Thick-shelled, grazer-protected diatoms decouple ocean carbon and silicon cycles in the iron-limited Antarctic Circumpolar Current

Direct and indirect effects of copepod grazers on community structure

Ecological theory and empirical research show that both direct lethal effects and indirect non-lethal effects can structure the composition of communities. While the direct effects of grazers on marine phytoplankton communities are well studied, their indirect effects are still poorly understood. Direct and indirect effects are inherently difficult to disentangle in plankton food webs. In this study we evaluate the indirect effects of copepod grazers on community function and structure using isolated chemical alarm signals, copepodamides. We expose intact summer and spring communities to direct grazing from copepods, or to chemical alarm cues without the presence of grazers in controlled experiments. The effects of direct grazing on ecosystem function were moderate in both experiments as indicated by levels of chlorophyll and primary production. Indirect and direct effects resulted in changes in the composition of both the eukaryote and prokaryote communities as shown by metabarcoding of 18S and 16S rRNA. Size structure analysis suggests that direct grazing and copepodamide exposure both favoured smaller organisms (< 10-15 μm) corroborating the size-structuring effect of copepod grazers. We conclude that the well-established effect of copepods on phytoplankton communities results from a combination of direct and indirect effects. This is a first attempt to isolate indirect effects of copepods on community structure and the results suggest that a full mechanistic understanding of the structuring effect of copepods will require insights to both direct and indirect effects of consumers as demonstrated for other ecosystems components.

Molecular physiology of Antarctic diatom natural assemblages and bloom event reveal insights into strategies contributing to their ecological success

The continental shelf of the Western Antarctic Peninsula (WAP) is a highly variable system characterized by strong cross-shelf gradients, rapid regional change, and large blooms of phytoplankton, notably diatoms. Rapid environmental changes coincide with shifts in plankton community composition and productivity, food web dynamics, and biogeochemistry. Despite the progress in identifying important environmental factors influencing plankton community composition in the WAP, the molecular basis for their survival in this oceanic region, as well as variations in species abundance, metabolism, and distribution, remains largely unresolved. Across a gradient of physicochemical parameters, we analyzed the metabolic profiles of phytoplankton as assessed through metatranscriptomic sequencing. Distinct phytoplankton communities and metabolisms closely mirrored the strong gradients in oceanographic parameters that existed from coastal to offshore regions. Diatoms were abundant in coastal, southern regions, where colder and fresher waters were conducive to a bloom of the centric diatom, Actinocyclus. Members of this genus invested heavily in growth and energy production; carbohydrate, amino acid, and nucleotide biosynthesis pathways; and coping with oxidative stress, resulting in uniquely expressed metabolic profiles compared to other diatoms. We observed strong molecular evidence for iron limitation in shelf and slope regions of the WAP, where diatoms in these regions employed iron-starvation induced proteins, a geranylgeranyl reductase, aquaporins, and urease, among other strategies, while limiting the use of iron-containing proteins. The metatranscriptomic survey performed here reveals functional differences in diatom communities and provides further insight into the environmental factors influencing the growth of diatoms and their predicted response to changes in ocean conditions.

IMPORTANCE

In the Southern Ocean, phytoplankton must cope with harsh environmental conditions such as low light and growth-limiting concentrations of the micronutrient iron. Using metratranscriptomics, we assessed the influence of oceanographic variables on the diversity of the phytoplankton community composition and on the metabolic strategies of diatoms along the Western Antarctic Peninsula, a region undergoing rapid climate change. We found that cross-shelf differences in oceanographic parameters such as temperature and variable nutrient concentrations account for most of the differences in phytoplankton community composition and metabolism. We opportunistically characterized the metabolic underpinnings of a large bloom of the centric diatom Actinocyclus in coastal waters of the WAP. Our results indicate that physicochemical differences from onshore to offshore are stronger than between southern and northern regions of the WAP; however, these trends could change in the future, resulting in poleward shifts in functional differences in diatom communities and phytoplankton blooms.

Deviation from neutral species abundance distributions unveils geographical differences in the structure of diatom communities

In recent years, the application of metagenomics techniques has advanced our understanding of plankton communities and their global distribution. Despite this progress, the relationship between the abundance distribution of diatom species and varying marine environmental conditions remains poorly understood. This study, leveraging data from the Tara Oceans expedition, tests the hypothesis that diatoms in sampled stations display a consistent species abundance distribution structure, as though they were sampled from a single ocean-wide metacommunity. Using a neutral sampling theory, we thus develop a framework to estimate the structure and diversity of diatom communities at each sampling station given the shape of the species abundance distribution of the metacommunity and the information of a reference station. Our analysis reveals a substantial temperature gradient in the discrepancies between predicted and observed biodiversity across the sampled stations. These findings challenge the hypothesis of a single neutral metacommunity, indicating that environmental differences substantially influence both the composition and structure of diatom communities.

Effects and mechanisms of glyphosate as phosphorus nutrient on element stoichiometry and metabolism in the diatom Phaeodactylum tricornutum

The ability to utilize dissolved organic phosphorus (DOP) gives phytoplankton competitive advantages in P-limited environments. Our previous research indicates that the diatom Phaeodactylum tricornutum could grow on glyphosate, a DOP with carbon-phosphorus (C-P) bond and an herbicide, as sole P source. However, direct evidence and mechanism of glyphosate utilization are still lacking. In this study, using physiological and isotopic analysis, combined with transcriptomic profiling, we demonstrated the uptake of glyphosate by P. tricornutum and revealed the candidate responsible genes. Our data showed a low efficiency of glyphosate utilization by P. tricornutum, suggesting that glyphosate utilization costs energy and that the alga possessed an herbicide-resistant type of 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase. Compared to the P-limited cultures, the glyphosate-grown P. tricornutum cells up-regulated genes involved in DNA replication, cell growth, transcription, translation, carbon metabolism, and many genes encoding antioxidants. Additionally, cellular C and silicon (Si) increased remarkably while cellular nitrogen (N) declined in the glyphosate-grown P. tricornutum, leading to higher Si:C and Si:N ratios, which corresponded to the up-regulation of genes involved in the C metabolism and Si uptake and the down-regulation of those encoding N uptake. This has the potential to enhance C and Si export to the deep sea when P is limited but phosphonate is available. In sum, our study documented how P. tricornutum could utilize the herbicide glyphosate as P nutrient and how glyphosate utilization may affect the element content and stoichiometry in this diatom, which have important ecological implications in the future ocean.IMPORTANCEGlyphosate is the most widely used herbicide in the world and could be utilized as phosphorus (P) source by some bacteria. Our study first revealed that glyphosate could be transported into Phaeodactylum tricornutum cells for utilization and identified putative genes responsible for glyphosate uptake. This uncovers an alternative strategy of phytoplankton to cope with P deficiency considering phosphonate accounts for about 25% of the total dissolved organic phosphorus (DOP) in the ocean. Additionally, accumulation of carbon (C) and silicon (Si), as well as elevation of Si:C ratio in P. tricornutum cells when grown on glyphosate indicates glyphosate as the source of P nutrient has the potential to result in more C and Si export into the deep ocean. This, along with the differential ability to utilize glyphosate among different species, glyphosate supply in dissolved inorganic phosphorus (DIP)-depleted ecosystems may cause changes in phytoplankton community structure. These insights have implications in evaluating the effects of human activities (use of Roundup) and climate change (potentially reducing DIP supply in sunlit layer) on phytoplankton in the future ocean.

