Culturable Diversity and Lipid Production Profile of Labyrinthulomycete Protists Isolated from Coastal Mangrove Habitats of China

Labyrinthulomycetes thrives in organic matter-rich waters with ecological partitioning in the Pearl River Estuary

Labyrinthulomycetes play an important role in marine biogeochemical cycles, but their diversity, distribution patterns, and key regulatory factors remain unclear. This study measured the abundance and diversity of Labyrinthulomycetes in the Pearl River Estuary (PRE) to understand its distribution pattern and relationship with environmental and biological factors. The abundance of Labyrinthulomycetes ranged from 24 to 500 cells·mL-1, with an average of 144.37 ± 94.65 cells·mL-1, and its community composition showed obvious ecological partitioning in the PRE. The results of statistical analysis indicated that CDOM, salinity, and chlorophyll a contributed significantly (P < 0.01) to the community composition, explaining 46.59%, 11.34%, and 4.38% of the variance, respectively. The Labyrinthulomycetes distribution pattern combined with the niches of dominant species was revealed; low-salinity species mainly use terrigenous organic matter occupied dominant positions in the upper estuary and showed the highest abundance; moderate-salinity species that can use phytoplankton-derived resources thrived in the middle estuary; and seawater species dominated the lower estuary with the highest diversity but the lowest abundance. In addition, the results of phylogenetic tree analysis indicated that the existence of a novel lineage, and further study on the diversity and ecological functions of Labyrinthulomycetes is needed.IMPORTANCELabyrinthulomycetes play important roles in organic matter remineralization, carbon sinks, and food webs. However, the true diversity of Labyrinthulomycetes is still unclear due to limitations in isolation and culture methods. In addition, previous studies on their relationship with environmental factors are inconsistent and even contradictory, and it is speculated that their community composition may have spatial heterogeneity along the environmental gradient. In this study, the distribution pattern and key regulators of Labyrinthulomycetes in the PRE were revealed. Combining the niche of dominant species, it is suggested that salinity determines the spatial differences in Labyrinthulomycetes diversity, and the resources of substrate (terrestrial input or phytoplankton-derived) determine the dominant species, and its abundance is mainly determined by organic matter concentrations. Our study provided new information on the Labyrinthulomycetes diversity and verified the spatial heterogeneity of Labyrinthulomycetes community composition, providing reliable explanations for the inconsistencies in previous studies.

Lipid Production of Schizochytrium sp. HBW10 Isolated from Coastal Waters of Northern China Cultivated in Food Waste Hydrolysate

Marine oleaginous thraustochytrids have attracted increasing attention for their great potential in producing high-value active metabolites using various industrial and agricultural waste. Food waste containing abundant nutrients is considered as an excellent feedstock for microbial fermentation. In this study, a thraustochytrid strain Schizochytrium sp. HBW10 was isolated from a water column in Bohai Bay in Northern China for the first time. Further lipid production characteristics of S. sp. HBW10 were investigated utilizing sulfuric acid hydrolysate of food waste (FWH) from two different restaurants (FWH1 and FWH2) with the initial pH value adjusted by NaOH or NaHCO3. Results showed that the highest concentration of total fatty acids (TFAs) was observed in FWH2 medium with the 50% content level on the fifth day, reaching up to 0.34 g/L. A higher initial pH promoted the growth and saturated fatty acid (SFA) accumulation of S. sp. HBW10, achieving nearly 100% of the sum of saturated and monounsaturated fatty acids (SMUFAs) in TFAs with initial pH7 and pH8 in FWH1 medium. This work demonstrates a possible way for lipid production by thraustochytrids using food waste hydrolysate with a higher initial pH (pH7~pH8) adjusted by NaHCO3.

