Analysis of the Proteome of the Marine Diatom Phaeodactylum tricornutum Exposed to Aluminum Providing Insights into Aluminum Toxicity Mechanisms

A Brief Review of Effects of Aluminum on Marine Diatoms

Aluminum (Al) is the most abundant metal element in the Earth's crust, yet it is present in trace levels in seawater. Growing evidence suggests potential effects of Al on the biogeochemical cycles of carbon (C) and silicon (Si) in the marine environment. By accumulation, sinking, and deposition, diatoms play a center role in coupling these three elements' biocycles in the oceans. However, it is still a challenge to elucidate the behaviors of diatoms influenced by Al. Our review aims to present the current knowledge of Al biogeochemistry in marine environment and its impact on marine phytoplankton, with a focus on how Al influences diatoms. Previous researches indicate that Al can promote the growth of diatoms, and diatoms have the ability to incorporate Al into their frustules. Given this, we paid particular attention on the interaction between Al and diatom frustules, and the influences of Al on the physiology and ecology of diatoms. Furthermore, it is suggested that Al alters the accumulation of other nutrients such as nitrogen, phosphorus and iron in diatoms; the subsequent responses of diatoms are also discussed. The objective of this review is to address the potential roles of Al in diatoms and offer insights into the possible biogeochemistry implications.

Microalgal multiomics-based approaches in bioremediation of hazardous contaminants

The enhanced industrial growth and higher living standards owing to the incessant population growth have caused heightened production of various chemicals in different manufacturing sectors globally, resulting in pollution of aquatic systems and soil with hazardous chemical contaminants. The bioremediation of such hazardous pollutants through microalgal processes is a viable and sustainable approach. Accomplishing microalgal-based bioremediation of polluted wastewater requires a comprehensive understanding of microalgal metabolic and physiological dynamics. Microalgae-bacterial consortia have emerged as a sustainable agent for synergistic bioremediation and metabolite production. Effective bioremediation involves proper consortium functioning and dynamics. The present review highlights the mechanistic processes employed through microalgae in reducing contaminants present in wastewater. It discusses the multi-omics approaches and their advantages in understanding the biological processes, monitoring, and dynamics among the partners in consortium through metagenomics. Transcriptomics, proteomics, and metabolomics enable an understanding of microalgal cell response toward the contaminants in the wastewater. Finally, the challenges and future research endeavors are summarised to provide an outlook on microalgae-based bioremediation.

Multi-omic insights into the cellular response of Phaeodactylum tricornutum (Bacillariophyta) strains under grazing pressure

Background/Aims

Phaeodactylum tricornutum, a model organism of diatoms, plays a crucial role in Earth's primary productivity. Investigating its cellular response to grazing pressure is highly significant for the marine ecological environment. Furthermore, the integration of multi-omics approaches has enhanced the understanding of its response mechanism.

Methods

To assess the molecular and cellular responses of P.tricornutum to grazer presence, we conducted transcriptomic, proteomic, and metabolomic analyses, combined with phenotypic data from previous studies. Sequencing data were obtained by Illumina RNA sequencing, TMT Labeled Quantitative Proteomics and Non-targeted Metabolomics, and WGCNA analysis and statistical analysis were performed.

Results

Among the differentially expressed genes, we observed complex expression patterns of the core genes involved in the phenotypic changes of P.tricornutum under grazing pressure across different strains and multi-omics datasets. These core genes primarily regulate the levels of various proteins and fatty acids, as well as the cellular response to diverse signals.

Conclusion

Our research reveals the association of multi-omics in four strains responses to grazing effects in P.tricornutum. Grazing pressure significantly impacted cell growth, fatty acid composition, stress response, and the core genes involved in phenotype transformation.

Aluminium-based galvanic anode impacts the photosynthesis of microphytobenthos and supports the bioaccumulation of metals released

Very few studies have looked at the potential biological effects of degradation products of galvanic anodes particularly on primary producers which are central to food webs in marine ecosystems. The galvanic anode cathodic protection system (GACP) is widely used to protect submerged metallic structures from corrosion. Aluminium (Al) and zinc (Zn) are the main constituents of galvanic anodes and are therefore released in the marine environment by oxidation process to form ions or oxy-hydroxides. The main objective of our study was to evaluate the effects of the metals released from an aluminium-based galvanic anode on microphytobenthos performance in term of biofilm growing through the analysis of photosynthetic parameters, the determination of chlorophyll and extracellular polymeric substances (EPS). The bioaccumulation of Al and Zn were measured in the microphytobenthic compartment collected at the surface of polyvinyl chloride (PVC) plates exposed during 13 days to seawaters enriched in different concentrations of metals released from dissolution of one anode. Determination of bioconcentration factors confirmed that the microphytobenthos has incorporated Al. A significative effect was observed on the Chl a concentration for the higher tested concentration ([Al] = 210.1 ± 60.2 µg L ^- 1; [Zn] = 20.2 ± 1.4 µg L ^- 1). The seawater exposed to the anode affected the MPB productivity (ETRII_max) with consequences on acclimatation light (Ek), absorption cross section of PSII (σ_PII), F_v/F_m and NPQ. Regarding the EPS production, the anode degradation presented an impact on high and low molecular weight of both carbohydrates and protein fractions of microphytobenthos suggesting that EPS play an essential role in sequestering metal contaminants to maintain the integrity of the biological membranes and the functionality of the cellular organelles. The accumulation of Al released by GACP in microphytobenthos cells could lead to physiologic problems in photosynthetic organisms.