Nanoplankton: The dominant vector for carbon export across the Atlantic Southern Ocean in spring

Across the Southern Ocean, large (≥20 μm) diatoms are generally assumed to be the primary vector for carbon export, although this assumption derives mainly from summertime observations. Here, we investigated carbon production and export potential during the Atlantic Southern Ocean's spring bloom from size-fractionated measurements of net primary production (NPP), nitrogen (nitrate, ammonium, urea) and iron (labile inorganic iron, organically complexed iron) uptake, and a high-resolution characterization of phytoplankton community composition. The nanoplankton-sized (2.7 to 20 μm) diatom, Chaetoceros spp., dominated the biomass, NPP, and nitrate uptake across the basin (40°S to 56°S), which we attribute to their low iron requirement, rapid response to increased light, and ability to escape grazing when aggregated into chains. We estimate that the spring Chaetoceros bloom accounted for >25% of annual export production across the Atlantic Southern Ocean, a finding consistent with recent observations from other regions highlighting the central role of the phytoplankton "middle class" in carbon export.

Iron and manganese availability drives primary production and carbon export in the Weddell Sea

Next to iron (Fe), recent phytoplankton-enrichment experiments identified manganese (Mn) to (co-)limit Southern Ocean phytoplankton biomass and species composition. Since taxonomic diversity affects aggregation time and sinking rate, the efficiency of the biological carbon pump is directly affected by community structure. However, the impact of FeMn co-limitation on Antarctic primary production, community composition, and the subsequent export of carbon to depth requires more investigation. In situ samplings of 6 stations in the understudied southern Weddell Sea revealed that surface Fe and Mn concentrations, primary production, and carbon export rates were all low, suggesting a FeMn co-limited phytoplankton community. An Fe and Mn addition experiment examined how changes in the species composition drive the aggregation capability of a natural phytoplankton community. Primary production rates were highest when Fe and Mn were added together, due to an increased abundance of the colonial prymnesiophyte Phaeocystis antarctica. Although the community remained diatom dominated, the increase in Phaeocystis abundance led to highly carbon-enriched aggregates and a 4-fold increase in the carbon export potential compared to the control, whereas it only doubled in the Fe treatment. Based on the outcome of the FeMn-enrichment experiment, this region may suffer from FeMn co-limitation. As the Weddell Sea represents one of the most productive Antarctic marginal ice zones, our findings highlight that in response to greater Fe and Mn supply, changes in plankton community composition and primary production can have a disproportionally larger effect on the carbon export potential.

Ocean iron fertilization may amplify climate change pressures on marine animal biomass for limited climate benefit

Climate change scenarios suggest that large-scale carbon dioxide removal (CDR) will be required to maintain global warming below 2°C, leading to renewed attention on ocean iron fertilization (OIF). Previous OIF modelling has found that while carbon export increases, nutrient transport to lower latitude ecosystems declines, resulting in a modest impact on atmospheric CO2 . However, the interaction of these CDR responses with ongoing climate change is unknown. Here, we combine global ocean biogeochemistry and ecosystem models to show that, while stimulating carbon sequestration, OIF may amplify climate-induced declines in tropical ocean productivity and ecosystem biomass under a high-emission scenario, with very limited potential atmospheric CO2 drawdown. The 'biogeochemical fingerprint' of climate change, that leads to depletion of upper ocean major nutrients due to upper ocean stratification, is reinforced by OIF due to greater major nutrient consumption. Our simulations show that reductions in upper trophic level animal biomass in tropical regions due to climate change would be exacerbated by OIF within ~20 years, especially in coastal exclusive economic zones (EEZs), with potential implications for fisheries that underpin the livelihoods and economies of coastal communities. Any fertilization-based CDR should therefore consider its interaction with ongoing climate-driven changes and the ensuing ecosystem impacts in national EEZs.

Rice husk as a potential source of silicate to oceanic phytoplankton

Global oceans are witnessing changes in the phytoplankton community composition due to various environmental stressors such as rising temperature, stratification, nutrient limitation, and ocean acidification. The Arabian Sea is undergoing changes in its phytoplankton community composition, especially during winter, with the diatoms being replaced by harmful algal blooms (HABs) of dinoflagellates. Recent studies have already highlighted dissolved silicate (DSi) limitation and change in Silicon (Si)/Nitrogen (N) ratios as the factors responsible for the observed changes in the phytoplankton community in the Arabian Sea. Our investigation also revealed Si/N < 1 in the northern Arabian Sea, indicating DSi limitation, especially during winter. Here, we demonstrate that rice husk with its phytoliths is an important source of bioavailable DSi for oceanic phytoplankton. Our experiment showed that a rice husk can release ∼12 μM of DSi in 15 days and can release DSi for ∼20 days. The DSi availability increased diatom abundance up to ∼9 times. The major benefitted diatom species from DSi enrichment were Nitzshia spp., Striatella spp., Navicula spp., Dactiliosolen spp., and Leptocylindrus spp. The increase in diatom abundance was accompanied by an increase in fucoxanthin and dimethyl sulphide (DMS), an anti-greenhouse gas. Thus, the rice husk with its buoyancy and slow DSi release has the potential to reduce HABs, and increase diatoms and fishery resources in addition to carbon dioxide (CO₂) sequestration in DSi-limited oceanic regions such as the Arabian Sea. Rice husk if released at the formation site of the Subantarctic mode water in the Southern Ocean could supply DSi to the thermocline in the global oceans thereby increasing diatom blooms and consequently the biotic carbon sequestration potential of the entire ocean.

Morphological, physiological, and transcriptional responses of the freshwater diatom Fragilaria crotonensis to elevated pH conditions

Harmful algal blooms (HABs) caused by the toxin-producing cyanobacteria Microcystis spp., can increase water column pH. While the effect(s) of these basified conditions on the bloom formers are a high research priority, how these pH shifts affect other biota remains understudied. Recently, it was shown these high pH levels decrease growth and Si deposition rates in the freshwater diatom Fragilaria crotonensis and natural Lake Erie (Canada-US) diatom populations. However, the physiological mechanisms and transcriptional responses of diatoms associated with these observations remain to be documented. Here, we examined F. crotonensis with a set of morphological, physiological, and transcriptomic tools to identify cellular responses to high pH. We suggest 2 potential mechanisms that may contribute to morphological and physiological pH effects observed in F. crotonensis. Moreover, we identified a significant upregulation of mobile genetic elements in the F. crotonensis genome which appear to be an extreme transcriptional response to this abiotic stress to enhance cellular evolution rates-a process we have termed "genomic roulette." We discuss the ecological and biogeochemical effects high pH conditions impose on fresh waters and suggest a means by which freshwater diatoms such as F. crotonensis may evade high pH stress to survive in a "basified" future.

