Siti Khodijah Chaerun is an associate professor who studies recycling metals using microbes and plants. Her educational background includes degrees in environmental engineering and geomicrobiology. She conducts research on using microbes like bacteria and fungi to extract metals from ores, mine wastes, and electronic wastes through bioleaching. Plants can also be used to extract and accumulate metals from contaminated soils through phytomining. This approach has advantages like being environmentally friendly and having potential applications for metal recovery from low-grade ores and mine tailings.

1. Summer course (IVC)
27 August 2021
Recycling of metals using
microbes and plants
SITI KHODIJAH CHAERUN
Department of Metallurgical Engineering, Faculty of Mining & Petroleum Engineering, Institut Teknologi Bandung
Biosciences and Biotechnology Research Center (BBRC), Institut Teknologi Bandung

2. Educational and Work Background:
 B.Eng (Ir.) – Environ Engineering, ITB, Indonesia (1988-1993)
 M.Eng (M.T.) – Environ Bioengineering, ITB, Indonesia (1996-1999)
 PhD. – Petroleum and Environ Geomicrobiology,
Biomining/Biometallurgy, Minerals Biotechnology, Bioremediation,
Dept of Earth Sciences, Kanazawa University, Japan (2001-2004)
 Postdoctoral Researcher, ZALF Centre, Berlin, Germany (2006)
 Visiting Scientist, Tokyo University of Agriculture and Technology,
Japan (2007)
 Postdoctoral Associate, Dept. of Microbiology, Atlanta, Georgia, USA
(2008-2009)
 Visiting Research Fellow, Dept. of Energy & Resources Engineering,
Peking University, Beijing, China (2011-2014)
Current Position:
Associate Professor
Department of Metallurgical Engineering, Faculty of Mining
and Petroleum Engineering, Institut Teknologi Bandung (ITB),
Indonesia

3. Metal Resources
Naturally occurring resources
(Primary sources)
Secondary resources
bisnis.tempo.co
www.google.com
“Urban mine” resources
Tailings
slags
wikipedia
Biomining (biohydrometallurgy)
Spent catalyst: Ledoux&Co

4. Kennecott: The largest copper mine in the world! Kennecott provides approximately 13 percent of the
country's copper with production of over 300,000
tons of refined copper each year.
Copper bioleaching at the Kennecott Copper
Bingham Mine, in Utah, USA since the 1950s
Biohydrometallurgy technology

5. Use of microbes (bacteria, archaea, fungi) to recover metals
from low-grade ores, mine wastes and metallic wastes
Biomining: a technology that harnesses the
abilities of certain microbes to accelerate the
dissolution of minerals, thereby facilitating the
recovery of metals of value (Johnson, 2010)
Biomining: the use of microorganisms to recover
precious and base metals from mineral ores and
concentrates (Rawlings & Johnson, 2007)
Biomining is the use of microorganisms to extract
metals from sulfide and/or iron-containing ores
and mineral concentrates (Rawlings et al., 2003)
Biohydrometallurgy
BioMineWiki
Interdisciplinary study field that involves processes that:
•make the use of microbes, usually bacteria, archaea, fungi---- BIO
•mainly take place in aqueous environment-------------- HYDRO
•deal with metal production & treatment of metal-containing
materials and solution --------------------- METALLURGY

6. -Low cost (less energy intensive)
-Processing of lower-grade ores
-Processing of complex ores (polymetallics)
-Recovery of by-product
-Environmentally friendly
-No emission of any harmful gas or chemical in the environment
-Selective, enhanced bioleaching
(Johnson, 2010; Brierley, 2010; Rawlings, 2004)
Czichos, 1987

7. (Bio-) Hydrometallurgy
(Aqueous chemistry)
Chemical Leaching
Bioleaching
Bio-reactor
Heaps
Low cost
Low-grade ores
Pyrometallurgy
(thermal treatment)
Smelting process
Melting furnace
High cost
High-grade ores

8. Microbes playing roles in biohydrometallurgy
No protein coat
No DNA or RNA

9. • Chemolithotrophs/chemolithoautotrophs/chemoautotrophs
• Chemoorganotrophs/heterotrophs
• Mixotrophs
• Iron-oxidizing
• Sulfur oxidizing
• Acidophilic
• Metals-resistant
• Biosurfactant-producing (e.g., EPS)
• Organic acid-producing
From the viewpoint of microbial metabolism
Fungi/Fungus
Bacteria/Bacterium
Expected microbes for biomining process:

10. Indigenous Fungi
Indigenous Bacteria (Chemoorganotrophs and Mixotrophs)

11. Taxonomy level in Microbial systematics
(Classification, identification, nomenclature)
Bergey's International Society for Microbial Systematics
Prokaryotes
Aspergillus sp.
Bacillus sp.
Eukaryotes
Aspergillus spp.
Bacillus spp.

