Metabolomic Insights into Marine Phytoplankton Diversity

From nets to networks: tools for deciphering phytoplankton metabolic interactions within communities and their global significance

Our oceans are populated with a wide diversity of planktonic organisms that form complex dynamic communities at the base of marine trophic networks. Within such communities are phytoplankton, unicellular photosynthetic taxa that provide an estimated half of global primary production and support biogeochemical cycles, along with other essential ecosystem services. One of the major challenges for microbial ecologists has been to try to make sense of this complexity. While phytoplankton distributions can be well explained by abiotic factors such as temperature and nutrient availability, there is increasing evidence that their ecological roles are tightly linked to their metabolic interactions with other plankton members through complex mechanisms (e.g. competition and symbiosis). Therefore, unravelling phytoplankton metabolic interactions is the key for inferring their dependency on, or antagonism with, other taxa and better integrating them into the context of carbon and nutrient fluxes in marine trophic networks. In this review, we attempt to summarize the current knowledge brought by ecophysiology, organismal imaging, in silico predictions and co-occurrence networks using 'omics data, highlighting successful combinations of approaches that may be helpful for future investigations of phytoplankton metabolic interactions within their complex communities.This article is part of the theme issue 'Connected interactions: enriching food web research by spatial and social interactions'.

Evaluation of Developmental Toxicity and Oxidative Stress Caused by Zinc Oxide Nanoparticles in Zebra Fish Embryos/ Larvae

Zinc oxide nanoparticles (ZnO NPs) are used in various fields, including biological ones. ZnO NPs are eventually disposed of in the environment where they may affect natural systems, and there is no international law to regulate their manufacture, usage, and disposal. Hence, this present study is carried out to synthesise a more non-toxic and bioactive ZnO NPs from the marine algae Sargassum polycystum. The ZnO NPs were biologically produced using the marine algae Sargassum polycystum. The dynamic light scattering result describes that synthesised particles' average size is about 100 nm in diameter. Transmission electron microscopy (TEM) analysis demonstrated the rod-like morphology of ZnO NPs. Fourier tranform-infrared spectroscopy (FT-IR) results revealed the presence of functional groups in ZnO NPs. The selected area electron diffraction (SAED) results strongly suggested the ZnO NPs crystallinity. ZnO NPs surface morphology and compositions were identified by scanning electron microscopy (SEM- EDX) values. To analyse the toxicity of synthesised nanoparticles, zebra fish larvae were used, which involved subjecting embryos to various ZnO NPs concentrations at 1 hpf and analysing the results at 96 hpf. The 60 and 80 ppm sub-lethal doses were chosen for further studies based on the LC50 (82.23 ppm). In the ZnO NPs-treated groups, a significant slowdown in pulse rate and a delay in hatching were seen, both of which impacted the embryonic processes. A teratogenic study revealed a dose-dependent increase in the incidence of developmental deformities in the treated groups. Along with increased oxidants and a corresponding reduction in antioxidant enzymes, Na+ K+-ATPase and AChE activity changes were seen in ZnO NPs-treated zebra fish larvae groups. The apoptosis process was increased in ZnO NPs-treated groups revealed by acridine orange staining. These results indicate that the green synthesis process cannot mitigate the oxidative stress induced by ZnO NPs on oxidative signalling.

Inferring and comparing metabolism across heterogeneous sets of annotated genomes using AuCoMe

Comparative analysis of genome-scale metabolic networks (GSMNs) may yield important information on the biology, evolution, and adaptation of species. However, it is impeded by the high heterogeneity of the quality and completeness of structural and functional genome annotations, which may bias the results of such comparisons. To address this issue, we developed AuCoMe, a pipeline to automatically reconstruct homogeneous GSMNs from a heterogeneous set of annotated genomes without discarding available manual annotations. We tested AuCoMe with three data sets, one bacterial, one fungal, and one algal, and showed that it successfully reduces technical biases while capturing the metabolic specificities of each organism. Our results also point out shared and divergent metabolic traits among evolutionarily distant algae, underlining the potential of AuCoMe to accelerate the broad exploration of metabolic evolution across the tree of life.

