factors influencing connectivity, including Lagrangian travel time, as proxies of oceanic current effects. We found that oceanic currents were the main population genetic connectivity drivers, together with temperature and salinity. Finally, we classified the 113 taxa into parameter-driven groups and showed that plankton taxa belonging to the same taxonomic rank such as phylum, class or order presented genomic differentiation driven by different environmental factors.

CONCLUSION

Our results validate the isolation-by-current hypothesis for a non-negligible proportion of taxa and highlight the role of other physicochemical parameters in large-scale plankton genetic connectivity. The reference-free approach used in this study offers a new systematic framework to analyse the population genomics of non-model and undocumented marine organisms from a large-scale and holistic point of view.

Global analysis of ocean phytoplankton nutrient limitation reveals high prevalence of co-limitation

Nutrient availability limits phytoplankton growth throughout much of the global ocean. Here we synthesize available experimental data to identify three dominant nutrient limitation regimes: nitrogen is limiting in the stratified subtropical gyres and in the summertime Arctic Ocean, iron is most commonly limiting in upwelling regions, and both nutrients are frequently co-limiting in regions in between the nitrogen and iron limited systems. Manganese can be co-limiting with iron in parts of the Southern Ocean, whilst phosphate and cobalt can be co-/serially limiting in some settings. Overall, an analysis of experimental responses showed that phytoplankton net growth can be significantly enhanced through increasing the number of different nutrients supplied, regardless of latitude, temperature, or trophic status, implying surface seawaters are often approaching nutrient co-limitation. Assessments of nutrient deficiency based on seawater nutrient concentrations and nutrient stress diagnosed via molecular biomarkers showed good agreement with experimentally-assessed nutrient limitation, validating conceptual and theoretical links between nutrient stoichiometry and microbial ecophysiology.

Elemental stoichiometry of the key calcifying marine phytoplankton Emiliania huxleyi under ocean climate change: A meta-analysis

The elemental composition of marine microorganisms (their C:N:P ratio, or stoichiometry) is central to understanding the biotic and biogeochemical processes underlying key marine ecosystem functions. Phytoplankton C:N:P is species specific and flexible to changing environmental conditions. However, bulk or fixed phytoplankton stoichiometry is usually assumed in biogeochemical and ecological models because more realistic, environmentally responsive C:N:P ratios have yet to be defined for key functional groups. Here, a comprehensive meta-analysis of experimental laboratory data reveals the variable C:N:P stoichiometry of Emiliania huxleyi, a globally significant calcifying phytoplankton species. Mean C:N:P of E. huxleyi is 124C:16N:1P under control conditions (i.e. growth not limited by one or more environmental stressors) and shows a range of responses to changes in nutrient and light availability, temperature and pCO2 . Macronutrient limitation caused strong shifts in stoichiometry, increasing N:P and C:P under P deficiency (by 305% and 493% respectively) and doubling C:N under N deficiency. Responses to light, temperature and pCO2 were mixed but typically shifted cellular elemental content and C:N:P stoichiometry by ca. 30% or less. Besides these independent effects, the interactive effects of multiple environmental changes on E. huxleyi stoichiometry under future ocean conditions could be additive, synergistic or antagonistic. To synthesise our meta-analysis results, we explored how the cellular elemental content and C:N:P stoichiometry of E. huxleyi may respond to two hypothetical future ocean scenarios (increased temperature, irradiance and pCO2 combined with either N deficiency or P deficiency) if an additive effect is assumed. Both future scenarios indicate decreased calcification (which is predominantly sensitive to elevated pCO2 ), increased C:N, and up to fourfold shifts in C:P and N:P. Our results strongly suggest that climate change will significantly alter the role of E. huxleyi (and potentially other calcifying phytoplankton species) in marine biogeochemical processes.

