Photosynthetic physiological performance and proteomic profiling of the oleaginous algae Scenedesmus acuminatus reveal the mechanism of lipid accumulation under low and high nitrogen supplies

Environmental Proteomics Elucidates Phototrophic Biofilm Responses to Ornamental Lighting on Stone-built Heritage

Recent studies are showing that some lights suitable for illuminating the urban fabric (i.e. that do not include the red, green and blue sets of primary colours) may halt biological colonisation on monuments, mainly that caused by phototrophic subaerial biofilms (SABs), which may exacerbate the biodeterioration of substrates. However, the light-triggered mechanisms that cause changes in the growth of the phototrophs remain unknown. Environmental proteomics could be used to provide information about the changes in the SAB metabolism under stress inflicted by nocturnal lighting. Here, laboratory-produced SABs, composed of Chlorophyta, Streptophyta and Cyanobacteriota, were subjected to three types of lighting used for monuments: cool white, warm white and amber + green (potentially with a biostatic effect). A control without light (i.e. darkness) was also included for comparison. The nocturnal lighting impaired the capacity of the SABs to decompose superoxide radicals and thus protect themselves from oxidative stress. Cool white and warm white light both strongly affected the proteomes of the SABs and reduced the total peptide content, with the extent of the reduction depending on the genera of the organisms involved. Analysis of the photo-damaging effect of amber + green light on the biofilm metabolism revealed a negative impact on photosystems I and II and production of photosystem antenna protein-like, as well as a triggering effect on protein metabolism (synthesis, folding and degradation). This research provides, for the first-time, a description of the proteomic changes induced by lighting on SABs colonising illuminated monuments in urban areas.

Composition of carbohydrate, protein and lipid derived from microalgae using thermally pretreated solid waste

Microalgae are widely recognized for their capacity to generate value-added products in a variety of sectors, including the pharmaceutical and food industries, bioenergy industries and wastewater industries. The quality of a microalga is significantly influenced by its proliferation. Along with growth, the biochemical profile may also vary based on the nutrient that is supplemented. The majority of the supplemented nutrients utilized are not in a functional state, as they are typically extracted in liquid form or pretreated prior to use. Parallel to numerous commonly applied pretreatment processes, including chemical, mechanical and biological, thermal pretreatment appears to receive less attention. Hence it is crucial to comprehend the potential for thermal pretreatment as well as its mechanism in militating the solid waste to release additional nutrients in order to enhance the biochemical profile of microalgae. The current review takes a closer look at the impact of various thermal pretreatments on solid waste on influencing microalgal performance in terms of their overall biochemical profiles such as carbohydrates, proteins and lipids. This approach is likely to enhance the circular economy by utilizing waste products and effectively closing the loop on waste. © 2024 Society of Chemical Industry.

Mixotrophic growth of a ubiquitous marine diatom

Diatoms are major players in the global carbon cycle, and their metabolism is affected by ocean conditions. Understanding the impact of changing inorganic nutrients in the oceans on diatoms is crucial, given the changes in global carbon dioxide levels. Here, we present a genome-scale metabolic model (iMK1961) for Cylindrotheca closterium, an in silico resource to understand uncharacterized metabolic functions in this ubiquitous diatom. iMK1961 represents the largest diatom metabolic model to date, comprising 1961 open reading frames and 6718 reactions. With iMK1961, we identified the metabolic response signature to cope with drastic changes in growth conditions. Comparing model predictions with Tara Oceans transcriptomics data unraveled C. closterium's metabolism in situ. Unexpectedly, the diatom only grows photoautotrophically in 21% of the sunlit ocean samples, while the majority of the samples indicate a mixotrophic (71%) or, in some cases, even a heterotrophic (8%) lifestyle in the light. Our findings highlight C. closterium's metabolic flexibility and its potential role in global carbon cycling.