Algal nutraceuticals: A perspective on metabolic diversity, current food applications, and prospects in the field of metabolomics

The current consumers' demand for food naturalness is urging the search for new functional foods of natural origin with enhanced health-promoting properties. In this sense, algae constitute an underexplored biological source of nutraceuticals that can be used to fortify food products. Both marine macroalgae (or seaweeds) and microalgae exhibit a myriad of chemical constituents with associated features as a result of their primary and secondary metabolism. Thus, primary metabolites, especially polysaccharides and phycobiliproteins, present interesting properties to improve the rheological and nutritional properties of food matrices, whereas secondary metabolites, such as polyphenols and xanthophylls, may provide interesting bioactivities, including antioxidant or cytotoxic effects. Due to the interest in algae as a source of nutraceuticals by the food and related industries, novel strategies should be undertaken to add value to their derived functional components. As a result, metabolomics is considered a high throughput technology to get insight into the full metabolic profile of biological samples, and it opens a wide perspective in the study of algae metabolism, whose knowledge is still little explored. This review focuses on algae metabolism and its applications in the food industry, paying attention to the promising metabolomic approaches to be developed aiming at the functional characterization of these organisms.

On the Fate of Butyl Methoxydibenzoylmethane (Avobenzone) in Coral Tissue and Its Effect on Coral Metabolome

The intensive use of sunscreen products has raised concerns regarding their environmental toxicity and the adverse impacts of ultraviolet (UV) filters on ecologically important coral communities. Prior metabolomic analyses on symbiotic coral Pocillopora damicornis exposed to the UV filter butyl methoxydibenzoylmethane (BM, avobenzone) revealed unidentified ions in the holobiont metabolome. In the present study, follow-up differential metabolomic analyses in BM-exposed P. damicornis detected 57 ions with significantly different relative concentrations in exposed corals. The results showed an accumulation of 17 BM derivatives produced through BM reduction and esterification. The major derivative identified C16:0-dihydroBM, which was synthesized and used as a standard to quantify BM derivatives in coral extracts. The results indicated that relative amounts of BM derivatives made up to 95% of the total BM (w/w) absorbed in coral tissue after 7 days of exposure. Among the remaining metabolites annotated, seven compounds significantly affected by BM exposure could be attributed to the coral dinoflagellate symbiont, indicating that BM exposure might impair the photosynthetic capacity of the holobiont. The present results suggest that the potential role of BM in coral bleaching in anthropogenic areas should be investigated and that BM derivatives should be considered in future assessments on the fate and effects of BM in the environment.

Bacterial transcriptional response to labile exometabolites from photosynthetic picoeukaryote Micromonas commoda

Dissolved primary production released into seawater by marine phytoplankton is a major source of carbon fueling heterotrophic bacterial production in the ocean. The composition of the organic compounds released by healthy phytoplankton is poorly known and difficult to assess with existing chemical methods. Here, expression of transporter and catabolic genes by three model marine bacteria (Ruegeria pomeroyi DSS-3, Stenotrophomonas sp. SKA14, and Polaribacter dokdonensis MED152) was used as a biological sensor of metabolites released from the picoeukaryote Micromonas commoda RCC299. Bacterial expression responses indicated that the three species together recognized 38 picoeukaryote metabolites. This was consistent with the Micromonas expression of genes for starch metabolism and synthesis of peptidoglycan-like intermediates. A comparison of the hypothesized Micromonas exometabolite pool with that of the diatom Thalassiosira pseudonana CCMP1335, analyzed previously with the same biological sensor method, indicated that both phytoplankton released organic acids, nucleosides, and amino acids, but differed in polysaccharide and organic nitrogen release. Future ocean conditions are expected to favor picoeukaryotic phytoplankton over larger-celled microphytoplankton. Results from this study suggest that such a shift could alter the substrate pool available to heterotrophic bacterioplankton.

