BIOENGINEERED

2022, VOL. 13, NO. 1, 1073–1089

https://doi.org/10.1080/21655979.2021.2017624

REVIEW

Composting and its application in bioremediation of organic contaminants

Chitsan Lina,b, Nicholas Kiprotich Cheruiyotb, Xuan-Thanh Buic,d, and Huu Hao Ngoe
a
Maritime Science and Technology, College of Maritime, National Kaohsiung University of Science and Technology, Kaohsiung, Taiwan (R.O.
C.); bDepartment of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung, Taiwan (R.O.
C.); cKey Laboratory of Advanced Waste Treatment Technology, Ho Chi Minh City University of Technology (HCMUT), Vietnam National
University Ho Chi Minh (VNU-HCM), Ho Chi Minh City, Vietnam; dFaculty of Environment & Natural Resources, Ho Chi Minh City University of
Technology (Hcmut), Ho Chi Minh City, Vietnam; eCentre for Technology in Water and Wastewater, School of Civil and Environmental
Engineering, University of Technology Sydney, Sydney, Australia

ABSTRACT ARTICLE HISTORY

This review investigates the findings of the most up-to-date literature on bioremediation via Received 18 October 2021
composting technology. Studies on bioremediation via composting began during the 1990s and Revised 7 December 2021
have exponentially increased over the years. A total of 655 articles have been published since Accepted 7 December 2021
then, with 40% published in the last six years. The robustness, low cost, and easy operation of KEYWORDS
composting technology make it an attractive bioremediation strategy for organic contaminants Aerobic biodegradation;
prevalent in soils and sediment. Successful pilot-and large-scale bioremediation of organic con­ bioaugmentation; bio-
taminants, e.g., total petroleum hydrocarbons, plasticizers, and persistent organic pollutants stimulation; green
(POPs) by composting, has been documented in the literature. For example, composting could technology; microbial
remediate >90% diesel with concentrations as high as 26,315 mg kg−a of initial composting community; recalcitrant
material after 24 days. Composting has unique advantages over traditional single- and multi- organic contaminants
strain bioaugmentation approaches, including a diverse microbial community, ease of operation,
and the ability to handle higher concentrations. Bioremediation via composting depends on the
diverse microbial community; thus, key parameters, including nutrients (C/N ratio = 25–30),
moisture (55–65%), and oxygen content (O2 > 10%) should be optimized for successful bioreme­
diation. This review will provide bioremediation and composting researchers with the most recent
finding in the field and stimulate new research ideas.

1. Introduction aromatic hydrocarbons (PAHs) [1–3], total petro­

leum hydrocarbons (TPHs) [4], diesel [5], phtha­
Composting is a self-heating biological process
late-based plasticizers [6,7], organochlorine
that has been used for centuries as an organic
pesticides [8], polychlorinated dibenzo-p-dioxins
waste management solution. Apart from managing
and furans (PCDD/Fs) [9,10], and polychlorinated
organic waste, the composting product can be used
biphenyls (PCBs) [11].
as a soil amendment and organic fertilizer. The diverse microbial communities present in
Composting research has made substantial composting materials are responsible for the bio­
advances over the years, especially on shortening degradation of recalcitrant organic contaminants.
the composting process and improving compost This degradation process could take the form of
quality. The research has been aided by the knowl­ either complete mineralization/metabolism, co-
edge of parameters affecting the composting pro­ metabolism, or nonspecific extracellular oxidation.
cess, including initial particle size, nutrients, Several studies have identified species that can
oxygen content, moisture content, pH, and tem­ mineralize these contaminants. For instance,
perature. In addition, because composting can bio­ Acinetobacter lwoffii, Bacillus subtilis and
degrade organic products, researchers have been Raoultella ornithinolytica can degrade crude oil
interested in using this technology to treat recalci­ [12]. Moreover, high temperatures during the
trant organic contaminants, including polycyclic composting (thermophilic phase) also enhance

CONTACT Chitsan Lin [email protected] Ph.D. Program in Maritime Science and Technology, College of Maritime, National Kaohsiung University of
Science and Technology, Kaohsiung 81157, Taiwan (R.O.C.); Department of Marine Environmental Engineering, National Kaohsiung University of Science and
Technology, Kaohsiung 81157, Taiwan (R.O.C.); Huu Hao Ngo [email protected] Centre for Technology in Water and Wastewater, School of
Civil and Environmental Engineering, University of Technology Sydney, NSW 2007, Australia
© 2022 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted
use, distribution, and reproduction in any medium, provided the original work is properly cited.
1074 C. LIN ET AL.

