Engineering salt tolerance of photosynthetic cyanobacteria for seawater utilization

Improving salt-tolerant artificial consortium of Bacillus amyloliquefaciens for bioconverting food waste to lipopeptides

High-salt content in food waste (FW) affects its resource utilization during biotransformation. In this study, adaptive laboratory evolution (ALE), gene editing, and artificial consortia were performed out to improve the salt-tolerance of Bacillus amyloliquefaciens for producing lipopeptide under FW and seawater. High-salt stress significantly decreased lipopeptide production in the B. amyloliquefaciens HM618 and ALE strains. The total lipopeptide production in the recombinant B. amyloliquefaciens HM-4KSMSO after overexpressing the ion transportor gene ktrA and proline transporter gene opuE and replacing the promoter of gene mrp was 1.34 times higher than that in the strain HM618 in medium containing 30 g/L NaCl. Lipopeptide production under salt-tolerant consortia containing two strains (HM-4KSMSO and Corynebacterium glutamicum) and three-strains (HM-4KSMSO, salt-tolerant C. glutamicum, and Yarrowia lipolytica) was 1.81- and 2.28-fold higher than that under pure culture in a medium containing FW or both FW and seawater, respectively. These findings provide a new strategy for using high-salt FW and seawater to produce value-added chemicals.

Culture-free identification of fast-growing cyanobacteria cells by Raman-activated gravity-driven encapsulation and sequencing

By directly converting solar energy and carbon dioxide into biobased products, cyanobacteria are promising chassis for photosynthetic biosynthesis. To make cyanobacterial photosynthetic biosynthesis technology economically feasible on industrial scales, exploring and engineering cyanobacterial chassis and cell factories with fast growth rates and carbon fixation activities facing environmental stresses are of great significance. To simplify and accelerate the screening for fast-growing cyanobacteria strains, a method called Individual Cyanobacteria Vitality Tests and Screening (iCyanVS) was established. We show that the 13C incorporation ratio of carotenoids can be used to measure differences in cell growth and carbon fixation rates in individual cyanobacterial cells of distinct genotypes that differ in growth rates in bulk cultivations, thus greatly accelerating the process screening for fastest-growing cells. The feasibility of this approach is further demonstrated by phenotypically and then genotypically identifying individual cyanobacterial cells with higher salt tolerance from an artificial mutant library via Raman-activated gravity-driven encapsulation and sequencing. Therefore, this method should find broad applications in growth rate or carbon intake rate based screening of cyanobacteria and other photosynthetic cell factories.

Trophic status determination of the Egyptian Eastern Mediterranean Sea based on phytoplankton diversity and their biochemical contents

The present study attempted to test the applicability of using phytoplankton as a bioindicator for assessing water quality along the Eastern Alexandria coast, Egypt. Eight stations were selected to cover the different characteristics of seawater during the summer 2022. Six algal groups were detected in different ratios: Bacillariophyceae, Cyanophyceae, Dinophyceae, Chlorophyceae, Silicoflagellata, and Euglenophyceae. Phytoplankton abundance was found highest at the Port Said (PS) beach, and the lowest abundance was detected at Ras El Bar (RB) beach. According to the evaluation of phytoplankton abundance, all the studied stations are oligotrophic state except PS was eutrophic. Based on Chl a concentration, the selected stations could be described as good-bad from west to east. The Shannon diversity and Pielou evenness indexes classified the studied stations as being moderate pollution except for PS and RB stations. The existence of organic pollution indicators species like Navicula, Synedra, and Euglena is a warning indication of the declining water quality especially in B and M stations. The biochemical compositions of the collected phytoplankton were spatial fluctuated. Protein and carbohydrates were the dominant macromolecules in the phytoplankton community compared with lipids. These macromolecules are used to assess trophic states whereas the ratio between protein and carbohydrate > 1 represents a healthy coast as observed in some stations. Thus, phytoplankton should be considered a bioindicator within Water Framework Directive monitoring programs for the Mediterranean Sea. For the long-term monitoring of the Mediterranean Sea's ecosystem, it is recommended that the macromolecules of phytoplankton should be determined.

