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Environmental Science and Pollution Research (2023) 30:79654–79675

https://doi.org/10.1007/s11356-023-28123-6

REVIEW ARTICLE

A comprehensive review on microbial lipid production from wastes:


research updates and tendencies
Haishu Sun1,2 · Zhen Gao1 · Lirong Zhang3 · Xiaona Wang1,2 · Ming Gao1 · Qunhui Wang1,3

Received: 29 December 2022 / Accepted: 1 June 2023 / Published online: 16 June 2023
© The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2023

Abstract
Microbial lipids have recently attracted attention as an intriguing alternative for the biodiesel and oleochemical industries
to achieve sustainable energy generation. However, large-scale lipid production remains limited due to the high processing
costs. As multiple variables affect lipid synthesis, an up-to-date overview that will benefit researchers studying microbial
lipids is necessary. In this review, the most studied keywords from bibliometric studies are first reviewed. Based on the results,
the hot topics in the field were identified to be associated with microbiology studies that aim to enhance lipid synthesis and
reduce production costs, focusing on the biological and metabolic engineering involved. The research updates and tendencies
of microbial lipids were then analyzed in depth. In particular, feedstock and associated microbes, as well as feedstock and
corresponding products, were analyzed in detail. Strategies for lipid biomass enhancement were also discussed, including
feedstock adoption, value-added product synthesis, selection of oleaginous microbes, cultivation mode optimization, and
metabolic engineering strategies. Finally, the environmental implications of microbial lipid production and possible research
directions were presented.

Keywords Single cell oil · Feedstock · Oleaginous microbe · Cultivation mode · Metabolic engineering · Environmental
implication

Introduction as promising substitutes for the oleochemical industry in a


move toward renewable and sustainable energy production
Global climate change and other environmental problems (Chatterjee and Mohan 2020; Karamerou and Webb 2019).
resulting from the excessive consumption of fossil fuels Microbially derived lipids are particularly attractive because
are urgent concerns (Kim et al. 2019; Sundaramahalingam of their high quality, shorter cultivation time, independ-
et al. 2022). Faced with a shortage of petrochemical petro- ence from geographical or climatological conditions, lower
leum, the contradiction of food for oil, and deteriorating space requirements, and non-competitiveness with food sup-
environmental problems, it is urgent to develop renewable, ply (Chatterjee and Mohan 2020; Tomas-Pejo et al. 2021).
clean, and environmentally friendly energy sources such as However, large-scale microbial lipid development is limited
biofuels (Park et al. 2019). Microbial lipids have emerged by high processing costs and high prices of substrates (Cho
and Park 2018). Therefore, the exploration of cost-effective
feedstocks, combined with the use of waste substrates, which
Responsible Editor: Ta Yeong Wu are environmentally and economically sustainable, might be
a feasible alternative for reducing costs (Tan et al. 2022).
* Xiaona Wang
wangxiaona071@163.com Oleaginous microbes can utilize low-cost feedstocks
and waste substrates, such as lignocellulosic biomass and
1
School of Energy and Environmental Engineering, agro-residues, for higher lipid production (Garlapati et al.
University of Science and Technology Beijing, 2020). Oleaginous properties are inherent to certain spe-
Beijing 100083, China
cies of yeasts, microalgae, molds, and bacteria (Khot et al.
2
Shunde Innovation School, University of Science 2020), and the identification of excellent oleaginous strains
and Technology Beijing, Foshan 528399, China
is a prerequisite for the industrialization of microbial lipids.
3
Tianjin College, University of Science and Technology, Industrial production strains should be robust, stable, and
Beijing, Tianjin 301811, China

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highly productive, with the ability to assimilate a diverse Owing to the crucial role of microbial lipids in promoting
array of carbon (C) sources and be tolerant to a wide range environmental and economic sustainability, it is not surpris-
of inhibitors in complex substrates (Chaturvedi et al. 2019). ing that more than 3000 articles have been published on
In addition to the adoption of inexpensive raw materials, this topic over the last 2 decades (Fig. 1). However, most
the bioconversion of feedstock into value-added products review papers on microbial lipids focus on the effects of
could add value to fermentation processes. Therefore, a co- one or two factors on lipid production, and hardly any of
production system of microbial lipids with valuable com- these reviews provide comprehensive recommendations for
pounds, such as pigments and polyunsaturated fatty acids enhancing lipid biosynthesis (Park et al. 2019; Saha and
(PUFAs), not only improves the utilization of resources but Mukhopadhyay 2021). As multiple factors can affect lipid
also enhances the economics of microbial lipids (Chen et al. production, an up-to-date review that will benefit researchers
2021; Manowattana et al. 2018). studying microbial lipids is required. This review aimed to
To increase the economic competitiveness of the micro- summarize the research hotspots in microbial lipids, includ-
bial lipid manufacturing process, cultivation modes have ing feedstocks, oleaginous microbes, cultivation modes,
been optimized, and metabolic pathways have been modified research methods, and products. In particular, feedstock and
(Chen et al. 2021). Although microorganisms have inherent associated microbes, as well as feedstock and correspond-
metabolic pathways for the synthesis of microbial lipids, the ing products, were thoroughly evaluated. Recent advances
theoretical yield of microbial lipids is limited to approxi- and tendencies of the most studied keywords in research on
mately 0.2–0.3 g/g, which hinders industrial production microbial lipids were also discussed in depth, and an over-
and commercialization (Chen et al. 2021; Das et al. 2020). view of the cultivation modes and metabolic engineering
Biomass growth is the predominant process when C and N approaches to maximize microbial lipid production is also
are abundant; however, microbial lipids are generally syn- presented. Finally, the environmental implications of micro-
thesized under the prerequisites of sufficient C and limited bial lipid production and possible research directions were
nutrients (N, P, or S) (Ma et al. 2018). Therefore, optimizing discussed. Overall, this study aimed to provide an overview
cultivation modes is crucial because of the distinct nutri- of the current status of research in the field of microbial lipid
ent demands of the two stages. Maximum lipid yield occurs production and inspire further innovation in this area.
when minimal C flux is dedicated to the biomass (Yan and
Pfleger 2020). Metabolic engineering approaches can manip-
ulate the microbial C-energy balance and enhance the yield Research tendencies analysis based
and titer of lipids (Mehmood et al. 2021). Metabolic engi- on bibliometrics
neering involves modifying the genetics and metabolism of
microorganisms toward the desired biomass composition, In this study, keywords (“microb* lipid*” or “microb* oil*”
which can increase the titer, rate, and yield of the targeted or “single cell oil” or “single cell lipid*” or “oleaginous
metabolite (Kim et al. 2019). The overexpression of target micro*” or “oleaginous algae*” or “oleaginous yeast” or
enzymes and blockage of competitor pathways are two key “oleaginous bacteria*” or “oleaginous mold” or “oleaginous
metabolic engineering methods for boosting yield (Das et al. fung*”) were used as topic search phrases to acquire all the
2020; Yan and Pfleger 2020). index of articles published in the Web of Science database

Fig. 1  Number of publications


on microbial lipids during the
past 21 years (2000–2021)