Influence of Drought Stress on the Rhizosphere Bacterial Community Structure of Cassava (Manihot esculenta Crantz)

Drought presents a significant abiotic stress that threatens crop productivity worldwide. Rhizosphere bacteria play pivotal roles in modulating plant growth and resilience to environmental stresses. Despite this, the extent to which rhizosphere bacteria are instrumental in plant responses to drought, and whether distinct cassava (Manihot esculenta Crantz) varieties harbor specific rhizosphere bacterial assemblages, remains unclear. In this study, we measured the growth and physiological characteristics, as well as the physical and chemical properties of the rhizosphere soil of drought-tolerant (SC124) and drought-sensitive (SC8) cassava varieties under conditions of both well-watered and drought stress. Employing 16S rDNA high-throughput sequencing, we analyzed the composition and dynamics of the rhizosphere bacterial community. Under drought stress, biomass, plant height, stem diameter, quantum efficiency of photosystem II (Fv/Fm), and soluble sugar of cassava decreased for both SC8 and SC124. The two varieties' rhizosphere bacterial communities' overall taxonomic structure was highly similar, but there were slight differences in relative abundance. SC124 mainly relied on Gamma-proteobacteria and Acidobacteriae in response to drought stress, and the abundance of this class was positively correlated with soil acid phosphatase. SC8 mainly relied on Actinobacteria in response to drought stress, and the abundance of this class was positively correlated with soil urease and soil saccharase. Overall, this study confirmed the key role of drought-induced rhizosphere bacteria in improving the adaptation of cassava to drought stress and clarified that this process is significantly related to variety.

Growth and productivity of Haematococcus pluvialis and Coelastrella saipanensis by photosystem modulation for understanding the heterotrophic nutritional strategy for bioremediation application

In this study, Haematococcus pluvialis and Coelastrella saipanensis were evaluated for heterotrophic nutrition potential in dairy waste medium by blocking the PSII using DCMU. The study was done by four sets of experiments. In the first set, in the different concentrations DCMU-treatments, 20μL showed pronounced effect in H. pluvialis and C. saipanensis as 89 % and 83% decrease in cells (>30 and > 250 cells/mL) compared to control (536 ± 12.35 × 104 and 1167 ± 15.35 × 104 cells/mL, respectively). Damage to the PS II by DCMU interrupted the growth, which in turn produced a significant drop in the number of cells. In the second round of experiment, growth of algae in various dairy waste concentrations suggest that dairy wastewater (DWW) provides enough nutrients to produce 35.71 % and 64.74 % more cells in H. pluvialis and C. saipanensis, respectively compared to the control. In the third set, high DCMU concentration was added to microalgae cultures in DWW to assess the heterotrophic nutrition potential. Growth in cell number 34.4 ± 19 and 617.46 ± 60.44 cells/mL was recorded in H. pluvialis and C. saipanensis when grown control medium whereas addition of DCMU reduced the cell number to 1.53 ± 0.75 and 55.13 ± 0.75 cells/mL on 15th day, respectively. This shows cells in cultures treated with DCMU reveal that algae can sustain their metabolic activity by utilizing the nutrients of dairy waste inhibiting photosystem. Fourth round of experiments found that microalgae could resume their growth and productivity by adapting to heterotrophic nutritional behaviour when DCMU given in mild dose at different time interval. This study conclude as C. saipanensis grows more readily by absorbing dairy waste nutrients than H. pluvialis. Therefore, C. saipanensis is an excellent choice for wastewater treatment through sustainable environmentally benign process after scale-up investigation. These results provide useful information to advance to molecular study for measuring microalgae's capability for bioremediation application.

Panoptic elucidation of algicidal mechanism of Raoultella sp. S1 against the Microcystis aeruginosa by TMT quantitative proteomics