Effects of phytoplankton physiology on global ocean biogeochemistry and climate

The similarity of the average ratios of nitrogen (N) and phosphorus (P) in marine dissolved inorganic and particulate organic matter, dN:P and pN:P, respectively, indicates tight links between those pools in the world ocean. Here, we analyze this linkage by varying phytoplankton N and P subsistence quotas in an optimality-based ecosystem model coupled to an Earth system model. The analysis of our ensemble of simulations discloses various feedbacks between changes in the N and P quotas, N2 fixation, and denitrification that weaken the often-hypothesized tight coupling between dN:P and pN:P. We demonstrate the importance of particulate N:C and P:C ratios for regulating dN:P on the global scale, with marine oxygen level being an important control. Our analysis provides further insight into the potential interdependence of phytoplankton physiology and global climate conditions.

Microbial Interaction is Among the Key Factors for Isolation of Previous Uncultured Microbes

Pure cultivation of microbes is still limited by the challenges of microbial uncultivability, with most microbial strains unable to be cultivated under standard laboratory conditions. The experience accumulated from advanced techniques such as in situ cultivation has identified that microbial interactions exist in natural habitats but are absent in laboratory cultures. These microbial interactions are likely one of the key factors in isolating previously uncultured microbes. The need for better knowledge of the mechanisms operating in microbial interactions has led to various experiments that have utilized microbial interactions in different approaches to microbial cultivation. These new attempts to understand microbial interactions not only present a new perspective on microbial uncultivability but also provide an opportunity to access uncultured phylogenetically novel microbes with their potential biotechnology applications. In this review, we focus on studies of the mechanisms of microbial interaction where the growth of other microbes is affected. Additionally, we review some successful applications of microbial interactions in cultivation methods, an approach that can play an important role in the bioprospecting of untapped microbial resources.

Nutrient uptake plasticity in phytoplankton sustains future ocean net primary production

Annually, marine phytoplankton convert approximately 50 billion tons of dissolved inorganic carbon to particulate and dissolved organic carbon, a portion of which is exported to depth via the biological carbon pump. Despite its important roles in regulating atmospheric carbon dioxide via carbon sequestration and in sustaining marine ecosystems, model-projected future changes in marine net primary production are highly uncertain even in the sign of the change. Here, using an Earth system model, we show that frugal utilization of phosphorus by phytoplankton under phosphate-stressed conditions can overcompensate the previously projected 21st century declines due to ocean warming and enhanced stratification. Our results, which are supported by observations from the Hawaii Ocean Time-series program, suggest that nutrient uptake plasticity in the subtropical ocean plays a key role in sustaining phytoplankton productivity and carbon export production in a warmer world.

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.

Global patterns and predictors of C:N:P in marine ecosystems

Oceanic nutrient cycles are coupled, yet carbon-nitrogen-phosphorus (C:N:P) stoichiometry in marine ecosystems is variable through space and time, with no clear consensus on the controls on variability. Here, we analyze hydrographic, plankton genomic diversity, and particulate organic matter data from 1970 stations sampled during a global ocean observation program (Bio-GO-SHIP) to investigate the biogeography of surface ocean particulate organic matter stoichiometry. We find latitudinal variability in C:N:P stoichiometry, with surface temperature and macronutrient availability as strong predictors of stoichiometry at high latitudes. Genomic observations indicated community nutrient stress and suggested that nutrient supply rate and nitrogen-versus-phosphorus stress are predictive of hemispheric and regional variations in stoichiometry. Our data-derived statistical model suggests that C:P and N:P ratios will increase at high latitudes in the future, however, changes at low latitudes are uncertain. Our findings suggest systematic regulation of elemental stoichiometry among ocean ecosystems, but that future changes remain highly uncertain.

Utilization of diverse organophosphorus pollutants by marine bacteria

Anthropogenic organophosphorus compounds (AOPCs), such as phosphotriesters, are used extensively as plasticizers, flame retardants, nerve agents, and pesticides. To date, only a handful of soil bacteria bearing a phosphotriesterase (PTE), the key enzyme in the AOPC degradation pathway, have been identified. Therefore, the extent to which bacteria are capable of utilizing AOPCs as a phosphorus source, and how widespread this adaptation may be, remains unclear. Marine environments with phosphorus limitation and increasing levels of pollution by AOPCs may drive the emergence of PTE activity. Here, we report the utilization of diverse AOPCs by four model marine bacteria and 17 bacterial isolates from the Mediterranean Sea and the Red Sea. To unravel the details of AOPC utilization, two PTEs from marine bacteria were isolated and characterized, with one of the enzymes belonging to a protein family that, to our knowledge, has never before been associated with PTE activity. When expressed in Escherichia coli with a phosphodiesterase, a PTE isolated from a marine bacterium enabled growth on a pesticide analog as the sole phosphorus source. Utilization of AOPCs may provide bacteria a source of phosphorus in depleted environments and offers a prospect for the bioremediation of a pervasive class of anthropogenic pollutants.

