minerals

Review
Accumulated Copper Tailing Solid Wastes with Specific
Compositions Encourage Advances in Microbial Leaching
Juan Zhang 1,2, * , Xiaojun Liu 1 , Xinyue Du 1 , Xin Wang 1 , Yifan Zeng 3 and Shukai Fan 4

1 State Key Laboratory of Advanced Metallurgy, School of Metallurgical and Ecological Engineering,
University of Science and Technology Beijing, Beijing 100083, China; m202320346@xs.ustb.edu.cn (X.L.);
d202310160@xs.ustb.edu.cn (X.D.); m202120319@xs.ustb.edu.cn (X.W.)
2 Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-0032, Japan
3 National Engineering Research Center of Coal Mine Water Hazard Controlling, China University of Mining
and Technology Beijing, Beijing 100083, China; zengyf@cumtb.edu.cn
4 State Key Laboratory of Mineral Processing, Environmental Engineering Institute, BGRIMM Technology
Group, Beijing 100160, China; fanshukai@bgrimm.com
* Correspondence: zhangjuan85@ustb.edu.cn

Abstract: Against the backdrop of the increasing copper demand in a low-carbon economy, this
work statistically forecasted the distribution of China’s copper tailings for the first time, and then
characterized them as finely crushed and low-grade mining solid wastes containing copper mainly in
the form of chalcopyrite, bornite, covelline, enargite and chalcocite based on available research data.
China is the globally leading refined copper producer and consumer, where the typical commercial-
scale bioleaching of copper tailings is conducted in the Dexing, Zijinshan and Jinchuan mining
regions. And these leaching processes were compared in this study. Widely used chemolithoau-
totrophic and mesophilic bacteria are Acidithiobacillus, Leptospirillum, Acidiphilium, Alicyclobacillus
and Thiobacillus with varied metal resistance. They can be used to treat copper sulfide tailings such
as pyrite, chalcopyrite, enargite, chalcocite, bornite and covellite under sufficient dissolved oxygen
from 1.5 to 4.1 mg/L and pH values ranging from 0.5 to 7.2. Moderate thermophiles (Acidithiobacillus
Citation: Zhang, J.; Liu, X.; Du, X.; caldus, Acidimicrobium, Acidiplasma, Ferroplasma and Sulfobacillus) and extreme thermophilic archaea
Wang, X.; Zeng, Y.; Fan, S. (Acidianus, Metallosphaera, Sulfurococcus and Sulfolobus) are dominant in leaching systems with operat-
Accumulated Copper Tailing Solid ing temperatures higher than 40 ◦ C. However, these species are vulnerable to high pulp density and
Wastes with Specific Compositions heavy metals. Heterotrophic Acidiphilium multivorum, Ferrimicrobium, Thermoplasma and fungi use
Encourage Advances in Microbial
organic carbon as energy to treat copper oxides (malachite, chrysocolla and azurite) and weathered
Leaching. Minerals 2024, 14, 1051.
sulfides (bornite, chalcocite, digenite and covellite) under a wide pH range and high pulp density.
https://doi.org/10.3390/min14101051
We also compared autotrophs in a planktonic state or biofilm to treat different metal sulfides using
Academic Editors: Naoko Okibe, various sulfur-cycling enzymes involved in the polysulfide or thiosulfate pathways against fungi
Sossio Fabio Graziano, Rossana that produce various organic acids to chelate copper from oxides. Finally, we recommended a bioin-
Bellopede, Giovanna Antonella Dino formatic analysis of functional genes involved in Fe/S oxidization and C/N metabolism, as well as
and Nicola Careddu
advanced representation that can create new possibilities for the development of high-efficiency leach-
Received: 17 August 2024 ing microorganisms and insight into the mechanisms of bioleaching desired metals from complex
Revised: 24 September 2024 and low-grade copper tailings.
Accepted: 2 October 2024
Published: 20 October 2024 Keywords: copper mineral phases; predicted tailing distribution; microbial metabolism limitations;
mineral-dependent mechanisms; emerging technologies

Copyright: © 2024 by the authors.

Licensee MDPI, Basel, Switzerland.
1. Introduction
This article is an open access article
distributed under the terms and There is a large demand for copper as the second largest strategic raw material due to it
conditions of the Creative Commons being a soft, malleable and ductile metal with very high thermal and electrical conductivity,
Attribution (CC BY) license (https:// along with its essential role in the thermal and electrical transition of renewable energy
creativecommons.org/licenses/by/ systems [1,2]. A shortage of copper concentrate has forced a few smelters in China to
4.0/). cut output, and instead, copper production from secondary sources has achieved lower

Minerals 2024, 14, 1051. https://doi.org/10.3390/min14101051 https://www.mdpi.com/journal/minerals

Minerals 2024, 14, 1051 2 of 18

economic costs, a lower level of operational complexity and an environmental advantage

as compared to that from primary raw ores on the basis of life cycle assessment (LCA) [3,4].
The intensive modern copper production has caused a high volume of solid waste, and
the estimated global production of copper tailings in 2020 amounted to 4.3 billion tons
(data from www.snl.com accessed on 11 January 2023) with an average copper grade of
0.46% [5,6]. If not well managed, mine tailing waste would pose a threat to the environment
and human health by acid mine drainage (AMD) and dam failure [7,8]. The widely
used high temperatures and highly efficient pyrometallurgy for copper concentrate are
characterized by high costs, high emissions and high metal loss, whereas traditional acid
leaching does not work as well as bioleaching to recover copper from tailings with high
pyrite content [9–11].
As one of the most promising green technologies for low-grade minerals under gentle
conditions without additional power supply, the industrial applications of microbial leach-
ing have been conducted in the United States since the 1950s [12,13]. Recently, bioleaching
has been spread all over Australia (Whim Creek copper mine), using mesophilic and moder-
ately thermophilic bacteria leaching [10]; China, using natural microorganisms from AMD
or a mixed culture of bacteria [14,15]; Africa (Fairview gold mine), using the BIOX® process
(sourced from Johannesburg, South Africa) in the past and the MesoTHERM® process
(sourced from Kuusjärvi, Finland) since 2019 [16]; Finland (Vuonos Cu–Zn–Co mine), using
natural microorganisms from AMD [17]; and the Dominican Republic (Pueblo Viejo gold
mine), using THIOTEQTM technology (sourced from Balk, The Netherlands) [12,18]. And
bioleaching accounted for approximately 1.2% of global total copper production through
2020 [16]. Leaching microorganisms can recover multiple heavy metals from tailings and
immobilize fine-grained tailings to prevent their pulverization [7,19,20]. Furthermore,
bioleaching-based recycling technology has been developed for copper tailings [21], other
industrial residues [22,23] and e-waste [24,25].
The current chemical recoveries of single-Cu metal are acceptable for minerals with a
grade of more than 1.2% on the basis of LCA, and opportunities exist to replace the virgin
chemicals consumed in the assessed process with bio-based material substitutes [5]. It
is important to remember that beyond the need to have suitable mineralogy to support
bioleaching, the longer time required for bioleaching has also been a substantial barrier
to the deployment of this technology [16]. It is urgent to explore large-scale applications
of robust microbial strains to treat low-grade copper tailings with different mineralogical
compositions [26,27]. High-throughput screening has allowed deep insights into the
microbial diversity, metabolic pathways and mineral–microbe interactions [28,29]. Further
identification of pioneer species and ecological succession in extreme environments such as
volcanoes or sea floors could supply more efficient candidates for the microbial leaching of
low-grade tailings [30,31]. In addition, accelerating chemical representation development
has contributed to an improved understanding of biofilm and bioleaching dynamics within
the microbe–mineral interface at the nanometer scale [32].
Microbial leaching mechanisms for sulfide [33] and non-sulfide minerals [9,34], their
advantage over conventional metallurgical techniques [35] and their application to sec-
ondary resources [36], were reviewed. However, there was a lack of systematic reviews
focusing on copper tailings, the world’s growing solid wastes containing recyclable met-
als and unregulated toxic metals. This review aims to present massive productions and
distributions of copper tailings, as well as introduce typical commercial applications of
bioleaching in China that rank as the leading country in production and consumption of
refined Cu (grade A copper). In addition, we will compare potential bacterial, archaeal
and fungal species that can thrive under multiple influencing factors, including mineral
composition and particle size, temperature, pH, supplemental air and pulp density, to
reveal different types of microbe–mineral interactions in complicated bioleaching systems.
Future perspectives of bioleaching will be outlined with the development of robust func-
tional microbes with enhanced leaching efficiency and resource efficiency, and advanced
representation encoding molecular structures of microbe–mineral complexes.
Minerals 2024, 14, 1051 3 of 18

2. Materials and Methods

This review focuses on advances in study of copper tailings, leaching microorganisms
and their mechanisms over the past two decades, and the references were systematically
hand searched using Web of Science, Elsevier ScienceDirect, Springer Nature, ACS Pub-
lications, Taylor & Francis, Wiley, Frontiers databases and Google Scholar. A total of
196 articles were evaluated, including high-quality research papers, review articles, con-
ference publications, book chapters and official reports. The inclusion criteria were the
terms (“bioleaching” or “bioextraction” or “biorecovery” or “biotechnology” or “leaching
microorganisms” or “bacteria” or “fungi”) and (“copper” or “copper mine” or “copper
sulfides” or “chalcopyrite”) and (“tailings” or “secondary resource” or “mining waste”
or “low grade”) present in the main sections of articles, which were combined using the
Boolean operator “AND”. Each reference was systematically full-text screened based on
whether it focused on copper tailings, leaching microorganisms, or bioleaching mechanisms.
And supplementary literature search focused on the mineral composition of copper tailings
in China and the genome of microbial species in bioleaching.