Harmful algal blooms (HABs) due to eutrophication are becoming a serious ecological disaster worldwide, threatening human health and the optimal balance of aquatic ecosystems. The traditional approaches to eradicate HABs yield several drawbacks in practical application, while microbial algicidal technology is garnering mounting recognition due to its high efficiency, eco-friendliness, and low cost. In our previous study, we isolated a bacterium strain Raoultella sp. S1 from eutrophic water with high efficiency of algicidal properties. This study further investigated the flocculation and inactivation efficiency of S1 on Microcystis aeruginosa at different eutrophic stages by customizing the algal cell densities. The supernatant extract of S1 strain exhibited remarkable flocculation and inactivation effects against low (1 × 106 cell/mL)and medium (2.7 × 106 cell/mL)concentrations of algal cells, but unexceptional for higher densities. The results further revealed that algal cells at low and medium counts manifested a more apparent antioxidant defense response, while the photosynthetic efficiency and relative electron transport rate were considerably reduced within 24 h. TEM observations confirmed the disruption of thylakoid membranes and cell structure of algal cells by algicidal substances. Moreover, TMT proteomics revealed alterations in protein metabolic pathways of algal cells during the flocculation and lysis stages at the molecular biological level. This signified that the disruption of the photosynthetic system is the core algicidal mechanism of S1 supernatant. In contrast, the photosynthetic metabolic pathways in the HABs were significantly upregulated, increasing the energy supply for the NADPH dehydrogenation process and the upregulation of ATPases in oxidative phosphorylation. Insufficient energy provided by NADPH resulted in a dwindled electron transport rate, stagnation of carbon fixation in dark reactions, and blockage of light energy conversion into chemical energy. Nonetheless, carbohydrate metabolism (gluconeogenesis and glycolysis) proteins were down-regulated and hampered DNA replication and repair. This study aided in unveiling the bacterial management of eutrophication by Raoultella sp. S1 and further arrayed the proteomic mechanism of algal apoptosis.

Proteomic analysis reveals mechanisms of mixed wastewater with different N/P ratios affecting the growth and biochemical characteristics of Chlorella pyrenoidosa

Effects of different nutrient ratios on the biochemical compositions of microalgae and the changes were rarely studied at the molecular level. In this study, the impacts of various nitrogen to phosphorus (N/P) ratios on growing of C. pyrenoidosa, as well as biochemical compositions and the metabolic regulation mechanism in mixed sewage, were investigated. The results suggested that 18 was optimal N/P ratio, while the dry weight (1.0 g/L), chlorophyll-a (Chla) (3.63 mg/L), and lipid production (0.28 g/L) were all the highest comparing with other groups. In contrast, the protein production (0.37 g/L) was the least. The nature of the regulatory mechanisms inthe metabolic pathways of these biochemical compositions was revealed by proteomic results, and there were 62 different expression proteins (DEPs) taken part in fatty acid and lipid biosynthesis metabolism (FA), amino acid biosynthesis metabolism (AA), photosynthesis (PHO), carbon fixation in photosynthetic organisms (CFP), and central carbon metabolism (CCM).

Insights into the genetic and metabolic engineering approaches to enhance the competence of microalgae as biofuel resource: A review

Conventional fuel resources are overburden with speedy global energy demand which ensued the urgent need of alternate energy resources. Biofuel generation efficiency of microalgae is notable due to their comparatively rapid biomass production rate and high oil content. But, the employment of microalgae as biofuel resource is in infancy due to low productivity and high production cost. The issues can be addressed by employing engineered microalgal strains that would be able to efficiently generate enhanced levels of biomass with augmented lipid and/or carbohydrate content for proficient biofuel production. Genetic alterations and metabolic engineering of microalgal species might be helpful in developing high stress-tolerant strains with improved properties for biofuel generation. Various omics approaches appeared significant to upgrade the microalgal lipid production. Intervention of genetic and metabolic engineering approaches would facilitate the development of microalgae as a competent biofuel resource and inflate the economic commercialization of biofuels.

Acclimation to a broad range of nitrate strength on a euryhaline marine microalga Tetraselmis subcordiformis for photosynthetic nitrate removal and high-quality biomass production