12. Sulfide Minerals Oxide Minerals
Hematite: Fe2O3
Rutile: TiO2
Magnetite:Fe3O4
Goethite: αFeO(OH)
Quartz: SiO2
Calcite: CaCO3
Pyrite: FeS2
Galena: PbS
Sphalerite: ZnS
Chalcopyrite: CuFeS2
Tungstenite: (WS2)
Molybdenite: MoS2
Fundamental principles of biohydrometallurgy

13. Biooxidation Bioleaching
Pentlandite
Arsenopyrite
Johnson, 2010
Au(CN)2
-

14. Principle of Biooxidation

15. Contact Bioleaching Non-contact Bioleaching
Johnson, 2010
M0
Attached microbial
cells
Ore/material
M+
Liquid media
M0 M+
cells
pH ↓
M0
M+
M+

16. Thiosulfate mechanism Polysulfide mechanism
Schippers et al., 1999
Af: Acidithiobacillus ferrooxidans
Lf: Leptospirillum ferrooxidans
At: Acidithiobacillus thiooxidans
A B

17. Thiosulfate mechanism
Schippers et al., 1999
FeS2 , MoS2 , and WS2

18. Polysulfide mechanism
Schippers et al., 1999
e.g. ZnS (Sphalerite), CuFeS2 , or PbS (Galena)

19. Fungi: Genus Aspergillus & Penicillium
Fungi are capable of oxidizing substrate only partially
and then secreting it. This incomplete oxidation
causes the accumulation of organic acids, which are
able to extract metals from solid materials
Proton attack:
NiO + 2H+ ---- Ni2+ + H2O
CaCO3 + 2H+ ---- Ca2+ + H2O + CO2
Reduction: MnO2 + 2e- + 4H+ ---- Mn2+ + 2H2O
Complexation/Chelation:
Ni2+ + C6H5O7 ---- Ni(C6H5O7) + 3H+

20. Bioleaching of nickel laterite ores (saprolite and limonite)
High selective leaching:
The leaching using metabolic organic acids of Aspergillus
niger is selective to magnesium

21. Biooxidation of carbonaceous refractory gold ores
Control: without bacterial inoculation
AC: chemolithotropic bacterium
SKC1: iron-oxidizing mixotrophic bacterium
SKC2:sulfur-oxidizing mixtrophic bacterium

22. Bioleaching of copper sulfide ores
T1: bioleaching experiment without addition of
pyrite and sulfur adjusted to pH 3;
T2: bioleaching experiment with addition of 1%
w/v pyrite and 0.25% w/v sulfur adjusted to pH 3;
T3: bioleaching experiment with addition of 1%
w/v pyrite and 0.25% w/v sulfur without pH
adjustment;
T4: bioleaching experiment with addition of 5%
w/v pyrite and 2.5% w/v sulfur
adjusted to pH 3;
T5: bioleaching experiment with addition of 5%
w/v pyrite and 2.5% w/v sulfur
without pH adjustment;
T6: abiotic control without the bacterium which
was identical to
bioleaching experiment (T1)
29.25 g/l NaCl
T: 28 oC
a particle size = 75 μm
5% pulp density

23. Bioleaching of organic sulfur from coal
Treatment A: a combination of biooxidation
for 15 days and bioflotation;
Treatment B: a combination of biooxidation
for 40 days and bioflotation;
Treatment C: bioflotation;
Treatment D: column flotation

24. Recycling of metals from E-wastes
Primary source
Natural ores
Base metals:
Cu, Fe, Al
Platinum group
metals: Pd, Pt
Precious group
metals: Au, Ag
Other elements:
Plastic, ceramic
“Urban mine” resources
Secondary source