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from 2000 to 2021. The research on microbial lipids started terms of feedstock (Fig. 2b), the most frequently used carbon
relatively late, with only a few publications per year until source is glucose. Various waste substrates have been inves-
2008. However, since 2010, the number of articles on this tigated due to their low cost, with lignocellulose being the
topic has substantially increased, likely due to several factors most commonly researched feedstock. To enable the microbe
such as the emergence of active clinical and safety trials as to access the nutrients found in waste substrates, appropri-
well as the establishment and consolidation of organizations ate pretreatment methods such as enzymatic hydrolysis
engaged in the microbial lipids production (Palazzolo and are required (Cai et al. 2016). Additionally, glucose-based
Garcia-Perez 2022). A noteworthy trend is the fact that over wastes such as molasses have been utilized for lipid produc-
300 papers were published in 2021 alone, indicating a sig- tion. Among the oleaginous microbes (Fig. 2c), yeast had
nificant increase in researchers’ interest in microbial lipids. the highest occurrences, followed by microalgae, molds, and
The keywords associated with research on microbial bacteria. Proper cultivation modes are essential to promote
lipids include feedstocks, oleaginous microbes, products, high lipid generation by supplying the essential nutrients
research methods, cultivation modes, and products, as at the appropriate time (Karamerou and Webb 2019). The
illustrated in Fig. 2. Among these, oleaginous microbes batch mode is a well-studied and fundamental approach for
and products have received the most attention (Fig. 2a). In lipid production (Fig. 2d). Given that microbes compete for

Fig. 2  Keywords analysis of research on microbial lipids

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C sources in the two primary processes of cell proliferation


and lipid accumulation, metabolic pathways of microbial
lipids have gained increasing attention. Many studies have
tried to regulate C flow to produce lipids through research
methods such as metabolic engineering tools (Fig. 2e).
For product generation (Fig. 2f), one significant func-
tion of microbial lipids is their potential as substitutes for
valuable lipids, such as cocoa butter. This function is almost
impossible to achieve through “de novo” lipid production
because in many cases, the lipid composition of the micro-
organism remains relatively stable (Huang et al. 2013). For
example, the reserve lipids of Y. lipolytica can serve as a
substitute for cocoa butter due to the use of an oleic acid
donor as a co-substrate with stearin (Papanikolaou and
Aggelis 2010). Synthetic biology and metabolic engineer-
ing have enabled increased triacylglycerol (TAG) production
in oleaginous yeasts, such as Y. lipolytica and S. cerevisiae,
providing a potential solution for the production of cocoa Fig. 3  Frequently studied feedstocks and their associated microbes
butter substitutes via “de novo” lipid accumulation path- for lipid production
ways (Konzock et al. 2022; Wang et al. 2020b). Owing to
their high carbon-to-heteroatom ratios, microbial lipids are
desirable feedstocks for the production of renewable fuels. few studies have been conducted on feedstocks and their
These TAGs contain fatty acids that are suitable for bio- associated bacteria for lipid production, as they generally
diesel production (Kosa and Ragauskas 2011). Biodiesel, do not retain substantial amounts of lipids (Palazzolo and
similar to other renewable energy sources, has a high energy Garcia-Perez 2022). Oleaginous yeasts such as Lipomyces,
density and is nontoxic, biodegradable, and environmentally Rhodotorula, and Rhodosporidium are particularly note-
friendly (Zhang et al. 2021a). Additionally, the production of worthy for their ability to rapidly consume diverse organic
high-value products such as docosahexaenoic acid (DHA), materials and stably produce lipids, making them a popular
eicosapentaenoic acid (EPA), carotenoids, and arachidonic choice for microbial lipid production. Lipomyces can convert
acid (ARA), has garnered increasing interest (Jakhwal et al. hemicellulosic hydrolysate sugars into lipids without prior
2022). detoxification, making it a promising candidate for lipid
generation in the presence of toxic components (Qin et al.
2017). Furthermore, inhibitors are depleted throughout the
Feedstock fermentation process, probably due to yeast metabolism, as
the Lipomyces genome contains key genes involved in inhib-
Feedstock and associated microbes itor metabolism. Rhodotorula is a ubiquitous yeast species
used in the manufacture of natural carotenoids (Gujjala et al.
Oleaginous microbes can use hydrophilic and hydrophobic 2019). Rhodosporidium, another yeast genus, plays a vital
substrates to accumulate lipids via two pathways: de novo role in the environment and is beneficial as many species can
and ex novo lipid synthesis. It is noteworthy that both of convert lignocellulosic biomass into lipids. Yarrowia prefers
these pathways offer distinct advantages: de novo lipid fer- oil- and food-rich conditions. The genome of the model Yar-
mentation can generate a considerable quantity of lipids, rowia lipolytica was sequenced, which could facilitate syn-
while ex novo lipid fermentation can modify the lipid com- thetic biology and genetic engineering applications to boost
positions to satisfy the requirements of the chemical or food its lipid production performance (Madzak 2018).
industries (Huang et al. 2017). Together, these two strategies Glucose is the feedstock most commonly used by ole-
provide a powerful platform for the production of various aginous microbes to produce lipids because it is the most
lipids with different properties and applications. suitable carbon source for microbial growth. However, the
cost of large-scale lipid production using glucose as a raw
“De novo” lipid fermentation material is high; therefore, agro-industrial and municipal
wastes, as well as other non-food raw materials, are being
Oleaginous yeasts are among the most widely studied used to explore the feasibility of microbial lipid production.
microbes for lipid production, due to their ability to con- Microbial lipid production from wastewater with high
sume a broad range of low-cost materials (Fig. 3). Relatively levels of organic matter has been found to be slightly more