Light and carbon: Synthetic biology toward new cyanobacteria-based living biomaterials

Cyanobacteria are ideal candidates to use in developing carbon neutral and carbon negative technologies; they are efficient photosynthesizers and amenable to genetic manipulation. Over the past two decades, researchers have demonstrated that cyanobacteria can make sustainable, useful biomaterials, many of which are engineered living materials. However, we are only beginning to see such technologies applied at an industrial scale. In this review, we explore the ways in which synthetic biology tools enable the development of cyanobacteria-based biomaterials. First we give an overview of the ecological and biogeochemical importance of cyanobacteria and the work that has been done using cyanobacteria to create biomaterials so far. This is followed by a discussion of commonly used cyanobacteria strains and synthetic biology tools that exist to engineer cyanobacteria. Then, three case studies-bioconcrete, biocomposites, and biophotovoltaics-are explored as potential applications of synthetic biology in cyanobacteria-based materials. Finally, challenges and future directions of cyanobacterial biomaterials are discussed.

Production of Arthrospira platensis: Effects on Growth and Biochemical Composition of Long-Term Acclimatization at Different Salinities

Arthrospira platensis is an edible cyanobacterium with high nutritional value. Even though A. platensis is not a marine species, it can be adapted to higher salinities, a strategy that could allow mass cultivation using brackish or saline water. In this work A. platensis was long-term adapted at different salinities (5-60 g/L NaCl added as natural sea salt) to evaluate the growth and biochemical composition of the biomass produced. Biomass production was enhanced in salinity up to 40 g/L NaCl, while at 60 g/L NaCl biomass production slightly decreased. However, it displayed higher values compared to the conventional Zarrouk growth medium. By increasing the salinity, carbohydrate content increases, while proteins, phycocyanin, carotenoids, and total phenolics decreased. Biomass content in lipids, and chlorophyll along with the antioxidant capacity of extracts, was not significantly affected. A. platensis tended to increase the unsaturated fatty acids, while amino acid composition was not significantly affected by the increased salinity. However, in vitro protein digestibility was negatively affected when salinity was above 20 g/L NaCl. It was macroscopically observed that trichomes were longer at higher salinities, and especially at 40 g/L NaCl. The results suggest that A. platensis when acclimated in long-term can be grown successfully at various salinities.

Improved salt tolerance of Synechococcus elongatus PCC 7942 by heterologous synthesis of compatible solute ectoine

Salt stress is one of the essential abiotic stresses for the survival of cyanobacteria. However, the realization of large-scale cultivation of cyanobacteria is inseparable from the utilization of abundant seawater resources. Therefore, research on the regulatory mechanism, as well as the improvement of salt tolerance of cyanobacteria is fundamental. Ectoine, a compatible solute which was found in halophilic microorganisms, has potentiality to confer salt tolerance. Here in this article, the salt tolerance of Synechococcus elongatus PCC 7942 (Syn7942) was significantly improved via expressing the ectoine biosynthetic pathway, reaching an increased final OD₇₅₀ by 20% under 300 mM NaCl and 80% under 400 mM NaCl than that of wild-type (WT), respectively. Encouragingly, the engineered strain could even survive under 500 mM NaCl which was lethal to WT. In addition, by introducing the ectoine synthetic pathway into the sucrose-deficient strain, the salt tolerance of the obtained strain Syn7942/Δsps-ect was restored to the level of WT under 300 mM NaCl stress, demonstrating that ectoine could substitute for sucrose to combat against salt stress in Syn7942. In order to study the difference in the regulation of mechanism on the salt adaptation process after replacing sucrose with ectoine, transcriptomic analysis was performed for Syn7942/Δsps-ect and WT. The differentially expressed gene analysis successfully identified 19 up-regulated genes and 39 down-regulated genes in Syn7942/Δsps-ect compared with WT under salt stress condition. The results also showed that the global regulation of Syn7942/Δsps-ect and WT had certain differences in the process of salt adaptation, in which Syn7942/Δsps-ect reduced the demand for the intensity of sulfur metabolism in this process. This study provides a valuable reference for further salt tolerance engineering in cyanobacteria.