Saturated and Polyunsaturated Fatty Acids Production by Aurantiochytrium limacinum PKU#Mn4 on Enteromorpha Hydrolysate

Thraustochytrids are unicellular marine heterotrophic protists, which have recently shown a promising ability to produce omega-3 fatty acids from lignocellulosic hydrolysates and wastewaters. Here we studied the biorefinery potential of the dilute acid-pretreated marine macroalgae (Enteromorpha) in comparison with glucose via fermentation using a previously isolated thraustochytrid strain (Aurantiochytrium limacinum PKU#Mn4). The total reducing sugars in the Enteromorpha hydrolysate accounted for 43.93% of the dry cell weight (DCW). The strain was capable of producing the highest DCW (4.32 ± 0.09 g/L) and total fatty acids (TFA) content (0.65 ± 0.03 g/L) in the medium containing 100 g/L of hydrolysate. The maximum TFA yields of 0.164 ± 0.160 g/g DCW and 0.196 ± 0.010 g/g DCW were achieved at 80 g/L of hydrolysate and 40 g/L of glucose in the fermentation medium, respectively. Compositional analysis of TFA revealed the production of equivalent fractions (% TFA) of saturated and polyunsaturated fatty acids in hydrolysate or glucose medium. Furthermore, the strain yielded a much higher fraction (2.61-3.22%) of eicosapentaenoic acid (C20:5n-3) in the hydrolysate medium than that (0.25-0.49%) in the glucose medium. Overall, our findings suggest that Enteromorpha hydrolysate can be a potential natural substrate in the fermentative production of high-value fatty acids by thraustochytrids.

Screening and Identification of Coastal Chilean Thraustochytrids for Arachidonic Acid Production: Biotechnological Potential of Ulkenia visurgensis Lng2-Strain

Thraustochytrids are unicellular heterotrophic marine protists that have been described as producing a high content of polyunsaturated fatty acids (PUFAs). Among them, arachidonic acid (ARA) stands out as a precursor of several mediators of pivotal importance for the immune system. However, the biotechnological potential of thraustochytrids for ARA production has not been developed. The objective of this study is to isolate and identify native strains from different Chilean coastal environments and evaluate in vitro the effect of culture parameters such as C/N ratio (19 and 33) and temperature (15 °C and 23 °C) on biomass production and arachidonic acid content. A total of nine strains were identified and classified into four genera of the Thraustochitridae family. The Lng2 strain with 99% identity belongs to the species Ulkenia visurgenis and was the most prominent one for ARA production. Temperature had an effect on the PUFA profile but not on the ARA content nor on the biomass yield. Additionally, the C/N ratio has been identified as a key parameter. The ARA productivity increased by 92% (from 0.6 to 8.3 ARA mg/g-DW) and its total biomass by 62.7% (from 1.9 to 5.1 g/L) at a high C/N ratio (33) as compared to the control.

Comparative Genomic Analyses of Cellulolytic Machinery Reveal Two Nutritional Strategies of Marine Labyrinthulomycetes Protists

Labyrinthulomycetes are a group of ubiquitous and diverse unicellular Stramenopiles and have long been known for their vital role in ocean carbon cycling. However, their ecological function from the perspective of organic matter degradation remains poorly understood. This study reports high-quality genomes of two newly isolated Labyrinthulomycetes strains, namely, Botryochytrium sp. strain S-28 and Oblongichytrium sp. strain S-429, and provides molecular analysis of their ecological functions using comparative genomics and a biochemical assay. Our results suggest that Labyrinthulomycetes may occupy multiple ecological niches in marine ecosystems because of the significant differences in gene function among different genera. Certain strains could degrade wheat bran independently by secreting cellulase. The key glycoside hydrolase families (GH1, GH5, and GH9) related to cellulase and the functional domains of carbohydrate-active enzymes (CAZymes) were more enriched in their genomes. This group can actively participate in marine biochemical cycles as decomposers. In contrast, other strains that could not produce cellulase may thrive as "leftover scavengers" and act as a source of nutrients to the higher-trophic-level plankton. In addition, our findings emphasize the dual roles of endoglucanase, acting as both exo- and endoglucanases, in the process of cellulose degradation. Using genomic, biochemical, and phylogenetic analyses, our study provides a broader insight into the nutritional patterns and ecological functions of Labyrinthulomycetes. IMPORTANCE Unicellular heterotrophic eukaryotes are an important component of marine ecosystems. However, their ecological functions and modes of nutrition remain largely unknown. Our current understanding of marine microbial ecology is incomplete without integrating these heterotrophic microeukaryotes into the food web models. This study focuses on the unicellular fungus-like protists Labyrinthulomycetes and provides two high-quality genomes of cellulase-producing Labyrinthulomycetes. Our study uncovers the basis of their cellulase production by deciphering the results of genomic, biochemical, and phylogenetic analyses. This study instigates a further investigation of the molecular mechanism of organic matter utilization by Labyrinthulomycetes in the world's oceans.