Potential negative effects of ocean afforestation on offshore ecosystems

Our scientific understanding of climate change makes clear the necessity for both emission reduction and carbon dioxide removal (CDR). The ocean with its large surface area, great depths and long coastlines is central to developing CDR approaches commensurate with the scale needed to limit warming to below 2 °C. Many proposed marine CDR approaches rely on spatial upscaling along with enhancement and/or acceleration of the rates of naturally occurring processes. One such approach is 'ocean afforestation', which involves offshore transport and concurrent growth of nearshore macroalgae (seaweed), followed by their export into the deep ocean. The purposeful occupation for months of open ocean waters by macroalgae, which do not naturally occur there, will probably affect offshore ecosystems through a range of biological threats, including altered ocean chemistry and changed microbial physiology and ecology. Here, we present model simulations of ocean afforestation and link these to lessons from other examples of offshore dispersal, including rafting plastic debris, and discuss the ramifications for offshore ecosystems. We explore what additional metrics are required to assess the ecological implications of this proposed CDR. In our opinion, these ecological metrics must have equal weight to CDR capacity in the development of initial trials, pilot studies and potential licensing.

Phosphorus Limitation Enhances Diazotroph Zinc Quotas

Trichodesmium spp. is a colonial diazotrophic cyanobacterium found in the oligotrophic (sub)tropical oceans, where dissolved inorganic phosphorus (DIP) can be depleted. To cope with low P concentrations, P can be scavenged from the dissolved organic P (DOP) pool. This requires the deployment of multiple enzymes activated by trace metals, potentially enhancing metal requirements under stronger P limitations. To test this, we grew Trichodesmium under trace-metal-controlled conditions, where P was supplied as either DIP or DOP (methylphosphonic acid). Mean steady-state biomass under the DOP treatment was only 40% of that grown under equivalent DIP supply, carbon normalized alkaline phosphorus activity was elevated 4-fold, and the zinc (Zn)–carbon ratio was elevated 3.5-fold. Our finding matches the known, dominant Zn requirement across a diversity of enzymes involved in P stress responses and supports an important interaction in the oceanic cycles of these two nutrients.

Adaptive carbon export response to warming in the Sargasso Sea

Ocean ecosystem models predict that warming and increased surface ocean stratification will trigger a series of ecosystem events, reducing the biological export of particulate carbon to the ocean interior. We present a nearly three-decade time series from the open ocean that documents a biological response to ocean warming and nutrient reductions wherein particulate carbon export is maintained, counter to expectations. Carbon export is maintained through a combination of phytoplankton community change to favor cyanobacteria with high cellular carbon-to-phosphorus ratios and enhanced shallow phosphorus recycling leading to increased nutrient use efficiency. These results suggest that surface ocean ecosystems may be more responsive and adapt more rapidly to changes in the hydrographic system than is currently envisioned in earth ecosystem models, with positive consequences for ocean carbon uptake.

The ability of the ocean’s biota to sequester carbon is thought to be negatively affected by climate change. Here the authors use time-series data in the Sargasso Sea to show that biotic processes can buffer against these negative impacts.

Nutrient regulation of biological nitrogen fixation across the tropical western North Pacific

Nitrogen fixation is critical for the biological productivity of the ocean, but clear mechanistic controls on this process remain elusive. Here, we investigate the abundance, activity, and drivers of nitrogen-fixing diazotrophs across the tropical western North Pacific. We find a basin-scale coherence of diazotroph abundances and N₂ fixation rates with the supply ratio of iron:nitrogen to the upper ocean. Across a threshold of increasing supply ratios, the abundance of nifH genes and N₂ fixation rates increased, phosphate concentrations decreased, and bioassay experiments demonstrated evidence for N₂ fixation switching from iron to phosphate limitation. In the northern South China Sea, supply ratios were hypothesized to fall around this critical threshold and bioassay experiments suggested colimitation by both iron and phosphate. Our results provide evidence for iron:nitrogen supply ratios being the most important factor in regulating the distribution of N₂ fixation across the tropical ocean.