Particulate and dissolved fluorescent organic matter fractionation and composition: Abiotic and ecological controls in the Southern Ocean

Phytoplankton-derived organic matter sustains heterotrophic marine life in regions away from terrestrial inputs such as the Southern Ocean. Fluorescence spectroscopy has long been used to characterize the fluorescent organic matter (FOM) pool. However, most studies focus only in the dissolved FOM fraction (FDOM) disregarding the contribution of particles. In order to assess the dynamics and drivers of the dissolved and particulate fractions of FOM, we used a Lagrangian approach to follow the time evolution of phytoplankton proliferations at four different sites in the Southern Ocean and compared the FOM in filtered and unfiltered seawater aliquots. We found that filtration had little effects on FOM visible spectrum fluorescence intensities, implying that most of this signal was due to dissolved fluorophores. On the other hand, protein-like fluorescence was strongly supressed by filtration, with fluorescence of particles accounting for up to 90 % of the total protein-like FOM. Photobleaching was identified as the main driver of visible FDOM composition, which was better described by indices of phytoplankton photoacclimation than by measurements of the incident solar radiation dose. In contrast, protein-like FOM intensity and fractionation were primarily related to abundance, composition and physiological state of phytoplankton proliferations. The chlorophyll a concentration from non-diatom phytoplankton explained 91 % of the particulate protein-like FOM variability. The proportion of protein-like fluorescence found in the dissolved phase was predicted by the combination of potential viral and grazing pressures, which accounted for 51 and 29 % of its variability, respectively. Our results show that comparing FOM measurements from filtered and unfiltered seawater provides relevant information on the taxonomic composition and cell integrity of phytoplankton communities. A better understanding of the commonly overlooked FOM fractionation process is essential for the implementation of in situ fluorescence sensors and will also help us better understand the processes that govern OM cycling in marine systems.

Thermal trait variation may buffer Southern Ocean phytoplankton from anthropogenic warming

Despite the potential of standing genetic variation to rescue communities and shape future adaptation to climate change, high levels of uncertainty are associated with intraspecific trait variation in marine phytoplankton. Recent model intercomparisons have pointed to an urgent need to reduce uncertainty in the projected responses of marine ecosystems to climate change, including Southern Ocean (SO) surface waters, which are among the most rapidly warming habitats on Earth. Because SO phytoplankton growth responses to warming sea surface temperature (SST) are poorly constrained, we developed a high-throughput growth assay to simultaneously examine inter- and intra-specific thermal trait variation in a group of 43 taxonomically diverse and biogeochemically important SO phytoplankton called diatoms. We found significant differential growth performance among species across thermal traits, including optimum and maximum tolerated growth temperatures. Within species, coefficients of variation ranged from 3% to 48% among strains for those same key thermal traits. Using SO SST projections for 2100, we predicted biogeographic ranges that differed by up to 97% between the least and most tolerant strains for each species, illustrating the role that strain-specific differences in temperature response can play in shaping predictions of future phytoplankton biogeography. Our findings revealed the presence and scale of thermal trait variation in SO phytoplankton and suggest these communities may already harbour the thermal trait diversity required to withstand projected 21st-century SST change in the SO even under severe climate forcing scenarios.

Variety and Distribution of Diatom-Based Sea Ice Proxies in Antarctic Marine Sediments of the Past 2000 Years

Antarctic sea ice is an essential component of the global climate system. Reconstructions of Antarctic sea ice from marine sediment cores are a vital resource to improve the representation of Antarctic sea ice in climate models and to better understand natural variability in sea ice over centennial and sub-centennial timescales. The Thomas et al. (2019) review of Antarctic sea ice reconstructions from ice and marine cores highlighted the prominence of diatom-based proxies in this research. Here, focusing solely on the diatom-based proxy records in marine sediments, we review the composition of proxies, their advantages and limitations, as well as the spatial and temporal cover of the records over the past 2 ka in order to assess the scope for future assimilation and standardization. The archive comprises 112 records from 68 marine cores, with proxies based on more than 30 different combinations of diatom taxa as well as the relatively new, highly branched isoprenoid (HBI) biomarkers.

Diminished carbon and nitrate assimilation drive changes in diatom elemental stoichiometry independent of silicification in an iron-limited assemblage

In the California Current Ecosystem, upwelled water low in dissolved iron (Fe) can limit phytoplankton growth, altering the elemental stoichiometry of the particulate matter and dissolved macronutrients. Iron-limited diatoms can increase biogenic silica (bSi) content >2-fold relative to that of particulate organic carbon (C) and nitrogen (N), which has implications for carbon export efficiency given the ballasted nature of the silica-based diatom cell wall. Understanding the molecular and physiological drivers of this altered cellular stoichiometry would foster a predictive understanding of how low Fe affects diatom carbon export. In an artificial upwelling experiment, water from 96 m depth was incubated shipboard and left untreated or amended with dissolved Fe or the Fe-binding siderophore desferrioxamine-B (+DFB) to induce Fe-limitation. After 120 h, diatoms dominated the communities in all treatments and displayed hallmark signatures of Fe-limitation in the +DFB treatment, including elevated particulate Si:C and Si:N ratios. Single-cell, taxon-resolved measurements revealed no increase in bSi content during Fe-limitation despite higher transcript abundance of silicon transporters and silicanin-1. Based on these findings we posit that the observed increase in bSi relative to C and N was primarily due to reductions in C fixation and N assimilation, driven by lower transcript expression of key Fe-dependent genes.

A Large Silicon Pool in Small Picophytoplankton

Marine picophytoplankton (<2 μm) play a key role in supporting food web and energy flow in the ocean, and are major contributors to the global marine carbon (C) cycle. In recent years, picophytoplankton have been found to have significant silica (Si) accumulation, a finding which provides a new sight into the interaction of marine C and Si cycles and questions the overwhelming role of large diatoms (>2 μm) in the Si cycle. As picophytoplankton have high cell abundance and wide distribution in the open ocean, exploring their influences on the C and Si cycles as well as other element cycles are becoming new scientific hotspots. However, there are still few studies on the physiology and ecology of picophytoplankton, especially their potential roles in the biogeochemical Si cycle at present. Thus, it is necessary to accurately evaluate and quantify the contributions of picophytoplankton to the C and Si cycles, and to further understand their C and Si sinking mechanisms. In this review, we expect to have a novel understanding of picophytoplankton Si pool and regulation mechanism by conducting targeted studies on these scientific issues. This also provides a premise foundation and theoretical framework for further study of the role of small cells in the global ocean Si cycle and the coupling of C and Si cycles.

A dark-tolerant diatom (Chaetoceros) cultured from the deep sea

Although the extreme conditions of the deep sea are typically not suitable for the growth of photosynthetic algae, accumulating evidence indicates that there are diverse healthy phytoplankton living in this environment. However, living phytoplankton from the deep sea have rarely been isolated and cultivated, and so our understanding of where they come from and how they adapt to (or tolerate) the extreme deep-sea environment is limited. Here, under long-term dark stress and subsequent light treatment, we successfully isolated a diatom from a depth of 1,000 m in the Western Pacific Ocean. Morphological observations and molecular phylogenetic analysis revealed that it is affiliated to the genus Chaetoceros, and thus, we tentatively named it Chaetoceros sp. DS1. We observed that the chloroplast genome of this species, is most closely related to that of Chaetoceros simplex. It was shown to have a strong tolerance to darkness in that it maintained its morphological integrity and vitality for up to 3 months in complete darkness at room temperature. We also demonstrated that Chaetoceros sp. DS1 presented a facultative heterotrophic function. Its growth was promoted by many organic carbon sources (e.g., glycerine, ethanol, and sodium acetate) under low light conditions. However, under dark and high light conditions, the growth promotion effect of organic carbon was not obvious. Indeed, Chaetoceros sp. DS1 grew best under low light conditions, indicating that it likely came from the deeper layer of the euphotic zone. The facultative heterotrophic function of this diatom and tolerance to darkness may help it survive in these conditions or enter a dormant period in the deep sea.