Culturable Diversity of Thraustochytrids from Coastal Waters of Qingdao and Their Fatty Acids

Thraustochytrids have gained significant attention in recent years because of their considerable ecological and biotechnological importance. Yet, the influence of seasons and habitats on their culturable diversity and lipid profile remains poorly described. In this study, a total of 58 thraustochytrid strains were isolated from the coastal waters of Qingdao, China. These strains were phylogenetically close to five thraustochytrid genera, namely Botryochytrium, Oblongichytrium, Schizochytrium, Thraustochytrium, and Sicyoidochytrium. Most of the isolated strains were classified into the genera Thraustochytrium and Oblongichytrium. Further diversity analysis revealed that samples collected from nutrient-rich habitats and during summer/fall yielded significantly higher culturable diversity of thraustochytrids than those from low-nutrient habitats and winter/spring. Moreover, sampling habitats and seasons significantly impacted the fatty acid profiles of the strains. Particularly, the Oblongichytrium sp. OC931 strain produced a significant amount (153.99 mg/L) of eicosapentaenoic acid (EPA), accounting for 9.12% of the total fatty acids, which was significantly higher than that of the previously reported Aurantiochytrium strains. Overall, the results of this study fill the gap in our current understanding of the culturable diversity of thraustochytrids in the coastal waters and the impact of the sampling habitats and seasons on their capacity for lipid accumulation.

Thraustochytrids of Mangrove Habitats from Andaman Islands: Species Diversity, PUFA Profiles and Biotechnological Potential

Thraustochytrids are the most promising microbial source for the commercial production of docosahexaenoic acid (DHA) for its application in the human health, aquaculture, and nutraceutical sectors. The present study isolated 127 thraustochytrid strains from mangrove habitats of the south Andaman Islands, India to study their diversity, polyunsaturated fatty acids (PUFAs), and biotechnological potential. The predominant strains were identified as belonging to two major genera (Thraustochytrium, Aurantiochytrium) based on morphological and molecular characteristics. The strain ANVKK-06 produced the maximum biomass of 5.42 g·L^-1, while ANVKK-03 exhibited the maximum total lipid (71.03%). Omega-3 PUFAs such as eicosapentaenoic acid (EPA) accumulated up to 11.03% in ANVKK-04, docosapentaenoic acid (DPA) up to 8.65% in ANVKK-07, and DHA up to 47.19% in ANVKK-06. ANVKK-06 showed the maximum scavenging activity (84.79 ± 2.30%) while ANVKK-03 and ANVKK-10 displayed the highest antibacterial activity against human and fish pathogens, S. aureus (18.69 ± 1.2 mm) and V. parahaemolyticus (18.31 ± 1.0 mm), respectively. All strains were non-toxic as evident by negative blood agar hemolysis, thus, the thraustochytrids are suggested to be a potential source of DHA for application in the health care of human and fish.