degradation by making the contaminants less vis­ organic compounds such as sugars, organic acids
cous and more bioavailable. Biosurfactants, e.g., may be produced during the fermentation of these
rhamnolipids produced by certain microbial spe­ compounds, resulting in a pH drop into the acidic
cies during composting, also enhance biodegrada­ range. However, the pH will not stay in this range
tion by solubilizing the organic contaminants. for long due to the further decomposition of organic
Therefore, this review is aimed at presenting, acids, volatilization, and the production of NH3.
reviewing, and discussing the recent bioremedia­ This phase lasts until the temperature reaches
tion via composting literature. Past review papers, 55°C, ushering in the thermophilic phase. This
published in the past ten years, have only focused stage has the highest temperature during the com­
on specific organic contaminants, including TPH posting process.
[13], PAHs [14–17], and pesticides [16,18]. This Since temperature is an indicator of microbial
review will include all the organic contaminants activity, the initial stage of the thermophilic phase
that have been reported to degrade during com­ is considered the period with the highest activity.
posting. Because composting is a biological pro­ Mesophilic microbes are temperature sensitive and
cess and is influenced by some key deactivated during the thermophilic phase, while
physicochemical parameters, this review also thermophilic microbes populate the microbial
includes an overview of the composting process community. Less biodegradable and complex
and these parameters to enable the readers to organic substances like cellulose and hemicellulose
understand that the key to effective bioremedia­ start biodegrading during this phase. Ammonia
tion via composting lies in the optimization of the produced from the degradation of nitrogen-
parameters. In addition, the composting studies containing organic matter causes an increase in
are compared to commonly used single- and pH [19]. The high temperature in this period
multi-strain bioremediation approaches to gauge also destroys most human and animal pathogens
the competitiveness of this technology. We con­ such as Escherichia coli and Salmonella sp.
clude the review by offering some future perspec­ Microbial activity slows down as nutrient sources
tives in this research field that we believe would deplete, causing a decrease in temperature and the
stimulate research ideas that are equally beneficial beginning of the curing phase, which consists of
and interesting. the cooling and the maturation phase. The tem­
perature during the cooling phase is similar to the
mesophilic phase, and mesophilic organisms thrive
2. Overview of organic waste composting during this stage. The available nutrient source
process comprises complex organic materials that are lig­
nocellulosic. Macrofungi, which consume these
2.1. Basics of the composting process complex materials, are usually observed in the
The composting process has been neatly categorized compost, while the pH remains alkaline but
into four phases: mesophilic, thermophilic, cooling, drops slightly, approaching the neutral range.
and maturation. These phases have different tem­ The cooling phase generally takes several weeks
perature, oxygen demand, microbial community and can easily be mistaken for the maturation
structure, stability, carbon content, nitrogen con­ phase, the last stage of the composting process
tent, and pH profiles. After the initial composting when the compost is stable and mature. The end
mixture has been prepared, the mesophilic phase product is a humus-like substance with an earthy
commences. The microbes utilize readily degradable smell. At this period, the compost temperature is
organic matter as a nutrient source. As a result, the similar to the ambient temperature, and the pH is
temperature rises above the ambient temperature neutral or slightly alkaline. Several indicators,
after hours, or even a few days, depending on the including the germination index and soluble C/N
composting scale, initial material, and composting ratio, are used to determine the maturity and
conditions. If the compost mixture has soluble stability of the compost [20].
 BIOENGINEERED 1075

2.2. Key parameters for effective composting be present in a substrate, they must be in a form
that the microbes can utilize. Additionally, the
Composting, like other biological processes, is
decomposition depends on the enzymatic compo­
affected by nutrient availability and environmental
sition of individual microorganisms, strongly sug­
conditions. This subsection will discuss the key
gesting that some microbes can break down
parameters that influence the process and also
specific substrates while others might only break
include the optimal conditions for effective com­
down the intermediate products.
posting where necessary. Figure 1 summarizes
In composting, carbon and nitrogen contents of
these parameters and separates them into those
composting materials are described as the main
initially adjusted and those monitored and/or con­
nutritional characteristic of the substrate. Carbon
trolled throughout the composting process.
is used mainly as an energy source, while nitrogen
Moisture content, C/N ratio, particle size, and in
is necessary for cell growth and function. The C/N
some cases pH, are initially controlled to provide
ratio is used in composting to assess whether the
microorganisms with a suitable environment for
microbes have sufficient nutrients. Table 1 shows
thriving. Throughout the composting process,
the nitrogen content and C/N ratio of commonly
parameters, including oxygen and moisture con­
used composting materials. Generally, animal man­
tent, that influence microbial activity during the
ure and sewage sludge are usually rich in nitrogen
four stages of the process, are monitored and
from urine and have lower C/N ratios, while ligno­
controlled.
cellulosic materials such as wheat and rice straw
have more carbon and, therefore, a high C/N
2.2.1. Initial compost materials and nutrient ratio. The consensus among most researchers is
balance that an initial C/N ratio of 25–30 is ideal for the
The microorganisms in the compost require
macronutrients such as carbon, nitrogen, phos­
phorus, and potassium, and micronutrients, Table 1. Commonly used compost materials and their nitrogen
including essential metals and minerals. The and C/N ratio reported in literature.
source of these nutrients is the substrate or feed­ Compost materials Nitrogen C/N ratio Ref.
[92,93]
stock available for these microorganisms. Another Cow manure 2.3–2.6 13.8–15.8
[94,95]
Chicken manure 2.6–7.0 6.1–8.9
aspect to consider is how readily the microorgan­ Pig manure 2.5–3.0 16.8–17.2 [96,97]
[98,99]
isms can break down the substrates. For example, Sheep manure 2.1–2.8 17–17.1
[95,100]
Sewage sludge 1.7–4.5 11.3–11.5
recalcitrant substances like cellulose and lignin Sawdust 0.5–1.8 140–250 [100,101]

would take longer to break down compared to Rice straws 0.25–0.54 36.4–71.7 [92,93]
[102,103]
fructose. Consequently, although nutrients might Wheat straw 0.8–0.9 69.6–77.5

Figure 1. Overview of the key parameters during the composting process.

