Nutrient consumption and chain tuning in diatoms exposed to storm-like turbulence

Effects of turbulence on diatoms of the genus Pseudo-nitzschia spp. and associated bacteria

Turbulence is one of the least investigated environmental factors impacting the ecophysiology of phytoplankton, both at the community and individual species level. Here, we investigated, for the first time, the effect of a turbulence gradient (Reynolds number, from Reλ = 0 to Reλ = 360) on two species of the marine diatom Pseudo-nitzschia and their associated bacterial communities under laboratory conditions. Cell abundance, domoic acid (DA) production, chain formation, and Chl a content of P. fraudulenta and P. multiseries were higher for intermediate turbulence (Reλ = 160 or 240). DA was detectable only in P. multiseries samples. These observations were supported by transcriptomic analyses results, which suggested the turbulence related induction of the expression of the DA production locus, with a linkage to an increased photosynthetic activity of the total metatranscriptome. This study also highlighted a higher richness of the bacterial community associated with the nontoxic strain of P. fraudulenta in comparison to the toxic strain of P. multiseries. Bacillus was an important genus in P. multiseries cultures (relative abundance 15.5%) and its highest abundances coincided with the highest DA levels. However, associated bacterial communities of both Pseudo-nitzschia species did not show clear patterns relative to turbulence intensity.

Single cell dynamics and nitrogen transformations in the chain forming diatom Chaetoceros affinis

Colony formation in phytoplankton is often considered a disadvantage during nutrient limitation in aquatic systems. Using stable isotopic tracers combined with secondary ion mass spectrometry (SIMS), we unravel cell-specific activities of a chain-forming diatom and interactions with attached bacteria. The uptake of 13C-bicarbonate and15N-nitrate or 15N-ammonium was studied in Chaetoceros affinis during the stationary growth phase. Low cell-to-cell variance of 13C-bicarbonate and 15N-nitrate assimilation within diatom chains prevailed during the early stationary phase. Up to 5% of freshly assimilated 13C and 15N was detected in attached bacteria within 12 h and supported bacterial C- and N-growth rates up to 0.026 h-1. During the mid-stationary phase, diatom chain-length decreased and 13C and 15N-nitrate assimilation was significantly higher in solitary cells as compared to that in chain cells. During the late stationary phase, nitrate assimilation ceased and ammonium assimilation balanced C fixation. At this stage, we observed highly active cells neighboring inactive cells within the same chain. In N-limited regimes, bacterial remineralization of N and the short diffusion distance between neighbors in chains may support surviving cells. This combination of "microbial gardening" and nutrient transfer within diatom chains represents a strategy which challenges current paradigms of nutrient fluxes in plankton communities.

On the conditions promoting Pseudo-nitzschia spp. blooms in the eastern English Channel and southern North Sea

This study investigated the drivers of the blooms of Pseudo-nitzschia seriata and Pseudo-nitzschia delicatissima complexes in the eastern English Channel and southern North Sea. Phytoplankton data series acquired from 1992 to 2020 were analyzed with a multivariate statistical approach based on Hutchinson's niche concept. P. seriata and P. delicatissima complexes were found to be typically present year round, but they bloomed at different periods because they occupied different realized ecological niches. P. delicatissima complex occupied a more marginal niche and was less tolerant than P. seriata complex. P. delicatissima complex typically bloomed in April-May at the same time as Phaeocystis globosa while P. seriata complex blooms were more frequently observed in June during the decline of low intensity P. globosa blooms. P. delicatissima and P. seriata complexes were both favored by low-silicate environments and relatively low turbulence but they responded differently to water temperature, light, ammonium, phosphate and nitrite + nitrate conditions. Niche shifts and biotic interactions played important roles in the control of the blooms of P. delicatissima and P. seriata complexes. The two complexes occupied different sub-niches during their respective low abundance and bloom periods. The phytoplankton community structure and the number of other taxa presenting a niche overlapping the niches of P. delicatissima and P. seriata complexes also differed between these periods. P. globosa was the taxa contributing the most to the dissimilarity in community structure. P. globosa interacted positively with P. delicatissima complex and negatively with P. seriata complex.

