Comparative Shotgun Proteomic Analysis of Wastewater-Cultured Microalgae: Nitrogen Sensing and Carbon Fixation for Growth and Nutrient Removal in Chlamydomonas reinhardtii

Key Proteomics Tools for Fundamental and Applied Microalgal Research

Microscopic, photosynthetic prokaryotes and eukaryotes, collectively referred to as microalgae, are widely studied to improve our understanding of key metabolic pathways (e.g., photosynthesis) and for the development of biotechnological applications. Omics technologies, which are now common tools in biological research, have been shown to be critical in microalgal research. In the past decade, significant technological advancements have allowed omics technologies to become more affordable and efficient, with huge datasets being generated. In particular, where studies focused on a single or few proteins decades ago, it is now possible to study the whole proteome of a microalgae. The development of mass spectrometry-based methods has provided this leap forward with the high-throughput identification and quantification of proteins. This review specifically provides an overview of the use of proteomics in fundamental (e.g., photosynthesis) and applied (e.g., lipid production for biofuel) microalgal research, and presents future research directions in this field.

Algae: a frontline photosynthetic organism in the microplastic catastrophe

Recalcitrancy in microplastics (MPs) contributes to white pollution. Bioremediation can remove MPs and facilitate environmental sustainability. Although recent studies have been conducted on the interaction of algae and MPs, the role of algae in MP removal with the simultaneous implementation of 'omics studies has not yet been discussed. Here, we review the adverse effects of MPs on the environment and possible approaches to remove them from the aquatic environment by using algae. We highlight the mechanism of MP biodegradation, the algal species that have been used, and how these are affected by MPs. We propose that algomics, characterization of biodegrading enzymes, and genetic engineering could be effective strategies for optimizing MP degradation.

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.

Multi-omics approaches and genetic engineering of metabolism for improved biorefinery and wastewater treatment in microalgae

Microalgae, a group of photosynthetic microorganisms rich in diverse and novel bioactive metabolites, have been explored for the production of biofuels, high value-added compounds as food and feeds, and pharmaceutical chemicals as agents with therapeutic benefits. This article reviews the development of omics resources and genetic engineering techniques including gene transformation methodologies, mutagenesis, and genome-editing tools in microalgae biorefinery and wastewater treatment. The introduction of these enlisted techniques has simplified the understanding of complex metabolic pathways undergoing microalgal cells. The multiomics approach of the integrated omics datasets, big data analysis, and machine learning for the discovery of objective traits and genes responsible for metabolic pathways was reviewed. Recent advances and limitations of multiomics analysis and genetic bioengineering technology to facilitate the improvement of microalgae as the dual role of wastewater treatment and biorefinery feedstock production are discussed. This article is protected by copyright. All rights reserved.

Microalgae-based technology for antibiotics removal: From mechanisms to application of innovational hybrid systems

Antibiotics contamination is an emerging environmental concern, owing to its potential risks to ecosystems and human health. Microalgae-based technology has been widely reported as a promising alternative to conventional wastewater treatment, since it is a solar-power driven, ecologically friendly, cost-effective, and sustainable reclamation strategy. This review provides fundamental insights into the major mechanisms underpinning microalgae-based antibiotics removal, including bioadsorption, bioaccumulation, and biodegradation. The critical role of extracellular polymeric substances on bioadsorption and extracellular biodegradation of antibiotics are also covered. Moreover, this review sheds light on the important factors affecting the removal of antibiotics by microalgae, and summarizes several novel approaches to improve the removal efficiency, including acclimation, co-metabolism and microbial consortium. Besides, hybrid systems (such as, microalgae-based technologies combined with the conventional activated sludge, advanced oxidation processes, constructed wetlands, and microbial fuel cells), and genetic engineering are also recommended, which will be feasible for enhanced removal of antibiotics. Finally, this review also highlights the need for further studies aimed at optimizing microalgae-based technology, with emphasis on improving performance and expanding its application in large-scale settings, especially in terms of technical, environmental-friendly and economically competitiveness. Overall, this review summarizes current understanding on microalgae-based technologies for removal of antibiotics and outlines future research directions.