Chemotaxonomic characterization of the key genera of diatoms in the Northern Antarctic Peninsula

Diatoms are successful in occupying a wide range of ecological niches and biomes along the global ocean. Although there is a recognized importance of diatoms for the Southern Ocean ecosystems and biogeochemical cycles, the current knowledge on their ecology and distribution along the impacted Antarctic coastal regions remains generalized at best. HPLC-CHEMTAX approaches have been extensively used to this purpose, providing valuable information about the whole phytoplankton community, even for those small-size species which are normally difficult to identify by light microscopy. Despite that, the chemotaxonomic method has reserved minimal focus on great diversity of types associated with diatom genera or species. Here, we show a coupling between the key genera and the corresponding chemotaxonomic subgroup type-A or type-B of diatoms via HPLC-CHEMTAX and microscopic analysis, using chlorophyll-c 1 and chlorophyll-c 3 as biomarker pigments, respectively. The results demonstrated strong correlations for nine of the fifteen most abundant diatom genera observed along the Northern Antarctic Peninsula, from which five (four) were statistically associated with chlorophyll-c 1 (chlorophyll-c 3). Our study highlights the importance to observe diatoms in greater detail, beyond being only one functional group, for a better understanding on their responses under a climate change scenario.

Biochemical Characterization of a Novel Redox-Regulated Metacaspase in a Marine Diatom

Programmed cell death (PCD) in marine microalgae was suggested to be one of the mechanisms that facilitates bloom demise, yet its molecular components in phytoplankton are unknown. Phytoplankton are completely lacking any of the canonical components of PCD, such as caspases, but possess metacaspases. Metacaspases were shown to regulate PCD in plants and some protists, but their roles in algae and other organisms are still elusive. Here, we identified and biochemically characterized a type III metacaspase from the model diatom Phaeodactylum tricornutum, termed PtMCA-IIIc. Through expression of recombinant PtMCA-IIIc in E. coli, we revealed that PtMCA-IIIc exhibits a calcium-dependent protease activity, including auto-processing and cleavage after arginine. Similar metacaspase activity was detected in P. tricornutum cell extracts. PtMCA-IIIc overexpressing cells exhibited higher metacaspase activity, while CRISPR/Cas9-mediated knockout cells had decreased metacaspase activity compared to WT cells. Site-directed mutagenesis of cysteines that were predicted to form a disulfide bond decreased recombinant PtMCA-IIIc activity, suggesting its enhancement under oxidizing conditions. One of those cysteines was oxidized, detected in redox proteomics, specifically in response to lethal concentrations of hydrogen peroxide and a diatom derived aldehyde. Phylogenetic analysis revealed that this cysteine-pair is unique and widespread among diatom type III metacaspases. The characterization of a cell death associated protein in diatoms provides insights into the evolutionary origins of PCD and its ecological significance in algal bloom dynamics.

Restoration, conservation and phytoplankton hysteresis

Phytoplankton growth depends not only upon external factors that are not strongly altered by the presence of phytoplankton, such as temperature, but also upon factors that are strongly influenced by activity of phytoplankton, including photosynthetically active radiation, and the availability of the macronutrients carbon, nitrogen, phosphorus and, for some, silicate. Since phytoplankton therefore modify, and to an extent create, their own habitats, established phytoplankton communities can show resistance and resilience to change, including managed changes in nutrient regimes. Phytoplankton blooms and community structures can be predicted from the overall biogeochemical setting and inputs, but restorations may be influenced by the physiological responses of established phytoplankton taxa to nutrient inputs, temperature, second-order changes in illumination and nutrient recycling. In this review we discuss the contributions of phytoplankton ecophysiology to biogeochemical hysteresis and possible effects on community composition in the face of management, conservation or remediation plans.

Cellular costs underpin micronutrient limitation in phytoplankton

Micronutrients control phytoplankton growth in the ocean, influencing carbon export and fisheries. It is currently unclear how micronutrient scarcity affects cellular processes and how interdependence across micronutrients arises. We show that proximate causes of micronutrient growth limitation and interdependence are governed by cumulative cellular costs of acquiring and using micronutrients. Using a mechanistic proteomic allocation model of a polar diatom focused on iron and manganese, we demonstrate how cellular processes fundamentally underpin micronutrient limitation, and how they interact and compensate for each other to shape cellular elemental stoichiometry and resource interdependence. We coupled our model with metaproteomic and environmental data, yielding an approach for estimating biogeochemical metrics, including taxon-specific growth rates. Our results show that cumulative cellular costs govern how environmental conditions modify phytoplankton growth.

Molecular underpinnings and biogeochemical consequences of enhanced diatom growth in a warming Southern Ocean

Phytoplankton contribute to the Southern Ocean’s (SO) ability to absorb atmospheric CO₂ and shape the stoichiometry of northward macronutrient delivery. Climate change is altering the SO environment, yet we know little about how resident phytoplankton will react to these changes. Here, we studied a natural SO community and compared responses of two prevalent, bloom-forming diatom groups to changes in temperature and iron that are projected to occur by 2100 to 2300. We found that one group, Pseudo-nitzschia, grows better under warmer low-iron conditions by managing cellular iron demand and efficiently increasing photosynthetic capacity. This ability to grow and draw down nutrients in the face of warming, regardless of iron availability, has major implications for ocean ecosystems and global nutrient cycles.

The Southern Ocean (SO) harbors some of the most intense phytoplankton blooms on Earth. Changes in temperature and iron availability are expected to alter the intensity of SO phytoplankton blooms, but little is known about how these changes will influence community composition and downstream biogeochemical processes. We performed light-saturated experimental manipulations on surface ocean microbial communities from McMurdo Sound in the Ross Sea to examine the effects of increased iron availability (+2 nM) and warming (+3 and +6 °C) on nutrient uptake, as well as the growth and transcriptional responses of two dominant diatoms, Fragilariopsis and Pseudo-nitzschia. We found that community nutrient uptake and primary productivity were elevated under both warming conditions without iron addition (relative to ambient −0.5 °C). This effect was greater than additive under concurrent iron addition and warming. Pseudo-nitzschia became more abundant under warming without added iron (especially at 6 °C), while Fragilariopsis only became more abundant under warming in the iron-added treatments. We attribute the apparent advantage Pseudo-nitzschia shows under warming to up-regulation of iron-conserving photosynthetic processes, utilization of iron-economic nitrogen assimilation mechanisms, and increased iron uptake and storage. These data identify important molecular and physiological differences between dominant diatom groups and add to the growing body of evidence for Pseudo-nitzschia’s increasingly important role in warming SO ecosystems. This study also suggests that temperature-driven shifts in SO phytoplankton assemblages may increase utilization of the vast pool of excess nutrients in iron-limited SO surface waters and thereby influence global nutrient distribution and carbon cycling.