3. Accumulated Copper Tailings and Promising Bioleaching in China

China has been ranked third in global raw copper production with a continuous
increase from 2007 to 2022 based on US Geological Survey annual publications (2023) [37]
in Figure 1a and Table S1. There were eighty-three copper mines with copper production
of more than 1000 tons per year, where the up-to-date information on the production of
raw copper and grades of raw ores was collected from academic journals, S&P Global
Market Intelligence and annual reports of copper-producing companies (Figure 1b and
Table S1). The sum of production in the top twelve copper mining areas accounted for
54.8% of China’s raw copper output and their average copper ore grade was 0.68%, which
was higher than the reported average grade of 0.6% in China [38]. They were located in ten
provinces or the autonomous region—Jiangxi (Dexing copper mining areas), Tibet (Yulong,
Julong and Jiama), Heilongjiang (Duobaoshan), Yunnan (Pulang), Gansu (Jinchuan), Fujian
(Zijingshan), Inner Mongolia (Wunugetushan), Shanxi (Tongkuangyu), Xinjiang (Ashele),
and Anhui (Dongguashan) (Figure 1b and Table S2). Among them, the Dexing copper mine
located in southeastern China ranked first, where the production of copper ores reached
156 thousand tons, accounting for 8.2% of domestic output in 2022. In the same year, the
total output reached up to 414 thousand tons in the Pulang, Julong, Yulong, and Jiama
mining areas of southwestern China, which sharply increased by almost tenfold in the last
five years (Table S2).
However, China’s copper production from domestic raw ores contributed to only 14%
of total copper consumption [39], which imported up to 25.27 million tons of copper ores
and concentrates in 2022 [40]. Utilization of secondary copper resources creates a pathway
for navigating challenges of resources, environment and energy transition [4,41,42]. There
are fifty-one ponds registered by the Ministry of Ecology and Environment of China for
the disposal and storage of tailings from twenty-two copper mines with a large-scale
production of more than ten thousand tons per year in mainland China (Figure 1c and
Table S3). Three fitted linear models with good R-squared values of 1 were built to estimate
the annual production of tailings from porphyry copper mines that account for ~75% of
the world’s Cu production, volcanogenic massive sulfide mines and magmatic sulfide
mines (Figure 1), where the sampling size ranged from 32 to 109. The 3.76 million tons per
year of porphyry copper tailings are accumulated in Tibet, China’s largest scale of mining
and processing region. The 2.35 million tons per year of porphyry and magmatic sulfide
mine tailings are accumulated in Jiangxi Province, Asia’s largest open-pit copper mining
region. There are 1.36 million tons per year of porphyry copper tailings accumulated in
Heilongjiang Province; in addition, there are 1.36 million tons per year of tailings from
porphyry, volcanogenic massive sulfide and orogenic Au deposits in Yunnan Provinces.
Minerals 2024, 14, x FOR PEER REVIEW 4 of 19

accumulated in Heilongjiang Province; in addition, there are 1.36 million tons per year of
Minerals 2024, 14, 1051 tailings from porphyry, volcanogenic massive sulfide and orogenic Au deposits in Yunnan
4 of 18
Provinces.

Figure
Figure 1. Production and
1. Production and distribution
distribution of of copper
copper mines
mines and
and copper
copper tailings.
tailings. (a) Global production
(a) Global production ofof
raw
raw copper
copper and
andcopper
coppertailings
tailingsfrom
from2004 to to
2004 2022. (b)(b)
2022. China’s large-scale
China’s copper
large-scale mining
copper regions
mining (Cu
regions
production > 1000
(Cu production t/a).t/a).
> 1000 (c)(c)
China’s
China’s large-scale
large-scalecopper
coppertailing
tailingponds
ponds(Cu
(Cuproduction
production>>10,000
10,000 t/a).
t/a).
Data and
and references
referencesfor
forChina’s
China’scopper
copperoreoregrades
gradesand
andannual
annualproduction
production ofof
raw copper
raw copperareare
given in
given
in Table
Table S2;S2; more
more global
global datadata
forfor three
three types
types of copper
of copper oreore deposits
deposits sourced
sourced from from
Adrianto [5].[5].
Adrianto

Microbial species and their leaching mechanisms are dependent on the mineralogical
compositions
compositions and andphysical
physicalproperties
propertiesofof tailings
tailings [12,43].
[12,43]. Compared
Compared to raw
to raw copper
copper ores, ores,
cop-
copper mine tailings have specific particle composition and mineral composition,
per mine tailings have specific particle composition and mineral composition, which are which
are finely
finely crushed
crushed solid
solid wastes
wastes with
with a particle
a particle size
size ofofless
lessthan
than400400µm
µm andand contain
contain copper
copper
mainly
mainly in the form of bi/polymetallic sulfides such as chalcopyrite, bornite, covelline,
in the form of bi/polymetallic sulfides such as chalcopyrite, bornite, covelline,
enargite and chalcocite
enargite and chalcocite(Table
(Table1).
1).The
The tailing
tailing particle
particle size
size is inversely
is inversely proportional
proportional to
to the
the bioleaching
bioleaching rate,rate, but ultrafine
but the the ultrafine particles
particles havehave negative
negative effectseffects
on theonflow
the of
flow of leach
leach solu-
solution, cellular
tion, cellular integrity,
integrity, microbial
microbial metabolicactivities
metabolic activitiesand
andleaching
leaching behavior
behavior [44,45].
[44,45]. The
The
recommended particle size for stirred-tank leaching (lower than 500 µm) is much lower
than that for bioheap leaching (lower than 12 mm) (Table S4).
Minerals 2024, 14, 1051 5 of 18

Table 1. Mineral composition and particle size of raw ores and tailings from China’s copper mines.

Cu Minerals in
Copper Mines Cu Minerals in Raw Ore Tailing Particle Size (µm) References
Tailings
Copper sulfides (aikinite, bornite,
carrollite, chalcocite, chalcopyrite,
1 to 340 µm
cubanite, djurleite, emplectite,
Dexing Chalcopyrite with median diameter of [46,47]
tennantite), copper oxides
9 to 113 µm
(azurite–malachite, cuprite–tenorite
and malachite)
Copper oxides (malachite, azurite,
copper manganese aluminum silicon
oxides) and secondly in copper 86.60% of particles lower
Yulong Covellite [48]
sulfides (chalcocite, chalcopyrite, than 74 µm
chrysocolla, delafossite
and brochantite)
87.8% of particles ranging
Copper sulfides (chalcopyrite, bornite from 25 to 150 µm and 96%
Chalcopyrite and
Duobaoshan and covellite) and minor copper of particles lower than [49–51]
bornite
oxides (cuprite) 45 µm after
iso-flotability flotation
Copper sulfides (chalcopyrite and
87.8% of particles ranging
Pulang bornites) and minor copper Chalcopyrite [52,53]
from 5 to 75 µm
oxides (malachite)
More than 85% of particles
Jinchuan Copper sulfides (chalcopyrite) Chalcopyrite [54]
ranging from 2 to 250 µm
Copper sulfides (chalcopyrite, bornite Chalcopyrite,
Jiama Lower than 75 µm [55,56]
and minor tetrahedrite) chalcocite and bornite
Copper sulfides (chalcocite, covellite Chalcocite, covellite Particles ranging from 74 to
Zijinshan [21]
and enargite) and enargite 178 µm for Cu recovery
Copper sulfides (chalcopyrite, bornite,
chalcocite and tetrahedrite), malachite
Wunuge Tushan Not given Not given [57]
and covellite in the fracture surfaces of
altered rocks in the oxidation zone
Copper sulfides (chalcopyrite, bornite More than 99% of particles
Tongkuangyu Not given [58,59]
and minor chalcocite) lower than 150 µm
Copper sulfides (chalcopyrite,
Ashele tennantite, bornite, cubanite Chalcopyrite Lower than 75 µm [60,61]
and tetrahedrite)
Copper sulfides (chalcopyrite) Sulfides and Particles lower than 74 µm
Dabaoshan [62,63]
hosted in middle Devonian limestone oxyhydroxides for analysis
Copper oxides (malachite, cuprite, Malachite, chalcopyrite,
Yangla 2 to 281 µm [14,15]
chrysocolla and chessylite) covelline and chalcocite

Bioleaching is economically feasible for recovery of copper from an estimated

20 million tons of low-grade tailings with copper grades of higher than 0.1% [64,65].
China’s typical bioleaching application for copper tailings at a scale of 1000 t (Figure 2) can
be traced back to 1987 at Dexing copper mine, Asia’s largest open-pit copper mine and
ranking second in the world [66]. And 16.59% to 30% of copper was recoveried from tailings
with copper grades of higher than 0.12% using natural microorganisms from AMD [66,67].
The bioheap leaching was firstly scaled up to 10,000 t of copper tailings at the Zijinshan
mining region, which had a copper grade of higher than 0.15% and a multistage flotation
was combined with a microbial consortium that consists of Acidithiobacillus, Leptospirillum
and Sulfobacillus [21]. The Jinchuan nickle–copper mine tailings with a copper grade of
no less than 0.30% were treated by mixed Acidithiobacillus ferrooxidans, Acidithiobacillus
thiooxidans and Leptospirillum ferrooxidans [68].
 tailings with a copper grade of no less than 0.30% were treated by mixed Acidithiobacillus
ferrooxidans, Acidithiobacillus thiooxidans and Leptospirillum ferrooxidans [68].
In general, accumulated copper mine tailings have attracted much attention and
many studies have focused on bioleaching of copper sulfide tailings for potential
industrial practice (Table S4). However, industrial applications are limited owing to
Minerals 2024, 14, 1051 6 of 18
microbial metabolic activities that are susceptible to environmental influences, mineral
composition in particular.

Figure 2. Characterization of China’s typical commercial bioleaching of low-grade copper ores and
Figure 2. Characterization of China’s typical commercial bioleaching of low-grade copper ores
tailings.
and tailings.
4. Strengths and Weaknesses of Typical Microbes for Leaching Varied Cu Sulfides or
In general, accumulated copper mine tailings have attracted much attention and
Oxides
many studies have focused on bioleaching of copper sulfide tailings for potential indus-
Most leaching
trial practice (Table bacteria or archaea
S4). However, are autotrophic
industrial Fe and/or
applications sulfur oxidizers,
are limited owing toand the
microbial
specific metabolic properties allow them to be effective in dissolving the sulfide
metabolic activities that are susceptible to environmental influences, mineral composition minerals
ininparticular.
the copper tailings such as pyrite, chalcopyrite, enargite, chalcocite, bornite and covell-
ite (Figure 3 and Table S5). Supplemental oxygen is required for microbial oxidation and
4.dissolved
Strengths oxygen concentration
and Weaknesses ofshould
TypicalbeMicrobes
maintainedforbetween 1.5 Varied
Leaching mg/L andCu4.1 mg/L by
Sulfides
aeration,
or Oxides shaking and stirring [10,69,70]. Moreover, carbon dioxide from supplemental air
andMost
carbonate minerals is the primary carbon source for autotrophic metabolism
leaching bacteria or archaea are autotrophic Fe and/or sulfur oxidizers, and thevia the
specific metabolic properties allow cycle
classical Calvin–Benson–Bassham them[71,72].
to be effective in dissolving the sulfide minerals in
Temperature exerts an important influence on
the copper tailings such as pyrite, chalcopyrite, microbial
enargite, community
chalcocite, and passivation
bornite and covellite
of interface between microorganisms and minerals [73,74]. Mesophiles are normally op-
(Figure 3 and Table S5). Supplemental oxygen is required for microbial oxidation and
erated at a temperature of between 20 °C and 40 °C. Among them, Acidithiobacillus
dissolved oxygen concentration should be maintained between 1.5 mg/L and 4.1 mg/L by
aeration, shaking and stirring [10,69,70]. Moreover, carbon dioxide from supplemental air
and carbonate minerals is the primary carbon source for autotrophic metabolism via the
classical Calvin–Benson–Bassham cycle [71,72].
Temperature exerts an important influence on microbial community and passivation of
interface between microorganisms and minerals [73,74]. Mesophiles are normally operated
at a temperature of between 20 ◦ C and 40 ◦ C. Among them, Acidithiobacillus ferrooxidans is
an iron– and sulfur-oxidizing bacterium that inhabites in the early–stage liquid media [75].
And thus, it was first isolated in 1947, developed in bioleaching in 1958 at the U.S. Bingham
Canyon copper mine, and then was first used in BROGIM® system to treat sulfide tailings
from Uganda Kasese Cu–Co mine in 1999 [76,77]. On the contrary, mesophilic Leptospirillum
is favorably attached to the solids and is resistant to a high concentration of Fe (III) (60 g/L
at pH 1.0) and heavy metals through NADH:ubiquinone oxidoreductase, thiol/disulfide
Minerals 2024, 14, 1051 7 of 18

system and dihydroxy-acid dehydratase [28,70,78]. Moreover, A. ferrooxidans and L. ferroox-

idans can produce magnetosome to conserve available oxygen, accumulate excess iron and
heavy metals [79]. Acid pH plays important roles in proton–induced metal solubilization;
however, the growth and leaching rates of L. ferriphilum significantly decrease at the
Minerals 2024, 14, x FOR PEER REVIEW 8 of pH
19
value of lower than 1.0 or higher than 1.8 [33,80,81].