Marine natural products

Covering: 2020This review covers the literature published in 2020 for marine natural products (MNPs), with 757 citations (747 for the period January to December 2020) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1407 in 420 papers for 2020), together with the relevant biological activities, source organisms and country of origin. Pertinent reviews, biosynthetic studies, first syntheses, and syntheses that led to the revision of structures or stereochemistries, have been included. A meta analysis of bioactivity data relating to new MNPs reported over the last five years is also presented.

Effect of Physico-chemical Parameters on the Population Diversity of Potentially Harmful Micro-algae during Post-monsoon Season along the Malabar Coast

There are several toxic microalgae species known as Harmful algal bloom (HAB) causing serious effects to the environment and economy. Knowledge on these groups of marine micro-flora is scanty and several areas remain unexplored. The present study focuses on the analysis of microalgal diversity in the Malabar coastal areas at Southwest and Northeast monsoon. The diatoms, dinoflagellates and total microalgal population were analysed and quantified. Predominant species were identified. Physicochemical parameters of the seawater at different time intervals and Correlation between diatoms, dinoflagellates and total microalgae population with physicochemical parameters were identified. From the analysis, a total of 53 diatoms and 15 dinoflagellates were identified. The predominant species including toxic or harmful bloom-forming were found to be Dinophysis caudata, Noctiluca scintillans, Prorocentrum lima and Tripos furca. The total microalgae population varied from 18,592 cells/L to 7,832 cells/L in the months of April and December. Dinoflagellates were positively correlated with salinity (r = 0.848; p = 0.008), nitrite (r = 0.752; p = 0.032) and total phosphorous (r = 0.734, p = 0.038). Diatoms were positively correlated with temperature (r = 0.804; p = 0.016) and nitrate (r = 0.774, p = 0.024). Total microalgal density was positively correlated with temperature (r = 0.825; p = 0.012) and nitrate content (r = 0.811, p = 0.15).

Metabolomics of Chlorophylls and Carotenoids: Analytical Methods and Metabolome-Based Studies

Chlorophylls and carotenoids are two families of antioxidants present in daily ingested foods, whose recognition as added-value ingredients runs in parallel with the increasing number of demonstrated functional properties. Both groups include a complex and vast number of compounds, and extraction and analysis methods evolved recently to a modern protocol. New methodologies are more potent, precise, and accurate, but their application requires a better understanding of the technical and biological context. Therefore, the present review compiles the basic knowledge and recent advances of the metabolomics of chlorophylls and carotenoids, including the interrelation with the primary metabolism. The study includes material preparation and extraction protocols, the instrumental techniques for the acquisition of spectroscopic and spectrometric properties, the workflows and software tools for data pre-processing and analysis, and the application of mass spectrometry to pigment metabolomics. In addition, the review encompasses a critical description of studies where metabolomics analyses of chlorophylls and carotenoids were developed as an approach to analyzing the effects of biotic and abiotic stressors on living organisms.

Toxicity of Naphthenic Acids on the Chlorophyll Fluorescence Parameters and Antioxidant Enzyme Activity of Heterosigma akashiwo

Petroleum hydrocarbons can serve as a carbon source for marine phytoplankton; so, marine high-acid crude oil pollution events are likely to result in algal outbreaks or harmful algal blooms (HABs) in surface waters. Naphthenic acids (NAs) are the primary acidic component of crude oil, and red tide is of great concern due to its high diffusivity and strong destructive properties. It is important to study the mechanism of the toxic effect of NAs on the typical red tide algae, Heterosigma akashiwo, for the balance and stability of marine algae. The mechanism of NAs’ damage effect was investigated in terms of the antioxidant enzyme activity, cell number, the chlorophyll positive fluorescence parameters, and the cell morphology of microalgae. Experiments confirmed the hormesis of low-concentration (0.5, 2, and 4 mg/L) NAs on Heterosigma akashiwo, and the indicators of high-concentration (8 and 16 mg/L) NA exposures showed inhibition. In this study, the toxic effect of NAs on the target organism showed a clear concentration–dose relationship. The 16 mg/L NAs stress caused severe damage to the morphology and structure of the target biological cells in a short time (96 h), and the population growth decreased. The target organisms showed a staged oxidative stress response to NAs. The behavior in the low-concentration treatment groups showed toxicant excitatory effects on the photosynthetic efficiency and antioxidant enzyme activity of the target organisms. This study provides theoretical and practical data for the development of an important toxicological model of the toxicant’s excitement effects and antioxidant defense mechanisms. In addition, it provides prospective research data for the prediction and avoidance of ecological risk from NA pollution in marine environments.