Exploring biogeochemical and ecological redundancy in phytoplankton communities in the global ocean

Climate-change-induced alterations of oceanic conditions will lead to the ecological niches of some marine phytoplankton species disappearing, at least regionally. How will such losses affect the ecosystem and the coupled biogeochemical cycles? Here, we couch this question in terms of ecological redundancy (will other species be able to fill the ecological roles of the extinct species) and biogeochemical redundancy (can other species replace their biogeochemical roles). Prior laboratory and field studies point to a spectrum in the degree of redundancy. We use a global three-dimensional computer model with diverse planktonic communities to explore these questions further. The model includes 35 phytoplankton types that differ in size, biogeochemical function and trophic strategy. We run two series of experiments in which single phytoplankton types are either partially or fully eliminated. The niches of the targeted types were not completely reoccupied, often with a reduction in the transfer of matter from autotrophs to heterotrophs. Primary production was often decreased, but sometimes increased due to reduction in grazing pressure. Complex trophic interactions (such as a decrease in the stocks of a predator's grazer) led to unexpected reshuffling of the community structure. Alterations in resource utilization may cause impacts beyond the regions where the type went extinct. Our results suggest a lack of redundancy, especially in the 'knock on' effects on higher trophic levels. Redundancy appeared lowest for types on the edges of trait space (e.g. smallest) or with unique competitive strategies. Though highly idealized, our modelling findings suggest that the results from laboratory or field studies often do not adequately capture the ramifications of functional redundancy. The modelled, often counterintuitive, responses-via complex food web interactions and bottom-up versus top-down controls-indicate that changes in planktonic community will be key determinants of future ocean global change ecology and biogeochemistry.

Deep learning-based diatom taxonomy on virtual slides

Deep convolutional neural networks are emerging as the state of the art method for supervised classification of images also in the context of taxonomic identification. Different morphologies and imaging technologies applied across organismal groups lead to highly specific image domains, which need customization of deep learning solutions. Here we provide an example using deep convolutional neural networks (CNNs) for taxonomic identification of the morphologically diverse microalgal group of diatoms. Using a combination of high-resolution slide scanning microscopy, web-based collaborative image annotation and diatom-tailored image analysis, we assembled a diatom image database from two Southern Ocean expeditions. We use these data to investigate the effect of CNN architecture, background masking, data set size and possible concept drift upon image classification performance. Surprisingly, VGG16, a relatively old network architecture, showed the best performance and generalizing ability on our images. Different from a previous study, we found that background masking slightly improved performance. In general, training only a classifier on top of convolutional layers pre-trained on extensive, but not domain-specific image data showed surprisingly high performance (F1 scores around 97%) with already relatively few (100–300) examples per class, indicating that domain adaptation to a novel taxonomic group can be feasible with a limited investment of effort.

An intimate view into the silica deposition vesicles of diatoms

Diatoms are single-celled microalgae that produce silica-based cell walls with intricate nano- and micropatterns. Biogenesis of diatom biosilica is a bottom-up process that occurs in large intracellular compartments termed silica deposition vesicles (SDVs). Investigating the mechanisms of silica morphogenesis has so far been severely limited by the lack of methods for imaging the entire volume of an SDV with high spatial resolution during all stages of development. Here we have developed a method that allows for rapid identification and electron microscopy imaging of many different, full sized SDVs that are in the process of producing biosilica valves. This enabled visualizing the development of characteristic morphological biosilica features with unprecedented spatio-temporal resolution. During early to mid-term development, valve SDVs contained ~ 20 nm sized particles that were primarily associated with the radially expanding rib-like biosilica structures. The results from electron dispersive X-ray analysis suggests that the immature biosilica patterns are silica-organic composites. This supports the hypothesis that silica morphogenesis is dependent on organic biomolecules inside the SDV lumen.

Variation of biogeochemical cycle of riverine dissolved inorganic carbon and silicon with the cascade damming

To investigate the variation of the biogeochemical cycle of riverine dissolved inorganic carbon (DIC) and silicon (DSi) with the cascade damming, the bicarbonate ([Formula: see text]), dissolved silicon (DSi), and other environmental factors within the cascade reservoirs of the lower reaches of Yalongjiang River, passing through the southeastern Qinghai-Tibet Plateau, were systematically analyzed by collecting water samples during the wet season and dry season from 2018 to 2019, respectively. The results showed that the lower ratio of DSi to[Formula: see text] (0.044 ± 0.001) was mainly controlled by the domination of carbonate mineral in the sedimentary rock of the Yalongjiang River drainage basin. The DSi:[Formula: see text] ratio was positively correlated with discharge (P < 0.05), and negatively correlated with the water retention time (P < 0.01) and chlorophyll a, implying that the variations of DSi:[Formula: see text] ratio were mainly determined by the rock chemical weathering processes and the hydrologic process outside the reservoirs and the biological processes within the cascade reservoirs. The phytoplankton photosynthetic process stoichiometrically assimilated DSi and [Formula: see text], resulted in 3.46 × 10⁴ t·Si a^-1 and 1.89 × 10⁴ t·C a^-1 sequestering in the cascade reservoirs, respectively. Compared with the situation of dam-free in the lower reaches of Yalongjiang River, the export flux of [Formula: see text] and DSi at the mouth of Yalongjiang River was reduced by 11.87% and 62.50%, respectively; the ratio of DSi:[Formula: see text] decreased by 36.01% for only building the Ertan dam and 53.15% for the cascade damming, respectively. The water renewal time prolonged from 45 to 126.6 days due to the regulation of the cascade reservoirs in the mainstream. Ultimately, a conceptual model on migration-transformation of DIC and DSi within the cascade reservoirs in the lower reaches of Yalongjiang River was established. These findings demonstrated that riverine cascade damming could extend the biogeochemical coupling cycle of DIC and DSi within the inland aquatic ecosystems and ensure the ecological environment security in the hot-dry valley.

Preliminary Evidence for the Role Played by South Westerly Wind Strength on the Marine Diatom Content of an Antarctic Peninsula Ice Core (1980–2010)

Winds in the Southern Ocean drive exchanges of heat and carbon dioxide between the ocean and atmosphere. Wind dynamics also explain the dominant patterns of both basal and surface melting of glaciers and ice shelves in the Amundsen and Bellingshausen Seas. Long records of past wind strength and atmospheric circulation are needed to assess the significance of these recent changes. Here we present evidence for a novel proxy of past south westerly wind (SWW) strength over the Amundsen and Bellingshausen Seas, based on diatoms preserved in an Antarctic Peninsula ice core. Ecological affinities of the identified diatom taxa indicate an almost exclusively marine assemblage, dominated by open ocean taxa from the Northern Antarctic Zone (NAZ). Back-trajectory analysis shows the routes of air masses reaching the ice core site and reveals that many trajectories involve contact with surface waters in the NAZ of the Amundsen and Bellingshausen Seas. Correlation analyses between ice core diatom abundance and various wind vectors yield positive and robust coefficients for the 1980–2010 period, with average annual SWW speeds exhibiting the strongest match. Collectively, the data presented here provide new evidence that diatoms preserved in an Antarctic Peninsula ice core offer genuine potential as a new proxy for SWW strength.