Industrial wastewaters usually possess a wide range of nitrate strength. Microalgae-based nitrate-rich wastewater treatment could realize nitrate recovery along with CO₂ sequestration for sustainable biomass production, but the low tolerance of the microalgal strains to high-strength nitrate restricted the treatment process. The present study comprehensively evaluated a euryhaline marine microalga Tetraselmis subcordiformis for photosynthetic nitrate removal and biomass production in synthetic wastewater with a broad range of nitrate strength (0.24-7.0 g NO₃^--N/L). This alga could acclimate to high nitrate strength up to 3.5 g NO₃^--N/L (HN) without compromising biomass production. Nitrate could be completely removed within four days when low nitrate (0.24 g NO₃^--N/L, LN) was loaded. The maximum nitrate removal rate of 331 mg N/L/day and specific nitrate removal rate of 360 mg N/day/g cell was obtained under medium nitrate condition (1.8 g NO₃^--N/L, MN). High-nitrate stress under 7.0 g NO₃^--N/L (SHN) caused an increased light energy dissipation while decreased the density of photosystem II active reaction center, which partially protect the cells from photodamage and contributed to their acclimation to SHN. The algae also enhanced amino acid/fatty acid proportions essential for maintaining intracellular redox states to cope with the stress caused by LN or SHN. HN and SHN was in favor of protein accumulation and maintenance with enhanced proportion of essential amino acids, which entitled the algal biomass to be of high quality for animal feed applied in livestock graziery and aquaculture. LN facilitated productive starch and lipid accumulation with good quality for biofuels production. The nitrate removal rate and biomass productivity exceeded most of the microalgae reported in literature under similar conditions, which highlighted Tetraselmis subcordiformis as a potent strain for flexible nitrate-rich wastewater remediation coupled with fast CO₂ bio-mitigation and high-quality biomass production for sustainable algal biorefinery.

Nutritional Profiling and Preliminary Bioactivity Screening of Five Micro-Algae Strains Cultivated in Northwest Europe

This study aimed to map the nutritional profile and bioactivities of five microalgae that can be grown in Northwest Europe or areas with similar cultivation conditions. Next to the biochemical composition, the in vitro digestibility of carbohydrates, proteins, and lipids was studied for Chlamydomonas nivalis, Porphyridium purpureum, Chlorella vulgaris, Nannochloropsis gaditana, and Scenedesmus species biomass. These microalgae were also assessed for their ability to inhibit the angiotensin-1-converting enzyme (ACE-1, EC 3.4.15.1), which is known to play a role in the control of blood pressure in mammals. Large differences in organic matter solubility after digestion suggested that a cell disruption step is needed to unlock the majority of the nutrients from N. gaditana and Scenedesmus species biomass. Significant amounts of free glucose (16.4–25.5 g glucose/100 g dry algae) were detected after the digestion of C. nivalis, P. purpureum, and disrupted Scenedesmus. The fatty acid profiles showed major variations, with particularly high Ω-3 fatty acid levels found in N. gaditana (5.5 ± 0.5 g/100 g dry algae), while lipid digestibility ranged from 33.3 ± 6.5% (disrupted N. gaditana) to 67.1 ± 11.2% (P. purpureum). C. vulgaris and disrupted N. gaditana had the highest protein content (45–46% of dry matter), a nitrogen solubility after digestion of 65–71%, and the degree of protein hydrolysis was determined as 31% and 26%, respectively. Microalgae inhibited ACE-1 by 73.4–87.1% at physiologically relevant concentrations compared to a commercial control. These data can assist algae growers and processors in selecting the most suitable algae species for food or feed applications.

Trophic Transition Enhanced Biomass and Lipid Production of the Unicellular Green Alga Scenedesmus acuminatus