Modulation of salt stress in paddy field cyanobacteria with exogenous application of gibberellic acid: growth behavior and antioxidative status

The present study explores the possible function of gibberellic acid (GA: 20 µM) in reducing salt (NaCl) induced toxicity in two diazo-trophic cyanobacteria i.e. Nostoc muscorum and Phormidium foveolarum. The physiological and biochemical parameters viz. growth, photosynthetic pigments (chlorophyll a, carotenoids, and phycocyanin), photosynthetic and respiratory rates, oxidative stress biomarkers (superoxide radicle, hydrogen peroxide, and malondialdehyde contents) antioxidant activities (superoxide dismutase, peroxidase, catalase, and glutathione-S-transferase) and non-enzymatic antioxidants were studied under both the doses i.e. 40 mM (LC 10) and  mM (LC 30) of NaCl. The growth, photosynthetic pigments and photosynthetic rate were found to be declined under concentration-dependent manner of NaCl. Contrastingly, the respiratory rate, oxidative stress biomarkers, and the activity of antioxidant enzymes i.e. superoxide dismutase (SOD), peroxidases (POD), catalase (CAT), and glutathione-S-transferase (GST) together with contents of non-enzymatic antioxidants (proline and cysteine) were found to increase in the test cyanobacteria. PSII photochemistry in both the cyanobacteria was negatively affected showing an inhibitory effect of NaCl on JIP parameters, while an enhancement effect was noticed in the values related to energy flux parameters. Further, the addition of GA to the growth medium caused an alleviating effect as it completely mitigated NaCl toxicity induced by a lower dose i.e. 40 mM of NaCl, while it partially alleviated the growth and photosynthetic parameters of 80 mM NaCl stressed cyanobacteria. Supplementation of GA significantly reduced the contents of oxidative stress tested cyanobacteria due to an improved antioxidant system (increased activities of enzymatic and non-enzymatic antioxidants) as evident from the biochemical analysis. In brief, our findings reflect the possible role of GA as a potential modulator of salt toxicity.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-022-01266-5.

Tracking the influence of antibiotics, antibiotic resistomes, and salinity gradient in modulating microbial community assemblage of surface water and the ecological consequences

The ecological impacts of antibiotics and antibiotic resistance genes (ARGs) on water ecology remain elusive in natural environments. We investigated the influence of antibiotics, ARGs and salinity gradient on the surface water ecosystem. Cefquinome (104.2 ± 43.6 ng/L) and cefminox (16.2 ± 7.50 ng/L) cephalosporins were predominant in all sites. Antibiotic contamination was increased in the estuary ecosystems compared to the freshwater ecosystems by 6%. Bacterial diversity could resist changes in salinity, but the relative abundance of some bacterial genera; Pseudoalteromonas, Glaciecola, norank_f__Arcobacteraceae, and Pseudohongiella was increased in the estuary zone (salinity>0.2%). The eukaryotic composition was increased in the subsaline environments (<0.2%), but the higher salinity in the saline zone inhibited the eukaryotic diversity. The relative abundance of ARGs was significantly higher in the estuary than in freshwater ecosystems, and ARGs interactions and mobile elements (aac(6')-Ib(aka_aacA4)-01, tetR-02, aacC, intI1, intI-1(clinic), qacEdelta1-01, and strB) were the predominant factors responsible for the ARGs propagation. Antibiotics associated with corresponding and non-corresponding ARGs and potentially created an adverse environment that increased the predation and pathogenicity of the aquatic food web and inhibited the metabolic functions. Surface water are first-line-ecosystems receiving antibiotics and ARGs hence our findings provided vital insights into understanding their ecological consequences on surface water ecosystems.