Protist Interactions and Community Structure During Early Autumn in the Kerguelen Region (Southern Ocean)

This study investigated protist community composition and biotic interactions focusing on microplankton at four distinct sites around the Kerguelen Islands (Southern Ocean) after the summer phytoplankton bloom. Protist diversity in different size fractions, sampled with Niskin bottles and plankton nets, was assessed by sequencing of the V4 18S rDNA region. Combining different approaches, i.e. sequencing of different plankton size fractions, and isolation and sequencing of single cells, provided new insights into microbial interactions in protist communities. The communities displayed high variability, including short-term fluctuations in relative abundance of large protists (>35μm) highlighted by the plankton net samples. Size fractionation of protist communities showed high concentrations of free Syndiniales spores but relatively few Syndiniales associated with microplankton, suggesting low parasitic infection in early autumn. Co-variance network analyses and sequencing of individually isolated single cells highlighted the important role of Rhizaria as consumers of a wide range of different diatom taxa. The data also raised the hypothesis that different Syndiniales clades might be directly or indirectly associated with some diatom genera, thus suggesting a potentially wider host range of these parasites than has been previously reported. These associations and the potential impact on carbon fluxes are discussed.

Drivers of Carbon Export Efficiency in the Global Ocean

The export of organic carbon from the surface ocean forms the basis of the biological carbon pump, an important planetary carbon flux. Typically, only a small fraction of primary productivity (PP) is exported (quantified as the export efficiency: export/PP). Here we assemble a global data synthesis to reveal that very high export efficiency occasionally occurs. These events drive an apparent inverse relationship between PP and export efficiency, which is opposite to that typically used in empirical or mechanistic models. At the global scale, we find that low PP, high export efficiency regimes tend to occur when macrozooplankton and bacterial abundance are low. This implies that a decoupling between PP and upper ocean remineralization processes can result in a large fraction of PP being exported, likely as intact cells or phytoplankton-based aggregates. As the proportion of PP being exported declines, macrozooplankton and bacterial abundances rise. High export efficiency, high PP regimes also occur infrequently, possibly associated with nonbiologically mediated export of particles. A similar analysis at a biome scale reveals that the factors affecting export efficiency may be different at regional and global scales. Our results imply that the whole ecosystem structure, rather than just the phytoplankton community, is important in setting export efficiency. Further, the existence of low PP, high export efficiency regimes imply that biogeochemical models that parameterize export efficiency as increasing with PP may underestimate export flux during decoupled periods, such as at the start of the spring bloom.

Different iron storage strategies among bloom-forming diatoms

Diatoms are prominent eukaryotic phytoplankton despite being limited by the micronutrient iron in vast expanses of the ocean. As iron inputs are often sporadic, diatoms have evolved mechanisms such as the ability to store iron that enable them to bloom when iron is resupplied and then persist when low iron levels are reinstated. Two iron storage mechanisms have been previously described: the protein ferritin and vacuolar storage. To investigate the ecological role of these mechanisms among diatoms, iron addition and removal incubations were conducted using natural phytoplankton communities from varying iron environments. We show that among the predominant diatoms, Pseudo-nitzschia were favored by iron removal and displayed unique ferritin expression consistent with a long-term storage function. Meanwhile, Chaetoceros and Thalassiosira gene expression aligned with vacuolar storage mechanisms. Pseudo-nitzschia also showed exceptionally high iron storage under steady-state high and low iron conditions, as well as following iron resupply to iron-limited cells. We propose that bloom-forming diatoms use different iron storage mechanisms and that ferritin utilization may provide an advantage in areas of prolonged iron limitation with pulsed iron inputs. As iron distributions and availability change, this speculated ferritin-linked advantage may result in shifts in diatom community composition that can alter marine ecosystems and biogeochemical cycles.

Diatom populations in an upwelling environment decrease silica content to avoid growth limitation

A mix of adaptive strategies enable diatoms to sustain rapid growth in dynamic ocean regions, making diatoms one of the most productive primary producers in the world. We illustrate one such strategy off coastal California that facilitates continued, high, cell division rates despite silicic acid stress. Using a fluorescent dye to measure single-cell diatom silica production rates, silicification (silica per unit area) and growth rates we show diatoms decrease silicification and maintain growth rate when silicon concentration limits silica production rates. While this physiological response to silicon stress was similar across taxa, in situ silicic acid concentration limited silica production rates by varying degrees for taxa within the same community. Despite this variability among taxa, silicon stress did not alter the contribution of specific taxa to total community silica production or to community composition. Maintenance of division rate at the expense of frustule thickness decreases cell density which could affect regional biogeochemical cycles. The reduction in frustule silicification also creates an ecological tradeoff: thinner frustules increase susceptibility to predation but reducing Si quotas maximizes cell abundance for a given pulse of silicic acid, thereby favouring a larger eventual population size which facilitates diatom persistence in habitats with pulsed resource supplies.

Extreme drought decouples silicon and carbon geochemical linkages in lakes

Silicon and carbon geochemical linkages were usually regulated by chemical weathering and organism activity, but had not been investigated under the drought condition, and the magnitude and extent of drought effects remain poorly understood. We collected a comprehensive data set from a total of 13 sampling sites covering the main water body of the largest freshwater lake system in Australia, the Lower Lakes. Changes to water quality during drought (April 2008-September 2010) and post-drought (October 2010-October 2013) were compared to reveal the effects of drought on dissolved silica (DSi) and bicarbonate (HCO₃^-) and other environmental factors, including sodium (Na⁺), pH, electrical conductivity (EC), chlorophyll a (Chl-a), total dissolved solids (TDS), dissolved inorganic nitrogen (DIN), total nitrogen (TN), total phosphorus (TP) and water levels. Among the key observations, concentrations of DSi and DIN were markedly lower in drought than in post-drought period while pH, EC and concentrations of HCO₃^-, Na⁺, Chl-a, TDS, TN, TP and the ratio TN:TP had inverse trends. Stoichiometric ratios of DSi:HCO₃^-, DSi:Na⁺ and HCO₃^-:Na⁺ were significantly lower in the drought period. DSi exhibited significantly negative relationships with HCO₃^-, and DSi:Na⁺ was strongly correlated with HCO₃^-:Na⁺ in both drought and post-drought periods. The backward stepwise regression analysis that could avoid multicollinearity suggested that DSi:HCO₃^- ratio in drought period had significant relationships with fewer variables when compared to the post-drought, and was better predictable using nutrient variables during post-drought. Our results highlight the drought effects on variations of water constituents and point to the decoupling of silicon and carbon geochemical linkages in the Lower Lakes under drought conditions.

Seeing is Believing: Diatoms and the Ocean Carbon Cycle Revisited

Terrestrial ecologists and biogeochemists are in direct contact with their objects of study via sense organs evolved in those environments; they hence share a common awareness because they can all see the whole elephant, as in the ancient Indian parable. Pelagic ecologists and biogeochemists on the other hand are the blind men groping different parts of the elephant - the protist-dominated biome of the planet - in attempts to understand its structure and functioning in terms of organism life cycles and the biogenic elements of which they are made. The pelagial is an alien world for us that we can only sense through instruments of our making: the propensity for bias is enormous. Throughout my career I have been acutely aware of this fundamental problem faced by protist ecologists. In this essay I would like to convey an impression of the subjective driving forces that led me to the conclusions I reached on the relationships between ocean ecology and biogeochemistry in the light of evolution by natural selection. Key personal encounters with sinking diatom blooms are recounted to illustrate how my convictions grew that led me to challenge mainstream thinking of the time.

