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Microbiological and Biochemical Study during Wet Coffee (Coffea

arabica) Fermentation in Kintamani, Bangli, Bali


Sayi Hatiningsih1, Nyoman Semadi Antara2, I.B.W. Gunam3
123
Departement of Food Science and Technology, Udayana University, Bali, Indonesia
e-mail: sayihatiningsih16@gmail.com

Abstract
The excellent quality of the fermentation process is closely related to microbes in the
process fermentation belonging to the groups of aerobic microorganisms, bacteria, lactic acid
bacteria and yeast. The coffee cherries and the depulped coffee samples were collected during
fermentation from many different sites of each coffee plantation in Kintamani, Bangli, Bali. The
pH of the outside coffee bean and pH of the inner coffee bean decreased successively 4.50 to 3.90
and 5.80 to 5.37 and the pH of liquid fermented coffee bean increased from 3.80 to 4.70 after 16
hr fermentation. Bacteria, lactic acid bacteria and yeast were the predominant microorganisms
found throughout the process. The quantity of microflora in the sampling of coffee bean fluctuated
but trend to increased from the start until last of fermentation. The quantity of microflora in the
sampling of liquid fermented coffee bean increased from the start of fermentation and reached
their maxima up to 8 hr, then decreased after 8 hr of fermentation. Fungi was no detected in the
two sampling of coffee bean and liquid fermented coffee bean during the fermentation because
activity water very high, low pH, and fermentation period very short.
Keywords: Coffea arabica, wet process, coffee fermentation

Introduction
Indonesia is main coffee producing country in the world after Brazil and Vietnam (Foreign
Agricultural Services/ USDA, 2016). Indonesia coffee plantation covers 1.230.001 ha of land area
and produces 602.428 tonnes of dried coffee beans or nearly 8 % of coffee producing in the world.
The state of Kintamani-Bangli, located in the north of Bali, Indonesia, was responsible for
producing 2.456 tonnes in 2015 (Directorate General of Estate Crops, 2016). In fact, Kintamani
arabica coffee has had certificate protection of Geographical Indications and a bargaining position
in the international coffee market (Ministry of Industry of The Republic of Indonesia, 2016).
In general, coffee beans are produced by dry or wet process or semi-dry process. The wet-
processing technique is more sophisticated and generally produces a higher quality brew. Arabica
coffee (Coffea arabica) is usually wet processed (Farah, 2012) and is the main process for arabica
coffee processing in Kintamani, Bangli.
One of critical wet coffee processing stage which affect the end quality is fermentation
(Correa et al., 2014). Coffee fermentation is to degrade the pectin-containing mucilage adhering
firmly to coffee beans by pectinase. The mucilage which can be eliminated by natural fermentation
is made saccharide, enzymes, pectin lipids and protopectin (Masoud and Jespersen, 2006). During
fermentation, enzymes may be added, the silver skin is removed and acidity increases, the pH may
be reduced to 6.27 to 4.00 using natural microbes for 12-36 hours pr up to 48 hours. The seeds are
then extensively washed, polished and sun-dried and/ or air-dried (Farah, 2012; Nasanit and
Satayamut, 2015; East Java Plantation Office, 2016).
The excellent quality of the fermentation process is closely related to microbes in the
process fermentation. The composition of mucilage layer has high nutritional value, consists of
84,2 % of water; 4,1 % sugar; 8,9 % protein; 0,91 % concentrated acid and 0,7 % ash (Clifford &
Ramirez in Yusianto and Nugroho, 2014); or in 20,25 % dry matter consist 11,50 % of total sugars,
15,50 % protein; 2,80 % fat; 5,50 % total pectin; 28,50 % acid detergent fiber; 12,0 % lignin; 16,20
% cellulose and 8,0 % ash (Silva et al., 2013), which has potential as a medium for microbial
growth. During fermentation, a large number of microorganisms can produce pectinolytic enzymes
such as polygalacturonase (PG), pectin lyase (PL) and pectin methylesterase (PME) and
metabolites such as organic acids makes acidity increases and hydrolysis of pectin-containing
mucilage. Moreover, some microorganisms had the ability to produce a special flavor and aroma
(Silva et al., 2013; Feng et al., 2016; Nasanit and Satayamut, 2015).
Bacteria, yeast and filamentous fungi have been detected during coffee fermentation (Silva
et al., 2013; Feng et al., 2016; Nasanit and Satayamut, 2015). The research of coffee Arabica
fermentation in Thailand and China with wet method found that Enterobacteriaceae such as
Enterobacteriaceae bacterium, Enterobacter agglomerans, E. cowanii, Erwin dissolvens, Pantoea
agglomerans, Rahnella aquatilis, Escherichia coli and Klebsiella pneumonia were pre-dominan
bacteria, Weissella species, Leuconostoc mesenteroides, Lactobacillus brevis, Lactococcus
plantarum and Enterococcus casseliflavus were the predominant lactic acid bacteria, Bacillus
subtilis and B. cereus were the predominant gram-positive bacteria, Candida, Pichia,
Debaryomyces, Kluyveromyces and Saccharomyces such as Pichia kluyvery, P. fermentans and
Hanseniaspora uvarum were most common yeast. Filamentous fungi were minimal during the
fermentation and Penicillium was the predominant fungi and most of them are pectinase-producing
microorganisms (Leong et al., 2014; Feng et al., 2016; Nasanit and Satayamut, 2015). Until now,
there has been no report on the microbial communities and biochemical parameters present during
Arabica coffee production in Kintamani, Bangli-Bali. Therefore, the current study aimed to
determine the microbial and biochemical during coffee (Coffea arabica) fermentation in
Kintamani, Bangli, Bali.