The Genome of the Haptophyte Diacronema lutheri (Pavlova lutheri, Pavlovales): A Model for Lipid Biosynthesis in Eukaryotic Algae

Haptophytes are biogeochemically and industrially important protists with underexplored genomic diversity. We present a nuclear genome assembly for the class Pavlovales, which was assembled with PacBio long-read data into highly contiguous sequences. We sequenced strain Diacronema lutheri NIVA-4/92, formerly known as Pavlova lutheri, because it has established roles in aquaculture and has been a key organism for studying microalgal lipid biosynthesis. Our data show that D. lutheri has the smallest and most streamlined haptophycean genome assembled to date, with an assembly size of 43.503 Mb and 14,446 protein-coding genes. Together with its high nuclear GC content, Diacronema is an important genus for investigating selective pressures on haptophyte genome evolution, contrasting with the much larger and more repetitive genome of the coccolithophore Emiliania huxleyi. The D. lutheri genome will be a valuable resource for resolving the genetic basis of algal lipid biosynthesis and metabolic remodeling that takes place during adaptation and stress response in natural and engineered environments.

Susceptibility of phytoplankton to the increasing presence of active pharmaceutical ingredients (APIs) in the aquatic environment: A review

Human and veterinary pharmaceuticals either in the form of un-metabolized, incompletely metabolized, and metabolized drugs are increasingly present in aquatic ecosystems. These active pharmaceutical ingredients from pharmaceutical industries, hospitals, agricultural, and domestic discharges find their way into water systems - where they adversely affect non-target organisms like phytoplankton. Different aspects of phytoplankton life; ranging from growth, reproduction, morphology, physiology, biochemical composition, oxidative response, proteomics, and transcriptomics are altered by pharmaceuticals. This review discusses the currently available information on the susceptibility of phytoplankton to the ever-increasing presence of pharmaceutical products in the aquatic environment by focusing on the effect of APIs on the physiology, metabolome, and proteome profiles of phytoplankton. We also highlight gaps in literature concerning the salient underlining biochemical interactions between phytoplankton communities and pharmaceuticals that require an in-depth investigation. This is all in a bid to understand the imminent dangers of the contamination of water bodies with pharmaceutical products and how this process unfavorably affects aquatic food webs.

A unique approach to monitor stress in coral exposed to emerging pollutants

Metabolomic profiling of the hexacoral Pocillopora damicornis exposed to solar filters revealed a metabolomic signature of stress in this coral. It was demonstrated that the concentration of the known steroid (3β, 5α, 8α) -5, 8-epidioxy- ergosta- 6, 24(28) - dien- 3- ol (14) increased in response to octocrylene (OC) and ethylhexyl salicylate (ES) at 50 µg/L. Based on the overall coral response, we hypothesize that steroid 14 mediates coral response to stress. OC also specifically altered mitochondrial function at this concentration and above, while ES triggered a stress/inflammatory response at 300 µg/L and above as witnessed by the significant increases in the concentrations of polyunsaturated fatty acids, lysophosphatidylcholines and lysophosphatidylethanolamines. Benzophenone-3 increased the concentration of compound 14 at 2 mg/L, while the concentration of stress marker remained unchanged upon exposition to the other solar filters tested. Also, our results seemed to refute earlier suggestions that platelet-activating factor is involved in the coral inflammatory response.