A droplet-based microfluidic platform enables high-throughput combinatorial optimization of cyanobacterial cultivation

Cyanobacteria are fast-growing, genetically accessible, photoautotrophs. Therefore, they have attracted interest as sustainable production platforms. However, the lack of techniques to systematically optimize cultivation parameters in a high-throughput manner is holding back progress towards industrialization. To overcome this bottleneck, here we introduce a droplet-based microfluidic platform capable of one- (1D) and two-dimension (2D) screening of key parameters in cyanobacterial cultivation. We successfully grew three different unicellular, biotechnologically relevant, cyanobacteria: Synechocystis sp. PCC 6803, Synechococcus elongatus UTEX 2973 and Synechococcus sp. UTEX 3154. This was followed by a highly-resolved 1D screening of nitrate, phosphate, carbonate, and salt concentrations. The 1D screening results suggested that nitrate and/or phosphate may be limiting nutrients in standard cultivation media. Finally, we use 2D screening to determine the optimal N:P ratio of BG-11. Application of the improved medium composition in a high-density cultivation setup led to an increase in biomass yield of up to 15.7%. This study demonstrates that droplet-based microfluidics can decrease the volume required for cyanobacterial cultivation and screening up to a thousand times while significantly increasing the multiplexing capacity. Going forward, microfluidics have the potential to play a significant role in the industrial exploitation of cyanobacteria.

Characterizing sediment bacterial community and identifying the biological indicators in a seawater-freshwater transition zone during the wet and dry seasons

Seawater intrusion has a detrimental effect on agriculture, industry, and human health. One question of particular interest is how the microbial community responds to and reflects seawater intrusion with seasonal variation. The current study explored the seasonal changes in bacterial community composition and interaction in the vicinity of Pearl River Estuary in dry season (January) and wet season (September). Results indicated that the salinity of sediment samples obtained in dry season was higher than that in wet season. The salt stress induced a declined alpha diversity but resulted in a loosely connected and unstable biotic interaction network in the bacterial communities. Random forest prediction and redundancy analysis of bacterial community indicated that salinity substantially affected the bacterial communities. Multiple lines of evidence, including the enrichment of bacterial taxa in the high-salinity location, microbe-microbe interactions, environment-microbe interactions, and machine learning approach, demonstrated that the families Moraxellaceae and Planococcaceae were the keystone taxa and were resistant to salt stress, which suggested that both of them can be used as potential biological indicators of monitoring and controlling seawater intrusion in coastal zone areas.

Effect of filamentous algae in a microalgal-bacterial granular sludge system treating saline wastewater: Assessing stability, lipid production and nutrients removal

In this study modified microalgal-bacterial granular sludge (MBGS) was constructed and employed to compare the performance for treating 1%-5% saline wastewater with aerobic granular sludge (AGS). Filamentous algae were found to flourish at 1% salinity when nutrients were temporarily restricted to low level (COD 0, N 10 mg/L, P 0.5 mg/L). A significant improvement of granule stability was detected as the integrity coefficients of MBGS was only 0.12-0.24 rather than 0.19-0.48 of AGS under 1%-5% salinities, which reduced the risk of particle disintegration. Filamentous algae including Leptolyngbya and Geitlerinema occupied 91.2% of identified algae, and were beneficial for enhancing the biomass content and lipid production to about 1.27-1.37, 3.1-5.0 times than AGS. The MBGS had best nitrogen and phosphorus removal efficiencies of 93.4% and 64.6% at 1% salinity, and showed higher resistance to 3%-5% salinities. This study could provide meaningful information for using this modified MBGS technology in practice.

Effective Use of Water in Crop Plants in Dryland Agriculture: Implications of Reactive Oxygen Species and Antioxidative System

Under dryland conditions, annual and perennial food crops are exposed to dry spells, severely affecting crop productivity by limiting available soil moisture at critical and sensitive growth stages. Climate variability continues to be the primary cause of uncertainty, often making timing rather than quantity of precipitation the foremost concern. Therefore, mitigation and management of stress experienced by plants due to limited soil moisture are crucial for sustaining crop productivity under current and future harsher environments. Hence, the information generated so far through multiple investigations on mechanisms inducing drought tolerance in plants needs to be translated into tools and techniques for stress management. Scope to accomplish this exists in the inherent capacity of plants to manage stress at the cellular level through various mechanisms. One of the most extensively studied but not conclusive physiological phenomena is the balance between reactive oxygen species (ROS) production and scavenging them through an antioxidative system (AOS), which determines a wide range of damage to the cell, organ, and the plant. In this context, this review aims to examine the possible roles of the ROS-AOS balance in enhancing the effective use of water (EUW) by crops under water-limited dryland conditions. We refer to EUW as biomass produced by plants with available water under soil moisture stress rather than per unit of water (WUE). We hypothesize that EUW can be enhanced by an appropriate balance between water-saving and growth promotion at the whole-plant level during stress and post-stress recovery periods. The ROS-AOS interactions play a crucial role in water-saving mechanisms and biomass accumulation, resulting from growth processes that include cell division, cell expansion, photosynthesis, and translocation of assimilates. Hence, appropriate strategies for manipulating these processes through genetic improvement and/or application of exogenous compounds can provide practical solutions for improving EUW through the optimized ROS-AOS balance under water-limited dryland conditions. This review deals with the role of ROS-AOS in two major EUW determining processes, namely water use and plant growth. It describes implications of the ROS level or content, ROS-producing, and ROS-scavenging enzymes based on plant water status, which ultimately affects photosynthetic efficiency and growth of plants.