Color-Specific Recovery to Extreme High-Light Stress in Plants

Plants pigments, such as chlorophyll and carotenoids, absorb light within specific wavelength ranges, impacting their response to environmental light changes. Although the color-specific response of plants to natural levels of light is well described, extreme high-light stress is still being discussed as a general response, without considering the impact of wavelengths in particular response processes. In this study, we explored how the plant proteome coordinated the response and recovery to extreme light conditions (21,000 µmol m^-2 s^-1) under different wavelengths. Changes at the protein and mRNA levels were measured, together with the photosynthetic parameters of plants under extreme high-light conditions. The changes in abundance of four proteins involved in photoinhibition, and in the biosynthesis/assembly of PSII (PsbS, PsbH, PsbR, and Psb28) in both light treatments were measured. The blue-light treatment presented a three-fold higher non-photochemical quenching and did not change the level of the oxygen-evolving complex (OEC) or the photosystem II (PSII) complex components when compared to the control, but significantly increased psbS transcripts. The red-light treatment caused a higher abundance of PSII and OEC proteins but kept the level of psbS transcripts the same as the control. Interestingly, the blue light stimulated a more efficient energy dissipation mechanism when compared to the red light. In addition, extreme high-light stress mechanisms activated by blue light involve the role of OEC through increasing PsbS transcript levels. In the proteomics spatial analysis, we report disparate activation of multiple stress pathways under three differently damaged zones as the enriched function of light stress only found in the medium-damaged zone of the red LED treatment. The results indicate that the impact of extreme high-light stress on the proteomic level is wavelength-dependent.

Insights into upstream processing of microalgae: A review

The aim of this review is to provide insights into the upstream processing of microalgae, and to highlight the advantages of each step. This review discusses the most important steps of the upstream processing in microalgae research such as cultivation modes, photobioreactors design, preparation of culture medium, control of environmental factors, supply of microalgae seeds and monitoring of microalgal growth. An extensive list of bioreactors and their working volumes used, elemental composition of some well-known formulated cultivation media, different types of wastewater used for microalgal cultivation and environmental variables studied in microalgae research has been compiled in this review from the vast literature. This review also highlights existing challenges and knowledge gaps in upstream processing of microalgae and future research needs are suggested.

Omics approaches for microalgal applications: Prospects and challenges

In recent impetus of phycological research, microalgae have emerged as a potential candidate for various arena of application-driven research. Omics-based tactics are used for disentangling the regulation and network integration for biosynthesis/degradation of metabolic precursors, intermediates, end products, and identifying the networks that regulate the metabolic flux. Multi-omics coupled with data analytics have facilitated understanding of biological processes and allow ample access to diverse metabolic pathways utilized for genetic manipulations making microalgal factories more efficient. The present review discusses state-of-art "Algomics" and the prospect of microalgae and their role in symbiotic association by using omics approaches including genomics, transcriptomics, proteomics and metabolomics. Microalgal based uni- and multi-omics approaches are critically analyzed in wastewater treatment, metal toxicity and remediation, biofuel production, and therapeutics to provide an imminent outlook for an array of environmentally sustainable and economically viable microalgal applications.

Large Scale Proteomic Data and Network-Based Systems Biology Approaches to Explore the Plant World

The investigation of plant organisms by means of data-derived systems biology approaches based on network modeling is mainly characterized by genomic data, while the potential of proteomics is largely unexplored. This delay is mainly caused by the paucity of plant genomic/proteomic sequences and annotations which are fundamental to perform mass-spectrometry (MS) data interpretation. However, Next Generation Sequencing (NGS) techniques are contributing to filling this gap and an increasing number of studies are focusing on plant proteome profiling and protein-protein interactions (PPIs) identification. Interesting results were obtained by evaluating the topology of PPI networks in the context of organ-associated biological processes as well as plant-pathogen relationships. These examples foreshadow well the benefits that these approaches may provide to plant research. Thus, in addition to providing an overview of the main-omic technologies recently used on plant organisms, we will focus on studies that rely on concepts of module, hub and shortest path, and how they can contribute to the plant discovery processes. In this scenario, we will also consider gene co-expression networks, and some examples of integration with metabolomic data and genome-wide association studies (GWAS) to select candidate genes will be mentioned.

Microalgae: a robust "green bio-bridge" between energy and environment

Microalgae are a potential candidate for biofuel production and environmental treatment because of their specific characteristics (e.g. fast growth, carbon neutral, and rich lipid accumulations). However, several primary bottlenecks still exist in current technologies, including low biomass conversion efficiency, bio-invasion from the external environment, limited or costly nutrient sources, and high energy and capital input for harvest, and stalling its industrial progression. Coupling biofuel production with environmental treatment renders microalgae a more feasible feedstock. This review focuses on microalgae biotechnologies for both bioenergy generation and environmental treatment (e.g. CO₂ sequestration and wastewater reclamation). Different intelligent technologies have been developed, especially during the last decade, to eliminate the bottlenecks, including mixotrophic/heterotrophic cultivation, immobilization, and co-cultivation. It has been realized that any single purpose for the cultivation of microalgae is not an economically feasible option. Combinations of applications in biorefineries are gradually reckoned to be necessary as it provides more economically feasible and environmentally sustainable operations. This presents microalgae as a special niche occupier linking the fields of energy and environmental sciences and technologies. The integrated application of microalgae is also proven by most of the life-cycle analysis studies. This study summarizes the latest development of primary microalgal biotechnologies in the two areas that will bring researchers a comprehensive view towards industrialization with an economic perspective.