ARTP Mutagenesis of Schizochytrium sp. PKU#Mn4 and Clethodim-Based Mutant Screening for Enhanced Docosahexaenoic Acid Accumulation

Schizochytrium species are one of the best oleaginous thraustochytrids for high-yield production of docosahexaenoic acid (DHA, 22:6). However, the DHA yields from most wild-type (WT) strains of Schizochytrium are unsatisfactory for large-scale production. In this study, we applied the atmospheric and room-temperature plasma (ARTP) tool to obtain the mutant library of a previously isolated strain of Schizochytrium (i.e., PKU#Mn4). Two rounds of ARTP mutagenesis coupled with the acetyl-CoA carboxylase (ACCase) inhibitor (clethodim)-based screening yielded the mutant A78 that not only displayed better growth, glucose uptake and ACCase activity, but also increased (54.1%) DHA content than that of the WT strain. Subsequent optimization of medium components and supplementation improved the DHA content by 75.5 and 37.2%, respectively, compared with that of mutant A78 cultivated in the unoptimized medium. Interestingly, the ACCase activity of mutant A78 in a medium supplemented with biotin, citric acid or sodium citrate was significantly greater than that in a medium without supplementation. This study provides an effective bioengineering approach for improving the DHA accumulation in oleaginous microbes.

Exogenous Antioxidants Improve the Accumulation of Saturated and Polyunsaturated Fatty Acids in Schizochytrium sp. PKU#Mn4

Species of Schizochytrium are well known for their remarkable ability to produce lipids intracellularly. However, during their lipid accumulation, reactive oxygen species (ROS) are generated inevitably as byproducts, which if in excess results in lipid peroxidation. To alleviate such ROS-induced damage, seven different natural antioxidants (ascorbic acid, α-tocopherol, tea extract, melatonin, mannitol, sesamol, and butylated hydroxytoluene) were evaluated for their effects on the lipid accumulation in Schizochytrium sp. PKU#Mn4 using a fractional factorial design. Among the tested antioxidants, mannitol showed the best increment (44.98%) in total fatty acids concentration. However, the interaction effects of mannitol (1 g/L) and ascorbic acid (1 g/L) resulted in 2.26 ± 0.27 g/L and 1.45 ± 0.04 g/L of saturated and polyunsaturated fatty acids (SFA and PUFA), respectively, in batch fermentation. These concentrations were further increased to 7.68 ± 0.37 g/L (SFA) and 5.86 ± 0.03 g/L (PUFA) through fed-batch fermentation. Notably, the interaction effects yielded 103.7% and 49.6% increment in SFA and PUFA concentrations in batch fermentation. The possible mechanisms underlining those increments were an increased maximum growth rate of strain PKU#Mn4, alleviated ROS level, and the differential expression of lipid biosynthetic genes andupregulated catalase gene. This study provides an applicable strategy for improving the accumulation of SFA and PUFA in thraustochytrids by exogenous antioxidants and the underlying mechanisms.

Elemental Composition and Cell Mass Quantification of Cultured Thraustochytrids Unveil Their Large Contribution to Marine Carbon Pool

The element stoichiometry of bacteria has received considerable attention because of their significant role in marine ecosystems. However, relatively little is known about the composition of major structural elements of the unicellular heterotrophic protists—thraustochytrids, despite their widely recognized contribution to marine nutrient cycling. Here, we analyze the cell volume and elemental C, N, H, and S cell content of seven cultured thraustochytrids, isolated from different marine habitats, in the exponential and stationary growth phases. We further derive the relationships between the cell volume and elemental C and N content of the cultured thraustochytrids. The cell volumes varied significantly (p < 0.001) among the isolates, with median values of 96.9 and 212.5 μm³ in the exponential and stationary phases, respectively. Our results showed a significantly higher percentage of C (64.0 to 67.5) and H (9.9 to 13.2) but a lower percentage of N (1.86 to 2.16) and S (0.34 to 0.91) in the stationary phase, along with marked variations of C and N fractions among isolates in the exponential phase. The cell C (5.7 to 203.7 pg) and N (0.65 to 6.1 pg) content exhibited a significant (p < 0.001) linear relationship with the cell volume (27.7 to 510 μm³). On further analysis of the relationship across the two growth phases, we found the equation (cell C (pg) = 0.356 × cell volume (μm³) + 20.922) for stationary phase cells more appropriate for C estimation of natural thraustochytrids. This study provides the first experimental evidence of higher cell C density than the current estimate and relatively larger C contribution of thraustochytrids than bacteria to the marine organic pool.