Carotenoid Production from Microalgae: Biosynthesis, Salinity Responses and Novel Biotechnologies

Microalgae are excellent biological factories for high-value products and contain biofunctional carotenoids. Carotenoids are a group of natural pigments with high value in social production and human health. They have been widely used in food additives, pharmaceutics and cosmetics. Astaxanthin, β-carotene and lutein are currently the three carotenoids with the largest market share. Meanwhile, other less studied pigments, such as fucoxanthin and zeaxanthin, also exist in microalgae and have great biofunctional potentials. Since carotenoid accumulation is related to environments and cultivation of microalgae in seawater is a difficult biotechnological problem, the contributions of salt stress on carotenoid accumulation in microalgae need to be revealed for large-scale production. This review comprehensively summarizes the carotenoid biosynthesis and salinity responses of microalgae. Applications of salt stress to induce carotenoid accumulation, potentials of the Internet of Things in microalgae cultivation and future aspects for seawater cultivation are also discussed. As the global market share of carotenoids is still ascending, large-scale, economical and intelligent biotechnologies for carotenoid production play vital roles in the future microalgal economy.

Integrative analysis of the salt stress response in cyanobacteria

Microorganisms evolved specific acclimation strategies to thrive in environments of high or fluctuating salinities. Here, salt acclimation in the model cyanobacterium Synechocystis sp. PCC 6803 was analyzed by integrating transcriptomic, proteomic and metabolomic data. A dynamic reorganization of the transcriptome occurred during the first hours after salt shock, e.g. involving the upregulation of genes to activate compatible solute biochemistry balancing osmotic pressure. The massive accumulation of glucosylglycerol then had a measurable impact on the overall carbon and nitrogen metabolism. In addition, we observed the coordinated induction of putative regulatory RNAs and of several proteins known for their involvement in other stress responses. Overall, salt-induced changes in the proteome and transcriptome showed good correlations, especially among the stably up-regulated proteins and their transcripts. We define an extended salt stimulon comprising proteins directly or indirectly related to compatible solute metabolism, ion and water movements, and a distinct set of regulatory RNAs involved in post-transcriptional regulation. Our comprehensive data set provides the basis for engineering cyanobacterial salt tolerance and to further understand its regulation.

Transporter engineering for the development of cyanobacteria as cell factories: A text analytics guided survey

Cyanobacteria are attractive candidates for photoautotrophic production of platform chemicals due to their inherent ability to utilize carbon dioxide as the sole carbon source. Metabolic pathways can be engineered more readily in cyanobacteria compared to higher photosynthetic organisms. Although significant progress has been made in pathway engineering, intracellular accumulation of the product is a potential bottleneck in large-scale production. Likewise, substrate uptake is known to limit growth and product formation. These limitations can potentially be addressed by targeted and controlled expression of transporter proteins in the metabolically engineered strains. This review focuses on the transporters that have been explored in cyanobacteria. To highlight the progress on characterization and application of cyanobacterial transporters, we applied text analytics to extract relevant information from over 1000 publications. We have categorized the transporters based on their source, their function and the solute they transport. Further, the review provides insights into the potential of transporters in the metabolic engineering of cyanobacteria for improved product titer.