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prevalent using yeasts (Singh et al. 2022). Cryptococcus wheat straw hydrolysates into lipids. In batch cultivation,
such as Cryptococcus curvatus, Cryptococcus Laurentis, and this strain had a high lipid content of 18.1 g/L and a high
Cryptococcus podzolicus were frequently used for simulta- yield of 0.24 g/g carbon source (Brandenburg et al. 2021).
neous wastewater treatment and microbial lipid production Cheesy whey, a major byproduct of cheese manufacture
(Arous et al. 2019; Santos et al. 2014). Cryptococcus cur- in the dairy industry, is an appealing substrate for micro-
vatus had higher lipid production than Y. lipolytica in media bial lipid production because of its accessibility and high
made from primary wastewater (Chi et al. 2011). organic load (Chan et al. 2018). Various yeast strains, such
A suitable feedstock for biodiesel production is food as Candida sp., Cryptococcus sp., and Apiotrichum cur-
waste (Carmona-Cabello et al. 2021), a significant munici- vatum, have been found to be capable of producing large
pal solid waste with a high organic matter content (Xu et al. amounts of lipids when cultured in shake flasks. Carota
2022; Zhang et al. 2021c), rich in carbohydrates, proteins, et al. (2017) used ricotta cheese whey as a substrate for
and starch (Ma et al. 2022). Rhodosporidium, Cryptococ- microbial lipid generation in a shake flask and observed
cus, and Trichosporon were the most frequently studied gen- that Cryptococcus curvatus and Cryptococcus laurentii
era. Trichosporon differs from other yeasts for the ability to produced substantial quantities of lipids (6.8 and 5.1 g/L,
use highly diverse C sources, and it has a high tolerance to respectively). Furthermore, using cheese whey for cocoa
5-hydroxymethylfurfural (5-HMF), which is present in most butter substitute production is almost economically viable.
food waste (Arous et al. 2019). Our group has conducted A cocoa-butter substitute was synthesized from cheese
extensive studies on the microbial lipid production from whey using Apiotrichum curvatum ATCC 20509 culti-
food waste. Rhodosporidium toruloides 2.1389 can use food vated in a batch bioreactor (Davies et al. 1990). The pri-
waste saccharified liquid as a substrate for lipid production mary disaccharide in cheesy whey, lactose, is hydrolyzed
without the addition of external nutrients (Ma et al. 2019). by acid or an enzyme to produce glucose and galactose.
A variable pH control strategy was applied to the same ole- Tchakouteu et al. (2015a) observed that lactose acted as
aginous strain, resulting in a lipid yield of 11.10 g/kg of food a substrate that facilitated the accumulation of lipids by
waste (Gao et al. 2019). Cryptococcus curvatus. Mucor circinelloides was used to
Lignocellulose, which is present in agricultural and produce lipids on cheese hydrolyzed whey permeate, and
agro-industrial residues, is the most abundant sustainable the biomass yield and lipid yield plateaued at 9 g/L and
resource for the generation of advanced biofuels (Ruan 2.2 g/L, respectively (Chan et al. 2018).
et al. 2013). Biomass is mainly composed of three poly- Crude glycerol is a byproduct of biodiesel production,
meric components: cellulose, hemicellulose, and lignin. with approximately 10 kg generated per 100 kg of bio-
As most oleaginous microbes lack cellulase and hemi- diesel produced (Gao et al. 2016). To produce microbial
cellulose activities, lignocellulosic biomass is typically lipids, glycerol is utilized as a carbon source for several
subjected to hydrolysis to convert its polymers into fer- yeast strains such as Rhodotorula, Lipomyces, Rho-
mentable sugars, which can be used as a carbon source dosporidium, Cryptococcus, Trichosporonoides, and Yar-
for lipid production by oleaginous microbes (Santek et al. rowia (Qin et al. 2017). R. toruloides has been extensively
2018). However, the effective conversion of lignocellu- studied due to its ability to produce microbial lipids when
losic sugars into high-quality lipids remains a significant cultured on glycerol. R. toruloides strain AS2.1389 dis-
issue for oleaginous yeasts as they preferentially consume played exceptional lipid production performance, with a
glucose instead of other sugars present in lignocellulosic maximum yield of 26.7 g/L and a lipid content of 70% in a
hydrolysates (Qin et al. 2017). Despite these challenges, 5 L fermenter (Xu et al. 2012). The effect of impurities in
several studies have investigated the effectiveness of ole- crude glycerol on the lipid production of Rhodosporidium
aginous yeasts in utilizing lignocellulosic hydrolysates for toruloides 32489 was investigated. Methyl oleate, NaCl,
lipid production. Recently, significant lipid titers (39–45% and sodium oleate impurities boosted lipid production by
of the theoretical yield) have been observed for several 47.0%, 64.0%, and 68.0%, respectively, whereas methanol
strains of oleaginous yeasts cultivated on non-detoxified lowered lipid generation by 17.7%. However, the inhibi-
lignocellulosic hydrolysates. Yarrowia lipolytica cultivated tory effect of methanol was alleviated when mixed with
on hydrolysates of defatted rice bran had a lipid content of other impurities owing to their promoting effect (Gao et al.
48.02% (Tsigie et al. 2012). Fei et al. (2016) investigated 2016).
various fed-batch modes to optimize lipid production by Starch, an energy-storage polysaccharide formed by amy-
Rhodosporidium toruloides using corn stover hydrolysate. lopectin and amylose chain helix (Ledesma-Amaro et al.
Based on their findings, online sugar control was the most 2015), is one of the most abundant carbohydrates in nature
efficient approach, resulting in the highest lipid content (Ge et al. 2018). Mortierella and Cryptococcus typically
(59%). Rhodotorula babjevae has demonstrated remark- use starch for microbial lipid synthesis because fungi can
able potential as a fermentative strain for the conversion of produce starch hydrolysis enzymes (Zhang et al. 2016).

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“Ex novo” lipid fermentation hydrotreatment (Zhang et al. 2023). Thermochemical trans-
formations, such as pyrolysis, achieved by thermal pyrolysis
In hydrophobic environments, certain strains of microor- or catalytic cracking, are now widely employed. The selec-
ganisms produce lipids via an ex novo lipid accumulation tion of a suitable catalyst for this process is crucial to achieve
pathway. This process involves the conversion of hydropho- highly efficient biofuel production and resource separation
bic substrates to free fatty acids via microbial lipolytic pro- (Ahmed et al. 2022). The acid-catalyzed process utilizing
cesses, followed by active transport within microbial cells WCO has been found to be more technically viable and less
(Vyas et al. 2023). As microorganisms are only supplied complicated than the alkali-catalyzed approach, thereby
with hydrophobic substrates, this growth-oriented process presenting a competitive option for commercial biodiesel
is independent of nitrogen-limiting conditions (Huang et al. production (Zhang et al. 2003).
2017). Hydrophobic substrates can be used by oleaginous In general, when grown on N-limited substrates such as
yeasts, such as Rhodosporidium, Cryptococcus, Trichos- glucose or glycerol, strains of Yarrowia typically produce
poron, and Yarrowia (Patel and Matsakas 2019). limited quantities of lipids during the early growth stages,
Hydrophobic feedstocks, such as free fatty acids from with these lipids often being subjected to biodegradation
industrial waste liquids, waste cooking oils (WCOs), thereafter. Simultaneously, cells synthesize low-molecular-
fatty acid byproducts or wastes, animal or vegetable oils, weight compounds such as citric acid and polyols (Khot et al.
n-alkanes, and volatile fatty acids (VFAs), can serve as 2020). However, lipid production by wild-type strains of this
sources of lipids for oleaginous yeasts. Patel and Matsakas species is generally inferior to that of wild-type strains of
(2019) evaluated the potential of Cryptococcus curvatus to Rhodotorula, Rhodosporidium, Lipomyces, and other typical
utilize waste cooking oils. Based on their findings, ex novo oleaginous yeasts (Chatterjee and Mohan 2020). For exam-
lipid synthesis resulted in a significantly higher lipid con- ple, under ideal cultivation conditions, Rhodosporidium
centration, cell dry weight, and lipid content than growth toruloides can accumulate lipids in excess of 70% (w/w) of
on glucose. Additionally, VFAs derived from waste can be its biomass (Ma et al. 2021). The lipid contents of Lipomyces
utilized for biodiesel production using oleaginous yeasts, and Rhodotorula were reported to be as high as 77.8% and
such as Rhodosporidium toruloides, Cryptococcus curva- 68.0%, respectively, whereas some species of Yarrowia (e.g.,
tus, and Yarrowia lipolytica. Yarrowia lipolytica has been Yarrowia lipolytica) can only accumulate 38% of the lipid
found to effectively synthesize lipids using VFAs as a carbon content (Gujjala et al. 2019).
source, and the simultaneous biovalorization of VFAs and
glycerol or glucose resulted in a high lipid yield of 16.50 g/L Feedstock and corresponding products
(Fontanille et al. 2012).
In the “ex novo” lipid accumulation pathway, only Research on microbial lipid from numerous raw materials is
0.25–0.35 g of microbial lipid can be produced for every mainly focused on biodiesel (Fig. 4), because the FA com-
1.0 g of initial substrate fat consumed (Raut et al. 2022). positions of microbial lipid are comparable to vegetable oils
Additionally, after the conversion of extracellular lipids to commonly used for the synthesis of first-generation biodiesel
intracellular fat, a series of steps including breakage and (Santek et al. 2018). The utilization of microbial sources for
extraction are required, which increased production costs biodiesel production has been considered the most reliable
(Mendoza-Lopez et al. 2017). Thus, it is impractical to per- and appropriate strategy to meet the productive, technical,
form fat substrate fermentation solely to produce another and environmental demands (Sitepu et al. 2014). However,
intracellular fat. Gao et al. (2022) found that the combined the high cost of raw materials is a key factor that limits
use of glucose and WCO as feedstock resulted in a higher the popularity and application of microbial lipid (Cho and
lipid production of 5.65 g/L, which was 32.0% more than
that achieved by the two pure groups. This result was due to
the fatty acid salts generated from WCO under alkaline con-
ditions, which improved lipid production as a surface-active
agent. However, the mixed group had a substantially lower
WCO usage rate, indicating that the production of microbial
lipids from a single WCO is not economical.
The direct production of biodiesel from WCO is more
economical (Karmakar et al. 2021). Two main methods are
used to produce biodiesel from WCO: esterification and
thermal treatment. Esterification involves the conversion
of triglycerides into methylesters using methanol, whereas
thermal treatment involves thermal cracking, catalysts, and Fig. 4  Frequently studied feedstocks and the corresponding products