Microalgal heterotrophic cultivation is an emerging technology that can enable producing high cell-density algal cell cultures, which can be coupled with photoautotrophic cultivation for valuable chemicals such as lipids manufacturing. However, how the heterotrophically grown algal cells respond to the lipid-inducing conditions has not been fully elucidated so far. In this study, when the heterotrophically grown Scenedesmus acuminatus cells were subjected to the high light (HL) and nitrogen-limited (NL) conditions, both the biomass and lipid productivity were enhanced as compared to that of the photoautotrophically grown counterparts. The chlorophyll a fluorometry analysis showed that the Fv/Fm and Y(II) of the heterotrophically grown cells subjected to the HL and NL conditions was recovered to the maximum value of 0.75 and 0.43, respectively, much higher than those of the photoautotrophically grown cells under the same stress conditions. Transcriptomic analysis revealed that heterotrophically grown cells fully expressed the genes coding for the photosystems proteins, including the key photoprotective proteins D1, PsbS, light-harvesting-complex (LHC) I and LHC II. Meanwhile, downregulation of the carotenoid biosynthesis and upregulation of the glycolysis/gluconeogenesis, tricarboxylic acid (TCA) cycle and oxidative phosphorylation pathways were observed when the heterotrophically grown cells were subjected to the HL and N-limited conditions for lipid production. It was deduced that regulation of these pathways not only enhanced the light utilization but also provided the reducing power and ATP by which the biomass accumulation was significantly elevated. Besides, upregulation of the acetyl-CoA carboxylase/biotin carboxylase, digalactosyl diacylglycerol synthase and diacylglycerol acyltransferase 2 encoding genes may be attributable to the enhanced lipid production. Understanding the cellular responses during the trophic transition process could guide improvement of the strength of trophic transition enhancing microalgal biomass and lipid production.

iTRAQ-based quantitative glutelin proteomic analysis reveals differentially expressed proteins in the physiological metabolism process during endosperm development and their impacts on yield and quality in autotetraploid rice

Autotetraploid rice, which is developed through chromosome set doubling using diploid rice, produces high-quality kernels that are rich in storage proteins. However, little information is available about the content of different proteins in autotetraploid rice and their proteomic analysis. The dynamic changes in four storage proteins, namely, albumin, globulin, prolamin, and glutelin, were analyzed in the endosperm of autotetraploid rice (AJNT-4x) and in that of its diploid counterpart (AJNT-2x) for comparison. The contents of the four proteins were all higher during endosperm development in AJNT-4x than in AJNT-2x, but their change and composition were almost the same in the two materials. Then, iTRAQ was employed to analyze the glutelin profiles of AJNT-4x and AJNT-2x at 10 DAF, 15 DAF, and 20 DAF. A total of 1326 proteins were identified in AJNT-4x and AJNT-2x using high-throughput LC-MS/MS. Among the 1326 identified proteins, there were 362 DEPs in AJNT-4x compared with AJNT-2x and 372 DEPs between different developmental stages in AJNT-4x. Eight important upregulated proteins were identified by qRT-PCR, including B8AM24, B8ARJ0, B8AQM6, A2ZCE6, and P37833. Among them, B8AM24 and B8ARJ0 were related to the lysine biosynthesis process. GO enrichment analysis revealed that the critical functions of DEPs exhibited little overlap between the 10, 15, and 20 DAF groups. Endosperm glutelin accumulation was regulated mainly by different DEPs during the early stage, and 15 DAF was a critical regulating point for glutelin accumulation. KEGG pathway analysis showed that ribosomal proteins were significantly higher in AJNT-4x than in AJNT-2x at 10 DAF, and protein processing, biosynthesis, and metabolism of amino acids were higher and more active in AJNT-4x at 15 DAF, while the peroxisome was richer in AJNT-4x at 20 DAF. The PPI network showed that ribosomal proteins gradually decreased with increasing endosperm development. These results provide new insights into dynamic glutelin expression differences during endosperm development in autotetraploid rice, which will aid in the development of rice cultivars with increased yield and improved grain nutritional quality.

Antioxidant Adjustments of Olive Trees (Olea Europaea) under Field Stress Conditions

Extreme climate events are increasingly frequent, and the 2017 summer was particularly critical in the Mediterranean region. Olive is one of the most important species of this region, and these climatic events represent a threat to this culture. However, it remains unclear how olive trees adjust the antioxidant enzymatic system and modulate the metabolite profile under field stress conditions. Leaves from two distinct adjacent areas of an olive orchard, one dry and the other hydrated, were harvested. Tree water status, oxidative stress, antioxidant enzymes, and phenolic and lipophilic metabolite profiles were analyzed. The environmental conditions of the 2017 summer caused a water deficit in olive trees of the dry area, and this low leaf water availability was correlated with the reduction of long-chain alkanes and fatty acids. Hydrogen peroxide (H₂O₂) and superoxide radical (O₂^•–) levels increased in the trees collected from the dry area, but lipid peroxidation did not augment. The antioxidant response was predominantly marked by guaiacol peroxidase (GPOX) activity that regulates the H₂O₂ harmful effect and by the action of flavonoids (luteolin-7-O-glucuronide) that may act as reactive oxygen species scavengers. Secoiridoids adjustments may also contribute to stress regulation. This work highlights for the first time the protective role of some metabolite in olive trees under field drought conditions.