Phytoplankton community structure in the Kandla port ecosystem situated in a creek in the Gulf of Kutch, India

The port ecosystems are prone to deterioration due to the maritime and coastal activities and as a major source of the country's economy need efficient management. Phytoplankton communities can serve as reliable indicators of the prevailing environmental conditions due to their short life cycles. Seasonal sampling was conducted at 26 stations from October 2014 to February 2016 at Kandla port situated in a creek, along the west coast of India. The post-monsoon and monsoon water temperatures were higher (30 °C) whereas pre-monsoon were lower (21 °C). The salinity varied from polyhaline (18-30; monsoon) to euhaline (30 to 45; non-monsoon). The strong currents, high tidal activity, shallow depth areas, and the creek backwater systems make this ecosystem well-mixed and turbid. The annual average trophic index (TRIX) scores indicated very good water quality and low eutrophication, except during pre-monsoon (2.3 ± 0.7 to 4.1 ± 0.2). Based on the cell size, the phytoplankton community was classified into two main groups, i.e., nano-microphytoplankton, which comprised forty-seven species (represented by diatoms, dinoflagellates, and silicoflagellates) and picophytoplankton including two groups (picocyanophytes and picoeukaryotes). The diatoms and picophytoplankton dominated the total biomass and cell abundance, respectively. Only the picophytoplankton exhibited significant seasonal variations in cell abundance and carbon biomass. The lowest monsoon phytoplankton abundance coincided with high turbidity and vice versa during the post-monsoon. The hypersaline pre-monsoon environment with lower annual temperature, relatively lower turbid waters, and increased nutrients favoured higher diatom diversity. These conditions also supported potentially harmful Gymnodinium sp. and bloom-forming Tripos furca and Pyrophacus sp. Overall, ten non-toxic but bloom-forming species were observed. The study provides insights into the phytoplankton community's response to environmental conditions that can have repercussions on the ecosystem's functioning.

Quantitative Analysis of the Trade-Offs of Colony Formation for Trichodesmium

There is considerable debate about the benefits and trade-offs for colony formation in a major marine nitrogen fixer, Trichodesmium. To quantitatively analyze the trade-offs, we developed a metabolic model based on carbon fluxes to compare the performance of Trichodesmium colonies and free trichomes under different scenarios. Despite reported reductions in carbon fixation and nitrogen fixation rates for colonies relative to free trichomes, we found that model colonies can outperform individual cells in several cases. The formation of colonies can be advantageous when respiration rates account for a high proportion of the carbon fixation rate. Negative external influence on vital rates, such as mortality due to predation or micronutrient limitations, can also create a net benefit for colony formation relative to individual cells. In contrast, free trichomes also outcompete colonies in many scenarios, such as when respiration rates are equal for both colonies and individual cells or when there is a net positive external influence on rate processes (i.e., optimal environmental conditions regarding light and temperature or high nutrient availability). For both colonies and free trichomes, an increase in carbon fixation relative to nitrogen fixation rates would increase their relative competitiveness. These findings suggest that the formation of colonies in Trichodesmium might be linked to specific environmental and ecological circumstances. Our results provide a road map for empirical studies and models to evaluate the conditions under which colony formation in marine phytoplankton can be sustained in the natural environment. IMPORTANCE Trichodesmium is a marine filamentous cyanobacterium that fixes nitrogen and is an important contributor to the global nitrogen cycle. In the natural environment, Trichodesmium can exist as individual cells (trichomes) or as colonies (puffs and tufts). In this paper, we try to answer a longstanding question in marine microbial ecology: how does colony formation benefit the survival of Trichodesmium? To answer this question, we developed a carbon flux model that utilizes existing published rates to evaluate whether and when colony formation can be sustained. Enhanced respiration rates, influential external factors such as environmental conditions and ecological interactions, and variable carbon and nitrogen fixation rates can all create scenarios for colony formation to be a viable strategy. Our results show that colony formation is an ecologically beneficial strategy under specific conditions, enabling Trichodesmium to be a globally significant organism.

Can the stable isotope variability in a zooplankton time series be explained by its key species?