Cultivation and diversity analysis of novel marine thraustochytrids

Thraustochytrids are a group of unicellular marine heterotrophic protists, and have long been known for their biotechnological potentials in producing squalene, polyunsaturated fatty acids (PUFAs) and other bioactive products. There are less than a hundred known strains from diverse marine habitats. Therefore, the discovery of new strains from natural environments is still one of the major limitations for fully exploring this interesting group of marine protists. At present, numerous attempts have been made to study thraustochytrids, mainly focusing on isolating new strains, analyzing the diversity in specific marine habitats, and increasing the yield of bioactive substances. There is a lack of a systematic study of the culturable diversity, and cultivation strategies. This paper reviews the distribution and diversity of culturable thraustochytrids from a range of marine environments, and describes in detail the most commonly used isolation methods and the control of culture parameters. Furthermore, the perspective approaches of isolation and cultivation for the discovery of new strains are discussed. Finally, the future directions of novel marine thraustochytrid research are proposed. The ultimate goal is to promote the awareness of biotechnological potentials of culturable thraustochytrid strains in industrial and biomedical applications.

Two-level factorial analysis of the effect of fructose on DHA biosynthetic capacity of Aurantiochytrium sp. SW1

Thraustochytrids are getting increasingly popular due to their high potential role as alternative producers of the high-valued ω-3 polyunsaturated fatty acids (PUFA), docosahexaenoic acid (DHA). While most thraustochytrids prefer glucose as the major carbon source, few strains have been reported to prefer fructose. One such strain is Aurantiochytrium sp. SW1. In this study, the effect of fructose on DHA accumulation by SW1 was investigated using a two-level full factorial design. Besides, biomass, lipid and DHA accumulation profiles of SW1 cultivated in fructose and glucose media were compared. Results revealed that fructose has a very significant positive effect on the volumetric DHA content. Meanwhile, its involvement in affecting DHA biosynthetic capacity, though significant, is not very profound. It was also found that when cultivated in fructose medium, SW1 had a less steep log phase compared to that of glucose medium. However, after 48h of cultivation, biomass and lipid accumulation in fructose medium outweighed the other. Volumetric DHA content in fructose medium at 96h was 11% higher than that of glucose medium. Overall, fructose was found to be a more suitable substrate for biomass, lipid and DHA accumulation in SW1 compared to the conventional source, glucose.

Different Classes of Phytohormones Act Synergistically to Enhance the Growth, Lipid and DHA Biosynthetic Capacity of Aurantiochytrium sp. SW1

In the present study, the impact of eight phytohormones from six different classes on the growth, lipid and docosahexaenoic acid (DHA) biosynthetic capacity of Aurantiochytrium sp. SW1 (SW1) was evaluated. Kinetin (KIN), jasmonic acid (JA) and gibberellic acid (GA) significantly enhanced the growth and DHA production of SW1 by 16%-28% and 66%-84% in comparison to the control, respectively. The synergistic effect of these three phytohormones, evaluated by the response surface methodology (RSM), showed that a combination of 3.6 mg/L GA, 2.0 mg/L KIN and 20.0 mg/L JA further increased the growth and DHA production of SW1 by 16% to 28% and 22% to 36%, respectively, in comparison to the individual supplementation. The synergistic effect of these phytohormones was also shown to be time-dependent, where feeding at 24 h of cultivation led to 15%, 26% and 35% further increments in the biomass, lipid and DHA production in comparison to that of 0 h, respectively. The determination of stress markers, antioxidant enzymes and key enzymes involved in fatty acid biosynthesis aided to elucidate the potential mechanism underlying the improvement of growth and DHA production by SW1 at various times of feeding. Supplementation with the phytohormones at 24 h exhibited the maximum impact on reducing the level of reactive oxygen species (ROS) and malondialdehyde (MDA), as well as augmented the antioxidants (superoxide dismutase and catalase) and key metabolic enzymes involved in lipogenesis (malic, glucose-6-phosphate dehydrogenase and ATP-citrate lyase) in comparison to the control and other time points. This study signifies the potential application of phytohormones for improving the growth, lipid and DHA production in Aurantiochytrium spp.