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Park 2018). For example, the cost of preparing biodiesel DHA production primarily focus on ensuring product safety,
from glucose and starch is over 20,000 yuan per tonne, with particularly regarding environmental contaminants. National
raw material costs accounting for 60–85% of the total cost governments have set maximum permitted levels of con-
(Shields-Menard et al. 2018). Therefore, the development of taminants in food products to decrease the risk of dietary
low-cost and easily available raw materials is one of the hot exposure and safeguard consumers. In addition to safety
spots for research into products derived from microbial lipid. restrictions, some governments and organizations enforce
In addition, it is worth noting that small amounts of quality criteria. The European Union (EU), China, and the
microbial lipid can also be very valuable. For example, 1 kg USA are key markets for DHA products and typically lead in
of DHA is worth 700 RMB, while 1 ton of biodiesel is worth setting regulations. Other national governments often follow
6000 RMB (Gao et al. 2019). Therefore, with constant yield, the regulations of these major consumer countries or adopt
if the lipid produced contains more than 0.86% DHA, the international guidelines, such as those set by the FAO/WHO
value of DHA in the lipid will be higher than that sold as CODEX Alimentarius (Auchterlonie and Bescoby 2021).
biodiesel. As a result, the valorization of low-cost raw mate- New products may require additional regulatory approval,
rials towards the production of value-added PUFAs such as such as the three algal oil products that have acquired EU
GLA, EPA, ARA, and DHA is attracting increasing interest. regulatory clearance for both food and innovative food uses
EPA, particularly ethyl esters, is commercialized for (Winwood 2013). National regulations, such as those in
hypertriglyceridemia treatments. Lignocellulosic biomass is China, aim to control contaminants in food products. The
a frequently studied source that can be utilized as a low-cost standards set by the China Administration for Quality Super-
C source for PUFA synthesis, not only because lignocellu- vision Inspection and Quarantine and the China Food and
losic biomass is a renewable supply of sugars for the produc- Drug Administration include both safety requirements and
tion of value-added products but also because it is a plentiful quality specifications. The CODEX ALIMENTARIUS and
waste stream (Arevalo-Gallegos et al. 2017). Moreover, as trade groups, such as the Global Organization DHA, pro-
pyrolysis becomes a profitable method for depolymerizing mote Chinese standards that include safety regulations, qual-
lignocellulose into assimilable C, the number of studies on ity criteria, and fair practices in international food trading
it grows dramatically (Palazzolo and Garcia-Perez 2022). (Auchterlonie and Bescoby 2021).
EPA could be produced by microalgae Nannochloropsis
and Crypthecodinium species with lignocellulose (Kar-
naouri et al. 2020; Palazzolo and Garcia-Perez 2022). Since Oleaginous microbes
microalgae Nannochloropsis contain abundant long-chain
polyunsaturated fatty acids and are commonly used for EPA Based on the bibliometric analysis, oleaginous microbes
production (Kumar et al. 2022). The use of wastewater for have emerged as a significant area of research in the field
EPA production has also been frequently investigated, with of microbial lipid production. Oleaginous microorganisms
studies indicating the possibility of using wastewater from are defined as microbes that can accumulate more than 20%
pesticides, pharmaceuticals, municipality sewage, petro- of their dry body mass as lipids, primarily in the form of
leum, and the paper industry as a growth medium for Nan- TAG and FA (Jin et al. 2015). The lipid contents of efficient
nochloropsis to produce EPA (Mitra et al. 2016; Polishchuk oleaginous microbes averagely reach 40% of their dry mass,
et al. 2015). Euglena gracilis grown in aquaculture waste- and even up to 70% of cell dry mass in some strains under
water showed the highest EPA content of 7.6 mg/g (Tos- optimal conditions (Palazzolo and Garcia-Perez 2022). Ole-
savainen et al. 2019). aginous microbes predominantly comprise bacteria, yeast,
DHA is essential for correct brain and visual development mold, and microalgae (Fig. 5). Among the several types of
in newborns (Palazzolo and Garcia-Perez 2022). Crypthe- most studied microorganisms, oleaginous yeast generally has
codinium cohnii is well-known for producing high amounts a higher biomass and lipid content.
of DHA-enriched lipids, with DHA content typically rang-
ing from 30 to 50%. To achieve efficient DHA production, Oleaginous bacteria
lignocellulosic hydrolysates are often used as feedstocks for
C. cohnii (Asimakopoulou et al. 2021; Karnaouri et al. 2020, Oleaginous bacteria generally accumulate polyhydroxyal-
2021). Thraustochytrids are good heterotrophic microorgan- kanoates (PHAs) for energy storage, while TAGs, mainly
isms for the commercial production of DHA (Patel et al. C16:0, C18:0, and C18:1, are synthesized by some strains
2020), and Aurantiochytrium and Schizochytrium are com- under N-limiting conditions, such as Mycobacterium, Nocar-
monly studied for wastewater treatment in combination with dia, Rhodococcus, and Streptomyces (Goswami et al. 2017).
DHA production because of their ability to accumulate large Rhodococcus spp., particularly R. opacus and R. jostii, are
quantities of DHA (Bagul and Annapure 2020; Chen et al. potential microbial cell factories for lipid generation and
2016b; Humaidah et al. 2020). The regulations governing have gained special interest due to their capacity to convert

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Fig. 5  Comparison of the


production of microbial lipids
among different oleaginous
microbes

agro-industrial wastes into value-added lipids (Cho et al. (Liang and Jiang 2013). Furthermore, unlike microalgae,
2020). Some other bacteria, such as cyanobacteria (Eun- mold can grow in traditional bioreactors, lowering the cost
grasamee et al. 2019) and Methylomicrobium buryatense of lipid synthesis (Chintagunta et al. 2021).
(Demidenko et al. 2017), could produce FAs and deriva-
tives using carbon dioxide ­(CO2) and methane, respectively.
Bacteria usually generate less lipid per gram of biomass than Oleaginous microalgae
other oleaginous microbes (Bellou et al. 2016). Furthermore,
lipids adhere strongly to the bacterial membrane, making Microalgae grow autotrophically and can convert ­CO 2
them difficult to extract (Bao et al. 2021). Thus, the indus- into high-value products by photosynthesis in most cases
trial application of bacteria for lipid production is limited. (Azarpour et al. 2022; Das et al. 2021). However, micro-
However, compared to other microbes, the genetic regulation algae can also be cultivated under heterotrophic condi-
mechanism of oleaginous bacteria in FAs synthesis is more tions or mixed conditions with organic C amendment (Liu
thorough, so bacteria could be genetically manipulated to et al. 2021). Compared to autotrophic microalgae, hetero-
enhance lipid production. For example, the titers of ethyl trophic microalgae have shown a 900% increase in lipid
esters FA and long-chain hydrocarbons produced by meta- yield (Tomas-Pejo et al. 2021). Under heterotrophic con-
bolically engineered R. opacus were obviously improved ditions, the microalgae could accumulate a high amount
(Kim et al. 2019). of omega-3 fatty acids such as DHA and EPA, as well
as omega-6 fatty acids such as GLA and AA (Das et al.
Oleaginous mold 2021; Karnaouri et al. 2020; Kumar et al. 2022). Further-
more, microalgae can grow in salt or seawater (Park et al.
Oleaginous molds include Mortierella, Aspergillus, 2019). Most microalgae generate small amounts of TAGs;
Dmsporangium, Cunnighamella, Mucor, Saprolegnia, and however, when exposed to salicylic acid stress, Nanno-
Pichia (Donot et al. 2014) and can store lipids up to 80% chloropsis sp. achieved a high TAG yield of 475 mg/L
of their biomass (Pinzi et al. 2014). Mold-produced micro- (Udayan et al. 2020). Among various microalgal species,
bial lipids are more unsaturated than yeast-produced lipids Chlorella vulgaris has been frequently used for TAG and
(Papanikolaou and Aggelis 2011), and most molds have FA production due to its potential for breeding on a large
been explored to produce special lipids rich in PUFAs, scale (Jeevan Kumar et al. 2020; Sakarika and Kornaros
such as DHA, EPA, γ-linolenic acid (GLA), and ARA, 2019). Microalgae exhibit several unique characteristics,
which have attracted much medical and dietetical inter- including high ­CO2 utilization efficiency, greater lipid pro-
est. Several microbial lipids derived from molds are now ductivity than most commercially used plants, minimum
commercially available, including GLA from Mucor cir- land requirement, and autotrophic mode of nutrition (Park
cinelloides and ARA from Mortierella alpina (Khot et al. et al. 2019). However, low growth rates and high dewater-
2020). However, mold lipid use for biodiesel synthesis is ing costs are the major drawbacks of microalgal FAs and
still at the laboratory scale, and there are few publications TAGs production (Cho et al. 2020).
on the utilization of mold lipids for biodiesel production

