In situ monitoring of chlorophyll a fluorescence in Nannochloropsis oceanica cultures to assess photochemical changes and the onset of lipid accumulation during nitrogen deprivation

Remodeling of the 3D chromatin architecture in the marine microalga Nannochloropsis oceanica during lipid accumulation

BACKGROUND

Genomic three-dimensional (3D) spatial organization plays a key role in shaping gene expression and associated chromatin modification, and it is highly sensitive to environmental stress conditions. In microalgae, exposure to nitrogen stress can drive lipid accumulation, yet the associated functional alterations in the spatial organization of the microalgal genome have yet to be effectively characterized.

RESULTS

Accordingly, the present study employed RNA-seq, Hi-C, and ChIP-seq approaches to explore the relationship between 3D chromosomal architecture and gene expression during lipid accumulation in the marine microalga Nannochloropsis oceanica in response to nitrogen deprivation (ND). These analyses revealed that ND resulted in various changes in chromosomal organization, including A/B compartment transitions, topologically associating domain (TAD) shifts, and the disruption of short-range interactions. Significantly higher levels of gene expression were evident in A compartments and TAD boundary regions relative to B compartments and TAD interior regions, consistent with observed histone modification enrichment in these areas. ND-induced differentially expressed genes (DEGs) were notably enriched in altered TAD-associated regions and regions exhibiting differential genomic contact. These DEGs were subjected to Gene Ontology (GO) term analyses that indicated they were enriched in the 'fatty acid metabolism', 'response to stress', 'carbon fixation' and 'photosynthesis' functional categories, in line with the ND treatment conditions used to conduct this study. These data indicate that Nannochloropsis cells exhibit a clear association between chromatin organization and transcriptional activity under nitrogen stress conditions. Pronounced and extensive histone modifications were evident in response to ND. Observed changes in chromatin architecture were linked to shifts in histone modifications and gene expression.

CONCLUSIONS

Overall, the reprogramming of many lipid metabolism-associated genes was evident under nitrogen stress conditions with respect to both histone modifications and chromosomal organization. Together these results revealed that higher-order chromatin architecture represents a new layer that can guide efforts to understand the transcriptional regulation of lipid metabolism in nitrogen-deprived microalgae.

On-Line Monitoring of Biological Parameters in Microalgal Bioprocesses Using Optical Methods

Microalgae are promising sources of fuels and other chemicals. To operate microalgal cultivations efficiently, process control based on monitoring of process variables is needed. On-line sensing has important advantages over off-line and other analytical and sensing methods in minimizing the measurement delay. Consequently, on-line, in-situ sensors are preferred. In this respect, optical sensors occupy a central position since they are versatile and readily implemented in an on-line format. In biotechnological processes, measurements are performed in three phases (gaseous, liquid and solid (biomass)), and monitored process variables can be classified as physical, chemical and biological. On-line sensing technologies that rely on standard industrial sensors employed in chemical processes are already well-established for monitoring the physical and chemical environment of an algal cultivation. In contrast, on-line sensors for the process variables of the biological phase, whether biomass, intracellular or extracellular products, or the physiological state of living cells, are at an earlier developmental stage and are the focus of this review. On-line monitoring of biological process variables is much more difficult and sometimes impossible and must rely on indirect measurement and extensive data processing. In contrast to other recent reviews, this review concentrates on current methods and technologies for monitoring of biological parameters in microalgal cultivations that are suitable for the on-line and in-situ implementation. These parameters include cell concentration, chlorophyll content, irradiance, and lipid and pigment concentration and are measured using NMR, IR spectrophotometry, dielectric scattering, and multispectral methods. An important part of the review is the computer-aided monitoring of microalgal cultivations in the form of software sensors, the use of multi-parameter measurements in mathematical process models, fuzzy logic and artificial neural networks. In the future, software sensors will play an increasing role in the real-time estimation of biological variables because of their flexibility and extendibility.

Impact of Light Stress on the Synthesis of Both Antioxidants Polyphenols and Carotenoids, as Fast Photoprotective Response in Chlamydomonas reinhardtii: New Prospective for Biotechnological Potential of This Microalga

The aim of this study was to investigate the potential role of the microalga Chlamydomonas reinhardtii as an antioxidant source of enriched biomass. This microalga is a model organism deeply investigated for physiological studies, particularly considering carotenoid synthesis in response to stress, to counteract the effects of the formation of free radicals. Less attention has been paid to the profile characterization of other antioxidant compounds, such as polyphenols, which can be synthesized, concomitantly with carotenoids, under photooxidative stress, especially high light. The cultures of C. reinhardtii were exposed to three different light intensities, 70, 800 and 1500 µmoles photons m−2 s−1. The increasing light intensity symmetrically induced the increasing accumulation of both carotenoids and phenolic compounds. The results showed that exposure to high light intensities caused the accumulation of electrons in the electron transport chain, with a reduction in photosynthetic activity. In the same cultures, high light intensity induced the strong increment of polyphenols such as gallic, chlorogenic and coumaric acids, which resulted 6.2-fold, 4-fold and 3.7-fold higher, respectively, than in cells exposed to the lowest intensities. As expected, at the highest light intensity, the strong induction of the xanthophyll cycle and the largest increment of loroxanthin, lutein, α-carotene and ß-carotene could be detected. Antioxidant properties doubled with respect to the initial time, both in acetone and methanol cellular extracts of these cultures, revealing a new potential role for biotechnological application of this microalga.