Microalgae-based wastewater treatment - Microalgae-bacteria consortia, multi-omics approaches and algal stress response

Sustainable environmental management is one of the important aspects of sustainable development goals. Increasing amounts of wastewaters (WW) from exponential economic growth is a major challenge, and conventional treatment methods entail a huge carbon footprint in terms of energy use and GHG emissions. Microalgae-based WW treatment is a potential candidate for sustainable WW treatment. The nutrients which are otherwise unutilized in the conventional processes are recovered in the beneficial microalgal biomass. This review presents comprehensive information regarding the potential of microalgae as sustainable bioremediation agents. Microalgae-bacterial consortia play a critical role in synergistic nutrient removal, supported by the complex nutritional and metabolite exchange between microalgae and the associated bacteria. Design of effective microalgae-bacteria consortia either by screening or by recent technologies such as synthetic biology approaches are highly required for efficient WW treatment. Furthermore, this review discusses the crucial research gap in microalgal WW treatment - the application of a multi-omics platform for understanding microalgal response towards WW conditions and the design of effective microalgal or microalgae-bacteria consortia based on genetic information. While metagenomics helps in the identification and monitoring of the microbial community throughout the treatment process, transcriptomics, proteomics and metabolomics aid in studying the algal cellular response towards the nutrients and pollutants in WW. It has been established that the integration of microalgal processes into conventional WW treatment systems is feasible. In this direction, future research directions for microalgal WW treatment emphasize the need for identifying the niche in WW treatment, while highlighting the pilot sale plants in existence. Microalgae-based WW treatment could be a potential phase in the waste hierarchy of circular economy and sustainability, considering WWs are a rich secondary source of finite resources such as nitrogen and phosphorus.

Comparative Proteomic Analysis of the Diatom Phaeodactylum tricornutum Reveals New Insights Into Intra- and Extra-Cellular Protein Contents of Its Oval, Fusiform, and Triradiate Morphotypes

Phaeodactylum tricornutum is an atypical diatom since it can display three main morphotypes: fusiform, triradiate, and oval. Such pleomorphism is possible thanks to an original metabolism, which is tightly regulated in order to acclimate to environmental conditions. Currently, studies dedicated to the comparison of each morphotype issued from one specific strain are scarce and little information is available regarding the physiological significance of this morphogenesis. In this study, we performed a comparative proteomic analysis of the three morphotypes from P. tricornutum. Cultures highly enriched in one dominant morphotype (fusiform, triradiate, or oval) of P. tricornutum Pt3 strain were used. Pairwise comparisons highlighted biological processes, which are up- and down-regulated in the oval (e.g., purine and cellular amino acid metabolism) and triradiate morphotypes (e.g., oxido-reduction and glycolytic processes) compared to the fusiform one used as a reference. Intersection analysis allowed us to identify the specific features of the oval morphotype. Results from this study confirmed previous transcriptomic RNA sequencing observation showing that the oval cells present a distinct metabolism with specific protein enrichment compared to fusiform and triradiate cells. Finally, the analysis of the secretome of each morphotype was also performed.

Evaluation of the acute toxic response induced by triazophos to the non-target green algae Chlorella pyrenoidosa

Residues of triazophos in aquatic ecosystems due to extensive use for controlling pests in agriculture has became worldwide concern, while the toxic response of triazophos on the non-target green algae in aquatic environment is not well studied. Therefore, the acute (96 h) toxic effects of 1 and 10 mg/L triazophos on green algae Chlorella pyrenoidosa were evaluated in present study. The results showed that the growth was notably inhibited when treated with triazophos and the 96 h-EC₅₀ (median inhibition concentration) were 12.79 mg/L. The content of photosynthetic pigments (including chl a, chl b, total-chl and carotinoids) clearly decreased under two treatments after 48 h and 96 h with exception for the values at 48 h exposure in 1 mg/L treatment. In addition, the transcript abundance of photosynthesis-related genes (psbA, psbC and rbcL) showed obvious decrease in above two treatments after exposure 96 h to triazophos. In response to 10 mg/L triazophos treatment, the morphology of thylakoid chloroplast of algal cells were obviously damaged. It was also found that starch granules increased with down-regulation of atpB gene expression in 10 mg/L treatment, which suggests that triazophos may inhibit the energy metabolism of C. pyrenoidosa. Moreover, the algal growth inhibition was along with the increase of intracellular reactive oxygen species (ROS), activity of antioxidant enzymes and malondialdehyde content indicating oxidative damage and lipid peroxidation in the algal cells. Our findings reveal that triazophos has potential toxicity and environmental risks to one of the primary producers green algae.