Figure 3. Autotrophs and heterotrophs involved in leaching of varied copper minerals and their
Figure 3. Autotrophs and heterotrophs involved in leaching of varied copper minerals and their
multiple influencing factors. Data and references on application of species in bacteria, archaea and
multiple influencing factors. Data and references on application of species in bacteria, archaea and
fungi for China’s copper sulfides or oxides are given in Table S5.
fungi for China’s copper sulfides or oxides are given in Table S5.
In addition, heterotrophic bacteria (Acidiphilium multivorum and Ferrimicrobium), ar-
chaea (Thermoplasma) and fungi (Aspergillus niger, Beauveria caledonica, Penicillium simpli-
cissimum and Rhodotorula mucilaginosa) can use organic compounds as energy sources to
treat copper oxides (malachite, chrysocolla and azurite) and weathered sulfides (bornite,
chalcocite, digenite and covellite) (Figure 3 and Table S5) [99–101]. Heterotrophic archaea
Minerals 2024, 14, 1051 8 of 18

With elevating heap temperature at the mid to late stage of the bioleaching process
that was found to be exothermic, thermophiles are dominant in the inner and middle
layers [20,67]. Moderate thermophiles that work at a temperature of between 40 ◦ C and
60 ◦ C, were first developed in BioCOPTM progress for bioleaching of Chile’s Chuquicamata
polymetallic chalcopyrite in 1997 [82,83]. Sulfobacillus spp. and Acidithiobacillus caldus are
moderately thermophilic bacteria, which were combined with mesophiles to treat low-
grade copper ores and tailings [20,84]. The A. caldus is an extremely acidophilic sulfur
oxidizer with highly frequent gene turnover to evolutionary adaptation, which can recover
more than 40% of copper from low-grade sulfides at 45 ◦ C [85,86]. When it was mixed with
S. thermosulfidooxidan that is a facultatively chemolithotrophic Fe and sulfur oxidizer in
the presence of organic matter due to putative archaeal cluster of sulfocyanins, more than
90% of copper can be recovered from tailings at 45 ◦ C [87,88]. A. caldus and S. acidophilus
were mixed with Ferroplasma thermophilum to improve copper leaching from chalcopyrite at
a high pulp density of 20%, where F. thermophilum is mixotrophic iron-oxidizing archaea
and was dominant in the final stage corresponding to declining pH and increasing organic
matters [79,89]. The activities of mixed moderate thermophiles and leaching efficiency
were optimized at pH values of 1.0 to 3.0 [80], owing to effects of pH on electric charges of
tailings surfaces and their attachment to bacteria [25,90,91].
The stable passivation layer is more readily formed at pH values of 2.0 to 2.6 and
30 ◦ C, while it is hardly formed at a temperature of 60 ◦ C to 80 ◦ C [13,67]. Therefore,
more extreme thermophilic archaea belonging to Acidianus, Metallosphaera and Sulfolobus
have been explored in bioreactor of copper sulfide concentrates at operating tempera-
tures higher than 65 ◦ C over a decade ago [92,93]. Among them, Sulfolobus ubiquitously
distributed throughout vacanic fields worldwide is recommended for a wide variety of
industrial applications, and appears robust under considerable temperature fluctuations,
high concentrations of copper and solids [92,94]. S. acidocaldarius is a thermoacidophilic
archaeon with strong genetic stability, reduced susceptibility to mobile genetic elements
and environmental change [95]. S. acidocaldarius can recover more than 97% of copper from
chalcopyrite at 70 ◦ C [96]. Extreme thermophiles and hyperthermophiles grow well at a
temperature above 70 ◦ C or 80 ◦ C [92,95,97], and have been explored in bioleaching at
high temperatures and low oxidation potential to prevent passivation. Although higher
leaching rates can be obtained by thermophilic archaea, they lack peptidoglycan and acidic
groups in cell walls and are more sensitive to higher pulp density and heavy metals than
mesophiles [92,98].
In addition, heterotrophic bacteria (Acidiphilium multivorum and Ferrimicrobium), ar-
chaea (Thermoplasma) and fungi (Aspergillus niger, Beauveria caledonica, Penicillium simpli-
cissimum and Rhodotorula mucilaginosa) can use organic compounds as energy sources to
treat copper oxides (malachite, chrysocolla and azurite) and weathered sulfides (bornite,
chalcocite, digenite and covellite) (Figure 3 and Table S5) [99–101]. Heterotrophic archaea
Thermoplasma acidophilum was first isolated from coal waste dumps in 1970, where organic
matter is commonly occurring [102]. Fungi can reutilize carbohydrate-based agricultural
wastes as their exogenous nutrients and carbon resources to form complexes with met-
als [103,104]. Therefore, T. acidophilum and A. niger have been used to recover multiple
metals from e-wastes containing organic pollutants [105,106]. Fungi can thrive in bioleach-
ing systems with a wide range of pH values from 1.4 to 9.8 (Figure 3 and Table S5). However,
the processes consume considerable amounts of energy and carbon sources, resulting in a
lower leaching rate than bacteria [36]. Fungi can perform well at a high pulp density of 18%,
whereas the highest recovery of copper was obtained for A. ferrooxidans with resistance to
high levels of heavy metals at a pulp density of 5% [107,108]. In fact, copper tailings at
low pulp densities of 1% to 2% can provide essential metal ions for bacterial growth and
activity, which should be controlled to avoid accumulation of toxic products, a decrease in
agitation rate, and/or mass transfer limitation in bioreactors [85,109].
Chemolithoautotrophic and mesophilic bacteria are widely used to treat copper sulfide
tailings mainly in the form of chalcopyrite. Moderate thermophilic bacteria and extreme
Minerals 2024, 14, 1051 9 of 18

thermophilic archaea can be used as the operating temperature increases at the late stage
or to prevent passivation, but they are sensitive to high levels of pulp density and heavy
metals. Heterotrophic species thriving at a wide pH range and high pulp density, have
been develped to treat copper oxides and weathered sulfides, but their leaching rates are
lowered by high energy and carbon source consumption.

5. Mineral Composition-Dependent Leaching Mechanisms for Autotrophs and Heterotrophs

Bacteria produce chemical agents to dissolve the metals from tailings in modes of
bacteria–mineral contact, non-contact and cooperative leaching, known as indirect bioleach-
ing (Figure 4). For contact leaching, bacteria secrete extracellular polymeric substances (EPS)
to form biofilm by their adhesion to the surface of low-grade copper minerals [110,111].
The cycling of Fe (III) –S and Fe (II) –S proteins results in accumulation of Fe (III) in biofilm
and oxidative dissolution of metals from sulfide minerals, along with the release of Fe
(II) ions, sulfur colloids (S8 ), sulfur intermediates (H2 Sn and S2 O3 2− ) and the desired met-
als (Cu2+ ) [33,112]. Owing to different types of sulfide components in tailings [34,113],
autotrophic bacteria produce different sulfur intermediates via polysulfide pathway and
Minerals 2024, 14, x FOR PEER REVIEW
thiosulfate pathway under aerobic conditions (Figure 4). For non-contact leaching,10plank- of 19
tonic cells oxidize free Fe (II) ions in pore solution to generate Fe (III), driving solubilization
of sulfide minerals [33,114]. In the mode of cooperative leaching, planktonic cells utilize Fe
and ions,
(II) sulfur (Rhd),
rhodanese intermediates,
which was sulfur colloids
mixed with and mineral fragments
A. ferrooxidans originated
to generate from cells
more energy, in-
withinstress
crease the biofilm [115].and treat pyrite in tailings [11,119].
resistance

Figure
Figure 4.
4. Indirect
Indirect bioleaching
bioleachingof of copper
copper sulfide
sulfide tailings
tailings through
through bacterial
bacterial contact,
contact, non-contact
non-contact and
and
cooperative modes (a) for sulfide oxidation via polysulfide and thiosulfate pathways
cooperative modes (a) for sulfide oxidation via polysulfide and thiosulfate pathways (b). (b).

Different from bioleaching of copper sulfides by autotrophs, fungi extract valuable

metals from oxides in tailings through processes of acidolysis, complexolysis, and redox-
olysis in Figure 5 [34,103]. In acidolysis, organic acids dissociate to release H+ ions, includ-
ing oxalic, citric, gluconic, malic and itaconic acids produced by Aspergillus, lactic and fu-
maric acids produced by Rhizopus [124–126]. In fungal mitochondria, glycolysis occurs to
generate pyruvate, which is catalyzed by carboxylase to form an oxaloacetic acid and by
Minerals 2024, 14, 1051 10 of 18