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

Extremophile enzymes for food additives and fertilizers

The use of extremophile enzymes for industrial purposes has become very significant since the beginning of this century and it is envisaged an ample use of enzymes for environmental applications (fertilisers, food and feed additives, biodegradation, pharma) as well as in the biosynthesis of compounds through design of novel biosynthetic pathways.

Functional characterisation of substrate-binding proteins to address nutrient uptake in marine picocyanobacteria

Marine cyanobacteria are key primary producers, contributing significantly to the microbial food web and biogeochemical cycles by releasing and importing many essential nutrients cycled through the environment. A subgroup of these, the picocyanobacteria (Synechococcus and Prochlorococcus), have colonised almost all marine ecosystems, covering a range of distinct light and temperature conditions, and nutrient profiles. The intra-clade diversities displayed by this monophyletic branch of cyanobacteria is indicative of their success across a broad range of environments. Part of this diversity is due to nutrient acquisition mechanisms, such as the use of high-affinity ATP-binding cassette (ABC) transporters to competitively acquire nutrients, particularly in oligotrophic (nutrient scarce) marine environments. The specificity of nutrient uptake in ABC transporters is primarily determined by the peripheral substrate-binding protein (SBP), a receptor protein that mediates ligand recognition and initiates translocation into the cell. The recent availability of large numbers of sequenced picocyanobacterial genomes indicates both Synechococcus and Prochlorococcus apportion >50% of their transport capacity to ABC transport systems. However, the low degree of sequence homology among the SBP family limits the reliability of functional assignments using sequence annotation and prediction tools. This review highlights the use of known SBP structural representatives for the uptake of key nutrient classes by cyanobacteria to compare with predicted SBP functionalities within sequenced marine picocyanobacteria genomes. This review shows the broad range of conserved biochemical functions of picocyanobacteria and the range of novel and hypothetical ABC transport systems that require further functional characterisation.

Modeled temperature dependencies of macromolecular allocation and elemental stoichiometry in phytoplankton

Warming oceans may affect how phytoplankton allocate nutrients to essential cellular processes. Despite the potential impact of such processes on future biogeochemical cycles, questions remain about how temperature affects macromolecular allocation and elemental stoichiometry within phytoplankton cells. Here, we present a macromolecular model of phytoplankton and the effect of increasing temperature on the intracellular allocation of nutrients at a constant growth rate. When temperature increases under nitrogen (N) and phosphorus (P) co-limitation, the model shows less investment in phosphorus-rich RNA molecules relative to nitrogen-rich proteins, leading to a more severe decrease in cellular P:C than N:C causing increased cellular N:P values. Under P limitation, the model shows a similar pattern, but when excess P is available under N limitation, we predict lowered N:P due to the effect of luxury uptake of P. We reflected our model result on the surface ocean showing similar latitudinal patterns in N:P and P:C to observation and other model predictions, suggesting a considerable impact of temperature on constraining the elemental stoichiometry in the ocean.

Nanomolar phosphate supply and its recycling drive net community production in the subtropical North Pacific

Seasonal drawdown of dissolved inorganic carbon (DIC) in the subtropical upper ocean makes a significant contribution to net community production (NCP) globally. Although NCP requires macronutrient supply, surface macronutrients are chronically depleted, and their supply has been unable to balance the NCP demand. Here, we report nanomolar increases in surface nitrate plus nitrite (N+N, ~20 nM) and phosphate (PO₄, ~15 nM) from summer to winter in the western subtropical North Pacific. Molar ratios of upward fluxes of DIC:N+N:PO₄ to the euphotic zone (< 100 m) were in near-stoichiometric balance with microbial C:N:P ratios (107~243:16~35:1). Comparison of these upward influxes with other atmospheric and marine sources demonstrated that total supply is largely driven by the other sources for C and N (93~96%), but not for P (10%), suggesting that nanomolar upward supply of P and its preferential recycling play a vital role in sustaining the NCP.