Dewaterability improvement and environmental risk mitigation of waste activated sludge using peroxymonosulfate activated by zero-valent metals: Fe0 vs. Al0

The stabilization and dewaterability of waste activated sludge (WAS) are essential factors for downstream disposal or reuse. Herein, two types of zero-valent metals, zero-valent iron (Fe⁰) and zero-valent aluminum (Al⁰), were compared for their ability to activate peroxymonosulfate (PMS) during the WAS conditioning process, with the effects of PMS activation by these two metals on WAS dewaterability and the potential environmental risks evaluated. Results showed that compared to Al⁰/PMS treatment, Fe⁰/PMS treatment achieved superior WAS dewaterability and reduced operational costs. Using PMS combined with Fe⁰ and Al⁰ treatments under optimal conditions, the water content (Wc) of dewatered sludge decreased to 55.7 ± 2.7 wt% and 59.4 ± 1.3 wt%, respectively. Meanwhile, application of the Fe⁰/PMS treatment system reduced the total annual cost by approximately 33.1%, compared to the Al⁰/PMS treatment. Analysis of the dewatering mechanism demonstrated that in the Fe⁰/PMS treatment, Fe³⁺/Fe²⁺ flocculation played an important role in the enhancement of WAS dewatering, while sulfate radical (SO₄^•-) oxidation was the dominant factor for WAS dewaterability improvement in Al⁰/PMS treatment. The greater enhancement of WAS dewaterability by Fe⁰/PMS treatment, was mainly attributed to more efficient reduction of hydrophilic extracellular polymeric substances (EPS) and an increase in surface charge neutralization. Environmental risk evaluation results indicated that Fe⁰/PMS and Al⁰/PMS treatments both effectively alleviated the environmental risks of heavy metals and faecal coliforms in dewatered sludge. Overall, this study proposes a novel perspective for the selection of an optimal PMS activator in sludge treatment.

Pollutant toxicology with respect to microalgae and cyanobacteria

Microalgae and cyanobacteria are fundamental components of aquatic ecosystems. Pollution in aquatic environment is a worldwide problem. Toxicological research on microalgae and cyanobacteria can help to establish a solid foundation for aquatic ecotoxicological assessments. Algae and cyanobacteria occupy a large proportion of the biomass in aquatic environments; thus, their toxicological responses have been investigated extensively. However, the depth of toxic mechanisms and breadth of toxicological investigations need to be improved. While existing pollutants are being discharged into the environment daily, new ones are also being produced continuously. As a result, the phenomenon of water pollution has become unprecedentedly complex. In this review, we summarize the latest findings on five kinds of aquatic pollutants, namely, metals, nanomaterials, pesticides, pharmaceutical and personal care products (PPCPs), and persistent organic pollutants (POPs). Further, we present information on emerging pollutants such as graphene, microplastics, and ionic liquids. Efforts in studying the toxicological effects of pollutants on microalgae and cyanobacteria must be increased in order to better predict the potential risks posed by these materials to aquatic ecosystems as well as human health.

The Importance of Protein Phosphorylation for Signaling and Metabolism in Response to Diel Light Cycling and Nutrient Availability in a Marine Diatom

Diatoms are major contributors to global primary production and their populations in the modern oceans are affected by availability of iron, nitrogen, phosphate, silica, and other trace metals, vitamins, and infochemicals. However, little is known about the role of phosphorylation in diatoms and its role in regulation and signaling. We report a total of 2759 phosphorylation sites on 1502 proteins detected in Phaeodactylum tricornutum. Conditionally phosphorylated peptides were detected at low iron (n = 108), during the diel cycle (n = 149), and due to nitrogen availability (n = 137). Through a multi-omic comparison of transcript, protein, phosphorylation, and protein homology, we identify numerous proteins and key cellular processes that are likely under control of phospho-regulation. We show that phosphorylation regulates: (1) carbon retrenchment and reallocation during growth under low iron, (2) carbon flux towards lipid biosynthesis after the lights turn on, (3) coordination of transcription and translation over the diel cycle and (4) in response to nitrogen depletion. We also uncover phosphorylation sites for proteins that play major roles in diatom Fe sensing and utilization, including flavodoxin and phytotransferrin (ISIP2A), as well as identify phospho-regulated stress proteins and kinases. These findings provide much needed insight into the roles of protein phosphorylation in diel cycling and nutrient sensing in diatoms.

Phosphorus deficiency induced by aluminum in a marine nitrogen-fixing cyanobacterium Crocosphaera watsonii WH0003

Large amounts of aluminum (Al) enter the ocean through atmospheric dust deposition and river runoffs. However, few studies have reported the effects of Al on marine phytoplankton, especially nitrogen-fixing cyanobacteria. By using the isotope tracer method and quantitative reverse transcription PCR (RT-qPCR), we examined the physiological effect of Al (0.2, 2 and 20 μM) on the unicellular marine nitrogen-fixing cyanobacterium Crocosphaera watsonii in Aquil* medium. We show that Al has an inhibitory physiological effect on C. watsonii, including changes in growth rate, nitrogen fixation rate, carbon fixation rate, cell size, fast rise chlorophyll fluorescence kinetics, cellular photosynthetic pigment and C/N/P content, the same as that of the phosphorus deficient treatment. The ratio of cellular elements C:N:P showed that phosphorus was deficient in the cell of C. watsonii after Al treatment (2 and 20 μM). In addition, Al stimulated the expression of phosphorus-related genes pstS, phoH, phoU, ppK and ppX in C. watsonii. All these results suggest that Al-treated C. watsonii is phosphorus-limited, and that the phosphorus deficiency induced by Al may be one mechanism behind aluminum's toxicity.