25. Au Ag
Cu Fe
Al Pd Pt
Year 2016

26. Proposed reactions of copper bioleaching from PCBs
(Ilyas et al., 2013; Zhu et al., 2011; Xiang et al., 2010)
Indirect mechanism
4Fe2+ + O2  4Fe3+ + H2O
2Fe3+ + Cu0  2Fe2+ +Cu2+
Direct mechanism, in the absence of Fe, elemental sulfur as the energy source. Cu is
solubilized by protons, although in such case, molecular O2 is involved
S0 + H2O  H+ + SO4
2-
2Cu0 + 4H+ + O2  2Cu2+ + 2H2O
Acidithiobacillus sp. Ferrimicrobium
acidiphilum
Ferroplasma
acidimicrobium
Leptospirillum sp.
Microorganisms involved: Fe/S-Oxidizing bacteria and archaea

27. Microorganisms involved: cyanogenic bacteria and archaea
Au dissolution by (bio)cyanidation consists of an anodic and a cathodic reaction
4Au + 8CN-  4Au(CN)2
- + 4e- (anodic)
O2 + 2H2O + 4e-  4OH- (cathodic)
The overall reaction is known as Elsner’s equation (Hedley and Tabachnick, 1953)
4Au + 8CN- + O2 + 2H2O  4Au(CN)2
- + 4OH-
Pseudomonas plecoglossicida

28. Principles of Phytomining
1997
The Streptanthus polygaloides plant is a hyperaccumulator of
nickel, with hyperaccumulation defined as the presence of at
least 1,000 µg nickel per gram of dry mass. This species
averages 2,430 to 18,600 µg/g. This trait helps protect the plant
against many types of pathogens.

29. Sheoran, 2009
- Extraction of metals
from soil into the plant
roots by active transport
or sorption
Phytoextraction
- From the roots transfer/
translocation into the
shoot parts
Willscher, 2018

30. SEM-EDX image of the plant Miscanthus sinensis shows the adsorption ability of elements Si,
P, S, Cl, K, Ca, Fe, Cu, Zn, Pb (Tazaki & Chaerun, 2008).
Phytoaccumulation

31. Brooks et al., 1997

32. Requirements for the application
Bioavailability of the metals/ metalloids (mobility)
Occurrence of the metals in the rhizosphere
Tolerance of the plants to high metal concentrations
Satisfying growth of the plants

33. Phytomining
Substrates for application
- Low grade ores
- Overburden material
- Mill tailings
- Remainders of dump leaching
- Mineralized soil
- in all substrates uneconomical for conventional mining/ processing
- A large part of the processed mineral material contains low metal concentrations
- After the closedown of mining operations for the removal of lower amounts of the
mined metals and first revegetation/ stabilization Photo of Crop of Ni metals: SKC Lab
Willscher, 2018

34. Advantages of phytomining
- Less intrusive, low energy demand
- Soil recovering effect (improvement of soil ecology)
- Groundwater protection for the case of not too extensive application of
chemicals
- No erosion effects like other mining activities
- For sustainable closure of mining sites
- Reduction of acid mine drainage formation
Challenges
- Solubility and availability as one of the key factors
Appliction of lixiviates (mostly complex forming agents)
- Phytoextraction only in the root zone of the plants
Engineering for mass transport
Willscher, 2018

35. Sheoran et al., 2013

36. A Proposed phytomining concept: SKC
Mine
Crushing plant
Phytomining
(Concentrator)
Improved phyto-extraction parameters
Tailings, low-grade ores, the closedown of mining operations
-2 mm
Plant Harvesting
Crop of metals (Biomass)
Biomass burning
Leaching/Bioleaching
ashes
Biomass drying
under sunlight/oven
Biomass Grinding Bioenergy = Biogas
www.portonews.com

37. Summary
- Utilization of low grade ores, tailings and remainders
- Removal of valuable or toxic metals
- Better soil functions/ revitalization
- Improved soil fertility
- Coupled process with renewable energy production
- Lowering of the process costs
Advantages of the method
- Environmentally benign
- Non-invasive for the soil
- Low energy demand
Sumeks.co
shopee.co.id
Vetiveria zizanioides (Rumput vetiver = ilalang akar wangi)