1076 C. LIN ET AL.

composting process. However, since the range particle sizes in their investigations, for instance,
assumes complete carbon mineralization, lower C/ ≤ 1 cm in food waste composting [9,20,31] and
N ratios of up to 14 have been shown to work 1.5–3.0 cm in composting of cattle, chicken,
well [21]. kitchen, and municipal solid waste [21]. Some
Lower ratios in excess of the requirements of the researchers have studied the effect of particle
microbial population would lead to nitrogen loss as size of the bulking agents on the composting
volatilized ammonia [22], leading to malodor pollu­ process. For example, He, et al. [32] found that
tion. On the other hand, higher ratios lead to longer granular biochar reduced methane emissions dur­
composting processes due to limited nitrogen ing pig manure and wheat straw composting by
resources. Therefore, the initial C/N ratio is usually 22.2%, while powdered biochar increased emis­
adjusted before composting. Materials such as sions by 56.8%. This observation implies that
sucrose [23–25], glucose [26], spent mushroom [24], anaerobic conditions occurred more frequently
and cellulose [26] have been used to increase the C/N in the treatments with powdered biochar since
ratio of the compost mixture and reduce ammonia methane is produced by methanogens which are
loss. For instance, Meng, et al. [26] showed that 4% anaerobic microorganisms. Bulking agents are
addition of sucrose to sewage sludge increased the C/ supposed to give compost structural integrity,
N ratio from 8.06 to 9.56 and decreased nitrogen loss and the powdered biochar was too fine, resulting
by 46.3%. Dry leaves and straw, which are common in poor air and water penetration. For the engi­
bulking agents, have a very high C/N ratio and, when neering and financial aspects, the grinding/cutting
added to the compost mixture, increase the initial C/ cost versus the additional benefit should be
N ratio. However, the types of carbon, for instance, weighed when choosing the preferred particle
lignin in these bulking agents, are complex and diffi­ size.
cult to degrade. Another strategy that has been used
to inhibit nutrient loss, and most specifically nitrogen 2.2.3. Moisture content
loss in the form of ammonia, comprises biochar and Moisture content is an important parameter in the
other adsorbents [27,28]. These substances have high composting process because microorganisms need
surface areas and adsorb ammonia preventing volati­ adequate moisture to survive. Water is necessary for
lization. High C/N ratios have been adjusted using the transport of nutrients, making them accessible
ammonium fertilizers to decrease the C/N ratio, espe­ to microbes. Moisture influences air penetration,
cially for some commercial-scale composting facilities nutrients, oxygen uptake, and temperature. Higher
[29]. However, this adds to the operational cost. moisture (usually >70%) content during the com­
posting process forms waterlogs that lead to anae­
2.2.2. Initial particle size robic conditions. Lower moisture content (usually
The particle size of the initial composting materi­ <40%) could cause early dehydration during com­
als is important in two aspects. First, the size of posting, hindering the biological process. However,
the particle determines the surface area on which the optimal moisture content depends on the feed­
microbes can consume. Second, the particle size stock’s physical characteristics, including the particle
dictates how homogenous the initial materials size and water-holding capacity, but a range of 55–
mix. Smaller particles have larger surface areas 65% has been utilized by most composting studies
which would allow for effective degradation. treating various types of organic materials [13,31–
They also improve the homogenous mixing of 33]. The moisture content will also vary throughout
the initial materials. However, small particles the composting process depending on the tempera­
might also inhibit air and water penetration ture and aeration. For this reason, the moisture
within the mixture leading to anaerobic zones. content is continuously adjusted, especially during
Conversely, larger particle sizes can lead to exces­ the thermophilic phase.
sive ventilation, diminished water holding capa­
city, and slower degradation [30]. There is no 2.2.4. Oxygen content
consensus about the best possible particle size The aerobic microorganisms in compost require
for composting. Studies have used different oxygen for respiration, so oxygen supply is crucial
 BIOENGINEERED 1077

during composting. It is important that the micro­ heat influences moisture and microbial commu­
organisms are provided with adequate oxygen to nity structure [37]. High temperatures have been
maintain their metabolic activities throughout shown to dry out the compost and inhibit the
composting. The oxygen content of > 10% in the composting process. In addition, the microbial
compost gas throughout composting is recom­ diversity decreases in high temperatures, and
mended [13]. Oxygen is supplied either through only thermophiles, e.g., Thermus genus, survive
turning the compost manually or mechanically or and thrive under such conditions. For instance,
with the aid of an aeration pump using positive or Yu, et al. [38] observed that the Shannon index,
negative pressure depending on the size of the a measure of microbial diversity, dropped from
compost and resources. Among all other para­ 7.86 at day 0 to 4.03 at day 3 when the temperature
meters mentioned in this review, aeration is the reached 93.4°C, during hyperthermophilic com­
most influenced by the technology. In addition to posting. However, this is not necessarily a bad
supplying oxygen, aeration influences temperature thing. Hyperthermophilic composting is garnering
and moisture during composting. Inadequate aera­ growing interest among researchers because of the
tion leads to anaerobic conditions, while too high shorter composting period and less nitrogen being
might dry out the compost and inhibit the com­ lost compared to conventional composting
posting process [34]. Furthermore, since oxygen [39–41].
demand is proportional to microbial activities, Ambient temperature has also been reported to
aeration should be the highest during the thermo­ influence the composting period. This effect is
philic phase and the lowest during the curing more pronounced for composting carried out­
phases. doors, e.g., windrow and onsite composting that
Besides the composting scale, the desired aera­ are exposed to the elements [42–44]. Zhou, et al.
tion rate will depend on the characteristics of the [43] studied windrow composting in summer and
composting materials, including particle size and winter and concluded that the temperature took
moisture content [35,36]. Specifically, the particle one day longer to increase during winter. The
size of the bulking agents, which provide the struc­ maximum temperature reached during the ther­
tural integrity of the compost mixture, will influ­ mophilic phase was also lower. Heat loss from the
ence the oxygen supply in the compost. Therefore, surface of the compost to the environment is also
a bulking agent that provides adequate voids that more pronounced in colder temperatures. In large-
allow oxygen penetration throughout the compost scale composting operation, uneven temperature
is recommended. As Cao, et al. [35] showed, pow­ distribution may occur due to non-homogeneous
dered bulking agents increased methane emissions. mixing or aeration and may end up affecting the
Water and air compete for these interstitial voids, compost quality.
and therefore high moisture implies that the voids
are occupied with water instead of air. In their 2.2.6. pH
extensive literature review, Tran, et al. [13] con­ The initial pH of the composting materials is
cluded that an optimal aeration rate of 1–2 L kg dry influenced by the type of organic wastes. For
−1
wt. min−1 could meet the aeration requirements instance, food waste is slightly acidic, while animal
for a successful pilot-scale composting process. manure is alkaline. Furthermore, the bacterial
However, it is not possible to maintain complete community in the compost prefers neutral or
aerobic conditions during composting, especially near-neutral pHs, while the fungal community
for large-scale composting. Therefore, the goal is prefers slightly acidic conditions [45]. Therefore,
to maximize aeration within the constraints of the optimal pH range varies noticeably for com­
financial feasibility. posting, 5.5–8.0 [27,35,46,47]. This explains why
pH is not usually adjusted during composting
2.2.5. Temperature when compared to other biological treatment tech­
Composting is a self-heating biological process, nologies. However, lower pH values have been
and the heat is a product of aerobic microbial shown to influence composting negatively
degradation of organic matter. The produced [35,48]. For example, Cao, et al. [35] demonstrated
1078 C. LIN ET AL.