Most of the copper tailings contain orpiment (As2 S3 ), covellite (CuS), chalcopyrite
(CuFeS2 ), bornite (Cu5 FeS4 ), pyrrhotite (Fe7 S8 ), hauerite (MnS2 ), and sphalerite (ZnS),
which are acid-soluble and oxidized to form polysulfides (H2 Sn ) through polysulfide
pathway [116]. This process is driven by electron extraction using iron-oxidizing bacteria
produced Fe (III) ions, along with proton attack [117,118]. And then sulfur-oxidizing bacte-
ria facilitate oxidation of polysulfides to form sulfur colloids (S8 ), finally to H2 SO4 [33,43].
As for A. ferrooxidans, the hydrogen sulfide–Fe(III) oxidoreductase, sulfuric acid–Fe(III)
oxidoreductase and Fe(II) oxidoreductase are involved in this aerobic process, using both
Fe(II) and sulfur as substrates [119,120]. In contrast, thiosulfate pathway is carried out for
acid-insoluble tailings containing pyrite (FeS2 ) and molybdenite (MoS2 ) [116,121]. They are
oxidized to thiosulfate (S2 O3 2− ), and then to tetrathionate (S4 O6 2− ) as sulfur intermediates,
finally to sulfate (SO4 2− ) [122,123]. Through this pathway, A. ferrooxidans utilizes thiosul-
fate:quinone oxidoreductase (doxD) and tetrathionate hydrolase (tetH) and thiosulfate de-
hydrogenase (TSD) to shuttle electrons. And instead, A. thiooxidans can metabolize reduced
inorganic sulfur compounds (RISCs) by the sulfur oxidase complex (Sox), tetrathionate
hydrolase (TetH), sulfide quinone reductase (Sqr), heterodisulfate reductase (Hdr) and
rhodanese (Rhd), which was mixed with A. ferrooxidans to generate more energy, increase
stress resistance and treat pyrite in tailings [11,119].
Different from bioleaching of copper sulfides by autotrophs, fungi extract valuable
metals from oxides in tailings through processes of acidolysis, complexolysis, and redoxol-
ysis in Figure 5 [34,103]. In acidolysis, organic acids dissociate to release H+ ions, including
oxalic, citric, gluconic, malic and itaconic acids produced by Aspergillus, lactic and fu-
maric acids produced by Rhizopus [124–126]. In fungal mitochondria, glycolysis occurs to
generate pyruvate, which is catalyzed by carboxylase to form an oxaloacetic acid and by
dehydrogenase complex to form an acetyl group. After that, a condensation reaction occurs
to form citric acid, and then to malic acid via multistep decarboxylation, dehydrogenation
and hydration [127,128]. These organic acids transport across plasma membrane, where
the generated H+ ions react with oxide tailings to release Cu2+ . In complexolysis, stronger
bonds are formed between metal ions and functional groups of organic acids than lattice
energy, defined by attraction between metal ions and other ions in solids. The generated
metal–organic acid complexes enhance the release of copper from tailings [103,129,130].
There are different stability constants for copper and organic acid complexes as follows:
pyruvic = galacturonic < malic < citric [131]. In addition, the fungal adhesion to tailings
stimulates the production of EPS containing hydroxyl, carboxyl and amino groups, result-
ing in further complexation with metal ions [33,95,132]. In redoxolysis, the organic acids
or H+ ions can act as electron donor in an acidic environment, where Fe (III) and/or Mn
(IV) are catalytically reduced to release Fe (II) and Mn (II), depending on oxidation states of
multiple metals in tailings [103,133,134].
Autotrophs in a planktonic state or biofilm use different sulfur-cycling enzymes to
treat acid-soluble sulfides in polysulfide pathway and acid-insoluble sulfides in thiosulfate
pathway. For fungi, multiple enzymes are involved in production and transfer of various
organic acids to chelate copper from oxides. The proteins and functional genes associ-
ated with these processes remain poorly characterized, which provide limited insights
into bioleaching.
 Autotrophs in a planktonic state or biofilm use different sulfur-cycling enzymes to
treat acid-soluble sulfides in polysulfide pathway and acid-insoluble sulfides in thiosul-
fate pathway. For fungi, multiple enzymes are involved in production and transfer of var-
ious organic acids to chelate copper from oxides. The proteins and functional genes asso-
Minerals 2024, 14, 1051 ciated with these processes remain poorly characterized, which provide limited insights
11 of 18
into bioleaching.

Figure 5. Fungi and their principal mechanisms for leaching copper oxides in low-grade ores and
Figure 5. Fungi and their principal mechanisms for leaching copper oxides in low-grade ores and
tailings using
tailings using mutiple
mutiple organic
organic acids.
acids.

6. Advanced Genome, Microscopy and Spectroscopy-Driven Bioleaching

6. Advanced Genome, Microscopy and Spectroscopy-Driven Bioleaching
With the advances in bioinformatics, research has been moving forward on phylogenetic
and With the advances
functional diversityinofbioinformatics,
native microbial research has been
communities in moving
leachingforward
systemson phyloge-It
[135,136].
netic and functional diversity of native microbial communities
has been revealed that genes encoding tetrathionate hydrolase, Sox sulfur-oxidizingsystems
in leaching enzyme
[135,136]. It has been
system, thiosulfate revealed thatsulfur
dehydrogenase, genesoxygenase
encodingreductase,
tetrathionate hydrolase,
thiosulfate Sox sulfur-
sulfurtransferase,
oxidizing enzyme
heterodisulfide system,complex,
reductase thiosulfate dehydrogenase,enzymes,
sulfate-activating sulfur oxygenase reductase,
sulfide quinone thio-
reductase,
sulfate sulfurtransferase, heterodisulfide reductase complex, sulfate-activating
thiosulfate:quinone oxidoreductase, terminal oxidase and cytochrome bc1 complexes are enzymes,
sulfide quinone
associated with reductase, thiosulfate:quinone
sulfur oxidation oxidoreductase,
in Acidithiobacillus terminal oxidase
spp. and Leptospirillum and cy-
spp. [137,138].
tochrome bc1 complexes are associated with sulfur oxidation in Acidithiobacillus
And genes encoding iron oxidation functions have been identified in Acidithiobacillus spp., spp. and
Leptospirillum spp. [137,138]. And genes encoding iron oxidation functions
Leptospirillum spp. and Archaea (Ferroplasma spp., Sulfolobus spp. and Metallosphaera spp.), have been iden-
tified in Acidithiobacillus
including outer membrane spp.,cytochrome
Leptospirillumc, spp.
copperandprotein
Archaea (Ferroplasmairon
rusticyanin, spp.,oxidase,
Sulfolobuscy-
spp. and Metallosphaera
tochrome spp.), including
579, inner membrane outer membrane
peripheral cytochromecytochrome c, copper oxidase
c, inner membrane protein rus-
and
ticyanin,
cytochromeironbc1
oxidase, cytochrome
complexes) 579,Carbon
[137,138]. inner membrane
response inperipheral
Leptospirillumcytochrome
ferriphilum c, inner
from
membrane oxidase and cytochrome bc1 complexes) [137,138]. Carbon
Chile’s bioleaching heap of copper was revealed by genes encoding 2–oxoglutarate-acceptor response in Lepto-
spirillum ferriphilum
oxidoreductase, from Chile’s
glycogen bioleaching
phosphorilase heap of copper
and glycogen synthase was revealed
[139]. Thereby was genes en-
a signifi-
coding 2–oxoglutarate-acceptor
cant shift in genes encoding nitrogenase oxidoreductase,
iron proteinglycogen phosphorilase
and ammonium and glycogen
transporter protein
synthase [139]. There
of Leptospirillum was a significant
ferriphilum, shift inrelated
as well as urease genes protein
encoding nitrogenase
genes iron protein
from China’s copper
and ammonium
producing areas,transporter
which repliedprotein of Leptospirillum
to essential nitrogen ferriphilum, as well asBased
sources [139,140]. ureaseon related
deep
protein
insightsgenes frominvolved
into genes China’s copper producing
in bioleaching, areas, which
genetically replied
engineered to essential nitrogen
microorganisms opened
up new [139,140].
sources possibilities for design
Based on deep and construction
insights of robust
into genes microorganisms
involved in bioleaching,with enhanced
genetically
leaching efficiency
engineered and resource
microorganisms efficiency
opened up new [33,141]. It can be
possibilities fordesigned
design and to improve
constructiongrowthof
via overexpression of essential Fe–S protein ABCE1 and translation initiation factor a/eIF2(–
γ) in Sulfolobus solfataricus, to enhance sulfur and iron oxidation via overexpression of
rusticyanin, phosphofructokinase, sulfur dioxygenases and tetrathionate hydrolase in
Acidithiobacillus ferrooxidans, to obtain highly efficient CO2 fixation, iron oxidation or Fe3+
chelating capability of licanantase-rich biofilms in Acidithiobacillus ferrooxidans [142,143].
Minerals 2024, 14, 1051 12 of 18

Advanced microscopy and spectroscopy facilitate characterization of minerals, at-

tached microbial cells and EPS within biofilms to explore interactions between microorgan-
ism and minerals, especially for the formation of stable passivation layers [18,95]. Scanning
electron microscopy coupled with energy dispersive X–ray spectroscopy (SEM/EDX) can
identify elements with variable oxidation states, which reveals accumulation of Fe (III) ions
in EPS produced by Acidithiobacillus ferrooxidans, as well as its contribution to the improve-
ment of Cu recovery from chalcopyrite [143,144]. The adhesion forces between microbial
EPS and copper minerals can be determined by atomic force microscopy (AFM) and epiflu-
orescence microscopy (EFM), and further composition analysis of EPS can be conducted by
Fourier transmission infrared spectroscopy (FTIR) [145]. It can be emphasized that surface
cracks/imperfections have effects on attachment of microbial cell to minerals using AFM,
EFM and confocal laser microscopy (CLSM) [146,147]. The micro-Raman excitation and
FTIR spectroscopies, double-pulse laser-induced breakdown spectroscopy (DP–LIBS) with
high sensitivity to Fe and Cu, or expensive nano secondary ion mass spectrometry (SIMS)
for rare isotopes provide opportunities to differentiate EPS from the chemically stable
covellite-like and jarosite-like surface layers that prevent further dissolution of copper and
map them in real time [18,148,149].
The development of biological sciences and molecular representation can help break
bottlenecks in bioleaching technology by building robust functional microbes with en-
hanced leaching efficiency and resource efficiency, and designing molecular structures of
microbe–mineral complexes.

7. Conclusions
On the basis of three fitted linear models, China’s annual production of copper tail-
ings from porphyry, volcanogenic massive sulfide, and magmatic sulfide deposits were
estimated. And tailing piles are accumulated mainly in the Tibet autonomous region with
an annual production of 3.76 million tons, Jiangxi Province (2.35 million tons), Heilongjiang
Province (1.36 million tons) and Yunnan Province (1.36 million tons). As a green technology,
commercial bioleaching has been built for low-grade copper ores and tailings at the Dexing,
Jinchuan and Zijinshan mining regions in China using natural microorganisms from AMD
or a mixed culture of bacteria. Aerobic and autotrophic Fe and/or S oxidizers are domi-
nant in bioleaching systems of copper sulfide tailings mainly in the form of chalcopyrite.
Mesophilic Acidithiobacillus, Acidiphilium, Alicyclobacillus, Leptospirillum and Thiobacillus
have been commonly mixed with moderate thermophiles (Acidithiobacillus caldus, Acidimi-
crobium, Acidiplasma, Ferroplasma and Sulfobacillus). Although higher leaching rates can be
obtained by thermophilic archaea (Acidianus, Metallosphaera, Sulfurococcus and Sulfolobus)
at an operating temperature over 65 ◦ C to prevent passivation, they are more sensitive
to high levels of pulp density and heavy metals. Heterotrophic Acidiphilium multivorum,
Ferrimicrobium, Thermoplasma and fungi thriving at wide ranges of pH values and tempera-
tures below 47 ◦ C can be used for copper oxides (malachite, chrysocolla and azurite) and
weathered sulfides, requiring higher energy and organic carbon than autotrophs. Owing
to different acidic solubilities of sulfides, various sulfur-cycling enzymes are involved
in the autotrophic polysulfide and thiosulfate pathways under contact, non-contact and
cooperative modes. However, heterotrophic fungi such as Aspergillus and Rhizopus produce
organic acids to release copper from oxide minerals through acidolysis, complexolysis and
redoxolysis. As functional genes have been successively identified in leaching systems us-
ing molecular biology and bioinformatics, genetically engineered microorganisms are built
to improve microbial growth and utilization of iron, sulfur, carbon and nitrogen sources.
In addition, advanced characterization of microbe–mineral interface provides insight into
bioleaching mechanisms for complex minerals in low-grade tailings to improve leaching
efficiency. Advances in biological sciences and molecular representation will unlock the
bioleaching barriers resulting from microbial metabolic activities susceptible to mineral
composition and other environmental factors.
Minerals 2024, 14, 1051 13 of 18

Supplementary Materials: The following supporting information can be downloaded at: https:
//www.mdpi.com/article/10.3390/min14101051/s1, Table S1. Annual production of raw copper
and copper tailings in China from 2007 to 2022; Table S2. Detailed characteristics of large-scale copper
mines in China; Table S3. Detailed characteristics of tailing ponds at large-scale copper mines in
China; Table S4. Survey on bioleaching technologies with potential industrial applications for copper
sulfide tailings; Table S5. Culture conditions of leaching bacteria, archaea and fungi applicable for
copper minerals.
Author Contributions: Conceptualization, J.Z.; methodology, X.D.; validation, X.D.; formal analysis,
X.L.; data curation, X.L. and X.D.; writing—original draft, X.L. and X.W.; writing—review and editing,
J.Z., Y.Z. and S.F.; visualization, J.Z., X.W. and Y.Z.; funding acquisition, J.Z. and S.F. All authors have
read and agreed to the published version of the manuscript.
Funding: This research was funded by the National Natural Science Foundation of China (No.
52170149) and the National Key R&D Program of China (No. 2018YFC1802101 and 2018YFC1801702).
Data Availability Statement: Data from this study are available from the corresponding author
upon request.
Acknowledgments: The authors also thank Minghua Zhang who retired from her position in
University of California, Davis for language editing.
Conflicts of Interest: The authors declare no conflicts of interest.