Stable isotope (SI) analysis is a standard tool to study marine food webs, usually based on the measurement of a few individuals from a small list of subjectively pre-defined species. The main objective of this study was to find out which species are significantly associated with the temporal variability of the SI composition of zooplankton in a tropical marine ecosystem. We investigated this by means of a novel species-biomass-isotopes-mixture (SBIM) approach that uses a relative biomass matrix to explain the SI signature of the zooplankton community. Furthermore, SBIM was applied to detect key taxa that can be considered bioindicators for important descriptors of ecosystem state (e.g., oligotrophy, carbon sources, mean trophic level). Plankton samples (64 μm mesh size) were obtained in Tamandaré Bay (northeastern Brazil) from June 2013 to August 2019. One aliquot of each sample was taken for stable isotope measurements and one for taxonomic identification and estimation of size and relative biomass. Total zooplankton biomass differed significantly between years, seasons and stations. Total zooplankton δ13C values ranged from -21.0 to -18.2‰ (mean ± standard deviation: -19.7 ± 0.7‰ in the dry season, and -19.4 ± 0.8‰ in the rainy season). Total zooplankton δ15N values ranged from 3.8 to 9.0‰ (7.0 ± 1.0‰ in the dry season, and 6.5 ± 1.2‰ rainy season). Total zooplankton C/N ratios ranged from 3.5 to 5.0 (4.2 ± 0.4 in the dry season and 4.2 ± 0.3 in the rainy season). The sparsely abundant and relatively large-sized copepod Pseudodiaptomus acutus was the most important species for explaining the variability in δ15N (22% of the total variability). Relative biomass (%) of P. acutus showed a strong positive correlation with δ15N, indicating a high trophic level (TL). Our results highlight the importance of less abundant taxa for marine food webs. Small-sized invertebrate larvae were negatively correlated with δ15N, indicating a TL below average. The copepod Dioithona oculata was the most important organism in explaining the δ13C of zooplankton (17.7% of the total variability, positive correlation with δ13C), indicating possible selective use of a13C-enriched food source (e.g., diatoms) by this cyclopoid copepod. Oithona spp. juveniles showed a negative relationship with zooplankton C/N ratio, which can be indicators of an oligotrophic ecosystem state and lipid-poor zooplankton. The tintinnid F. ehrenbergii showed a positive correlation with C/N, being an indicator for turbid "green waters'', during the rainy season, when the ecosystem was in a eutrophic state, with high lipid contents in the zooplankton community. The proposed SBIM approach opens up a novel pathway to understanding the factors and species that shape the temporal variability of food webs.

Characterization of Fine-Scale Turbulence Generated in a Laboratory Orbital Shaker and Its Influence on Skeletonema costatum

Turbulence is one of the ubiquitous aspects of aquatic systems and affects many physical and biological processes. Based on direct velocity measurements and a computational fluid dynamics (CFD) simulation, we characterized the distribution of the turbulent kinetic dissipations rates (ε) in an orbital shaker system within a range of rotation frequencies. CFD was able to estimate the ε distribution in containers accurately, which was confirmed by other two methods and was independent of velocity measurement. The results showed that ε was linearly correlated with the rotational frequencies. Despite the existence of gradients of ε and the fact that a mean circular horizontal flow was formed within the tank, the energy levels of the whole tank varied spatially within an order of magnitude and the ε distributions at different rotational frequencies were similar, suggesting that the ε distribution in the whole tank could be seen as quasi-homogeneous. To investigate the influence of turbulence on algae growth, culture experiments of a typical diatom—Skeletonema costatum were carried out under different turbulence conditions. Our results suggested turbulence mixing promoted nutrient uptake and growth of Skeletonema costatum, which could be attributed to the break of the diffusion-limited resource concentration boundary layer surrounding phytoplankton.

Solvable Model for the Linear Separability of Structured Data

Linear separability, a core concept in supervised machine learning, refers to whether the labels of a data set can be captured by the simplest possible machine: a linear classifier. In order to quantify linear separability beyond this single bit of information, one needs models of data structure parameterized by interpretable quantities, and tractable analytically. Here, I address one class of models with these properties, and show how a combinatorial method allows for the computation, in a mean field approximation, of two useful descriptors of linear separability, one of which is closely related to the popular concept of storage capacity. I motivate the need for multiple metrics by quantifying linear separability in a simple synthetic data set with controlled correlations between the points and their labels, as well as in the benchmark data set MNIST, where the capacity alone paints an incomplete picture. The analytical results indicate a high degree of “universality”, or robustness with respect to the microscopic parameters controlling data structure.