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Oleaginous yeast methods (Fig. 6). To obtain high cell density and product
yield, the fed-batch mode is preferred over other cultiva-
Oleaginous yeasts are the most studied microbes owing to tion strategies (Chatterjee and Mohan 2020). Owing to the
their rapid growth rate, viral infection resistance, and capac- different needs of oleaginous microbes at different stages,
ity to reach high cell densities (Kamineni and Shaw 2020). two-stage fermentation or two-stage fed-batch cultivation
The FA distribution in oleaginous yeast is relatively sim- have received substantial attention in recent years (Boonyarit
ple, with hexadecanoic acid and octadecanoic acid as the et al. 2020; Polburee and Limtong 2020; Poontawee and
main fatty acids, similar to many vegetable oils. The TAG Limtong 2020).
content is high in lipids produced by yeast, accounting for
90% of the storage of lipids (Donot et al. 2014). Among Batch mode
oleaginous microorganisms, yeast shows the greatest genus
diversity (Palazzolo and Garcia-Perez 2022). Approximately Batch culture refers to adding all the reaction components
5% of the 1600 known yeast species are oleaginous (Garay into the flask or bioreactor at the beginning. It is a funda-
et al. 2016). The extensively studied lipid-producing yeasts mental and well-studied mode for lipid synthesis (Karam-
include Rhodotorula glutinis, Lipomyces Starkey, Rho- erou and Webb 2019). The batch mode in flasks is frequently
dosporidium toruloides, Cryptococcus curvatus, and Yar- used for media optimization or exploring the lipid produc-
rowia lipolytica (Ma et al. 2021). Y. lipolytica possesses an tion capacities of oleaginous strains (Chang et al. 2015;
evolutionarily advanced C-to-lipid flow, which is activated Huang et al. 2016b; Tchakouteu et al. 2015a). When cultured
during the stationary growth phase under N limited and in a bioreactor, optimal fermentation conditions for lipid
C surplus conditions (Takaku et al. 2020). R. toruloides synthesis were studied, including pH (Cavero-Olguin et al.
and L. starkeyi exhibit greater metabolic flexibility than Y. 2021) and nutrient concentrations (Cho et al. 2017). The
lipolytica (Spagnuolo et al. 2019). Oleaginous yeasts have results of batch cultivations are shown in Table 1. Because
significant benefits over other forms of oleaginous microor- a small amount of N was supplied in batch mode, the initial
ganisms, including ease of culture and resistance to bacte- concentration of nutrients in the medium limits the growth
rial contamination (Santamauro et al. 2014). In addition, as of bacteria. Simply increasing the initial concentration of
oleaginous yeast can utilize different low-cost feedstocks, nutrients may sometimes fail to improve the biomass and
they are promising alternative lipid sources (Karamerou and lipid yield; on the contrary, it may have a toxic effect on the
Webb 2019). strains (Christophe et al. 2012). Many researchers have real-
ized that it is difficult to improve the lipid content in batch
mode, so other culture modes have been studied and applied.
Cultivation modes of oleaginous microbes
Fed‑batch mode
The culture mode can affect the yield and productivity of
microbial lipid (Karamerou and Webb 2019). The primary Fed-batch fermentation refers to adding substrates into
culture modes may be categorized into batch, fed-batch, the reactor multiple times (Kumar et al. 2021; Zhao et al.
and continuous based on the various nutrient amendment 2022). One of the most frequent strategies for microbial

Fig. 6  Comparison of several


common cultivation modes
utilized for lipid production

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Table 1  A summary of the yields produced during batch fermentation on different substrates
Strain Carbon source Scale DCW (g/L) Lipid content (%) Ref

Rhodosporidium toruloides Crude glycerol Shake flask 14.85 41.76 (Gao et al. 2016)
Rhodosporidium toruloides Glucose 3.5 L bioreactor 36.2 65.1 (Tchakouteu et al. 2017)
Rhodosporidium paludigenum Enzymatic corncob hydrolysate 3.0 L bioreactor 27.77 70 (Chaiyaso et al. 2019)
Rhodosporidium toruloides Glycerol 1 L bioreactor 17.7 42.13 (Lopes et al. 2020)
Rhodotorula graminis Corn stover hydrolysate 1 L bioreactor 48 34 (Galafassi et al. 2012)
Rhodotorula glutinis Pure glycerol 2 L bioreactor 5.3 33 (Karamerou et al. 2016)
Lipomyces starkeyi Crude glycerol Shake flask 16.2 54.3 (Tchakouteu et al. 2015b)
Lipomyces starkeyi Hemicellulose hydrolysate 1.3 L bioreactor 9.6 26.1 (Xavier et al. 2017)
Cryptococcus curvatus Waste spent yeast Shake flask 50.4 37.7 (Ryu et al. 2013)

lipid synthesis in this process is the intermittent supply Continuous mode


of glucose without the removal of the fermentation broth
(Chang et al. 2013). Fed-batch cultivation is an effective Continuous mode involves continuously adding fresh sub-
mode for achieving higher cell densities, lipid content, strates to a well-stirred culture at a certain speed, and prod-
and lipid yield (Anschau et al. 2014; Chen et al. 2018). ucts and cells are withdrawn at the same speed to maintain a
Results obtained from fed-batch cultivation modes are stable C/N ratio in the fermentation system (Christophe et al.
displayed in Table 2. Compared to batch mode, fed-batch 2012). Continuous culture outperforms batch mode in terms
culture minimizes the inhibition of high concentrations of of lipid productivity and economic viability since it enables
substrate and end-products on the growth and metabolism the collection of products during the fermentation process
of the oleaginous microbes (Fei et al. 2016). In addition, (Karamerou and Webb 2019). In addition, the continuous
the operation of the fed-batch mode is as easy and reli- feeding supply prevents the cells from being inhibited by
able as batch mode (Salehmin et al. 2013). However, the a large amount of substrate. Continuous mode allows for
performance of the fed-batch mode is strongly reliant on parameter isolation and exploration of its impact on lipid
the feeding strategy used during culture (Chen et al. 2018; synthesis while maintaining the other parameters constant,
Kumar et al. 2021). Due to their relatively simple and low such as cell concentration, growth, and substrate absorp-
cost, simple indirect feedback control strategies combin- tion (Anschau et al. 2014). In continuous cultivation, the
ing substrate feeding with pH or dissolved oxygen (DO) main factor that affects lipid productivity is the dilution rate
determination have been employed for many years. Nev- (Karamerou and Webb 2019). Since cell proliferation and
ertheless, the sluggish response of cells to the changes product synthesis could be inhibited under high concentra-
in pH or DO caused by substrate usage could result in tions of such wastes. In a broader context, continuous feed-
over- or under-feeding, which might affect microbial lipid ing at low dilution rates is more advantageous for the utili-
production (Fei et al. 2016). zation of low-cost wastes rich in C, such as lignocellulosic
hydrolysates and crude glycerol, because these wastes often
contain a large number of toxic compounds (Gorte et al.
2020). The lipid production during continuous cultivations