Spatial and seasonal variations in coastal water characteristics at Kalpakkam, western Bay of Bengal, Southeast India: a multivariate statistical approach

A study was carried out in the coastal waters of Kalpakkam with the objectives to evaluate the seasonality in hydrobiological parameters in surface and bottom waters, and assess the anthropogenic stress and monsoonal flux on a spatiotemporal scale. The study covered an area of approximately 100 km² in the coastal environment. Relatively high values for pH, temperature, and TP were observed during the post-monsoon (POM) season. The monsoon (MON) season was linked with TN, ammonia, and DO concentrations as all these parameters have shown increased values during this season due to freshwater input. The summer (SUM) season was characterized by salinity, turbidity, nitrate, phosphate, and silicate, indicating a true marine environmental condition for plankton production. Principal component analysis (PCA) and cluster analysis (CA) indicated the presence of distinct coastal water masses with respect to seasons and sampling regions. The spatial pattern indicated the distinctness of the coastal nearshore water (CNW) and coastal offshore water (COW) with respect to water quality. The CNW was more dynamic due to direct external influence as compared to the relatively stable COW environment. Similarly, the study region in the northern part, which is continuously exposed to the backwater inputs and tourism activities, was statistically different from the southern part.

Arsenolipids in Plankton from High- and Low-Nutrient Oceanic Waters Along a Transect in the North Atlantic

Although the natural occurrence of arsenic-containing lipids (arsenolipids) in marine organisms is now well established, the possible role of these unusual compounds in organisms and in the cycling of arsenic in marine systems remains largely unexplored. We report the finding of arsenolipids in 61 plankton samples collected from surface marine waters of high- and low-nutrient content along a transect spanning the Gulf Stream in the North Atlantic Ocean. Using high-performance liquid chromatography (HPLC) coupled to both elemental and molecular mass spectrometry, we show that all 61 plankton samples contained six identifiable arsenolipids, namely, three arsenosugar phospholipids (AsPL958, 10-13%; AsPL978, 13-25%; and AsPL1006, 7-10% of total arsenolipids), two arsenic-containing hydrocarbons (AsHC332, 4-10% and AsHC360, 1-2%), and a methoxy-sugar arsenolipid that contained phytol (AsSugPhytol, 1-3%). The relative amounts of the six arsenolipids showed clear dependence on the nutrient status of the ambient water with plankton collected from high-nutrient waters having less of the arsenosugar phospholipids and more of the three non-P containing arsenolipids compared to low-nutrient waters. By combining these first field data of arsenolipids in plankton with reported global phytoplankton productivity, we estimate that the oceans' phytoplankton transform per year 50 000-100 000 tons of arsenic into arsenolipids.

Metagenomic analysis reveals global-scale patterns of ocean nutrient limitation

Nutrient supply regulates the activity of phytoplankton, but the global biogeography of nutrient limitation and co-limitation is poorly understood. Prochlorococcus adapt to local environments by gene gains and losses, and we used genomic changes as an indicator of adaptation to nutrient stress. We collected metagenomes from all major ocean regions as part of the Global Ocean Ship-based Hydrographic Investigations Program (Bio-GO-SHIP) and quantified shifts in genes involved in nitrogen, phosphorus, and iron assimilation. We found regional transitions in stress type and severity as well as widespread co-stress. Prochlorococcus stress genes, bottle experiments, and Earth system model predictions were correlated. We propose that the biogeography of multinutrient stress is stoichiometrically linked by controls on nitrogen fixation. Our omics-based description of phytoplankton resource use provides a nuanced and highly resolved description of nutrient stress in the global ocean.