Taxon-specific contributions to silica production in natural diatom assemblages

The metabolic activity and growth of phytoplankton taxa drives their ecological function and contribution to biogeochemical processes. We present the first quantitative, taxon-resolved silica production rates, growth rates, and silica content estimates for co-occurring diatoms along two cross-shelf transects off the California coast using the fluorescent tracer PDMPO (2-(4-pyridyl)-5-((4-(2-dimethylaminoethylaminocarbamoyl)methoxy)phenyl)oxazole), and confocal microscopy. Taxon contribution to total diatom community silica production was predominantly a function of the surface area of new frustule that each taxon created as opposed to cell abundance or frustule thickness. The influential role of surface area made large diatoms disproportionately important to community silica production over short time scales (<1 d). In some cases, large taxa that comprised only ~15% of numerical cell abundance accounted for over 50% of total community silica production. Over longer time scales relevant to bloom dynamics, the importance of surface area declines and growth rate becomes the dominant influence on contribution to production. The relative importance of surface area and growth rate in relation to silica production was modeled as the time needed for a smaller, faster-growing taxon to create more surface area than a larger, slower-growing taxon. Differences in growth rate between the taxa effected the model outcome more than differences in surface area. Shifts in relative silica production among taxa are time restricted by finite resources that limit the duration of a bloom. These patterns offer clues as to how taxa respond to their environment and the consequences for both species succession and the potential diatom contribution to elemental cycling.

Nanoplanktonic diatoms are globally overlooked but play a role in spring blooms and carbon export

Diatoms are one of the major primary producers in the ocean, responsible annually for ~20% of photosynthetically fixed CO₂ on Earth. In oceanic models, they are typically represented as large (>20 µm) microphytoplankton. However, many diatoms belong to the nanophytoplankton (2–20 µm) and a few species even overlap with the picoplanktonic size-class (<2 µm). Due to their minute size and difficulty of detection they are poorly characterized. Here we describe a massive spring bloom of the smallest known diatom (Minidiscus) in the northwestern Mediterranean Sea. Analysis of Tara Oceans data, together with literature review, reveal a general oversight of the significance of these small diatoms at the global scale. We further evidence that they can reach the seafloor at high sinking rates, implying the need to revise our classical binary vision of pico- and nanoplanktonic cells fueling the microbial loop, while only microphytoplankton sustain secondary trophic levels and carbon export.

Diatoms are major oceanic primary producers, but some species belonging to the nano- and even picoplankton size are poorly characterized. Here the authors describe a massive spring bloom of the smallest known diatom in the Mediterranean Sea and reveal their general oversight at the global scale.

Specific eukaryotic plankton are good predictors of net community production in the Western Antarctic Peninsula

Despite our current realization of the tremendous diversity that exists in plankton communities, we have little understanding of how this biodiversity influences the biological carbon pump other than broad paradigms such as diatoms contributing disproportionally to carbon export. Here we combine high-resolution underway O₂/Ar, which provides an estimate of net community production, with high-throughput 18 S ribosomal DNA sequencing to elucidate the relationship between eukaryotic plankton community structure and carbon export potential at the Western Antarctica Peninsula (WAP), a region which has experienced rapid warming and ecosystem changes. Our results show that in a diverse plankton system comprised of ~464 operational taxonomic units (OTUs) with at least 97% 18 S identity, as few as two or three key OTUs, i.e. large diatoms, Phaeocystis, and mixotrophic/phagotrophic dinoflagellates, can explain a large majority of the spatial variability in the carbon export potential (76-92%). Moreover, we find based on a community co-occurrence network analysis that ecosystems with lower export potential have more tightly coupled communities. Our results indicate that defining plankton communities at a deeper taxonomic resolution than by functional groups and accounting for the differences in size and coupling between groups can substantially improve organic carbon flux predictions.

Resistance of Arctic phytoplankton to ocean acidification and enhanced irradiance

The Arctic Ocean is a region particularly prone to ongoing ocean acidification (OA) and climate-driven changes. The influence of these changes on Arctic phytoplankton assemblages, however, remains poorly understood. In order to understand how OA and enhanced irradiances (e.g., resulting from sea–ice retreat) will alter the species composition, primary production, and eco-physiology of Arctic phytoplankton, we conducted an incubation experiment with an assemblage from Baffin Bay (71°N, 68°W) under different carbonate chemistry and irradiance regimes. Seawater was collected from just below the deep Chl a maximum, and the resident phytoplankton were exposed to 380 and 1000 µatm pCO₂ at both 15 and 35% incident irradiance. On-deck incubations, in which temperatures were 6 °C above in situ conditions, were monitored for phytoplankton growth, biomass stoichiometry, net primary production, photo-physiology, and taxonomic composition. During the 8-day experiment, taxonomic diversity decreased and the diatom Chaetoceros socialis became increasingly dominant irrespective of light or CO₂ levels. We found no statistically significant effects from either higher CO₂ or light on physiological properties of phytoplankton during the experiment. We did, however, observe an initial 2-day stress response in all treatments, and slight photo-physiological responses to higher CO₂ and light during the first five days of the incubation. Our results thus indicate high resistance of Arctic phytoplankton to OA and enhanced irradiance levels, challenging the commonly predicted stimulatory effects of enhanced CO₂ and light availability for primary production.

Dynamic responses to silicon in Thalasiossira pseudonana - Identification, characterisation and classification of signature genes and their corresponding protein motifs

The diatom cell wall, or frustule, is a highly complex, three-dimensional structure consisting of nanopatterned silica as well as proteins and other organic components. While some key components have been identified, knowledge on frustule biosynthesis is still fragmented. The model diatom Thalassiosira pseudonana was subjected to silicon (Si) shift-up and shift-down situations. Cellular and molecular signatures, dynamic changes and co-regulated clusters representing the hallmarks of cellular and molecular responses to changing Si availabilities were characterised. Ten new proteins with silaffin-like motifs, two kinases and a novel family of putatively frustule-associated transmembrane proteins induced by Si shift-up with a possible role in frustule biosynthesis were identified. A separate cluster analysis performed on all significantly regulated silaffin-like proteins (SFLPs), as well as silaffin-like motifs, resulted in the classification of silaffins, cingulins and SFLPs into distinct clusters. A majority of the genes in the Si-responsive clusters are highly divergent, but positive selection does not seem to be the driver behind this variability. This study provides a high-resolution map over transcriptional responses to changes in Si availability in T. pseudonana. Hallmark Si-responsive genes are identified, characteristic motifs and domains are classified, and taxonomic and evolutionary implications outlined and discussed.

Inter-annual variability of transparent exopolymer particles in the Arctic Ocean reveals high sensitivity to ecosystem changes

Transparent exopolymer particles (TEP) are a class of marine gel particles and important links between surface ocean biology and atmospheric processes. Derived from marine microorganisms, these particles can facilitate the biological pumping of carbon dioxide to the deep sea, or act as cloud condensation and ice nucleation particles in the atmosphere. Yet, environmental controls on TEP abundance in the ocean are poorly known. Here, we investigated some of these controls during the first multiyear time-series on TEP abundance for the Fram Strait, the Atlantic gateway to the Central Arctic Ocean. Data collected at the Long-Term Ecological Research observatory HAUSGARTEN during 2009 to 2014 indicate a strong biological control with highest abundance co-occurring with the prymnesiophyte Phaeocystis pouchetii. Higher occurrence of P. pouchetii in the Arctic Ocean has previously been related to northward advection of warmer Atlantic waters, which is expected to increase in the future. Our study highlights the role of plankton key species in driving climate relevant processes; thus, changes in plankton distribution need to be accounted for when estimating the ocean's biogeochemical response to global change.