Ecological responses of autotrophic microplankton to the eutrophication of the coastal upwelling along the Southwest coast of India

The primary ecological effects of the eutrophication of upwelling in the nearshore waters are the triggering and sustenance of phytoplankton (diatom) blooms. Here, we present the changes in the morphological characteristics and body size of microautotrophs associated with the nutrient enrichment of coastal upwelling along the southwest coast of India. The FlowCAM data of microautotrophs representing two time series locations in the coastal environment along the southwest coast of India at 18 weekly/biweekly frequencies showed the following features. The most significant response of the microautotrophs to the eutrophication associated with coastal upwelling during the Southwest Monsoon (June-September) was an increase in their mean bio-volume, either by increasing the individual cell size or by forming large colonies. During the Southwest Monsoon, large colonies of Thalassiosira (~ 8 cells/colony), Thalassionema (> 16 cells/colony), and Asterionellopsis (> 8 cells/colony) become very abundant. Streptotheca formed large mat-like colonies (av. 192350 ± 348 μm³/individual), and Fragilariopsis grew as very long ribbons (av. 272997 ± 5071 μm³/individual). Large-sized Chaetoceros (av. 45715 ± 1273 μm³/individual) with longer setae were also plentiful during the Southwest Monsoon. All these changes in the morphology and life forms of microautotrophs would help them to rapidly assimilate nitrate under turbulent conditions during the Southwest Monsoon.

Mobilization and Cellular Distribution of Phosphate in the Diatom Phaeodactylum tricornutum

Unicellular organisms that live in marine environments must cope with considerable fluctuations in the availability of inorganic phosphate (P_i). Here, we investigated the extracellular P_i concentration-dependent expression, as well as the intracellular or extracellular localization, of phosphatases and phosphate transporters of the diatom Phaeodactylum tricornutum. We identified P_i-regulated plasma membrane-localized, ER-localized, and secreted phosphatases, in addition to plasma membrane-localized, vacuolar membrane-localized, and plastid-surrounding membrane-localized phosphate transporters that were also regulated in a P_i concentration-dependent manner. These studies not only add further knowledge to already existing transcriptomic data, but also highlight the capacity of the diatom to distribute P_i intracellularly and to mobilize P_i from extracellular and intracellular resources.

The effects of turbulence on phytoplankton and implications for energy transfer with an integrated water quality-ecosystem model in a shallow lake

Turbulence has significant influences on the growth rate and community structure of phytoplankton in large shallow lakes. Phytoplankton in moving water may be influenced by turbulence and nutrient concentration gradients on a short time scale. To assess this issue, our research used an ensemble water quality and ecological model by internally coupling the three-dimensional hydrodynamic model, the Environmental Fluid Dynamics Code (EFDC), and the one-dimensional ecosystem model, PCLake. The results showed that turbulence dramatically inhibited phytoplankton growth, while nutrients had the opposite effect. In addition, turbulence was the key factor contributing to phytoplankton growth. However, the effects of turbulence on phytoplankton correlated with nutrient concentrations. For lower nutrient concentrations, phytoplankton growth was controlled by nutrients. Logistic regression models were established with the modeled chlorophyll a, total nitrogen (TN), total phosphorus (TP) and turbulent kinetic energy (K_e). The results also showed that turbulence could improve nutrient uptake by phytoplankton, especially at low nutrient levels. The effects of turbulence on phytoplankton may imply that energy transfer occurs between water turbulence and phytoplankton. Our study will provide insight into management and remediation strategies of ecosystems based on energy processes in the future.

Meta-omics reveals genetic flexibility of diatom nitrogen transporters in response to environmental changes

Diatoms (Bacillariophyta), one of the most abundant and diverse groups of marine phytoplankton, respond rapidly to the supply of new nutrients, often out-competing other phytoplankton. Herein, we integrated analyses of the evolution, distribution and expression modulation of two gene families involved in diatom nitrogen uptake (DiAMT1 and DiNRT2), in order to infer the main drivers of divergence in a key functional trait of phytoplankton. Our results suggest that major steps in the evolution of the two gene families reflected key events triggering diatom radiation and diversification. Their expression is modulated in the contemporary ocean by seawater temperature, nitrate and iron concentrations. Moreover, the differences in diversity and expression of these gene families throughout the water column hint at a possible link with bacterial activity. This study represents a proof-of-concept of how a holistic approach may shed light on the functional biology of organisms in their natural environment.