Toward a versatile flow technique: Development and application of reverse flow dual-injection analysis (rFDIA) for determining dissolved iron redox species and soluble reactive phosphorus in seawater

A versatile flow analyzer that extended the features of reverse flow injection analysis (rFIA) was developed in this study and named reverse flow dual-injection analysis (rFDIA). Compared with typical rFIA, the analyzer requires less reagent and is more environmentally friendly, which has two injection valves and two reagent loops for the accurate and successive injection of two reagents. With a 2-m long liquid waveguide capillary cell (LWCC) and a spectrophotometer, the analyzer was applied to underway determination of dissolved iron redox species in estuarine and coastal waters. Detection limits of 0.18 and 0.20 nmol L^-1 were achieved for Fe(II) and Fe(II + III), respectively and a linear dynamic range of 0.5-450 nmol L^-1 was obtained for both Fe(II) and Fe(II + III). The sample throughput for the simultaneous measurement of Fe(II) and Fe(II + III) was 12 h^-1, and each analysis consumed only 8 mL sample, 520 μL ferrozine solution, and 260 μL ascorbic acid solution. The analyzer was also used to measure nanomolar amounts of soluble reactive phosphorus (SRP) in seawater. The detection limit and the linear dynamic range for the SRP assay were 0.5 nmol L^-1 and 1.5-850 nmol L^-1. For SRP determination, the sample throughput was 20 h^-1, and each analysis required 9 mL of sample, 130 μL of mixed reagent solution and 260 μL of ascorbic acid. The analytical results were reproducible, with a relative standard deviation of 1.4% (2.5 nmol L^-1, n = 10), 2.1% (2.5 nmol L^-1, n = 10), and 2.1% (10 nmol L^-1, n = 11) for Fe(II), Fe(II + III), and SRP, respectively.

Longitudinal and Vertical Variations of Dissolved Labile Phosphoric Monoesters and Diesters in the Subtropical North Pacific

The labile fraction of dissolved organic phosphorus (DOP) – predominantly consisting of phosphoric esters – is an important microbial P source in the subtropical oligotrophic ocean. However, unlike phosphate, knowledge for labile DOP is still limited due to the scarcity of broad and intensive observations. In this study, we examined the concentrations and size-fractionated hydrolysis rates of labile phosphoric monoesters and diesters along a >10,000 km longitudinal transect in the North Pacific (23°N; upper 200-m layer). Depth-integrated monoesters decreased westward with a maximum difference of fivefold. Vertical profiles of monoesters in the eastern and western basins showed decreasing and increasing trends with depth, respectively. The monoester-depleted shallow layer of the western basin was associated with phosphate depletion and monoesterase activity was predominant in the large size fraction (>0.8 μm), suggesting that monoesters are significant P sources particularly for large microbes. In contrast, diester concentrations were generally lower than monoester concentrations and showed no obvious horizontal or vertical variation in the study area. Despite the unclear distribution pattern of diesters, diesterase activity in the particulate fraction (>0.2 μm) increased in the phosphate-depleted shallow layer of the western basin, suggesting that the targeted diesters in the assay were also important microbial P sources. Diesterase activities in the dissolved fraction (<0.2 μm) were not correlated with ambient phosphate concentrations; however, cell-free diesterase likely played a key role in P cycling, as dissolved diesterase activities were substantially higher than those in the particulate fraction. The horizontal and vertical variability of labile monoesters in the subtropical North Pacific were therefore predominantly regulated by P stress in particularly large microbes, whereas the distributions of labile diesters and diesterase activities were generally independent of microbial P stress, indicating a more complex regulation of diesters to that of monoesters.

Benthic phosphorus cycling within the Eurasian marginal sea ice zone

The Arctic Ocean region is currently undergoing dramatic changes, which will likely alter the nutrient cycles that underpin Arctic marine ecosystems. Phosphate is a key limiting nutrient for marine life but gaps in our understanding of the Arctic phosphorus (P) cycle persist. In this study, we investigate the benthic burial and recycling of phosphorus using sediments and pore waters from the Eurasian Arctic margin, including the Barents Sea slope and the Yermak Plateau. Our results highlight that P is generally lost from sediments with depth during organic matter respiration. On the Yermak Plateau, remobilization of P results in a diffusive flux of P to the seafloor of between 96 and 261 µmol m-2 yr-1. On the Barents Sea slope, diffusive fluxes of P are much larger (1736-2449 µmol m-2 yr-1), but these fluxes are into near-surface sediments rather than to the bottom waters. The difference in cycling on the Barents Sea slope is controlled by higher fluxes of fresh organic matter and active iron cycling. As changes in primary productivity, ocean circulation and glacial melt continue, benthic P cycling is likely to be altered with implications for P imported into the Arctic Ocean Basin. This article is part of the theme issue 'The changing Arctic Ocean: consequences for biological communities, biogeochemical processes and ecosystem functioning'.