References
1. Giachino, A.; Focarelli, F.; Marles-Wright, J.; Waldron, K.J. Synthetic biology approaches to copper remediation: Bioleaching,
accumulation and recycling. FEMS Microbiol. Ecol. 2021, 97, fiaa249. [CrossRef] [PubMed]
2. Zhang, J.; Shi, Q.; Fan, S.; Zhang, Y.; Zhang, M.; Zhang, J. Distinction between Cr and other heavy–metal–resistant bacteria
involved in C/N cycling in contaminated soils of copper producing sites. J. Hazard. Mater. 2021, 402, 123454. [CrossRef] [PubMed]
3. Chen, J.; Wang, Z.; Wu, Y.; Li, L.; Li, B.; Pan, D.A.; Zuo, T. Environmental benefits of secondary copper from primary copper
based on life cycle assessment in China. Resour. Conserv. Recycl. 2019, 146, 35–44. [CrossRef]
4. Zhang, J.; Tian, X.; Chen, W.; Geng, Y.; Wilson, J. Measuring environmental impacts from primary and secondary copper
production under the upgraded technologies in key Chinese enterprises. Environ. Impact Assess. Rev. 2022, 96, 106855. [CrossRef]
5. Adrianto, L.R.; Pfister, S. Prospective environmental assessment of reprocessing and valorization alternatives for sulfidic copper
tailings. Resour. Conserv. Recycl. 2022, 186, 106567. [CrossRef]
6. Valenta, R.K.; Lèbre, É.; Antonio, C.; Franks, D.M.; Jokovic, V.; Micklethwaite, S.; Parbhakar-Fox, A.; Runge, K.; Savinova, E.;
Segura-Salazar, J.; et al. Decarbonisation to drive dramatic increase in mining waste–Options for reduction. Resour. Conserv.
Recycl. 2023, 190, 106859. [CrossRef]
7. Furnell, E.; Bilaniuk, K.; Goldbaum, M.; Shoaib, M.; Wani, O.; Tian, X.; Chen, Z.; Boucher, D.; Bobicki, E.R. Dewatered and stacked
mine tailings: A review. ACS ES T Eng. 2022, 2, 728–745. [CrossRef]
8. Mokarian, P.; Bakhshayeshi, I.; Taghikhah, F.; Boroumand, Y.; Erfani, E.; Razmjou, A. The advanced design of bioleaching process
for metal recovery: A machine learning approach. Sep. Purif. Technol. 2022, 291, 120919. [CrossRef]
9. Mishra, S.; Panda, S.; Akcil, A.; Dembele, S. Biotechnological avenues in mineral processing: Fundamentals, applications and
advances in bioleaching and bio-beneficiation. Miner. Process. Extr. Metall. Rev. 2023, 44, 22–51. [CrossRef]
10. Tezyapar Kara, I.; Kremser, K.; Wagland, S.T.; Coulon, F. Bioleaching metal-bearing wastes and by-products for resource recovery:
A review. Environ. Chem. Lett. 2023, 21, 3329–3350. [CrossRef]
11. Zhang, R.; Hedrich, S.; Römer, F.; Goldmann, D.; Schippers, A. Bioleaching of cobalt from Cu/Co-rich sulfidic mine tailings from
the polymetallic Rammelsberg mine, Germany. Hydrometallurgy 2020, 197, 105443. [CrossRef]
12. Kaksonen, A.H.; Deng, X.; Bohu, T.; Zea, L.; Khaleque, H.N.; Gumulya, Y.; Boxall, N.J.; Morris, C.; Cheng, K.Y. Prospective
directions for biohydrometallurgy. Hydrometallurgy 2020, 195, 105376. [CrossRef]
13. Zhao, H.; Zhang, Y.; Zhang, X.; Qian, L.; Sun, M.; Yang, Y.; Zhang, Y.; Wang, J.; Kim, H.; Qiu, G. The dissolution and passivation
mechanism of chalcopyrite in bioleaching: An overview. Miner. Eng. 2019, 136, 140–154. [CrossRef]
14. Yin, S.; Wang, L.; Wu, A.; Free, M.L.; Kabwe, E. Enhancement of copper recovery by acid leaching of high-mud copper oxides: A
case study at Yangla copper mine, China. J. Clean. Prod. 2018, 202, 321–331. [CrossRef]
15. Yin, S.; Wang, L.; Wu, A.; Kabwe, E.; Chen, X.; Yan, R. Copper recycle from sulfide tailings using combined leaching of ammonia
solution and alkaline bacteria. J. Clean. Prod. 2018, 189, 746–753. [CrossRef]
16. Roberto, F.F.; Schippers, A. Progress in bioleaching: Part B, applications of microbial processes by the minerals industries. Appl.
Microbiol. Biotechnol. 2022, 106, 5913–5928. [CrossRef] [PubMed]
17. Mäkinen, J.; Salo, M.; Khoshkhoo, M.; Sundkvist, J.-E.; Kinnunen, P. Bioleaching of cobalt from sulfide mining tailings; a mini-pilot
study. Hydrometallurgy 2020, 196, 105418. [CrossRef]
Minerals 2024, 14, 1051 14 of 18

18. Kaksonen, A.H.; Boxall, N.J.; Gumulya, Y.; Khaleque, H.N.; Morris, C.; Bohu, T.; Cheng, K.Y.; Usher, K.M.; Lakaniemi, A.-M.
Recent progress in biohydrometallurgy and microbial characterisation. Hydrometallurgy 2018, 180, 7–25. [CrossRef]
19. De Oliveira, D.; Horn, E.J.; Randall, D.G. Copper mine tailings valorization using microbial induced calcium carbonate precipita-
tion. J. Environ. Manag. 2021, 298, 113440. [CrossRef]
20. Wang, Y.; Chen, X.; Zhou, H. Disentangling effects of temperature on microbial community and copper extraction in column
bioleaching of low grade copper sulfide. Bioresour. Technol. 2018, 268, 480–487. [CrossRef]
21. Chen, J.; Guo, X.J.; Li, H. Implementation and practice of an integrated process to recover copper from low grade ore at Zijinshan
mine. Hydrometallurgy 2020, 195, 105394. [CrossRef]
22. Mikoda, B.; Potysz, A.; Kmiecik, E. Bacterial leaching of critical metal values from polish copper metallurgical slags using
Acidithiobacillus thiooxidans. J. Environ. Manag. 2019, 236, 436–445. [CrossRef]
23. Panda, S. Magnetic separation of ferrous fractions linked to improved bioleaching of metals from waste-to-energy incinerator
bottom ash (IBA): A green approach. Environ. Sci. Pollut. Res. 2020, 27, 9475–9489. [CrossRef] [PubMed]
24. Ilyas, S.; Srivastava, R.R.; Kim, H.; Ilyas, N. Biotechnological recycling of hazardous waste PCBs using Sulfobacillus thermosulfi-
dooxidans through pretreatment of toxicant metals: Process optimization and kinetic studies. Chemosphere 2022, 286, 131978.
[CrossRef]
25. Pourhossein, F.; Mousavi, S.M. A novel step-wise indirect bioleaching using biogenic ferric agent for enhancement recovery of
valuable metals from waste light emitting diode (WLED). J. Hazard. Mater. 2019, 378, 120648. [CrossRef]
26. Cacciuttolo, C.; Valenzuela, F. Efficient use of water in tailings management: New technologies and environmental strategies for
the future of mining. Water 2022, 14, 1741. [CrossRef]
27. Ghomi, A.G.; Asasian-Kolur, N.; Sharifian, S.; Golnaraghi, A. Biosorpion for sustainable recovery of precious metals from
wastewater. J. Environ. Chem. Eng. 2020, 8, 103996. [CrossRef]
28. Javier, R.A.; Matías, R.; Alonso, F.; Renato, C.; Gloria, L. A novel gene from the acidophilic bacterium Leptospirillum sp. CF-1 and
its role in oxidative stress and chromate tolerance. Biol. Res. 2022, 55, 19. [CrossRef]
29. Zhang, J.; Guo, Y.; Fan, S.; Wang, S.; Shi, Q.; Zhang, M.; Zhang, J. Detoxification of heavy metals attributed to biological and
non–biological complexes in soils around copper producing areas throughout China. J. Clean. Prod. 2021, 292, 125999. [CrossRef]
30. Hofmann, M.; Norris, P.R.; Malik, L.; Schippers, A.; Schmidt, G.; Wolf, J.; Neumann-Schaal, M.; Hedrich, S. Metallosphaera javensis
sp. nov., a novel species of thermoacidophilic archaea, isolated from a volcanic area. Int. J. Syst. Evol. Microbiol. 2022, 72, 005536.
[CrossRef]
31. Noguchi, H.; Okibe, N. The role of bioleaching microorganisms in saline water leaching of chalcopyrite concentrate. Hydrometal-
lurgy 2020, 195, 105397. [CrossRef]
32. Zea, L.; Mclean, R.J.C.; Rook, T.A.; Angle, G.; Carter, D.L.; Delegard, A.; Denvir, A.; Gerlach, R.; Gorti, S.; Mcilwaine, D.; et al.
Potential biofilm control strategies for extended spaceflight missions. Biofilm 2020, 2, 100026. [CrossRef] [PubMed]
33. Vera, M.; Schippers, A.; Hedrich, S.; Sand, W. Progress in bioleaching: Fundamentals and mechanisms of microbial metal sulfide
oxidation—Part A. Appl. Microbiol. Biotechnol. 2022, 106, 6933–6952. [CrossRef]
34. Liapun, V.; Motola, M. Current overview and future perspective in fungal biorecovery of metals from secondary sources.
J. Environ. Manag. 2023, 332, 117345. [CrossRef]
35. Nkuna, R.; Ijoma, G.N.; Matambo, T.S.; Chimwani, N. Accessing metals from low-grade ores and the environmental impact
considerations: A review of the perspectives of conventional versus bioleaching strategies. Minerals 2022, 12, 506. [CrossRef]
36. Nguyen, T.H.; Won, S.; Ha, M.-G.; Nguyen, D.D.; Kang, H.Y. Bioleaching for environmental remediation of toxic metals and
metalloids: A review on soils, sediments, and mine tailings. Chemosphere 2021, 282, 131108. [CrossRef]
37. Copper Statistics and Information. Available online: https://www.usgs.gov/centers/national-minerals-information-center/
copper-statistics-and-information/ (accessed on 17 April 2024).
38. Wang, J.; Liu, W.; Chen, L.; Li, X.; Wen, Z. Analysis of China’s non-ferrous metals industry’s path to peak carbon: A whole life
cycle industry chain based on copper. Sci. Total Environ. 2023, 892, 164454. [CrossRef]
39. Liu, S.; Liu, W.; Tan, Q.; Li, J.; Qin, W.; Yang, C. The impact of China’s import ban on global copper scrap flow network and the
domestic copper sustainability. Resour. Conserv. Recycl. 2021, 169, 105525. [CrossRef]
40. Copper Ores and Concentrates Imports by Country in 2022. Available online: https://wits.worldbank.org/trade/comtrade/en/
country/ALL/year/2022/tradeflow/Imports/partner/WLD/product/260300/ (accessed on 17 April 2024).
41. Dong, D.; Van Oers, L.; Tukker, A.; Van Der Voet, E. Assessing the future environmental impacts of copper production in China:
Implications of the energy transition. J. Clean. Prod. 2020, 274, 122825. [CrossRef]
42. Renaud, K.M.; Manley, R.; Nassar, N.T. A comparison of copper use in China and India as a proxy for their economic development.
Resour. Policy 2023, 80, 103195. [CrossRef]
43. Medina-Díaz, H.L.; Acosta, I.; Muñoz, M.; López Bellido, F.J.; Villaseñor, J.; Llanos, J.; Rodríguez, L.; Fernández-Morales, F.J. A
classical modelling of abandoned mine tailings’ bioleaching by an autochthonous microbial culture. J. Environ. Manag. 2022, 323,
116251. [CrossRef] [PubMed]
44. Chen, J.; Tang, D.; Zhong, S.; Zhong, W.; Li, B. The influence of micro-cracks on copper extraction by bioleaching. Hydrometallurgy
2020, 191, 105243. [CrossRef]
45. Manafi, Z.; Kargar, M.; Kafilzadeh, F. Tank bioleaching of a copper concentrate using the moderately thermophilic microorganisms
Sulfobacillus thermosulfidoxidans KMM3 and Sulfobacillus acidophilus. Rev. Metal. 2021, 57, e207. [CrossRef]
Minerals 2024, 14, 1051 15 of 18