Role of nutrient concentrations and water movement on diatom's productivity in culture

Microalgal growth maximization is becoming a duty for enhancing the biotechnological fate of these photosynthetic microorganisms. This study, based on an extensive set of data, aims to revisit diatom’s cultivation in laboratory with the objective to increase growth rate and biomass production. We investigated the growth ability and resource requirements of the coastal diatom Skeletonema marinoi Sarno & Zingone grown in laboratory in the conventional f/2 medium with aeration and in two modified conditions: (i) the same medium with water movement inside and (ii) an enriched medium with the same water movement. Results revealed that, by doubling the concentration of phosphate, silicate, microelements and vitamins, growth rate was successfully enhanced, preventing phosphate or silicate limitation in the f/2 culture medium. Yet, irrespective of the media (f/2 or enriched one), water movement induced an increase of growth efficiency compared to aeration, affecting nutrients’ requirement and consumption by diatoms. This study is an important step for enhancing diatom biomass production, reducing its cost, as required in the blue biotechnology context.

RNA-seq and flow-cytometry of conventional, scalp, and palmoplantar psoriasis reveal shared and distinct molecular pathways

It has long been recognized that anatomic location is an important feature for defining distinct subtypes of plaque psoriasis. However, little is known about the molecular differences between scalp, palmoplantar, and conventional plaque psoriasis. To investigate the molecular heterogeneity of these psoriasis subtypes, we performed RNA-seq and flow cytometry on skin samples from individuals with scalp, palmoplantar, and conventional plaque psoriasis, along with samples from healthy control patients. We performed differential expression analysis and network analysis using weighted gene coexpression network analysis (WGCNA). Our analysis revealed a core set of 763 differentially expressed genes common to all sub-types of psoriasis. In contrast, we identified 605, 632, and 262 genes uniquely differentially expressed in conventional, scalp, and palmoplantar psoriasis, respectively. WGCNA and pathway analysis revealed biological processes for the core genes as well as subtype-specific genes. Flow cytometry analysis revealed a shared increase in the percentage of CD4+ T regulatory cells in all psoriasis subtypes relative to controls, whereas distinct psoriasis subtypes displayed differences in IL-17A, IFN-gamma, and IL-22 production. This work reveals the molecular heterogeneity of plaque psoriasis and identifies subtype-specific signaling pathways that will aid in the development of therapy that is appropriate for each subtype of plaque psoriasis.

Selective chemoattraction of the benthic diatom Seminavis robusta to phosphate but not to inorganic nitrogen sources contributes to biofilm structuring

Diatoms frequently dominate marine and freshwater biofilms as major primary producers. Nutrient resources in these biofilms are patchily distributed and fluctuate dynamically over time. We recently reported that this spatially and temporally structured environment can be exploited by motile diatoms that use chemoattraction to dissolved silicate (dSi) under Si starvation. Here, we show that the behavioral response of diatoms is more complex and selective as cells are also responding to gradients of dissolved phosphate (dP) when starved in this nutrient. In contrast, neither nitrate nor ammonium (dN) triggers an attractive response under nitrogen limitation. Video monitoring and movement pattern analysis of the model diatom Seminavis robusta revealed that dP attraction is mediated by a combined chemokinetic and chemotactic response. After locating nutrient hotspots, the microalgae slow down and recover from the limitation. The fastest recovery in terms of growth was observed after dSi limitation. In agreement with the lack of directional response, recovery from dN limitation was slowest, indicating that no short-term benefit would be drawn by the algae from the location of transient hotspots of this resource. Our results highlight the ability of diatoms to adapt to nutrient limitation by active foraging and might explain their success in patchy benthic environments.

Marine diatoms change their gene expression profile when exposed to microscale turbulence under nutrient replete conditions

Diatoms are a fundamental microalgal phylum that thrives in turbulent environments. Despite several experimental and numerical studies, if and how diatoms may profit from turbulence is still an open question. One of the leading arguments is that turbulence favours nutrient uptake. Morphological features, such as the absence of flagella, the presence of a rigid exoskeleton and the micrometre size would support the possible passive but beneficial role of turbulence on diatoms. We demonstrate that in fact diatoms actively respond to turbulence in non-limiting nutrient conditions. TURBOGEN, a prototypic instrument to generate natural levels of microscale turbulence, was used to expose diatoms to the mechanical stimulus. Differential expression analyses, coupled with microscopy inspections, enabled us to study the morphological and transcriptional response of Chaetoceros decipiens to turbulence. Our target species responds to turbulence by activating energy storage pathways like fatty acid biosynthesis and by modifying its cell chain spectrum. Two other ecologically important species were examined and the occurrence of a morphological response was confirmed. These results challenge the view of phytoplankton as unsophisticated passive organisms.