that the initial pH of 5 delayed degradation by of compost on plant growth, and the hygienization
seven to ten days and also increased the electrical aspects of composting [51,52]. Well-known com­
conductivity of the final mature compost above the posting technologies such as the aerated static pile
acceptable standards (≤4 mS cm−1). Such low pHs were invented during this period [53]. Zheng, et al.
are characteristic of food waste composting, and [54] refer to this period as the budding stage of
some researchers have increased the initial pH of composting technology based on the number of
the compost mixture [49]. patents filed worldwide. The period between 1990
The pH also varies throughout the composting and 2007 was designated as the developing stage
process. When the process commences, the pro­ and more recent years as the expanding stage.
duction of organic acids lowers the pH of the Their comprehensive bibliometric analysis sug­
compost. The production of ammonia from the gests that composting technology research interest
decomposition of nitrogen-containing organic has grown steadily over the years, especially with
matter increases the pH in the thermophilic stage the rise of the sustainable development movement
[33]. NH4+ and HCO3−, other decomposition pro­ and efforts to minimize wastage and needless
ducts, act as buffers that maintain the high pH pollution.
throughout the composting process [35]. Figure 2 represents the cumulative publications
on composting covering the years 1989 to 2021.
2.3. The history and current state of the The data was accessed from the Web of Science
composting process database and only included Scientific Citation
Composting has a long history that evolved along­ Index Expanded (SCIE) research, review, and
side human settlements and the practice of agri­ early access articles. According to Figure 2(a),
culture. Diaz and De Bertoldi [50] present an a total of 24,000 articles were published in the
exhaustive history of composting from the past three decades. Interest in composting research
Neolithic period to the 20th century. Research on can also be seen to increase over the period stea­
the composting process and influencing factors dily. The research has primarily focused on opti­
can be traced back to the late 1940s and 1950s. mizing and shortening the composting process
Mechanization of composting technology also [55,56], odor control [57,58], microbial commu­
began during this period, with composting diges­ nity structure [47,59,60], composting application
ters such as the Hardy digester and Dano drums including heat recovery [61–63] and bioremedia­
becoming commercially available. The 1960s tion [6,9,31]. Figure 2(b) shows the publication of
through to the 1980s witnessed more research on articles on bioremediation in those three decades.
the technical aspects and financial viability of Based on the exponential growth, bioremediation
composting facilities, use of compost, the effect research via composting appears to be on the rise.

Figure 2. (a) The cumulative number of composting articles (b) bioremediation via composting articles published from 1989 to 2020.
The data was sourced from the Web of Science database on August 28th, 2020.
 BIOENGINEERED 1079