Offspring toxicity of silver nanoparticles to Arabidopsis thaliana flowering and floral development

Many studies have considered silver nanoparticles (AgNPs) cytotoxicity to mammalian and human cell lines and plant growth. However, only few studies considered toxic effects of AgNPs on plant offspring, especially on flowering. Arabidopsis thaliana was treated with 12.5 mg/kg AgNPs employing parental-(P-AgNPs) and offspring-generation (O-AgNPs) exposure to study the effects of AgNPs on flowering and floral development. Exposure to P-AgNPs was found to significantly decrease petal and pollen viability and subsequently reduced pod production. The inhibition of A. thaliana vegetative growth caused by P-AgNPs exposure was transferred to offspring and even became more severe in the O-AgNPs group. Further, the transcription of genes related to flowering and floral organ development in P-AgNPs and O-Con plants was downregulated by approximately 10-40% compared to the transcription in P-Con plants and showed a stronger decrease in the O-AgNPs group to 30-50% of that in the P-AgNPs group. This resulted in a delay in flowering of 4, 3 and 8 days in P-AgNPs, O-Con and O-AgNPs plants, respectively. Our research shows that the negative effects on floral development can be transferred to the offspring in A. thaliana, which may have significant implications with regard to the risks posed by NPs to food safety and security.

Insights into the transcriptional responses of a microbial community to silver nanoparticles in a freshwater microcosm

Silver nanoparticles (AgNPs) are widely used because of their excellent antibacterial properties. They are, however, easily discharged into the water environment, causing potential adverse environmental effects. Meta-transcriptomic analyses are helpful to study the transcriptional response of prokaryotic and eukaryotic aquatic microorganisms to AgNPs. In the present study, microcosms were used to investigate the toxicity of AgNPs to a natural aquatic microbial community. It was found that a 7-day exposure to 10 μg L^-1 silver nanoparticles (AgNPs) dramatically affected the structure of the microbial community. Aquatic micro eukaryota (including eukaryotic algae, fungi, and zooplankton) and bacteria (i.e., heterotrophic bacteria and cyanobacteria) responded differently to the AgNPs stress. Meta-transcriptomic analyses demonstrated that eukaryota could use multiple cellular strategies to cope with AgNPs stress, such as enhancing nitrogen and sulfur metabolism, over-expressing genes related to translation, amino acids biosynthesis, and promoting bacterial-eukaryotic algae interactions. By contrast, bacteria were negatively affected by AgNPs with less signs of detoxification than in case of eukaryota; various pathways related to energy metabolism, DNA replication and genetic repair were seriously inhibited by AgNPs. As a result, eukaryotic algae (mainly Chlorophyta) dominated over cyanobacteria in the AgNPs treated microcosms over the 7-d exposure. The present study helps to understand the effects of AgNPs on aquatic microorganisms and provides insights into the contrasting AgNPs toxicity in eukaryota and bacteria.

Aluminum distribution heterogeneity and relationship with nitrogen, phosphorus and humic acid content in the eutrophic lake sediment

Increasing amount of aluminum (Al) gets into aquatic ecosystem through anthropogenic activity, but the knowledge about Al migration and relationships with sediments possessing different physico-chemical properties in eutrophic lakes is limited. Here, the Al migration rule and relationships with sediment nutritions in the Hangzhou West Lake, China was investigated, where a certain amount of residual Al-salts can enter because of the pre-treatment of the Qiantang River diversion project every day. Results revealed the obvious spatial distribution heterogeneity of Al in sediment vertical direction and horizontal direction following water flow. The Al content in sediment ranged 0.463-1.154 g kg^-1 in Maojiabu Lake, and ranged 9.862-40.442 g kg^-1 in Xiaonanhu Lake. Higher Al content distributed in upper layer sediment in lake with more disturbance. Total nitrogen (TN) contents were higher 0.917-3.387 mg g^-1 and 0.627-0.786 mg g^-1 in upper layer sediment than that in lower layer in Maojiabu Lake and Xiaonanhu Lake, respectively. Total phosphorus (TP) content ranged 0.779-2.580 mg g^-1, in which IP and Fe/Al-P contributed 24.9-80.8% and 17.0-51.6%, respectively. Correlations between Al content with nutrition, humic acid (HA) etc. of sediment regionally varied in Maojiabu and Xiaonanhu Lake. Spatial distribution of Al-salt in eutrophic lakes closely related with the physico-chemical characteristics of nutrients, humus, human disturbance and water division parameters. Results provides new insight into Al-salts migration and references for Al-risk evaluating in eutrophic lakes.