46. Tabelin, C.B.; Park, I.; Phengsaart, T.; Jeon, S.; Villacorte-Tabelin, M.; Alonzo, D.; Yoo, K.; Ito, M.; Hiroyoshi, N. Copper and
critical metals production from porphyry ores and E-wastes: A review of resource availability, processing/recycling challenges,
socio-environmental aspects, and sustainability issues. Resour. Conserv. Recycl. 2021, 170, 105610. [CrossRef]
47. Pan, H.; Cheng, Z.; Zhou, G.; Yang, R.; Sun, B.; He, L.; Zeng, D.; Wang, J. Geochemical and mineralogical characterization of
tailings of the Dexing copper mine, Jiangxi Province, China. Geochem.-Explor. Environ. Anal. 2017, 17, 334–344. [CrossRef]
48. Han, J.; Xiao, J.; Qin, W.; Chen, D.; Liu, W. Copper recovery from yulong complex copper oxide ore by flotation and magnetic
separation. JOM 2017, 69, 1563–1569. [CrossRef]
49. Mo, Z. Study on the effect of pulp pH value on the reconcentration of Duobaoshan copper molybdenum sulfide tailings. Min.
Metall. 2022, 31, 41–46. (In Chinese) [CrossRef]
50. Yin, S.H.; Wu, A.X.; Qiu, G.Z. Bioleaching of low-grade copper sulphides. Trans. Nonferrous Met. Soc. China 2008, 18, 707–713.
[CrossRef]
51. Zhang, S.; Ju, N.; Zhang, G.B.; Zhao, Y.D.; Ren, Y.S.; Liu, B.S.; Wang, H.; Guo, R.R.; Yang, Q.; Sun, Z.M.; et al. Geology and
mineralization of the Duobaoshan supergiant porphyry Cu-Au-Mo-Ag deposit (2.36 Mt) in Heilongjiang Province, China: A
review. China Geol. 2023, 6, 100–136. [CrossRef]
52. Li, W.C.; Zhang, X.F.; Yu, H.J.; Tao, D.; Liu, X.L. Geology and mineralization of the Pulang supergiant porphyry copper deposit
(5.11 Mt) in Shangri-la, Yunnan Province, China: A review. China Geol. 2022, 5, 662–695. [CrossRef]
53. Zhu, K.; He, Y.; Feng, D.; Jiang, W.; Zhang, K. Leaching behavior of copper tailings solidified/stabilized using hydantoin epoxy
resin and red clay. J. Environ. Manag. 2023, 345, 118876. [CrossRef]
54. Wang, L.; Li, Y.; Wang, H.; Cui, X.; Wang, X.; Lu, A.; Wang, X.; Wang, C.; Gan, D. Weathering behavior and metal mobility of
tailings under an extremely arid climate at Jinchuan Cu-Ni sulfide deposit, Western China. J. Geochem. Explor. 2017, 173, 1–12.
[CrossRef]
55. Zheng, W.; Tang, J.; Zhong, K.; Ying, L.; Leng, Q.; Ding, S.; Lin, B. Geology of the Jiama porphyry copper–polymetallic system,
Lhasa Region, China. Ore Geol. Rev. 2016, 74, 151–169. [CrossRef]
56. Weng, R.; Chen, G.; Huang, X.; Tian, F.; Ni, L.; Peng, L.; Liao, D.; Xi, B. Geochemical characteristics of tailings from typical metal
mining areas in Tibet autonomous region. Minerals 2022, 12, 697. [CrossRef]
57. Chen, Z.; Zhang, L.; Wan, B.; Wu, H.; Cleven, N. Geochronology and geochemistry of the Wunugetushan porphyry Cu–Mo
deposit in NE china, and their geological significance. Ore Geol. Rev. 2011, 43, 92–105. [CrossRef]
58. Zhang, Y.; Liu, H.; Ma, T.; Chen, C.; Gu, G.; Wang, J.; Shang, X. Experimental assessment of utilizing copper tailings as alkali-
activated materials and fine aggregates to prepare geopolymer composite. Constr. Build. Mater. 2023, 408, 133751. [CrossRef]
59. Meng, X.; Richards, J.; Mao, J.; Ye, H.; Dufrane, S.A.; Creaser, R.; Marsh, J.; Petrus, J. The Tongkuangyu Cu deposit, Trans-North
China orogen: A metamorphosed paleoproterozoic porphyry Cu deposit. Econ. Geol. 2020, 115, 51–77. [CrossRef]
60. Yang, F.; Geng, X.; Wang, R.; Zhang, Z.; Guo, X. A synthesis of mineralization styles and geodynamic settings of the Paleozoic
and Mesozoic metallic ore deposits in the Altay Mountains, NW China. J. Asian Earth Sci. 2018, 159, 233–258. [CrossRef]
61. Lu, D.K.; Shi, L.F.; Jin, Z.N. Research on chloride leaching of Cu, Zn and Ag from flotation tailings. Adv. Mater. Res. 2012, 391–392,
1138–1142. [CrossRef]
62. Shu, X.-H.; Zhang, Q.; Lu, G.-N.; Yi, X.-Y.; Dang, Z. Pollution characteristics and assessment of sulfide tailings from the Dabaoshan
Mine, China. Int. Biodeterior. Biodegrad. 2018, 128, 122–128. [CrossRef]
63. Mao, W.; Rusk, B.; Yang, F.; Zhang, M. Physical and chemical evolution of the dabaoshan porphyry Mo deposit, south China:
Insights from fluid inclusions, cathodoluminescence, and trace elements in Quartz. Econ. Geol. 2017, 112, 889–918. [CrossRef]
64. Qiu, G.-Z.; Liu, X.-D. Biotech key to unlock mineral resources value. Trans. Nonferrous Met. Soc. China 2022, 32, 2309–2317.
[CrossRef]
65. Singer, D.A. Future copper resources. Ore Geol. Rev. 2017, 86, 271–279. [CrossRef]
66. Wu, A.; Yin, S.; Wang, H.; Qin, W.; Qiu, G. Technological assessment of a mining-waste dump at the Dexing copper mine, China,
for possible conversion to an in situ bioleaching operation. Bioresour. Technol. 2009, 100, 1931–1936. [CrossRef]
67. Li, J.; Yang, H.; Tong, L.; Sand, W. Some aspects of industrial heap bioleaching technology: From basics to practice. Miner. Process.
Extr. Metall. Rev. 2022, 43, 510–528. [CrossRef]
68. Qin, W.; Zhen, S.; Yan, Z.; Campbell, M.; Wang, J.; Liu, K.; Zhang, Y. Heap bioleaching of a low-grade nickel-bearing sulfide ore
containing high levels of magnesium as olivine, chlorite and antigorite. Hydrometallurgy 2009, 98, 58–65. [CrossRef]
69. Bryan, C.G.; Harrison, S.T.L. Microbial ecology of bioheaps, stirred tanks, and mine wastes. In Biomining Technologies; Johnson,
D.B., Bryan, C.G., Schlömann, M., Roberto, F.F., Eds.; Springer: Cham, Switzerland, 2023; pp. 133–149. [CrossRef]
70. Lee, J.; Mahandra, H.; Hein, G.A.; Ramsay, J.; Ghahreman, A. Toward sustainable solution for biooxidation of waste and refractory
materials using neutrophilic and alkaliphilic microorganisms—A Review. ACS Appl. Biol. Mater. 2021, 4, 2274–2292. [CrossRef]
71. Chen, W.; Yin, S.; Ilankoon, I. Effects of forced aeration on community dynamics of free and attached bacteria in copper sulphide
ore bioleaching. Int. J. Miner. Metall. Mater. 2022, 29, 59–69. [CrossRef]
72. Guezennec, A.-G.; Joulian, C.; Delort, C.; Bodénan, F.; Hedrich, S.; D’hugues, P. CO2 mass transfer in bioleaching reactors: CO2
enrichment applied to a complex copper concentrate. Hydrometallurgy 2018, 180, 277–286. [CrossRef]
73. Liu, W.; Granata, G. Temperature control in copper heap bioleaching. Hydrometallurgy 2018, 176, 26–32. [CrossRef]
74. Srichandan, H.; Mohapatra, R.K.; Singh, P.K.; Mishra, S.; Parhi, P.K.; Naik, K. Column bioleaching applications, process
development, mechanism, parametric effect and modelling: A review. J. Ind. Eng. Chem. 2020, 90, 1–16. [CrossRef]
Minerals 2024, 14, 1051 16 of 18