A total of 655 articles have been published certain compounds by making them less viscous.
between 1990 to 2021, with 40% published in the Furthermore, some species can produce biosurfac­
last six years. tants that increase the bioavailability of the com­
pounds [65].
This section presents the bioremediation of
3. Bioremediation of recalcitrant organic some common recalcitrant organic pollutants
contaminants
found in the pedosphere and sediment, including
Bioremediation technologies employ microorgan­ polycyclic aromatic hydrocarbons (PAHs), di
isms to degrade organic contaminants. This degra­ (2-ethylhexyl) phthalate (DEHP), polychlorinated
dation process can occur via three main pathways: dibenzo-p-dioxins/furans (PCDD/Fs), total petro­
(i) mineralization or metabolism, whereby the leum hydrocarbons (TPH), and pesticides. These
microorganisms utilize the contaminant as compounds are highly hydrophobic and prevalent
a nutrient source; (ii) co-metabolism, whereby in the environment as a result of anthropogenic
contaminants that do not serve as a nutrient activities. Bioremediation studies, including com­
source are broken down in parallel with metabolic posting, single- and multi-strain bioremediation,
reactions; and (iii) nonspecific oxidation, which and biostimulation approaches, published in the
involves the extracellular degradation of contami­ past ten years, are presented in Tables 2–5.
nants [64]. Traditionally, bioremediation has been
carried out in various ways, including bioaugmen­
3.1. Bioremediation of petroleum and
tation and biostimulation. Bioaugmentation
petroleum-related organic contaminations
involves incorporating specific microbial species
capable of mineralizing a contaminant and using Petroleum contaminants are among the most pre­
it as a nutrient source into a contaminated envir­ valent organic contaminants in the environment
onment. Biostimulation involves providing rate- because of anthropogenic activities, including pet­
limiting nutrients such as phosphorus and nitro­ roleum extraction, processing, transportation, sto­
gen and supplements such as biosurfactants to rage, and usage. Table 2 presents results from
microorganisms in a contaminated environment. recent studies on the bioremediation of petroleum
Bioaugmentation has been conducted using single and petroleum-related contaminants at different
or multiple strains of bacteria or fungi scales. Petroleum-related contaminants that have
(mycoremediation). been remediated via bioremediation include diesel,
Bioremediation via composting presents unique PAH, and TPH. It can be observed that the effi­
advantages over single- or multi-strain bioreme­ ciency in removing petroleum contaminants utiliz­
diation. Firstly, the composting process comprises ing biological approaches varies according to the
several microorganisms that participate in mutua­ initial concentration, biological approach, and
listic, synergistic, and/or competitive relationships. scale. Except for composting, other bioremediation
In this diverse microbial structure, a handful of approaches were generally small-scale. This is an
species could completely mineralize or metabolize advantage of composting in that the scale of reme­
a contaminant, while other species are only able to diating TPH can be increased without significantly
co-metabolize or nonspecifically oxidize the con­ compromising the removal efficiency. For exam­
taminants. This makes the composting process ple, Lin, et al. [5] showed that over 90% of diesel of
robust and highly effective in degrading organic the initial concentration of 26,315 mg kg−1 was
contaminants. In addition, the composting process degraded via composting for 24 days. This suggests
undergoes certain physicochemical transforma­ that petroleum products are relatively easier to
tions that govern the fate of the organic contami­ biodegrade.
nant in the compost. For example, the high Numerous microbial species capable of miner­
temperatures during the thermophilic stage could alizing petroleum and petroleum-related com­
cause the volatilization of volatile and semi-volatile pounds have been reported in various studies
compounds. On the other hand, the high tempera­ [12]. These species have been isolated from petro­
tures might also increase the bioavailability of leum-contaminated environments, cultured, and
1080 C. LIN ET AL.

Table 2. Bioremediation and composting of petroleum and petroleum-related contaminants by biological treatment approaches.
Biological Target Initial Reduction
approaches pollutants concentration Size Period (days) (%) Details Ref.
Biostimulation and TPH 41,065– 2.5–3.0 kg 105 23–40 Contaminated soil mixed with [104]
bioaugmentation 60,153 mg uncontaminated soil in equal
kg−1 of the parts and molasses, compost,
mixture sludge, or activated carbon.
[105]
Phytoremediation, TPH 2,500– 0.5 kg of soil in 60 50–62 Bacillus genus (e.g., Bacillus,
biostimulation, 13,200 mg pots Pseudomonas, Listeria, Rothia,
and kg−1 of soil Corynebacterium, and
bioaugmentation Rhodococcus) with molasses,
nutrients, biosurfactants, and/
or H2O2.
[4]
Multi-strain TPH 54,074 mg Lab-scale 60 47.6 Lambertella, Penicillium,
mycoremediation kg−1 of 100 mL Malt Clonostachys, and Mucor
sediment Extract Broth supplemented with wood
chips. Bacterial species were
also said to participate in the
degradation
Biosurfactant TPH 2,642 mg 2.5 kg 28 61.8 Used biosurfactant produced by [106]
kg−1of soil Bacillus Malacitensis isolated
from aromatic hydrocarbon-
contaminated soil
Composting and TPH 31,823 mg 67.5 kg (2:1 203 (63 d composting 48 Yard trimmings, cactus, and urea. [107]
phytoremediation kg−1 of soil mass ratio; and 140
soil: compost d phytoremediation)
material)
[5]
Composting Diesel 26,315 mg 130 kg 24 90–92 Food waste, sawdust, and mature
kg−1 of compost
initial
composting
material
Composting PAHs 13.5–15.9 mg 0.02 m3 closed 39 58.7–76.4 Used Sewage sludge and [1]

kg−1 of reactor mushroom residue composting

sewage to degrade 6 PAHs
sludge
Biostimulation and PAHs 332 mg kg−1 0.04 m3 15 80 Bioaugmented the bioslurry with [108]

bioaugmentation of soil stainless- Rhodocccus erythropolis and

with two steel reactor Pseudomonas stuzeri.
bacterial strains (1:5 ratio; Biostimulated the process with
soil: distilled N, P, and biosurfactants.
water)
[2]
Composting PAHs 6–10 mg Commercial- 50 62.4–75.2 Sewage sludge, green forest
kg−1of scale waste, and mature compost.
sewage windrow
sludge (1.5 m wide,
1.2 m high,
and 10 m
long)
Composting PAHs 0.082 mg kg−1 Commercial 110 57 ± 31 Dewatered sewage sludge and [3]

sewage scale food industry waste

sludge
Remarks: TPH – Total petroleum hydrocarbons; PAHs – Polycyclic aromatic hydrocarbons.