Leaching behavior of fluorescent additives from microplastics and the toxicity of leachate to Chlorella vulgaris

Chemical additives leaching from microplastics and their effects on physiology of microalgae are of environmental significance. So far, these issues remain unclear. Here, the leaching behavior of fluorescent additives from polyurethane sponge microplastics in simulated (acidic, saline, and basic water) and natural waters (river, lake, wetland, and sea water) was investigated. Release amount of additives increased with increasing solution pH and leaching time. The maximum release amount was reached at the leaching time of 12-24 h and the 3,3'-diaminobenzidine-like substances were identified in the leachate. The leached concentrations of fluorescent additives in simulated and natural waters followed the order of basic water > saline water > seawater > West Lake > River > Wetland. Effects of leachate and microplastics on growth and photosynthesis of Chlorella vulgaris were further evaluated. The maximum quantum efficiency of photosystem II (F_v/F_m) decreased with increasing leachate concentrations. Only high content (1.6 g L^-1) of microplastics exerted significant inhibitory influence on cell photosynthesis when microalgae were exposed to microplastics alone. Retention of algal cells inside the porous sponge microplastics did not change their photosynthetic efficiency. These findings indicate that leaching process of additives from microplastics depends mainly on water environments and the leached chemicals may pose ecological risks to aquatic organisms.

Aquatic ecotoxicity of an antidepressant, sertraline hydrochloride, on microbial communities

Sertraline hydrochloride (Ser-HCl), a widely used antidepressant, becomes an aquatic contaminant via metabolic excretion and improper disposal; however, it is unknown how Ser-HCl affects aquatic microbial communities. The present study investigated the effects of Ser on the structures of aquatic microbial communities via high-throughput sequencing analyses. Ser-HCl treatment inhibited the growth of two model algae (the green alga, Chlorella vulgaris, and the cyanobacterium, Microcystis aeruginosa) and decreased the chlorophyll a (Chl-a) concentration in the microcosm to reduce the photosynthetic efficiency. High-throughput sequencing analyses showed that exposure to Ser-HCl disturbed the balance of cyanobacteria species by stimulating the growth of specific cyanobacteria. Among eukaryotes, the richness as well as the diversity indices were significantly enhanced after 5 days of Ser-HCl treatment but sharply decreased with exposure time. Nucleariida occupied an absolute majority (97.83%) within the eukaryotes, implicating that Ser-HCl disturbed the ecological equilibrium in microcosms. Ser-HCl will continue to be an environmental contaminant due to its wide usage and production. Our current study clarified the potential ecological risk of Ser-HCl to aquatic microorganisms. These findings suggest that more attention should be given to the negative effects of these bioactive pollutants on aquatic environments.

Linking Exoproteome Function and Structure to Anammox Biofilm Development

Extracellular proteins are of paramount importance in the cell-cell interactions of anammox biofilms. However, the inherent aggregation mechanisms of anammox have largely remained elusive. Herein, using a quartz sand extraction protocol and follow-up iTRAQ-based quantitative proteomics, we identified 367 extracellular proteins from initial colonizers, mature biofilm, and detached biofilm. The extracellular proteins were mainly membrane-associated. Most of the recovered proteins (226, 72.5%) originated from the phylum Planctomycetes. In summary, 215 and 190 of the 367 proteins recovered were up- and/or downregulated at least 1.2-fold during the biofilm formation and detachment periods, respectively. These differentially expressed proteins were dominantly involved in metal ion binding, which was regarded as strong evidence for their abilities to enhance ionic bridges in extracellular polymeric substances (EPS). Scanning electron microscopy-energy-dispersive X-ray spectroscopy (SEM-EDX) analysis of the biofilms further showed substantial levels of calcium and iron minerals. Critically, representative Sec-dependent secretory proteins affiliated with coccoid Planctomycetes, rod-shaped Proteobacteria, and filamentous Chloroflexi (11, 4, and 2 with differential expression, respectively) were found to have typical and abundant inner β-sheet structures, wherein hydrophobic moieties can promote anammox aggregation. Overall, these findings highlight links between differentially expressed protein functions and morphologic traits of anammox consortia during biofilm development.

Acute toxicity of the fungicide azoxystrobin on the diatom Phaeodactylum tricornutum

Azoxystrobin (AZ) is an effective broad-spectrum fungicide. Due to its extensive application, AZ is detectable in aquatic ecosystems and thus influences aquatic organisms. In this study, the acute toxicity (96 h) of AZ at concentrations of 1.0 mg/L and 5.0 mg/L on the diatom Phaeodactylum tricornutum were examined. At the tested concentrations, AZ significantly inhibited P. tricornutum growth and destroyed its cellular structure. Furthermore, the mechanisms of AZ-induced toxicity on P. tricornutum changed as the exposure time extended. Forty-eight hours after exposure, AZ inhibited P. tricornutum growth primarily via inducing oxidative stress, which increased the activity of two main antioxidant enzymes, superoxide dismutase and peroxidase, and inhibited energy metabolism. However, after 96 h of treatment, the decline in the photosynthetic capacity of P. tricornutum demonstrated that the photosystem was the main AZ target. The pigment content and expression levels of genes related to photosynthetic electron transfer reactions were also significantly decreased. The present study describes AZ toxicity in P. tricornutum and is very valuable for assessing the environmental risk of AZ.