Developing robust protein analysis profiles to identify bacterial acid phosphatases in genomes and metagenomic libraries

Phylogenetic analysis of more than 4000 annotated bacterial acid phosphatases was carried out. Our analysis enabled us to sort these enzymes into the following three types: (1) class B acid phosphatases, which were distantly related to the other types, (2) class C acid phosphatases and (3) generic acid phosphatases (GAP). Although class B phosphatases are found in a limited number of bacterial families, which include known pathogens, class C acid phosphatases and GAP proteins are found in a variety of microbes that inhabit soil, fresh water and marine environments. As part of our analysis, we developed three profiles, named Pfr-B-Phos, Pfr-C-Phos and Pfr-GAP, to describe the three groups of acid phosphatases. These sequence-based profiles were then used to scan genomes and metagenomes to identify a large number of formerly unknown acid phosphatases. A number of proteins in databases annotated as hypothetical proteins were also identified by these profiles as putative acid phosphatases. To validate these in silico results, we cloned genes encoding candidate acid phosphatases from genomic DNA or recovered from metagenomic libraries or genes synthesized in vitro based on protein sequences recovered from metagenomic data. Expression of a number of these genes, followed by enzymatic analysis of the proteins, further confirmed that sequence similarity searches using our profiles could successfully identify previously unknown acid phosphatases.

Linking regional shifts in microbial genome adaptation with surface ocean biogeochemistry

Linking 'omics measurements with biogeochemical cycles is a widespread challenge in microbial community ecology. Here, we propose applying genomic adaptation as 'biosensors' for microbial investments to overcome nutrient stress. We then integrate this genomic information with a trait-based model to predict regional shifts in the elemental composition of marine plankton communities. We evaluated this approach using metagenomic and particulate organic matter samples from the Atlantic, Indian and Pacific Oceans. We find that our genome-based trait model significantly improves our prediction of particulate C : P (carbon : phosphorus) across ocean regions. Furthermore, we detect previously unrecognized ocean areas of iron, nitrogen and phosphorus stress. In many ecosystems, it can be very challenging to quantify microbial stress. Thus, a carefully calibrated genomic approach could become a widespread tool for understanding microbial responses to environmental changes and the biogeochemical outcomes. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.

Automated Determination of Dissolved Reactive Phosphorus at Nanomolar to Micromolar Levels in Natural Waters Using a Portable Flow Analyzer

Automated in-field methods for measuring dissolved reactive phosphorus (DRP) over a large concentration range are in high demand for the purpose of better understanding the biogeochemistry of phosphorus in the river-estuary-coast continuum to the open ocean. Here, an automated portable and robust analyzer was described for the determination of nanomolar to micromolar levels of DRP in natural waters. The quantification of DRP was based on classic phosphomolybdenum blue (PMB) chemistry. All the components of the analyzer were computer-controlled using LabVIEW-based laboratory-programmed software. When equipped with a 3 cm Z-type flow cell, the system demonstrated linearity with concentrations up to 12 μmol L^-1, a sampling rate of 20 h^-1, a limit of detection of 0.11 μmol L^-1, and relative standard deviations (RSDs) of 0.4-4.6% (n = 11-576). When a solid-phase extraction cartridge was combined with the analyzer, the PMB formed from the sample was automatically concentrated on the hydrophilic-lipophilic balanced sorbent. The concentrated PMB compound was eluted with NaOH solution and measured in the spectrophotometric system. Under optimal conditions, the nanomolar-level mode afforded a sampling rate of 8 h^-1, a limit of detection of 1.7 nmol L^-1, and RSDs of 3.0-5.7% (n = 11-120). The system exhibited advantages that included a wide linear range, high sensitivity and reproducibility, low reagent consumption, and insignificant interference from salinity, silicate, arsenate, and other P-containing compounds. The system was successfully applied for discrete sample analysis, fixed site online monitoring, and the real-time underway measurement of DRP in riverine-estuarine-coastal waters.