Table 2  Summary of lipid productions obtained via fed-batch cultivation


Strain Carbon source Scale DCW (g/L) Lipid content (%) Ref

Rhodosporidium toruloides Glucose 15 L bioreactor 106.5 67.5 (Li et al. 2007)


Rhodosporidium toruloides Cornstalk hydrolysate 15 L bioreactor 78.7 61.8 (Zhao et al. 2011)
Rhodosporidium paludigenum Enzymatic corncob hydrolysate 3.0 L bioreactor 36.06 70 (Chaiyaso et al. 2019)
Cryptococcus sp. Glucose and corncob hydrolysate Shake flask 10.8 61.3 (Chang et al. 2013)
Lipomyces starkeyi Glucose and xylose 1 L bioreactor 86.4 36.2 (Anschau et al. 2014)
Rhodotorula glutinis Crude glycerol 50 L bioreactor 39.2 43.3 (Yen et al. 2015)
Trichosporon oleaginosus Crude glycerol 15 L bioreactor 21.87 49.89 (Chen et al. 2017)
Cutaneotrichosporon oleagino- Alkaline organosolv-pretreated Shake flask 50.7 61.7 (Gong et al. 2020)
sum corn stover

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at various dilution rates is summarized in Table 3. The con- et al. 2021b). Two-stage fermentation can be implemented
tinuous mode may be superior to the batch mode because of in both fed-batch and continuous modes and allows easy
its long-term operation and consistent biomass. Long-term adjustment of the two stages by modifying the nutrient input
fermentation, on the other hand, may result in blockages due (Karamerou and Webb 2019). Boonyarit et al. (2020) used
to biofilm development or medium sedimentation, as well a two-stage batch mode strategy with sugarcane top and
as contamination and changes in cell viability, which may crude glycerol as feedstocks, R. fluvialis used sugarcane top
reduce overall yield (Karamerou and Webb 2019). hydrolysate as a substrate for cell proliferation at 200 r/min
and 28 °C, and crude glycerol solution was utilized for lipid
Two‑stage fermentation synthesis in the second stage. A high lipid concentration and
lipid content of 15.85 g/L and 73.04%, respectively, were
Microbial lipid production consists of two stages, in which observed (Table 4). Two-stage fermentation is not limited
the biomass first grows, and then lipid accumulation occurs. to nutrients; other factors, such as pH (Zhang et al. 2019a),
The cell proliferation phase requires a rich medium, whereas C/N ratio (Fu et al. 2018), DO (Zhang et al. 2019b), and tem-
the lipid accumulation requires only a carbon source (Xu perature (Polburee et al. 2016), could be adjusted to ensure
et al. 2017). The difference in nutritional demand between that the culture conditions are more targeted for both phases.
biomass growth and lipid yield presents a dilemma (Fei Zhang et al. (2019a) developed a two-stage fed-batch pH
et al. 2015; Xu et al. 2017). Two-stage cultivation is used regulation strategy using acetate as a substrate by R. glutinis.
to separate the cell proliferation and lipid accumulation As a result, a promoted biomass of 67.2 g/L at pH 6.6 and
phases, thereby creating an environment suitable for biomass an enhanced lipid titer of 29.3 g/L at pH 7.0 were achieved.
growth and lipid accumulation. This mode allows oleaginous The biomass and lipid titer increased 15.6-fold and 19.1-
microbes to increase biomass under suitable conditions and fold, respectively, compared to those in the one-stage batch
then transfer to another system for lipid accumulation, which mode. Optimizing the DO concentration during the growth
has been demonstrated to improve lipid production (Zhang and lipogenesis phases can enhance the lipid content of T.

Table 3  The effect of the dilution rates on the lipid production under continuous cultivations
Strain Carbon source Dilution rate DCW (g/L) Lipid con- Ref
­(h−1) tent (%)

Schizochytrium sp. Glucose and glutamate 0.02 7.7 31 (Ganuza and Izquierdo 2007)
Rhodosporidium toruloides Glucose 0.02 8.67 8.66 (Shen et al. 2013)
Cryptococcus curvatus Acetate 0.04 1.34 56.7 (Gong et al. 2015)
Lipomyces starkeyi Glucose and xylose 0.06 10 43.3 (Anschau et al. 2014)
Yarrowia lipolytica Crude glycerol 0.03 8.1 43.3 (Papanikolaou and Aggelis 2002)
Yarrowia lipolytica Glycerol 0.01 59.8 31 (Rakicka et al. 2015)
Rhodotorula glutinis Glucose 0.02 27 35.2 (Shen et al. 2020)

Table 4  Overview of lipid production on two-stage cultivations


Strain Operation DCW (g/L) Lipid content (%) Ref

Rhodosporidium toruloides Cultivation in glucose medium followed by resuspen- 6.75 50.1 (Huang et al. 2016b)
sion in acetic acid
Lipomyces starkeyi Growth in a 15 L bioreactor using glucose-rich medium 104.6 64.9 (Lin et al. 2011)
and resuspension in a 7 L bioreactor using glucose
media
Cryptococcus curvatus Cultivation in N-acetylglucosamine media and resus- 16.8 54.2 (Tang et al. 2018)
pension to N-glucosamine solution
Rhodosporidiobolus fluvialis Cultivation in sugarcane top hydrolysate medium fol- 21.07 73.04 (Boonyarit et al. 2020)
lowed by resuspension in crude glycerol
Rhodosporidium toruloides Cultivation in food waste hydrolysate with pH of 4.0 13.86 50 (Gao et al. 2019)
and resuspension with pH of 11.0 in shake flask
Yarrowia lipolytica 60 h of growth in glycerol medium followed by the 41.02 34.59 (Fontanille et al. 2012)
addition of VFAs in a 7 L bioreactor