Genome Annotation of a Model Diatom Phaeodactylum tricornutum Using an Integrated Proteogenomic Pipeline

Diatoms comprise a diverse and ecologically important group of eukaryotic phytoplankton that significantly contributes to marine primary production and global carbon cycling. Phaeodactylum tricornutum is commonly used as a model organism for studying diatom biology. Although its genome was sequenced in 2008, a high-quality genome annotation is still not available for this diatom. Here we report the development of an integrated proteogenomic pipeline and its application for improved annotation of P. tricornutum genome using mass spectrometry (MS)-based proteomics data. Our proteogenomic analysis unambiguously identified approximately 8300 genes and revealed 606 novel proteins, 506 revised genes, 94 splice variants, 58 single amino acid variants, and a holistic view of post-translational modifications in P. tricornutum. We experimentally confirmed a subset of novel events and obtained MS evidence for more than 200 micropeptides in P. tricornutum. These findings expand the genomic landscape of P. tricornutum and provide a rich resource for the study of diatom biology. The proteogenomic pipeline we developed in this study is applicable to any sequenced eukaryote and thus represents a significant contribution to the toolset for eukaryotic proteogenomic analysis. The pipeline and its source code are freely available at https://sourceforge.net/projects/gapeproteogenomic.

Phytoplankton responses to aluminum enrichment in the South China Sea

Compared to extensive studies reporting the aluminum (Al) toxicity to terrestrial plants and freshwater organisms, very little is known about how marine phytoplankton responds to Al in the field. Here we report the marine phytoplankton responses to Al enrichment in the South China Sea (SCS) using on-deck bottle incubation experiments during eight cruises from May 2010 to November 2013. Generally, Al addition alone enhanced the growth of diatom and Trichodesmium, and nitrogen fixation, but it inhibited the growth of dinoflagellates and Synechococcus. Nevertheless, Al addition alone did not influence the chlorophyll a concentration of the entire phytoplankton assemblages. By adding nitrate and phosphate simultaneously, Al enrichment led to substantial increases in chlorophyll a concentration (especially that of the picophytoplankton<3μm), and cell abundances of diatom and photosynthetic picoeukaryotes. These results indicate varied responses of phytoplankton in different size fractions and taxonomic groups to Al enrichment. Further, by simultaneously adding different macronutrients and/or sufficient trace metals including iron, we found that the phytoplankton responses to Al enrichment were relevant to nutrients coexisting in the environment. Al enrichment may give some phytoplankton a competitive edge over using nutrients, especially the limited ones. The possible influences of Al on the competitors and grazers (predators) of some phytoplankton might indirectly contribute to the positive responses of the phytoplankton to Al enrichment. Our results indicate that Al may influence marine carbon cycle by impacting phytoplankton growth and structure in natural seawater.

Evaluation of the toxic response induced by azoxystrobin in the non-target green alga Chlorella pyrenoidosa

The top-selling strobilurin, azoxystrobin (AZ), is a broad-spectrum fungicide that protects against many kinds of pathogenic fungi by preventing their ATP production. The extensive use of AZ can have negative consequences on non-target species and its effects and toxic mechanisms on algae are still poorly understood. In this work, Chlorella pyrenoidosa that had been grown in BG-11 medium was exposed to AZ (0.5-10 mg L^-1) for 10 d. The physiological and molecular responses of the algae to AZ treatment, including photosynthetic efficiency, lipid peroxidation level, antioxidant enzyme activities, as well as transcriptome-based analysis of gene expression, were examined to investigate the potential toxic mechanism. Results shows that the photosynthetic pigment (per cell) increased slightly after AZ treatments, indicating that the photosystem of C. pyrenoidosa may have been strengthened. Glutathione and ascorbate contents were increased, and antioxidant enzyme activities were induced to relieve oxidative damage (e.g., from lipid peroxidation) in algae after AZ treatment. Transcriptome-based analysis of gene expression combined with physiological verification suggested that the 5 mg L^-1 AZ treatment did not inhibit ATP generation in C. pyrenoidosa, but did significantly alter amino acid metabolism, especially in aspartate- and glutamine-related reactions. Moreover, perturbation of ascorbate synthesis, fat acid metabolism, and RNA translation was also observed, suggesting that AZ inhibits algal cell growth through multiple pathways. The identification of AZ-responsive genes in the eukaryotic alga C. pyrenoidosa provides new insight into AZ stress responses in a non-target organism.

Molecular regulation of aluminum resistance and sulfur nutrition during root growth

Aluminum toxicity and sulfate deprivation both regulate microRNA395 expression, repressing its low-affinity sulfate transporter ( SULTR2;1 ) target. Sulfate deprivation also induces the high-affinity sulfate transporter gene ( SULTR12 ), allowing enhanced sulfate uptake. Few studies about the relationships between sulfate, a plant nutrient, and aluminum, a toxic ion, are available; hence, the molecular and physiological processes underpinning this interaction are poorly understood. The Al-sulfate interaction occurs in acidic soils, whereby relatively high concentrations of trivalent toxic aluminum (Al³⁺) may hamper root growth, limiting uptake of nutrients, including sulfur (S). On the other side, Al³⁺ may be detoxified by complexation with sulfate in the acid soil solution as well as in the root-cell vacuoles. In this review, we focus on recent insights into the mechanisms governing plant responses to Al toxicity and its relationship with sulfur nutrition, emphasizing the role of phytohormones, microRNAs, and ion transporters in higher plants. It is known that Al³⁺ disturbs gene expression and enzymes involved in biosynthesis of S-containing cysteine in root cells. On the other hand, Al³⁺ may induce ethylene biosynthesis, enhance reactive oxygen species production, alter phytohormone transport, trigger root growth inhibition and promote sulfate uptake under S deficiency. MicroRNA395, regulated by both Al toxicity and sulfate deprivation, represses its low-affinity Sulfate Transporter 2;1 (SULTR2;1) target. In addition, sulfate deprivation induces High Affinity Sulfate Transporters (HAST; SULTR1;2), improving sulfate uptake from low-sulfate soil solutions. Identification of new microRNAs and cloning of their target genes are necessary for a better understanding of the role of molecular regulation of plant resistance to Al stress and sulfate deprivation.