Transcriptional Orchestration of the Global Cellular Response of a Model Pennate Diatom to Diel Light Cycling under Iron Limitation

Environmental fluctuations affect distribution, growth and abundance of diatoms in nature, with iron (Fe) availability playing a central role. Studies on the response of diatoms to low Fe have either utilized continuous (24 hr) illumination or sampled a single time of day, missing any temporal dynamics. We profiled the physiology, metabolite composition, and global transcripts of the pennate diatom Phaeodactylum tricornutum during steady-state growth at low, intermediate, and high levels of dissolved Fe over light:dark cycles, to better understand fundamental aspects of genetic control of physiological acclimation to growth under Fe-limitation. We greatly expand the catalog of genes involved in the low Fe response, highlighting the importance of intracellular trafficking in Fe-limited diatoms. P. tricornutum exhibited transcriptomic hallmarks of slowed growth leading to prolonged periods of cell division/silica deposition, which could impact biogeochemical carbon sequestration in Fe-limited regions. Light harvesting and ribosome biogenesis transcripts were generally reduced under low Fe while transcript levels for genes putatively involved in the acquisition and recycling of Fe were increased. We also noted shifts in expression towards increased synthesis and catabolism of branched chain amino acids in P. tricornutum grown at low Fe whereas expression of genes involved in central core metabolism were relatively unaffected, indicating that essential cellular function is protected. Beyond the response of P. tricornutum to low Fe, we observed major coordinated shifts in transcript control of primary and intermediate metabolism over light:dark cycles which contribute to a new view of the significance of distinctive diatom pathways, such as mitochondrial glycolysis and the ornithine-urea cycle. This study provides new insight into transcriptional modulation of diatom physiology and metabolism across light:dark cycles in response to Fe availability, providing mechanistic understanding for the ability of diatoms to remain metabolically poised to respond quickly to Fe input and revealing strategies underlying their ecological success.

Oceanic diatoms live in constantly fluctuating environments to which they must adapt in order to survive. During sunlit hours, photosynthesis occurs allowing diatoms to store energy used at night to sustain energy demands. Cellular and molecular mechanisms for regulation of phytoplankton growth are important to understand because of their environmental roles at the base of food webs and in regulating carbon flux out of the atmosphere. In ocean ecosystems, the availability of iron (Fe) commonly limits phytoplankton growth and diatoms typically outcompete other phytoplankton when Fe is added, indicating they have adaptations allowing them to both survive at low Fe and rapidly respond to Fe additions. These adaptations may be unique depending on isolation from coastal or oceanic locations. To identify adaptive strategies, we characterized the response of a model diatom, Phaeodactylum tricornutum, to limiting Fe conditions over day:night cycles using a combination of gene expression analyses, metabolite, and physiology measurements. Major coordinated shifts in metabolism and growth were documented over diel cycles, with peak expression of low Fe expressed genes in the dark phase. Diatoms respond to limiting Fe by increasing Fe acquisition, while decreasing growth rate through slowed cell cycle progression, reduced energy acquisition, and subtle metabolic remodeling.

Composition of diatom communities and their contribution to plankton biomass in the naturally iron-fertilized region of Kerguelen in the Southern Ocean

In the naturally iron-fertilized surface waters of the northern Kerguelen Plateau region, the early spring diatom community composition and contribution to plankton carbon biomass were investigated and compared with the high nutrient, low chlorophyll (HNLC) surrounding waters. The large iron-induced blooms were dominated by small diatom species belonging to the genera Chaetoceros (Hyalochaete) and Thalassiosira, which rapidly responded to the onset of favorable light-conditions in the meander of the Polar Front. In comparison, the iron-limited HNLC area was typically characterized by autotrophic nanoeukaryote-dominated communities and by larger and more heavily silicified diatom species (e.g. Fragilariopsis spp.). Our results support the hypothesis that diatoms are valuable vectors of carbon export to depth in naturally iron-fertilized systems of the Southern Ocean. Furthermore, our results corroborate observations of the exported diatom assemblage from a sediment trap deployed in the iron-fertilized area, whereby the dominant Chaetoceros (Hyalochaete) cells were less efficiently exported than the less abundant, yet heavily silicified, cells of Thalassionema nitzschioides and Fragilariopsis kerguelensis Our observations emphasize the strong influence of species-specific diatom cell properties combined with trophic interactions on matter export efficiency, and illustrate the tight link between the specific composition of phytoplankton communities and the biogeochemical properties characterizing the study area.

Direct evidence of the molecular basis for biological silicon transport

Diatoms are an important group of eukaryotic algae with a curious evolutionary innovation: they sheath themselves in a cell wall made largely of silica. The cellular machinery responsible for silicification includes a family of membrane permeases that recognize and actively transport the soluble precursor of biosilica, silicic acid. However, the molecular basis of silicic acid transport remains obscure. Here, we identify experimentally tractable diatom silicic acid transporter (SIT) homologues and study their structure and function in vitro, enabled by the development of a new fluorescence method for studying substrate transport kinetics. We show that recombinant SITs are Na⁺/silicic acid symporters with a 1:1 protein: substrate stoichiometry and K_M for silicic acid of 20 μM. Protein mutagenesis supports the long-standing hypothesis that four conserved GXQ amino acid motifs are important in SIT function. This marks a step towards a detailed understanding of silicon transport with implications for biogeochemistry and bioinspired materials.

Diatoms sheath themselves in a self-made casing of silica, which requires the function of silicic acid transporters. Here, the authors identify versions of these transporters that are experimentally tractable, and develop a fluorescence method to study silicic acid transport in vitro.

Biochemical Composition and Assembly of Biosilica-associated Insoluble Organic Matrices from the Diatom Thalassiosira pseudonana

The nano- and micropatterned biosilica cell walls of diatoms are remarkable examples of biological morphogenesis and possess highly interesting material properties. Only recently has it been demonstrated that biosilica-associated organic structures with specific nanopatterns (termed insoluble organic matrices) are general components of diatom biosilica. The model diatom Thalassiosira pseudonana contains three types of insoluble organic matrices: chitin meshworks, organic microrings, and organic microplates, the latter being described in the present study for the first time. To date, little is known about the molecular composition, intracellular assembly, and biological functions of organic matrices. Here we have performed structural and functional analyses of the organic microrings and organic microplates from T. pseudonana. Proteomics analysis yielded seven proteins of unknown function (termed SiMat proteins) together with five known silica biomineralization proteins (four cingulins and one silaffin). The location of SiMat1-GFP in the insoluble organic microrings and the similarity of tyrosine- and lysine-rich functional domains identifies this protein as a new member of the cingulin protein family. Mass spectrometric analysis indicates that most of the lysine residues of cingulins and the other insoluble organic matrix proteins are post-translationally modified by short polyamine groups, which are known to enhance the silica formation activity of proteins. Studies with recombinant cingulins (rCinY2 and rCinW2) demonstrate that acidic conditions (pH 5.5) trigger the assembly of mixed cingulin aggregates that have silica formation activity. Our results suggest an important role for cingulins in the biogenesis of organic microrings and support the hypothesis that this type of insoluble organic matrix functions in biosilica morphogenesis.