Photosynthetic performance and photosynthesis-related gene expression coordinated in a shade-tolerant species Panax notoginseng under nitrogen regimes

BACKGROUND

Nitrogen (N) is an essential component of photosynthetic apparatus. However, the mechanism that photosynthetic capacity is suppressed by N is not completely understood. Photosynthetic capacity and photosynthesis-related genes were comparatively analyzed in a shade-tolerant species Panax notoginseng grown under the levels of low N (LN), moderate N (MN) and high N (HN).

RESULTS

Photosynthetic assimilation was significantly suppressed in the LN- and HN-grown plants. Compared with the MN-grown plants, the HN-grown plants showed thicker anatomic structure and larger chloroplast accompanied with decreased ratio of mesophyll conductance (gm) to Rubisco content (gm/Rubisco) and lower Rubisco activity. Meanwhile, LN-grown plants displayed smaller chloroplast and accordingly lower internal conductance (gi). LN- and HN-grown individuals allocated less N to light-harvesting system (NL) and carboxylation system (NC), respectively. N surplus negatively affected the expression of genes in Car biosynthesis (GGPS, DXR, PSY, IPI and DXS). The LN individuals outperformed others with respect to non-photochemical quenching. The expression of genes (FBA, PGK, RAF2, GAPC, CAB, PsbA and PsbH) encoding enzymes of Calvin cycle and structural protein of light reaction were obviously repressed in the LN individuals, accompanying with a reduction in Rubisco content and activity. Correspondingly, the expression of genes encoding RAF2, RPI4, CAB and PetE were repressed in the HN-grown plants.

CONCLUSIONS

LN-induced depression of photosynthetic capacity might be caused by the deceleration on Calvin cycle and light reaction of photosynthesis, and HN-induced depression of ones might derive from an increase in the form of inactivated Rubisco.

Integration of proteome and transcriptome refines key molecular processes underlying oil production in Nannochloropsis oceanica

BACKGROUND

Under nitrogen deficiency situation, Nannochloropsis spp. accumulate large amounts of lipids in the form of triacylglycerides (TAG). Mechanisms of this process from the perspective of transcriptome and metabolome have been obtained previously, yet proteome analysis is still sparse which hinders the analysis of dynamic adaption to nitrogen deficiency. Here, proteomes for 3 h, 6 h, 12 h, 24 h, 48 h and 10th day of nitrogen deplete (N-) and replete (N+) conditions were obtained and integrated with previous transcriptome data for N. oceanica.

RESULTS

Physiological adaptations to N- not apparent from transcriptome data were unveiled: (a) abundance of proteins related to photosynthesis only slightly decreased in the first 48 h, indicating that photosynthesis is still working efficiently, and protein amounts adjust gradually with reduction in chloroplast size. (b) Most proteins related to the TCA cycle were strongly upregulated after 48 h under N-, suggesting that respiration is enhanced after 48 h and that TCA cycle efflux supports the carbon required for lipid synthesis. (c) Proteins related to lipid accumulation via the Kennedy pathway increased their abundance at 48 h, synchronous with the previously reported diversification of fatty acids after 48 h.

CONCLUSIONS

This study adds a proteome perspective on the major pathways for TAG accumulation in Nannochloropsis spp. Temporal changes of proteome exhibited distinct adaptation phases that are usually delayed relative to transcriptomic responses. Notably, proteome data revealed that photosynthesis and carbon fixation are still ongoing even after 48 h of N-. Moreover, sometimes completely opposite trends in proteome and transcriptome demonstrate the relevance of underexplored post-transcriptional regulation for N- adaptation.