Salt-Tolerant Synechococcus elongatus UTEX 2973 Obtained via Engineering of Heterologous Synthesis of Compatible Solute Glucosylglycerol

The recently isolated cyanobacterium Synechococcus elongatus UTEX 2973 (Syn2973) is characterized by a faster growth rate and greater tolerance to high temperature and high light, making it a good candidate chassis for autotrophic photosynthetic microbial cell factories. However, Syn2973 is sensitive to salt stress, making it urgently important to improve the salt tolerance of Syn2973 for future biotechnological applications. Glucosylglycerol, a compatible solute, plays an important role in resisting salt stress in moderate and marine halotolerant cyanobacteria. In this study, the salt tolerance of Syn2973 was successfully improved by introducing the glucosylglycerol (GG) biosynthetic pathway (OD₇₅₀ improved by 24% at 60 h). In addition, the salt tolerance of Syn2973 was further enhanced by overexpressing the rate-limiting step of glycerol-3-phosphate dehydrogenase and downregulating the gene rfbA, which encodes UDP glucose pyrophosphorylase. Taken together, these results indicate that the growth of the end-point strain M-2522-GgpPS-drfbA was improved by 62% compared with the control strain M-pSI-pSII at 60 h under treatment with 0.5 M NaCl. Finally, a comparative metabolomic analysis between strains M-pSI-pSII and M-2522-GgpPS-drfbA was performed to characterize the carbon flux in the engineered M-2522-GgpPS-drfbA strain, and the results showed that more carbon flux was redirected from ADP-GLC to GG synthesis. This study provides important engineering strategies to improve salt tolerance and GG production in Syn2973 in the future.

Multi-Omic Analyses Reveal Habitat Adaptation of Marine Cyanobacterium Synechocystis sp. PCC 7338

Cyanobacteria are considered as promising microbial cell factories producing a wide array of bio-products. Among them, Synechocystis sp. PCC 7338 has the advantage of growing in seawater, rather than requiring arable land or freshwater. Nonetheless, how this marine cyanobacterium grows under the high salt stress condition remains unknown. Here, we determined its complete genome sequence with the embedded regulatory elements and analyzed the transcriptional changes in response to a high-salt environment. Complete genome sequencing revealed a 3.70 mega base pair genome and three plasmids with a total of 3,589 genes annotated. Differential RNA-seq and Term-seq data aligned to the complete genome provided genome-wide information on genetic regulatory elements, including promoters, ribosome-binding sites, 5'- and 3'-untranslated regions, and terminators. Comparison with freshwater Synechocystis species revealed Synechocystis sp. PCC 7338 genome encodes additional genes, whose functions are related to ion channels to facilitate the adaptation to high salt and high osmotic pressure. Furthermore, a ferric uptake regulator binding motif was found in regulatory regions of various genes including SigF and the genes involved in energy metabolism, suggesting the iron-regulatory network is connected to not only the iron acquisition, but also response to high salt stress and photosynthesis. In addition, the transcriptomics analysis demonstrated a cyclic electron transport through photosystem I was actively used by the strain to satisfy the demand for ATP under high-salt environment. Our comprehensive analyses provide pivotal information to elucidate the genomic functions and regulations in Synechocystis sp. PCC 7338.

Influence of Low Salt Concentration on Growth Behavior and General Biomass Composition in Lyngbya purpurem (Cyanobacteria)

Cyanobacteria are essential for the vast number of compounds they produce and the possible applications in the pharmaceutical, cosmetical, and food industries. As Lyngbya species' characterization is limited in the literature, we characterize this cyanobacterium's growth and biomass. L. purpureum was grown and analyzed under different salinities, culture media, and incubation times to determine the best conditions that favor its cell growth and the general production of proteins, carbohydrates, lipids, and some pigments as phycocyanin and chlorophyll a. In this study, each analyzed biomolecule's highest content was proteins 431.69 mg g^-1, carbohydrates 301.45 mg g^-1, lipids 131.5 mg g^-1, chlorophyll a 4.09 mg g^-1, and phycocyanin 40.4 mg g^-1. These results can provide a general context of the possible uses that can be given to biomass and give an opening to investigate possible biocompounds or bio metabolites that can be obtained from it.