75. Kinnunen, P.; Hedrich, S. Biotechnological strategies to recover value from waste. Hydrometallurgy 2023, 222, 106182. [CrossRef]
76. Morin, D.H.R.; d’Hugues, P. Bioleaching of a cobalt-containing pyrite in stirred reactors: A case study from laboratory scale to
industrial application. In Biomining; Rawlings, D.E., Johnson, D.B., Eds.; Springer: Berlin/Heidelberg, Germany, 2007; pp. 35–55.
[CrossRef]
77. Vera Véliz, M.; Videla Leiva, A.; Martínez Bellange, P. Copper bioleaching operations in Chile: Towards new challenges and
developments. In Biomining Technologies; Johnson, D.B., Bryan, C.G., Schlömann, M., Roberto, F.F., Eds.; Springer: Cham,
Switzerland, 2022; pp. 163–176. [CrossRef]
78. Penev, K.; Karamanev, D. Batch kinetics of ferrous iron oxidation by Leptospirillum ferriphilum at moderate to high total iron
concentration. Biochem. Eng. J. 2010, 50, 54–62. [CrossRef]
79. Yan, L.; Da, H.; Zhang, S.; López, V.M.; Wang, W. Bacterial magnetosome and its potential application. Microbiol. Res. 2017, 203,
19–28. [CrossRef]
80. Yu, R.; Shi, L.; Gu, G.; Zhou, D.; You, L.; Chen, M.; Qiu, G.; Zeng, W. The shift of microbial community under the adjustment of
initial and processing pH during bioleaching of chalcopyrite concentrate by moderate thermophiles. Bioresour. Technol. 2014, 162,
300–307. [CrossRef]
81. Ma, L.; Wang, X.; Feng, X.; Liang, Y.; Xiao, Y.; Hao, X.; Yin, H.; Liu, H.; Liu, X. Co-culture microorganisms with different initial
proportions reveal the mechanism of chalcopyrite bioleaching coupling with microbial community succession. Bioresour. Technol.
2017, 223, 121–130. [CrossRef]
82. Gericke, M.; Neale, J.; Van Staden, P. A Mintek perspective of the past 25 years in minerals bioleaching. Mol. Phylogenet. Evol.
2009, 109, 567–585.
83. Clark, M.E.; Batty, J.D.; Van Buuren, C.B.; Dew, D.W.; Eamon, M.A. Biotechnology in minerals processing: Technological
breakthroughs creating value. Hydrometallurgy 2006, 83, 3–9. [CrossRef]
84. Hao, X.D.; Liu, X.D.; Yang, Q.; Liu, H.W.; Yin, H.Q.; Qiu, G.Z.; Liang, Y.L. Comparative study on bioleaching of two different
types of low-grade copper tailings by mixed moderate thermophiles. Trans. Nonferrous Met. Soc. China 2018, 28, 1847–1853.
[CrossRef]
85. Feng, S.; Li, K.; Huang, Z.; Tong, Y.; Yang, H. Specific mechanism of Acidithiobacillus caldus extracellular polymeric substances
in the bioleaching of copper-bearing sulfide ore. PLoS ONE 2019, 14, e0213945. [CrossRef]
86. Zhang, X.; Liu, X.; He, Q.; Dong, W.; Zhang, X.; Fan, F.; Peng, D.; Huang, W.; Yin, H. Gene turnover contributes to the evolutionary
adaptation of Acidithiobacillus caldus: Insights from comparative genomics. Front. Microbiol. 2016, 7, 1960. [CrossRef] [PubMed]
87. Falagán, C.; Grail, B.M.; Johnson, D.B. New approaches for extracting and recovering metals from mine tailings. Miner. Eng. 2017,
106, 71–78. [CrossRef]
88. Zhang, X.; Liu, X.; Liang, Y.; Guo, X.; Xiao, Y.; Ma, L.; Miao, B.; Liu, H.; Peng, D.; Huang, W.; et al. Adaptive evolution of extreme
acidophile Sulfobacillus thermosulfidooxidans potentially driven by horizontal gene transfer and gene loss. Appl. Environ.
Microbiol. 2017, 83, e03098-16. [CrossRef] [PubMed]
89. Wang, Y.; Zeng, W.; Qiu, G.; Chen, X.; Zhou, H. A moderately thermophilic mixed microbial culture for bioleaching of chalcopyrite
concentrate at high pulp density. Appl. Environ. Microbiol. 2014, 80, 741–750. [CrossRef]
90. Huang, T.; Liu, L.; Zhang, S. Microbial fuel cells coupled with the bioleaching technique that enhances the recovery of Cu from
the secondary mine tailings in the bio-electrochemical system. Environ. Prog. Sustain. Energy 2019, 38, 13181. [CrossRef]
91. Pollmann, K.; Kutschke, S.; Matys, S.; Raff, J.; Hlawacek, G.; Lederer, F.L. Bio-recycling of metals: Recycling of technical products
using biological applications. Biotechnol. Adv. 2018, 36, 1048–1062. [CrossRef]
92. Norris, P.R.; Burton, N.P.; Clark, D.A. Mineral sulfide concentrate leaching in high temperature bioreactors. Miner. Eng. 2013, 48,
10–19. [CrossRef]
93. Albers, S.; Siebers, B. The Family Sulfolobaceae. In The Prokaryotes: Other Major Lineages of Bacteria and the Archaea; Rosenberg, E.,
DeLong, E.F., Lory, S., Stackebrandt, E., Thompson, F., Eds.; Springer: Berlin/Heidelberg, Germany, 2014; pp. 323–346. [CrossRef]
94. Quehenberger, J.; Shen, L.; Albers, S.V.; Siebers, B.; Spadiut, O. Sulfolobus—A potential key organism in future biotechnology.
Front. Microbiol. 2017, 8, 2474. [CrossRef]
95. Martins, F.L.; Leão, V.A. Bioleaching of two different chalcopyrite ores in chloride media. Braz. J. Chem. Eng. 2024, 41, 475–485.
[CrossRef]
96. Anderson, R.E.; Kouris, A.; Seward, C.H.; Campbell, K.M.; Whitaker, R.J. Structured populations of sulfolobus acidocaldarius
with susceptibility to mobile genetic elements. Biol. Evol. 2017, 9, 1699–1710. [CrossRef]
97. Rekadwad, B.N.; Li, W.-J.; Gonzalez, J.M.; Punchappady Devasya, R.; Ananthapadmanabha Bhagwath, A.; Urana, R.; Parwez, K.
Extremophiles: The species that evolve and survive under hostile conditions. 3 Biotech 2023, 13, 316. [CrossRef]
98. Norris, P.R.; Laigle, L.; Ogden, T.J.; Gould, O.J.P. Selection of thermophiles for base metal sulfide concentrate leaching, Part I:
Effect of temperature on copper concentrate leaching and silver recovery. Miner. Eng. 2017, 106, 7–12. [CrossRef]
99. Jafari, M.; Abdollahi, H.; Shafaei, S.Z.; Gharabaghi, M.; Jafari, H.; Akcil, A.; Panda, S. Acidophilic bioleaching: A review on the
process and effect of organic-inorganic reagents and materials on its efficiency. Miner. Process. Extr. Metall. Rev. 2019, 40, 87–107.
[CrossRef]
100. Sajjad, W.; Zheng, G.; Din, G.; Ma, X.; Rafiq, M.; Xu, W. Metals extraction from sulfide ores with microorganisms: The bioleaching
technology and recent developments. Trans. Indian Inst. Met. 2019, 72, 559–579. [CrossRef]
Minerals 2024, 14, 1051 17 of 18