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oleaginosus while reducing energy consumption. Zhang situ two-stage fermentation mode can tolerate greater lac-
et al. (2019b) found that maintaining a high DO concentra- tic acid concentrations in the substrate, whereas the in situ
tion during the growth stage and a low DO concentration fermentation mode enables greater lipid production and has
during the lipogenesis phase allowed the supply of only the the potential for practical use.
necessary oxygen for the yeast.
Our group developed a two-stage fermentation mode: ex
situ and in situ. As we found that lactic acid can promote
cell proliferation but inhibit lipid accumulation, a two-stage Metabolic engineering strategies and lipid
fermentation was developed using R. toruloides in differ- production
ent systems with high and low lactic acid concentrations.
After 4 days of cell proliferation in 100 mL of saccharified The yield of microbial lipid production is closely linked
food waste liquid (lactic acid concentration of 8.3 g/L), the to the flow of metabolic pathways in oleaginous microor-
bacteria were transferred to 100 mL of saccharified liquid ganisms. The use of glucose by oleaginous yeasts has been
(lactic acid concentration of 0.3 g/L) prepared from fresh extensively studied with respect to microbial lipid synthesis
food waste for 6 days for lipid accumulation. Compared to (Fig. 7). A condition in which there is an excess of C and
traditional one-stage fermentation, this ex situ two-stage fer- a deficiency of N can induce lipid synthesis (McNeil and
mentation resulted in a total lipid concentration of 9.19 g/L Stuart 2018). The depletion of N results in increased AMP
and a lipid yield of 0.204 g/g total sugar, which increased by deaminase activity, leading to the breakdown of adeno-
44.27% and 60.63%, respectively (Ma et al. 2019). In addi- sine monophosphate (AMP) into inosine 5′-monophos-
tion, as an acidic environment (pH 4.0) can promote the cell phate (IMP) and ammonia, and ammonia is an emergency
proliferation of R. toruloides and an alkaline environment response to N depletion. Low levels of AMP could dimin-
(pH 11.0) can promote lipid accumulation, an in situ two- ish the activity of isocitrate dehydrogenase (IDH), a unique
stage fermentation mode based on pH in the same medium effect found only in oleaginous species (Kosa and Ragauskas
was developed; that is, after adjusting the pH of the hydro- 2011), resulting in citrate accumulation in the mitochon-
lysate to 4.0, sterilization and inoculation for acid stage fer- dria (Zhang et al. 2022). The ATP-citrate lyase (ACL) will
mentation were conducted for 1 day. The pH value was then cleave the accumulated citrate into acetyl-CoA and oxaloac-
adjusted to 11.0, and the yeast was fermented in an alkaline etate (OAA) in the cytosol after it is exported by the cit-
stage for 5 days, in which the maximum lipid production was rate/malate translocase (CMT) (Chattopadhyay et al. 2021).
6.94 g/L, which was 84.6% higher than that in the traditional Subsequently, OAA is converted to malate, which is further
single-stage fermentation (Gao et al. 2019). Alkaline condi- converted to pyruvate in the presence of a malic enzyme
tions increase the degree of WCO hydrolysis in food waste (ME). Acetyl-CoA carboxylase (ACC) converts a part of
hydrolysis solutions, and the generated fatty acid salts act acetyl-CoA into malonyl-CoA (Kamineni and Shaw 2020).
as surfactants that promote the utilization of the substrate Then fatty acid synthase (FAS) involves both acetyl-CoA
by oleaginous yeast (Gao et al. 2022). In conclusion, the ex and malonyl-CoA in the synthesis of acyl-CoA, which is

Fig. 7  Simplified overview of


lipid synthesis and the regula-
tory pathways of oleaginous
yeast. ER, endoplasmic reticu-
lum; MT, mitochondria; ACL,
ATP-citrate lyase; MDH, malate
dehydrogenase; ME, malic
enzyme; ACC, acetyl-CoA
carboxylase; FAS, fatty acyl
synthetase; M-ACP, malonyl
acyl-carrier protein; G3P,
glycerol-3-phosphate; GPAT,
Acyl-CoA: glycerol-sn-3-phos-
phate acyltransferase; PA,
phosphatidic acid; DAG, diacyl-
glycerol; DGAT, diacylglycerol
acyltransferase; TAG, triacylg-
lycerol; PUFA, polyunsaturated
fatty acid

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then incorporated into the Kennedy pathway to form triacyl- related to lipid synthesis and knocking out competing
glycerol (TAG) in the endoplasmic reticulum (Zhang et al. pathways that flow to other byproducts (Table 5). Genes
2022). involved in FA and TAG syntheses, such as ACC1, ME,
Metabolic engineering strategies have been widely DGAT1, and DGA1, were generally overexpressed. Also,
employed in yeast and microalgae to reconfigure their genes that participated in the competing pathway, such
internal metabolic networks and enhance lipid produc- as ADP-glucose pyrophosphorylase (AGPase), UDP-glu-
tion (Jakhwal et al. 2022; Kamineni and Shaw 2020; Qiao cose pyrophosphorylase gene (UDPase), and lipase, were
et al. 2015). These strategies include overexpressing genes knocked out or knocked down (Kang et al. 2022).

Table 5  Overviews of metabolic engineering approaches to enhance lipid synthesis in oleaginous microbes
Gene Approach Strains Phenotypic changes REF

FA and TAG biosynthesis


ACC​ Overexpression of PtACC2 Phaeodactylum tricornutum 1.77-fold increase in lipid (Li et al. 2018)
content
ACC​ Overexpression of ACC​ Schizochytrium sp. 24% increase in DHA (Han et al. 2020)
ACC​ Heterologous expression of Saccharomyces cerevisiae 24% increase in lipid (Wang et al. 2016)
LsACC1 content
ME Heterologous expression Rhodotorula mucilaginosa 1.18-fold increase in lipid (Bandhu et al. 2019)
of ME production
ME Overexpression of NsME1 Nannochloropsis salina 53% increase in FA methyl (Jeon et al. 2021)
ester yield
ME Overexpression of ME Chlorella protothecoides 2.8-fold increase in lipid (Yan et al. 2019)
accumulation
FAS Overexpression of FAS1 and Saccharomyces cerevisiae 53% increase in lipid (Runguphan and Keasling
FAS2 content 2014)
FAS Overexpression of FAS1 Yarrowia lipolytica 33% increase in lipid titer (Silverman et al. 2016)
GPAT Overexpression of AGPAT1 Phaeodactylum tricornutum 1.81-fold increase in TAG (Balamurugan et al. 2017)
content
GPAT Overexpression of GPAT2 Phaeodactylum tricornutum 2.9-fold increase in TAG (Wang et al. 2020c)
content
GPAT Heterologous expression of Saccharomyces cerevisiae 1.3-fold in lipid content (Wei et al. 2017)
GPAT
DGAT​ Heterologous expression of Scenedesmus obliquus 2-fold increase in lipid (Chen et al. 2016a)
DGTT1 content
DGAT​ Overexpression of DGAT1 Nannochloropsis oceanica 2.4-fold and 47% increase in (Wei et al. 2017)
TAG content and yield
DGAT​ Overexpression of DGAT1 Phaeodactylum tricornutum 2.3-fold increase in TAG (Wang et al. 2018)
and LPAT1 content
DGAT​ Overexpression of DGA1 Yarrowia lipolytica 4-fold increase in lipid (Tai and Stephanopoulos
production 2013)
DGAT​ Overexpression of DGA1 Rhodosporidiobolus 2.5-fold increase in lipid (Polburee et al. 2018)
fluvialis content
DGAT​ Heterologous expression of Candida phangngensis 32% increase in lipid titer (Quarterman et al. 2018)
DGA1
Competitive pathways
AGPase Knockout Chlamydomonas 10-fold increase in TAG​ (Li et al. 2010)
UGPase Knockout Phaeodactylum tricornutum 45-fold increase in TAG​ (Daboussi et al. 2014)
YlGSY1 Knockout Yarrowia lipolytica 60% increase in TAG​ (Bhutada et al. 2017)
YlTGL3 and YlTGL4 Knockout Yarrowia lipolytica 10% increase in TAG (Dulermo et al. 2013)
content
CrACX2 Knockout Chlamydomonas 20% increase in TAG (Kong et al. 2017)
content