Are Diatoms "Green" Aluminosilicate Synthesis Microreactors for Future Catalyst Production?

Diatom biosilica may offer an interesting perspective in the search for sustainable solutions meeting the high demand for heterogeneous catalysts. Diatomaceous earth (diatomite), i.e., fossilized diatoms, is already used as adsorbent and carrier material. While diatomite is abundant and inexpensive, freshly harvested and cleaned diatom cell walls have other advantages, with respect to purity and uniformity. The present paper demonstrates an approach to modify diatoms both in vivo and in vitro to produce a porous aluminosilicate that is serving as a potential source for sustainable catalyst production. The obtained material was characterized at various processing stages with respect to morphology, elemental composition, surface area, and acidity. The cell walls appeared normal without morphological changes, while their aluminum content was raised from the molar ratio n(Al):n(Si) 1:600 up to 1:50. A specific surface area of 55 m²/g was measured. The acidity of the material increased from 149 to 320 µmol NH₃/g by ion exchange, as determined by NH₃ TPD. Finally, the biosilica was examined by an acid catalyzed test reaction, the alkylation of benzene. While the cleaned cell walls did not catalyze the reaction at all, and the ion exchanged material was catalytically active. This demonstrates that modified biosilica does indeed has potential as a basis for future catalytically active materials.

Enantioselective Phytotoxicity of Dichlorprop to Arabidopsis thaliana: The Effect of Cytochrome P450 Enzymes and the Role of Fe

The ecotoxicology effects of chiral herbicides have long been recognized and have drawn increasing attention. The toxic mechanisms of herbicides in plants are involved in production of reactive oxygen species (ROS) and cause damage to target enzymes, but the relationship between these two factors in the enantioselectivity of chiral herbicides has rarely been investigated. Furthermore, even though cytochromes P450 enzymes (CYP450s) have been related to the phytotoxicity of herbicides, their roles in the enantioselectivity of chiral herbicides have yet to be explored. To solve this puzzle, the CYP450s suicide inhibitor 1-aminobenzotriazole (ABT) was added to an exposure system made from dichlorprop (DCPP) enantiomers in the model plant Arabidopsis thaliana. The results indicated that different phytotoxicities of DCPP enantiomers by causing oxidative stress and acetyl-CoA carboxylase (ACCase) damage were observed in the presence and the absence of ABT. The addition of ABT decreased the toxicity of (R)-DCPP but was not significantly affected that of (S)-DCPP, resulting in smaller differences between enantiomers. Furthermore, profound differences were also observed in Fe uptake and distribution, exhibiting different distribution patterns in A. thaliana leaves exposed to DCPP and ABT, which helped bridge the relationship between ROS production and target enzyme ACCase damage through the function of CYP450s. These results offer an opportunity for a more-comprehensive understanding of chiral herbicide action mechanism and provide basic evidence for risk assessments of chiral herbicides in the environment.

Quantitative Proteomics Reveals Ecophysiological Effects of Light and Silver Stress on the Mixotrophic Protist Poterioochromonas malhamensis

Aquatic environments are heavily impacted by human activities including climate warming and the introduction of xenobiotics. Due to the application of silver nanoparticles as bactericidal agent the introduction of silver into the environment strongly has increased during the past years. Silver ions affect the primary metabolism of algae, in particular photosynthesis. Mixotrophic algae are an interesting test case as they do not exclusively rely on photosynthesis which may attenuate the harmful effect of silver. In order to study the effect of silver ions on mixotrophs, cultures of the chrysophyte Poterioochromonas malhamensis were treated in a replicate design in light and darkness with silver nitrate at a sub-lethal concentration. At five time points samples were taken for the identification and quantitation of proteins by mass spectrometry. In our analysis, relative quantitative protein mass spectrometry has shown to be a useful tool for functional analyses in conjunction with transcriptome reference sequences. A total of 3,952 proteins in 63 samples were identified and quantified, mapping to 4,829 transcripts of the sequenced and assembled transcriptome. Among them, 720 and 104 proteins performing various cellular functions were differentially expressed after eight days in light versus darkness and after three days of silver treatment, respectively. Specifically pathways of the energy and primary carbon metabolism were differentially affected by light and the utilization of expensive reactions hints to an energy surplus of P. malhamensis under light conditions. The excess energy is not invested in growth, but in the synthesis of storage metabolites. The effects of silver were less explicit, observable especially in the dark treatments where the light effect could not mask coinciding but weaker effects of silver. Photosynthesis, particularly the light harvesting complexes, and several sulphur containing enzymes were affected presumably due to a direct interference with the silver ions, mainly affecting energy supply.

iTRAQ quantitative proteomic analysis reveals the pathways for methanation of propionate facilitated by magnetite