used in bioremediation studies. For example, methane monooxygenases, which assist in the
Abena, et al. [12] identified crude oil-degrading breakdown of petroleum. For example, methane
bacterial strains belonging to Raoultella ornithino­ monooxygenase can oxidize the C-H bonds of
lytica, Bacillus subtilis, Serratia marcescens, and alkanes.
Acinetobacter lwoffii species and augmented the The aerobic bacterial degradation mechanism of
strains in contaminated soils, increasing the TPH- petroleum products, especially n-alkanes, is well
degradation to 48.1%. These species release certain documented [13,66]. The n-alkanes are broken
enzymes, including alkane hydroxylases and down into a carbon source for the bacteria
 BIOENGINEERED 1081

through the main pathways: terminal, subterminal, can occur at all stages of the composting
β-, and ω-oxidations. Details of the mechanisms process.
have been extensively presented in review papers
on petroleum degradation [66,67]. Briefly, these
3.2. Bioremediation of phthalate-based
pathways are catalyzed by monooxygenases to
plasticizers
convert them into alcohols. The dehydrogenases
catalyze the conversion of the alcohols into alde­ Phthalate-based plasticizers are common plastic
hydes and ketones, then further into fatty acids. and rubber additives that increase flexibility and
The fatty acids are further oxidized into tricar­ durability. Consequently, they have become quite
boxylic acid cycle (TCA) intermediates. On the prevalent in the environment. Environmentalists
other hand, the degradation mechanism of aro­ and public health experts are greatly concerned
matic petroleum compounds is more complicated about the links of these compounds to endocrine
and has been reported to be initiated via oxidative disruption. More toxic phthalates such as diethyl­
attack with the help of monooxygenases or dioxy­ hexyl phthalate (DEHP) and di-butyl phthalate
genases to produce catechol-like structures before (DBP) are already being phased out entirely or in
ring cleavage reactions by dioxygenases. The resul­ some products, e.g., children’s toys in the EU and
tant straight chain product goes through the the US. Few researchers have also shown interest
above-mentioned n-alkane oxidation reactions. in using bioremediation techniques to study the
Fungal species from genera such as Aspergillus, effectiveness of removing phthalates, as shown in
Alternaria, Penicillium, and Graphium have been Table 3. Composting can degrade multi-pollutants,
reported to degrade petroleum and petroleum- as shown by Fu, et al. [7]. Tran, et al. [6] also
related compounds [68]. The degradation of com­ showed that pilot-scale food waste composting
plex petroleum-related compounds like PAHs by removed 98% of DOTP with high concentrations
ligninolytic and non-ligninolytic fungi have been of 11,882 mg kg−1 after only 35 days of compost­
reported in detail by some studies [69,70]. ing. This was significantly higher than the single-
Ligninolytic fungi extracellularly degrade PAHs strain bioremediation study, which had lower con­
using lignin-degrading enzymes, including perox­ centrations and a scale over 1,000 times smaller.
idases and laccase. Both groups of compounds can The microbial degradation of phthalates
degrade these compounds intracellularly in reac­ involves a series of β-oxidation and de-
tions mediated by hydrolases and cytochrome esterification reactions to produce phthalic, ter­
P450 monooxygenases. The extracellular degrada­ ephthalic, or isophthalic acids [73–76]. Boll,
tion produces polar and water-soluble products et al. [77] detailed the most updated under­
that can be accessible for fungal and the other standing of microbial degradation of the resul­
microbial metabolisms in that environment. This tant acids. They reported that almost all the
process can occur during composting, and because aerobic microorganisms convert these com­
of the microbial diversity, there would be a high pounds into protocatechuate, a TCA intermedi­
probability of several species that would be able to ate. These reactions involve three steps for
metabolize these extracellular degradation phthalic acid; dioxygenation, dehydrogenation
products. and decarboxylation, and two steps for ter­
Several petroleum-degrading species have ephthalic and isophthalic acids; dioxygenation
been reported in literature, including mesophi­ and dehydrogenation. The involved enzymes
lic microbes such as Acinetobacter calcoaceti­ are decarboxylases, dehydrogenases, and dioxy­
cus, Bacillus simplex, Paenibacillus pabuli, genases. Several species were found in compost
Bacillus pumilus, and Pseudomonas aeruginosa; [6,33,78], e.g., Microbacterium sp and
and thermophilic microbes like Bacillus mega­ Rhodococcus erythropolis, Gordonia sp.
terium, Aspergillus sp, Pseudoxanthomonas sp., Pseudomonas sp. Bacillus sp., Rhizobium sp.,
Mucor sp, Rhizopus sp., and Shigella flexneri and Achromobacter sp. can completely metabo­
[13,17,71,72]. This suggests that biodegradation lize phthalates, even at high concentrations
1082 C. LIN ET AL.

Table 3. Bioremediation of phthalate-based plasticizers by biological treatment approaches.

Biological Period Reduction
approaches Target pollutants Initial concentration Size (days) (%) Details Ref.
Single-strain 3 PAEs (DEHP, DBP, and 1,000 mg kg−1 of soil 100 g 21 >55 Rhodococcus sp. strain WJ4 [109]
bioremediation DnOP) isolated from soil
Composting 5 PAEs (DEHP, BBP, DBP, 25.5 mg kg−1 of sewage sludge 3.6 60 32.2–78.1 Sewage sludge, rice straw [7]
DEP, and DMP) – and Pig manure
4.0 kg
Composting DOTP 11,882 mg kg−1 of initial 110 kg 35 98 Food waste, sawdust and [6]

compost material mixture matured compost

Remarks: DEHP – Di-(2-ethylhexyl) phthalate; DnOP – di-n-octyl phthalate; DMP – dimethyl phthalate; DEP – diethyl phthalate; DBP – di-n-butyl
phthalate; BBP – butyl benzyl phthalate; DOTP – dioctyl terephthalate .