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Enhancing FA and TAG synthesis via overexpressing Blocking enzymes involved in polysaccharide synthe-
of lipid synthesis‑related genes sis can favor lipid production in various microorganisms
(Dourou et al. 2018). For instance, Bhutada et al. (2017)
When it comes to lipid synthesis, acetyl-CoA carboxy- deleted the ylGSY1 gene, which encodes glycogen synthase
lase (ACC) and diacylglyceride acyl-transferases (DGAT) in Y. lipolytica, and achieved an up to 60% increase in TAG
are two enzymes that have received considerable attention accumulation. In microalgae, blocking starch synthesis and
(Tomas-Pejo et al. 2021). ACC catalyzes the first rate-limit- storage could be a more effective method to enhance TAG
ing step in FA production and has therefore been primarily accumulation than direct engineering of the lipid biosynthe-
targeted (Park et al. 2019). Overexpressions of the lipid path- sis pathway (Dourou et al. 2018). Several microalgal strains
way gene in oleaginous yeast, ACC1, have been reported, utilize C to produce starch as the main storage metabolite
but relatively smaller improvements have been achieved (Tai (Park et al. 2019). Inactivating AGPase in a Chlamydomonas
and Stephanopoulos 2013; Wang et al. 2016). In contrast, starchless mutant resulted in a tenfold rise in TAG (Li et al.
overexpression of endogenous ACC2 in microalgae P. tri- 2010). Disruption of the UDPase in Phaeodactylum tricor-
cornutum resulted in 1.77-fold increases in the neutral lipid nutum resulted in a 45-fold increase in TAG accumulation
content (Li et al. 2018). (Daboussi et al. 2014).
Oleaginous microbes are capable of synthesizing large Inhibiting β-oxidation is another potential strategy that
quantities of TAG under N-restricted conditions due to their focuses on TAG mobilization and oxidation pathways
high DGAT activity (Kosa and Ragauskas 2011). Therefore, (Probst et al. 2016). As β-oxidation occurs in peroxisomes,
multiple gene overexpression studies indicate that DGAT, genes involved in peroxisome biogenesis, such as PEX3,
responsible for the final step of TAG synthesis, has a promi- PEX10, and PEX11 in Y. lipolytica, have been deleted to
nent influence on productivity in oleaginous yeast (Blazeck prevent TAG degradation (Lazar et al. 2018; Wang et al.
et al. 2014; Kamineni and Shaw 2020; Tai and Stephanop- 2020a). TAG mobilization by TAG lipases (TGLs) is the
oulos 2013). DGA1 and DGA2 are two isozymes found in initial step in the breakdown process; therefore, the down-
oleaginous yeast, and overexpression of either has improved regulation of TGLs could inhibit TAG mobilization for
cell-specific lipid productivity (Kamineni and Shaw 2020). β-oxidation. Deletion of either or both YlTGL3 and YlTGL4
The overexpression of either DGA1 or DGA2 led to an in Y. lipolytica resulted in an increase of 10% in TAG content
increase in lipid content of up to 33.8% and 39%, respec- (Dulermo et al. 2013). Under N-limited circumstances, the
tively (Chattopadhyay et al. 2021). DGAT overexpression mutation of the CrACX2 gene, which encodes a member of
is also a commonly attempted approach in microalgae, and the acyl-CoA oxidase/dehydrogenase superfamily, led to a
lipid production has been found to increase in most cases 20% rise in lipid contents in Chlamydomonas (Kong et al.
(Iwai et al. 2014; Li et al. 2016). Microalgae have four types 2017).
of DGAT: DGAT1, DGAT2, DGAT3, and wax ester synthase/
acyl-coenzyme A (acyl-CoA): diacylglycerol acyltransferase
(WS/DGAT​) (Kang et al. 2022). Overexpression of DGAT1 Environmental implications and future
in Nannochloropsis oceanica increased TAG content and directions
yield by 2.4-fold and 47%, respectively (Wei et al. 2017).
The WS/DGAT​overexpression in Phaeodactylum tricornu- Several environmental issues have arisen as a result of
tum resulted in a 40% rise in TAG content (Cui et al. 2018). the use of fossil fuels, such as global warming caused by
greenhouse gas emissions produced during the combustion
of fossil fuels to generate electricity (Saha and Mukhopad-
Blocking the contribution of competitive pathways hyay 2021). The swift rise of renewable energy sources is
in line with the concept of “more energy, less carbon emis-
Another effective strategy for enhancing lipid production is sions”. Microbial lipid has been identified as an attractive
to block competing metabolic pathways. Various gene edit- possibility for biochemical production. Biodiesel produced
ing techniques, such as meganucleases and transcription from microbial lipids presents a number of benefits over
activator-like effector nucleases (TALENs), interfering, and traditional petroleum-based diesel, such as being a safer
antisense RNA methods (Levering et al. 2015), have been and cleaner alternative for the environment (Leong et al.
employed to knockdown and knockout genes responsible 2018). A recent study indicated that converting global food
for byproduct production. These genes are involved in low- waste into biodiesel could potentially replace around 27.9
molecular metabolites secretion (e.g., citric acid, polyols) million tonnes of mineral diesel, leading to a reduction
(Steiger et al. 2019), polysaccharide or PHA accumulation of roughly 0.31 million tonnes of C ­ O 2 emissions (Gao
(Bhutada et al. 2017), and the lipid degradation pathway et al. 2022). Also, microbial lipid can be generated by
(Shin et al. 2019). agro-industrial wastes, and part of it solves the problem

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of waste disposal (Cho and Park 2018). For example, the Conclusion
usage of WCO to produce biodiesel has become a criti-
cal development direction, where biodiesel production Microbial lipids, as renewable energy sources, may be a
from WCO not only replaces petroleum-based diesel and promising approach to tackle the problems of fossil fuel
reduces environmental pollution but also improves the depletion, environmental contamination, and climate
industrial added value of waste oil, ultimately achieving change. However, large-scale microbial lipid development
waste-to-energy goals (Gao et al. 2022). Additionally, lipid is still limited owing to high processing costs and low yields.
fermentation wastewater can be used in various applica- The main opportunity is to study feedstock supply and meta-
tions, such as bacterial cellulose production (Huang et al. bolic modifications to produce high-value-added products.
2016a) and phosphorus recovery (Wu et al. 2023). The However, to actualize this progress, low-cost, substantial,
treatment of lipid fermentation wastewater could not pos- and sustainable raw materials must be explored. Highly
sibly be another issue that increases the sustainability of effective oleaginous strains must be selected or encoded,
microbial production methods. and the involvement of two or more genes in lipid synthesis
Large-scale microbial lipid production has been exten- must be clarified. In a single study, focusing on a particular
sively studied in the past, but the high costs associated feedstock and examining its fermentation using a group of
with commercial application remain a major challenge oleaginous bacteria as both novel candidates and controls
(Chaturvedi et al. 2019). On the other hand, microbial con- were preferred. Simultaneously, exploring and stabilizing
version processes have low product concentrations, which the synthesis route of high-value-added products could
increase downstream processing costs (Rodionova et al. expand the commercial applications of microbial lipids.
2022). To address these challenges, several approaches
need to be considered. First, it is crucial to further explore
low-cost, substantial, and sustainable feedstocks for lipid Author contribution All authors contributed to the study’s concep-
tion and design. Material preparation, data collection, and analysis
synthesis. Waste streams for lipid production need to be were performed by Haishu Sun, Zhen Gao, and Lirong Zhang. Review
identified and adopted, such as lignocellulosic biomass, and editing were performed by Xiaona Wang, Ming Gao, and Qunhui
which is the most abundant for energy recovery. However, Wang. Supervision was performed by Xiaona Wang and Qunhui Wang.
lignin is difficult to degrade. The future studies should The first draft of the manuscript was written by Haishu Sun, and all
authors commented on previous versions of the manuscript. All authors
focus on the structural characterization of lignocellulosic read and approved the final manuscript.
waste, mechanisms of degradation, and process develop-
ment for valorization. The pretreatment of raw substrates Funding This work was supported by Tianjin Education Commission
is also necessary to enhance the efficiency of the process Scientific Research Planning Project [grant number 2021KJ064] and
Guangdong Basic and Applied Basic Research Foundation [grant num-
(Qin et al. 2017). Second, selecting or encoding new ber 2022A1515110943].
strains will definitively improve the lipid generation from
wastes. Although several key genes have been identified Data availability Not applicable
through genetic engineering and the effects of these genes
have been studied independently, future research should Declarations
explore theories that explain how two or more genes inter- Ethics approval and consent to participate Not applicable
act in the process. Furthermore, a systems biology technol-
ogy based on omics and computational models will aid in Consent for publication Not applicable
the design and reconstruction of superior strains for lipid
Competing interests The authors declare no competing interests.
production enhancement. Third, the fermentation process
is quite important to the total cost. Developing two-stage
fermentation modes might promote high lipid production
while supplying nutrients at the appropriate fermentation
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