Materials and Methods


Sampling
Coffee cherries (Coffea arabica) was handpicked at the mature stage was collected from
many different sites of each coffee plantation in Central Batur Village, Kintamani District, Bangli
Regency, Bali Province, Indonesia in Juli, 2017. The external mesocarp was mechanically
eliminated immediately after harvesting by wet pulping. Depulped beans were then conveyed in a
water stream to fermentation box and left to ferment for 16 h. The fermentation began at 6:00 pm,
outside temperature decreases, and ended at 10:00 am. Every 4 h, samples of coffee beans and
liquid fermented coffee beans were collected by collecting the samples from five different points
at the middle depth of the fermentation box and mixing. The temperature at each collection point
was measured with a portable electronic thermometer.
Measurement of pH of coffee beans
The measurement of the pH of the outside coffee beans was done by taking 5 g coffee
beans were gently swirled in 5 ml distilled water 5 ml (1:1) and the pH of the supernatant was
measured. The measurement of the pH of the inner coffee beans was done by crushing 5 g coffee
beans by blender and mixing in 5 ml distilled water (1:1) and the pH of the supernatant was
measured, while the pH liquid fermented coffee beans could be measured directly (Isnaini, 2011).

Microbiological analyses
Fermented coffee beans (10 g) and liquid fermented coffee beans (10 ml) were
homogenized in 90 ml of sterile distilled water (0,85 % NaCl) (1:10) with vortex. The microbial
culture suspension was taken 1 ml and diluted in 9 ml of sterile distilled water (10-2) and so on
until dilution 10-7. Lactic acid bacteria (LAB) were counted on De Man Rogosa and Shape Agar
(MRSA), yeast and fungi on Potato Dextrose Agar (PDA), aerobic microorganisms were
numbered on Plate Count Agar (PCA), bacteria on Nutrient Agar (NA). Plates were incubated in
incubator at 37 °C for 48 h for bacteria and lactic acid bacteria, at 30 ºC for 4-6 h for aerobic
microrganisms, yeast and fungi. Colony-forming units (CFU) were counted and data were
expressed as the mean of the decimal logarithm of the CFU/ml of fermented coffee beans or liquid
fermented coffee beans. Several isolates were purified and stored at -80 ºC in 40 % glycerol (v/v)
for further research (Isnaini, 2015; Nasanit et al., 2015).