101. Sklodowska, A.; Matlakowska, R. Bioleaching of Metals in Neutral And Slightly Alkaline Environment. In Microbial Processing of
Metal Sulfides; Donati, E.R., Sand, W., Eds.; Springer: Dordrecht, The Netherlands, 2007; pp. 121–129. [CrossRef]
102. Ruepp, A.; Graml, W.; Santos-Martinez, M.-L.; Koretke, K.K.; Volker, C.; Mewes, H.W.; Frishman, D.; Stocker, S.; Lupas, A.N.;
Baumeister, W. The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum. Nature 2000, 407, 508–513.
[CrossRef]
103. Dusengemungu, L.; Kasali, G.; Gwanama, C.; Mubemba, B. Overview of fungal bioleaching of metals. Environ. Adv. 2021, 5,
100083. [CrossRef]
104. Roy, J.J.; Cao, B.; Madhavi, S. A review on the recycling of spent lithium-ion batteries (LIBs) by the bioleaching approach.
Chemosphere 2021, 282, 130944. [CrossRef]
105. Madrigal-Arias, J.E.; Argumedo-Delira, R.; Alarcón, A.; Mendoza-López, M.; García-Barradas, O.; Cruz-Sánchez, J.S.;
Ferrera-Cerrato, R.; Jiménez-Fernández, M. Bioleaching of gold, copper and nickel from waste cellular phone PCBs and computer
goldfinger motherboards by two Aspergillus nigerstrains. Braz. J. Microbiol. 2015, 46, 707–713. [CrossRef]
106. Ilyas, S.; Lee, J.-C.; Chi, R.-A. Bioleaching of metals from electronic scrap and its potential for commercial exploitation. Hydromet-
allurgy 2013, 131–132, 138–143. [CrossRef]
107. Thompson, V.S.; Gupta, M.; Jin, H.; Vahidi, E.; Yim, M.; Jindra, M.A.; Nguyen, V.; Fujita, Y.; Sutherland, J.W.; Jiao, Y.; et al.
Techno-economic and life cycle analysis for bioleaching rare-earth elements from waste materials. ACS Sustain. Chem. Eng. 2018,
6, 1602–1609. [CrossRef]
108. Abhilash, D.; Mehta, K.D.; Pandey, B. Efficacy of bacterial adaptation on copper biodissolution from a low grade chalcopyrite ore
by A. ferrooxidans. Int. J. Nonferrous Metall. 2012, 1, 1–7. [CrossRef]
109. Jin, Z.; Huang, T.; Zhang, X.; Zhang, S. Bioelectrochemical-assisted bioleaching of chalcopyrite: Effect of pulp density, anode
material, and sliver ion. Process Saf. Environ. Prot. 2022, 159, 740–748. [CrossRef]
110. Quatrini, R.; Appia-Ayme, C.; Denis, Y.; Ratouchniak, J.; Veloso, F.; Valdes, J.; Lefimil, C.; Silver, S.; Roberto, F.; Orellana, O.; et al.
Insights into the iron and sulfur energetic metabolism of Acidithiobacillus ferrooxidans by microarray transcriptome profiling.
Hydrometallurgy 2006, 83, 263–272. [CrossRef]
111. Huang, Z.; Feng, S.; Tong, Y.; Yang, H. Enhanced “contact mechanism” for interaction of extracellular polymeric substances with
low-grade copper-bearing sulfide ore in bioleaching by moderately thermophilic Acidithiobacillus caldus. J. Environ. Manag. 2019,
242, 11–21. [CrossRef]
112. Osorio, H.C.; Mangold, S.; Denis, Y.; Ancucheo, I.; Esparza, M.; Johnson, D.B.; Bonnefoy, V.; Dopson, M.; Holmes David, S.
Anaerobic sulfur metabolism coupled to dissimilatory iron reduction in the extremophile Acidithiobacillus ferrooxidans.
Appl. Environ. Microbiol. 2013, 79, 2172–2181. [CrossRef]
113. Ji, G.; Liao, Y.; Wu, Y.; Xi, J.; Liu, Q. A review on the research of hydrometallurgical leaching of low-grade complex chalcopyrite.
J. Sustain. Metall. 2022, 8, 964–977. [CrossRef]
114. Zhang, R.; Hedrich, S.; Jin, D.; Breuker, A.; Schippers, A. Sulfobacillus harzensis sp. nov., an acidophilic bacterium inhabiting mine
tailings from a polymetallic mine. Int. J. Syst. Evol. Microbiol. 2021, 71, 004871. [CrossRef]
115. Rawlings, D.E. Heavy metal mining using microbes. Annu. Rev. Microbiol. 2002, 56, 65–91. [CrossRef]
116. Tanne, C.; Schippers, A. Electrochemical investigation of microbially and galvanically leached chalcopyrite. Hydrometallurgy 2021,
202, 105603. [CrossRef]
117. Zeng, W.M.; Peng, Y.P.; Peng, T.J.; Nan, M.H.; Chen, M.; Qiu, G.Z.; Shen, L. Electrochemical studies on dissolution and passivation
behavior of low temperature bioleaching of chalcopyrite by Acidithiobacillus ferrivorans YL15. Miner. Eng. 2020, 155, 106416.
[CrossRef]
118. Tao, H.; Dongwei, L. Presentation on mechanisms and applications of chalcopyrite and pyrite bioleaching in biohydrometallurgy—A
presentation. Biotechnol. Rep. 2014, 4, 107–119. [CrossRef] [PubMed]
119. Camacho, D.; Frazao, R.; Fouillen, A.; Nanci, A.; Lang, B.F.; Apte, S.C.; Baron, C.; Warren, L.A. New insights into Acidithiobacillus
thiooxidans sulfur metabolism through coupled gene expression, solution chemistry, microscopy, and spectroscopy analyses. Front.
Microbiol. 2020, 11, 411. [CrossRef] [PubMed]
120. Zhan, Y.; Yang, M.; Zhang, S.; Zhao, D.; Duan, J.; Wang, W.; Yan, L. Iron and sulfur oxidation pathways of Acidithiobacillus
ferrooxidans. World J. Microbiol. Biotechnol. 2019, 35, 60. [CrossRef] [PubMed]
121. Abdollahi, H.; Noaparast, M.; Shafaei, S.Z.; Manafi, Z.; Muñoz, J.A.; Tuovinen, O.H. Silver-catalyzed bioleaching of copper,
molybdenum and rhenium from a chalcopyrite–molybdenite concentrate. Int. Biodeterior. Biodegrad. 2015, 104, 194–200. [CrossRef]
122. Li, Q.; Zhu, J.Y.; Li, S.P.; Zhang, R.Y.; Xiao, T.F.; Sand, W. Interactions Between Cells of Sulfobacillus thermosulfidooxidans and
Leptospirillum ferriphilum during pyrite bioleaching. Front. Microbiol. 2020, 11, 44. [CrossRef]
123. Yin, Z.; Feng, S.; Tong, Y.; Yang, H. Adaptive mechanism of Acidithiobacillus thiooxidans CCTCC M 2012104 under stress during
bioleaching of low-grade chalcopyrite based on physiological and comparative transcriptomic analysis. J. Ind. Microbiol. Biotechnol.
2019, 46, 1643–1656. [CrossRef]
124. Ilyas, S.; Chi, R.A.; Lee, J.C. Fungal bioleaching of metals from mine tailing. Miner. Process. Extr. Metall. Rev. 2013, 34, 185–194.
[CrossRef]
125. Liaud, N.; Giniés, C.; Navarro, D.; Fabre, N.; Crapart, S.; Gimbert, I.H.; Levasseur, A.; Raouche, S.; Sigoillot, J.-C. Exploring fungal
biodiversity: Organic acid production by 66 strains of filamentous fungi. Fungal Biol. Biotechnol. 2014, 1, 1. [CrossRef]
Minerals 2024, 14, 1051 18 of 18

126. Xu, T.J.; Ramanathan, T.; Ting, Y.P. Bioleaching of incineration fly ash by Aspergillus niger—Precipitation of metallic salt crystals
and morphological alteration of the fungus. Biotechnol. Rep. 2014, 3, 8–14. [CrossRef]
127. Srichandan, H.; Mohapatra, R.K.; Parhi, P.K.; Mishra, S. Bioleaching approach for extraction of metal values from secondary solid
wastes: A critical review. Hydrometallurgy 2019, 189, 105122. [CrossRef]
128. Magnuson, J.K.; Lasure, L.L. Organic Acid Production by Filamentous Fungi. In Advances in Fungal Biotechnology for Industry,
Agriculture, and Medicine; Tkacz, J.S., Lange, L., Eds.; Springer: Boston, MA, USA, 2004; pp. 215–234. [CrossRef]
129. Mulligan, C.N.; Kamali, M. Bioleaching of copper and other metals from low-grade oxidized mining ores by Aspergillus niger.
J. Chem. Technol. Biotechnol. 2003, 78, 497–503. [CrossRef]
130. Martell, A.E.; Hancock, R.D. Metal Complexes in Aqueous Solutions; Springer: New York, NY, USA, 2013. [CrossRef]
131. Deiana, S.; Gessa, C.; Palma, A.; Premoli, A.; Senette, C. Influence of organic acids exuded by plants on the interaction of copper
with the polysaccharidic components of the root mucilages. Org. Geochem. 2003, 34, 651–660. [CrossRef]
132. Zhong, X.; Liu, F.; Wu, P.; Fan, F.; Zhu, J. Production of hydroxyl radicals from oxygenation of simulated acid mine drainage in
presence of extracellular polymers substances. Bull. Environ. Contam. Toxicol. 2022, 109, 771–775. [CrossRef] [PubMed]
133. Pathak, A.; Kothari, R.; Vinoba, M.; Habibi, N.; Tyagi, V.V. Fungal bioleaching of metals from refinery spent catalysts: A critical
review of current research, challenges, and future directions. J. Environ. Manag. 2021, 280, 111789. [CrossRef]
134. Shokri, Z.; Seidi, F.; Karami, S.; Li, C.; Saeb, M.R.; Xiao, H. Laccase immobilization onto natural polysaccharides for biosensing
and biodegradation. Carbohydr. Polym. 2021, 262, 117963. [CrossRef]
135. Dopson, M.; González-Rosales, C.; Holmes, D.S.; Mykytczuk, N. Eurypsychrophilic acidophiles: From (meta)genomes to
low-temperature biotechnologies. Front. Microbiol. 2023, 14, 1149903. [CrossRef]
136. Wang, Y.G.; Chen, X.H.; Zhou, H.B. Relationships between galvanic interaction, copper extraction and community dynamics
during bioleaching of chalcopyrite by a moderately thermophilic culture. Bioresour. Technol. 2018, 265, 581–585. [CrossRef]
137. Bonnefoy, V.; Holmes, D.S. Genomic insights into microbial iron oxidation and iron uptake strategies in extremely acidic
environments. Environ. Microbiol. 2012, 14, 1597–1611. [CrossRef]
138. Zhang, X.; Liu, X.; Liang, Y.; Fan, F.; Zhang, X.; Yin, H. Metabolic diversity and adaptive mechanisms of iron-and/or sulfur-
oxidizing autotrophic acidophiles in extremely acidic environments. Environ. Microbiol. Rep. 2016, 8, 738–751. [CrossRef]
139. Galleguillos, P.A.; Music, V.; Acosta, M.; Salazar, C.N.; Quatrini, R.; Shmaryahu, A.; Holmes, D.S.; Velásquez, A.; Espoz, C.; Pinilla,
C.; et al. Temporal dynamics of genes involved in metabolic pathways of C and N of L. ferriphilum, in the industrial bioleaching
process of escondida mine, Chile. Adv. Mater. Res. 2013, 825, 162–165. [CrossRef]
140. Zhang, J.; Wang, S.; Wang, X.; Zhang, M.; Fan, S. Detoxification pathways of multiple metals from intensive copper production by
indigenous ureolytic microbes coupled with soil nitrogen transformation. J. Clean. Prod. 2023, 384, 135643. [CrossRef]
141. Inaba, Y.; West, A.C.; Banta, S. Glutathione synthetase overexpression in Acidithiobacillus ferrooxidans improves halotolerance of
iron oxidation. Appl. Environ. Microbiol. 2021, 87, e0151821. [CrossRef] [PubMed]
142. Brar, K.K.; Magdouli, S.; Etteieb, S.; Zolfaghari, M.; Fathollahzadeh, H.; Calugaru, L.; Komtchou, S.-P.; Tanabene, R.; Brar, S.K.
Integrated bioleaching-electrometallurgy for copper recovery—A critical review. J. Clean. Prod. 2021, 291, 125257. [CrossRef]
143. Jung, H.J.; Inaba, Y.; Vardner, J.T.; West, A.C.; Banta, S. Overexpression of the licanantase protein in Acidithiobacillus ferrooxidans
leads to enhanced bioleaching of copper minerals. ACS Sustain. Chem. Eng. 2022, 10, 10888–10897. [CrossRef]
144. Nascimento, D.N.O.; Lucheta, A.R.; Palmieri, M.C.; Carmo, A.L.; Silva, P.M.; Ferreira, R.; Junca, E.; Grillo, F.; Alves, J. Bioleaching
for copper extraction of marginal ores from the Brazilian Amazon Region. Metals 2019, 9, 81. [CrossRef]
145. Li, Q.; Becker, T.; Zhang, R.; Xiao, T.; Sand, W. Investigation on adhesion of Sulfobacillus thermosulfidooxidans via atomic force
microscopy equipped with mineral probes. Colloids Surf. B Biointerfaces 2019, 173, 639–646. [CrossRef]
146. Zhang, R.; Neu, T.R.; Li, Q.; Blanchard, V.; Zhang, Y.; Schippers, A.; Sand, W. Insight into interactions of thermoacidophilic
archaea with elemental sulfur: Biofilm dynamics and EPS analysis. Front. Microbiol. 2019, 10, 896. [CrossRef]
147. Zhang, R.Y.; Vera, M.; Bellenberg, S.; Sand, W. Attachment to minerals and biofilm development of extremely acidophilic archaea.
Adv. Mater. Res. 2013, 825, 103–106. [CrossRef]
148. Varotsis, C.; Tselios, C.; Yiannakkos, K.A.; Andreou, C.; Papageorgiou, M.; Nicolaides, A. Application of double-pulse laser-
induced breakdown spectroscopy (DP-LIBS), Fourier transform infrared micro-spectroscopy and Raman microscopy for the
characterization of copper-sulfides. RSC Adv. 2022, 12, 631–639. [CrossRef] [PubMed]
149. Adamou, A.; Manos, G.; Messios, N.; Georgiou, L.; Xydas, C.; Varotsis, C. Probing the whole ore chalcopyrite–bacteria interactions
and jarosite biosynthesis by Raman and FTIR microspectroscopies. Bioresour. Technol. 2016, 214, 852–855. [CrossRef]

Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual
author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to
people or property resulting from any ideas, methods, instructions or products referred to in the content.