[73]. Therefore, composting is well equipped to lindaniclasticus, Alkaligens faecalis, and

degrade phthalates effectively. Pseudomonas aeruginosa as capable of dechlorinat­
ing lindane, Wang, et al. [84] reported that
Stroptomyces sp. strain can degrade DDT, and
3.3. Bioremediation of pesticides Seralathan, et al. [85] confirmed that Pseudomonas
aeruginosa, Ochrobacterium sp, and Achromobacter
Pesticides, including herbicides, insecticides, and
xylosoxidans degrade endosulfan and use it as
fungicides, have been extensively used in agriculture
a source of sulfur. These organochlorine pesticide-
to boost yield by keeping away pests and weeds.
degrading species contain genes, e.g., lin and Esd
Some of these pesticides from the organochlorine
genes that encode for dehalogenases, hydrolases,
group, e.g., dichlorodiphenyltrichloroethane
dehydrochlorinases, and monooxygenases enzymes
(DDT), lindane, endrin, dieldrin, endosulfan, and
that take part in mineralizing these compounds [86].
heptachlor, are part of the compounds listed in the
Hydrolysis, mediated by phosphotriesterase, is the
Stockholm Convention of POPs and are banned or
primary step in the bacterial degradation of organo­
restricted globally because of the environmental and
phosphate pesticides which causes the cleaving of
human health risk. However, these legacy pesticides
the P-O/F/S bond separating the two main moieties,
are highly persistent with incredibly long half-lives
which undergo further reactions to produce TCA
and are still found in soil [79] and sediment [80,81].
intermediates [86,87]. Since organophosphates have
Table 4 summarizes the results of some recent stu­
lower toxicity and less persistence in the environ­
dies on bioremediation of organochlorine and orga­
ment, many more microbial species documented by
nophosphate pesticides by biological treatment
Mulla, et al. [87] have been identified to degrade
approaches. Bioremediation of organochlorine
organophosphate pesticides.
(DDT, aldrin, lindane, α- and β-endosulfan)
appears slower than organophosphate (phorate
and chlorpyrifos) pesticides, which is attributable
3.4. Bioremediation of halogenated biphenyls,
to their higher toxicity. Egbe, et al. [82] reported
dioxins, and furans
that organochlorine pesticides reduced the number
of bacterial and fungal species when added to agri­ These persistent organic pollutants (POPs),
cultural soils, implying that these compounds are including polychlorinated dibenzo-p-dioxins and
toxic to some microorganisms. Bioremediation also dibenzofurans (PCDD/Fs) and polychlorinated
showed high removal efficiency. Ali, et al. [8] biphenyls (PCBs), stubbornly remain in the soil
reported that composting could simultaneously and sediments and are also carcinogenic and
degrade multiple legacy pesticides and achieve mutagenic. They constitute some of the most
high degradation efficiencies of 80–87% after toxic compounds known to man and were
100 days of composting. among the first listed compounds in the
Some specific strains found in compost can Stockholm Convention on POPs. PCBs were man­
degrade some pesticides. For example, Kumar and ufactured and widely used as coolants for many
Pannu [83] identified Rhodanobacter decades, but like PCDD/Fs, they can also be
 BIOENGINEERED 1083

Table 4. Bioremediation of pesticides by biological treatment approaches.

Biological Initial Period Reduction
approaches Target pollutants concentration Size (days) (%) Details Ref.
Multi-strain Phorate 100–300 mg 100 g 42 97.7–98.3 Brevibacterium [110]
bioaugmentation kg−1 of soil frigoritolerans, Bacillus
aerophilus and
Pseudomonas fulva.
Phytoremediation Dichlorodiphenyltrichloroethane 1.42 mg kg−1 1.5 kg 100 65.6 and Tall fescue, perennial [111]

+ Single-strain (DDT) of soil contaminated 65.9 ryegrass with

bioremediation soil in pots biosurfactant-producing
Pseudomonas sp. SB
(107 CFU g−1 dry soil per
pot).
Multi-strain Chlorpyrifos 50 mg kg−1 20 g 10 82 Pseudomonas, Klebsiella, [112]
bioaugmentation of soil Stenotrophomonas,
Ochrobactrumand
Bacillus.
Composting ● Aldrin ● 0.45– ~100 kg d−[1] of 100 ● 87.0 Vegetable waste, cow [8]

● α-endosulfan 0.65 mg waste fed in ● 86.4 dung, and sawdust.

● β-endosulfan kg−1 3.5 m3 ● 84.0
● Lindane ● 1.20– continuous ● 80.0
1.40 mg rotary drum
kg−1 composting.
● 0.65 mg
kg−1
● 0.35–
0.50 mg
kg−1of
raw
material

Remarks: Initial concentrations are per dry weight of soil or initial material mixture.

unintentionally produced during incomplete com­ found in compost include Sphingomonas sp.,
bustion. Therefore, all combustion sources such as Pseudomonas aeruginosa, Acinetobacter sp.,
engines, incinerators, and power plants, can pro­ Pseudomonas putida, Ralstonia sp., Burkholderia
duce these compounds. Since they are highly sp., Comamonas testosteroni, Novosphingobium
hydrophobic and have a high affinity to particles, sp., Burkholderia cepacia, and Pseudomonas sp.
they are found mostly in soil and sediments, where [9,89,90].
they have long half-lives that could last for more The aerobic bacterial degradation mechanism
than 100 years [88]. has been reported to be initiated via either angular
Table 5 documents some studies on the bior­ or lateral dioxygenation [91]. The degradation
emediation of these POPs published in the last mechanisms of these compounds have been car­
ten years. The first observation is that the initial ried out using non-chlorinated congeners because
concentrations, especially for PCDD/Fs, are they are less stable. The dioxygenation reaction
much lower than those used in the bioremedia­ involves the addition of OH to the angular or
tion of the other compounds presented in this lateral position. This initial reaction is catalyzed
review. This is probably because of the high by monooxygenases or hydroxylating dioxy­
toxicity of these compounds. Successful pilot- genases. The preceding oxygenation knocks down
scale bioremediation of these POPs via compost­ the planar structure of the molecule in the angular
ing has been reported [9,10] with removal effi­ dioxygenation, making the compound less toxic.
ciencies > 75%. Bacterial species with the The series of reactions proceed by opening the
dioxygenase encoding genes are capable of aromatic ring producing salicylic acid and cate­
degrading PCDD/F and PCDD/F-like com­ chol, which are further broken down to TCA
pounds. Some of these species that have been intermediates. The fungal degradation mechanism
1084 C. LIN ET AL.