Methanation of propionate requires syntrophic interaction of propionate-oxidizing bacteria and hydrogenotrophic methanogens, which is referred to as interspecies electron transfer. The present study showed that 10 mg/L conductive magnetite enhanced the methane production rate from propionate by around 44% in batch experiments, and both direct interspecies electron transfer and interspecies H₂ transfer were thermodynamically feasible with the addition of magnetite. The methanation of propionate facilitated by magnetite was also demonstrated in a long-term operated continuous reactor. The methane production rate from acetate by the enriched mixed culture with magnetite was higher than that without magnetite, while similar methane production rates were found from H₂/CO₂ by the enriched mixed culture with and without magnetite. The ability to utilize molecular H₂ indicated interspecies H₂ transfer played a role in the enriched culture with magnetite, and propionate-oxidizing bacteria relating with interspecies H₂ transfer were also detected by metagenomic sequencing. Metagenomic sequencing analysis also showed that Thauera, possibly relating with direct interspecies electron transfer, were enriched with the addition of magnetite. iTRAQ quantitative proteomic analysis, which was used in mixed culture for the first time, showed that magnetite induced the changes of protein expression levels involved in various pathways during the methanation of propionate. The up-regulation of proteins involved in propionate metabolism were found, and they were mainly originated from propionate-oxidizing bacteria which were not reported to be capable of direct interspecies electron transfer until now. Cytochrome c oxidase was also revealed as the possible protein relating with direct interspecies electron transfer considering its up-regulation with the addition of magnetite and origination from Thauera. Most of the up-regulated proteins in methane metabolism were originated from Methanosaeta, while most of the enzymes with down-regulated proteins were originated from Methanosarcina. However, the up-regulated proteins relating with hydrogenotrophic methanogenesis were originated from neither Methanosaeta nor Methanosarcina, indicating they were not involved in direct interspecies electron transfer. The hydrogenotrophic methanogens, e.g. Methanospirillum, Methanosphaerula et al., might be involved in direct interspecies electron transfer. Overall, the present study showed that both direct interspecies electron transfer and interspecies H₂ transfer were present during methanation of propionate facilitated by magnetite.

Global transcriptomic response of Anoxybacillus sp. SK 3-4 to aluminum exposure

Anoxybacillus sp. SK 3-4 is a Gram-positive, rod-shaped bacterium and a member of family Bacillaceae. We had previously reported that the strain is an aluminum resistant thermophilic bacterium. This is the first report to provide a detailed analysis of the global transcriptional response of Anoxybacillus when the cells were exposed to 600 mg L^-1 of aluminum. The transcriptome was sequenced using Illumina MiSeq sequencer. Total of 708 genes were differentially expressed (fold change >2.00) with 316 genes were up-regulated while 347 genes were down-regulated, in comparing to control with no aluminum added in the culture. Based on Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, the majority of genes encoding for cell metabolism such as glycolysis, sulfur metabolism, cysteine and methionine metabolism were up-regulated; while most of the gene associated with tricarboxylic acid cycle (TCA cycle) and valine, leucine and isoleucine metabolism were down-regulated. In addition, a significant number of the genes encoding ABC transporters, metal ions transporters, and some stress response proteins were also differentially expressed following aluminum exposure. The findings provide further insight and help us to understand on the resistance of Anoxybacillus sp. SK 3-4 toward aluminium.

Toxicity of dissolved and precipitated aluminium to marine diatoms

Localised aluminium contamination can lead to high concentrations in coastal waters, which have the potential for adverse effects on aquatic organisms. This research investigated the toxicity of 72-h exposures of aluminium to three marine diatoms (Ceratoneis closterium (formerly Nitzschia closterium), Minutocellus polymorphus and Phaeodactylum tricornutum) by measuring population growth rate inhibition and cell membrane damage (SYTOX Green) as endpoints. Toxicity was correlated to the time-averaged concentrations of different aluminium size-fractions, operationally defined as <0.025μm filtered, <0.45μm filtered (dissolved) and unfiltered (total) present in solution over the 72-h bioassay. The chronic population growth rate inhibition after aluminium exposure varied between diatom species. C. closterium was the most sensitive species (10% inhibition of growth rate (72-h IC10) of 80 (55-100)μg Al/L (95% confidence limits)) while M. polymorphus (540 (460-600)μg Al/L) and P. tricornutum (2100 (2000-2200)μg Al/L) were less sensitive (based on measured total aluminium). Dissolved aluminium was the primary contributor to toxicity in C. closterium, while a combination of dissolved and precipitated aluminium forms contributed to toxicity in M. polymorphus. In contrast, aluminium toxicity to the most tolerant diatom P. tricornutum was due predominantly to precipitated aluminium. Preliminary investigations revealed the sensitivity of C. closterium and M. polymorphus to aluminium was influenced by initial cell density with aluminium toxicity significantly (p<0.05) increasing with initial cell density from 10(3) to 10(5)cells/mL. No effects on plasma membrane permeability were observed for any of the three diatoms suggesting that mechanisms of aluminium toxicity to diatoms do not involve compromising the plasma membrane. These results indicate that marine diatoms have a broad range in sensitivity to aluminium with toxic mechanisms related to both dissolved and precipitated aluminium.