Table 5. Bioremediation and composting of halogenated biphenyls, dioxins, and furans by biological treatment approaches.
Biological Target Initial Period Reduction
approaches pollutants concentration Size (days) (%) Details Ref.
Multi-strain PCBs 23 mg kg−1 of 20 g 21 41–85 Bioaugmentation with R. ruber, A. xylosoxidans, [113]
bioaugmentation sediment R. ruber, S. maltophilia, O. anthropic and
A. xylosoxidans isolated from PCB-
contaminated sediment.
Composting PCBs 0.6 mg kg−1 of 0.2 m3 reactor 124 67 Sewage sludge, bark, and peat [11]

sewage sludge (1:2; sewage

sludge:peat
and peat)
Single-strain PCDD/Fs 260 ± 37 ng kg−1 150 g (dry 60 35 Penicillium Brasilianum and Fusarium Solani [114]

mycoremediation weight) 25 (isolated from PCDD/F-contaminated soil)

with wood and cardboard chips
[115]
Single-strain PCDD/Fs 6,238 ± 1110 ng Carried out in 72 96 Solid state fermentation coupled with
mycoremediation I-TEQ kg−1 of 250 mL glass Pleurotus pulmonarius
soil bottles (1:1;
soil:inocula)
[116]
Single-strain PCDD/Fs 4,432 ± 632 ng 300 g (dry 30 60 Solid state fermentation coupled with
mycoremediation WHO-TEQ kg−1 weight) (1:0.5; Pleurotus pulmonarius
of soil soil:inocula)
[10]
Composting PCDD/Fs 16,004 ng-TEQ 85 kg 42 75 Food waste, sawdust, and mature compost
kg−1
[9]
Composting PCDD/Fs 8,954 ng-TEQ 89 kg 35 81 Food waste, sawdust, and mature compost
kg−1 of soil
Remarks: PCBs – Polychlorinated biphenyls Octachlorodibenzofuran PCDD/Fs – Polychlorinated dibenzo-p-dioxins/dibenzofurans; I-TEQ –
International Toxic Equivalent; WHO-TEQ – World Health Organization Toxic Equivalent.

involves similar reactions in the degradation of compost gas have been recommended by research­
aromatic compounds previously mentioned in ers as optimal. However, the research on the opti­
Section 3.1. mal ranges of the other parameters is still
inadequate to draw any certain conclusions.
Interesting and important research directions that
4. Conclusions and future perspectives need further investigation include bio-augmenting
From reviewing the recent publications, we can /inoculating the composting process with specific
conclude that bioremediation via composting is microbes capable of degrading a contaminant at
still a nascent topic but has great potential to different composting stages. Another important
remove recalcitrant organic pollutants in soils and topic is studying the pairing of composting with
sediments. Some of the organic contaminants that other bioremediation technologies, e.g., using
have been successfully treated via composting mature compost with residual contamination in
include diesel, total petroleum hydrocarbons mycoremediation or phytoremediation. In addition,
(TPH), polycyclic aromatic hydrocarbons (PAHs), investigating the ability of composting to degrade
polychlorinated biphenyls (PCBs), diethylhexyl multiple organic contaminants simultaneously is
phthalate (DEHP), and polychlorinated dibenzo- another interesting research area. In conclusion,
p-dioxins and dibenzofurans (PCDD/Fs). composting is a suitable bioremediation technology
Generally, highly toxic compounds like PCDD/Fs that deserves more attention.
take longer to degrade, and only lower initial con­
centrations can be successfully treated. Since com­
posting is a biological process, ensuring that key Highlights
parameters, including particle size, nutrients, oxy­
gen content, and moisture content, are within the ● Composting can successfully bioremediate
suitable ranges of effective composting enhances the several recalcitrant organic contaminants
bioremediation. Moisture content of 55–65%, C/N ● The microbial diversity of composting offers
ratio of 25–30 and oxygen content of > 10% in the unique bioremediation merits
 BIOENGINEERED 1085

● Production of biosurfactants and the high during full-scale continuous rotary drum composting.
temperatures promote bioavailability Chemosphere. 2014;102:68–75.
[9] Tran HT, Lin C, Hoang HG, et al. Biodegradation of
● Ensuring optimal composting conditions
dioxin-contaminated soil via composting: identifica­
enhances the bioremediation tion and phylogenetic relationship of bacterial
● The exact degradation mechanism of con­ communities. Environ Technol Innov. 2020;19:101023.
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co-composting degradation of highly PCDD/
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Disclosure statement environmental quality assessment of composted sewage
No potential conflict of interest was reported by the author(s). sludge. Waste Manage. 2013;33(6):1451–1460.
[12] Abena MTB, Li T, Shah MN, et al. Biodegradation of
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Funding taminated soils by natural attenuation and
bioaugmentation. Chemosphere. 2019;234:864–874.
The author(s) reported there is no funding associated with [13] Tran H-T, Lin C, Bui X-T, et al. Aerobic composting
the work featured in this article. remediation of petroleum hydrocarbon-contaminated
soil. Current and Future Perspectives. Sci Total
Environ. 2021;753:142250.
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