Result
pH and temperature during coffee fermentation
The measurement of pH and temperature during fermentation was undertaken every 4 hr
during 16 hr fermentation. The pH values and temperatures during coffee fermentation were
determined as shown in Figure 1. As can be seen, the pH of the outside coffee bean and pH of the
inner coffee bean decreased gradually during the fermentation period of 16 hr, successively 4.50
to 3.90 and 5.80 to 5.37. But, the pH of liquid fermented coffee bean increased from 3.80 to 4.70.
The temperature in the coffee fermentation is fixed (± 20.70 °C ) because the outside temperature
is rather cold (15 °C), which corresponds to the night, but the temperature decreased in the last
fermentation period.
Microbial trend during coffee fermentation
The quantity of bacteria, aerobic bacteria, lactic acid bacteria, yeast and fungi were
determined in the two sampling of coffee bean and liquid fermented coffee bean are reported on a
logarithmic scale as shown in Figure 2 and Figure 3. The quantity of bacteria, aerobic bacteria,
lactic acid bacteria and yeast in the sampling of coffee bean fluctuated but trend to increased from
the start until last of fermentation as shown in Figure 2.
21.2 6.0

20.0
5.5

18.8
Temperature (°C)

5.0
17.6

pH
4.5
16.4

4.0
15.2

14.0 3.5
0 4 8 12 16
Time (hours)
Coffee temperature Ambient temperature
pH of the inner coffee bean pH of the outside coffee bean
pH liquid fermented coffee bean

Fig 1. Change of pH and temperature during 16 hr wet fermentation of coffee beans.

8.5

7.5

6.5
Log (cfu/ml)

5.5

4.5

3.5
0 4 8 12 16
Time (hours)
Aerobic microorganisms Lactic acid bacteria Bacteria Yeast

Fig 2. Coffee fermentation microflora in the sampling of coffee bean


8.0

7.4
Log (cfu/ml)

6.8

6.2

5.6

5.0
0 4 8 12 16
Time (hours)
Aerobic microorganisms Lactic acid bacteria Bacteria Yeast

Fig 3. Coffee fermentation microflora in the sampling of liquid fermented coffee bean

The quantity of bacteria, aerobic bacteria, lactic acid bacteria and yeast in the sampling of
liquid fermented coffee bean increased gradually from the start of fermentation and reached their
maxima up to 8 hr. These microorganisms decreased dramatically after 8 hr of fermentation as
shown in Figure 2. But, fungi was no detected in the two sampling of coffee bean and liquid
fermented coffee bean during the fermentation.

Discussion
The excellent quality of the fermentation process is closely related to microbes in the
process fermentation, which some microorganisms naturally exist on the surface of coffee cherry
(Yusianto and Widyotomo, 2013). They can produce pectinolytic enzymes to hydrolysis of pectin-
containing mucilage and organic compounds which the coffee bean can absorb. The initial coffee
fermentation microflora significantly can produce metabolites such as organic acids, oxalic was
the highest, followed by acetic and lactic acids makes acidity increases and pH decreases (Silva et
al., 2013; Feng et al., 2016; Nasanit and Satayamut, 2015).
In the current study, the depulped coffee was fermented in fermentation box for 16 hr to
remove the mucilage layer composes of pectin. In previous studies, bacteria, aerobic
microorganisms, lactic acid bacteria, yeast and fungi were detected during coffee fermentation
(Silva et al., 2013; Feng et al., 2016; Nasanit and Satayamut, 2015). The results showed that lactic
acid bacteria and yeast were the predominant microorganisms found from the start of fermentation,
whereas aerobic microflora and bacteria also growth because water was extensively used in the
process. At the end of the fermentation, yeasts, bacteria and lactic acid bacteria were predominant
microorganisms found when the pH was low because of their higher resistance to acid conditions.
Yeasts and lactic acid bacteria could be responsible for flavor and aroma of the coffee brew
(Nasanit and Satayamut, 2015).
Bacteria, lactic acid bacteria and yeast were predominant microorganisms, some of which
can produce pectinolytic enzymes (Silva et al., 2013). Enterobacteriaceae was predominant
bacteria species during coffee fermentation, Leuconostoc mesenteroides, Lactobacillus brevis,
Lactococcus plantarum and Enterococcus casseliflavus were the predominant lactic acid bacteria.
Furthermore, some lactic acid bacteria for example Ln. mesenteroides would play a role in the
solubilization of pectin substances (Feng et al., 2016; Nasanit and Satayamut, 2015). Several strain
of lactic acid bacteria such as produce lactic acid as describe for soygurt and yoghurt (Fauziah et
al., 2013; Leong et al., 2014; Wisti, 2014; Haryo et al., 2017; Martharini and Indratiningsih, 2017),
resulting in a decreased pH during coffee fermentation, which leads to optimum conditions for
yeast to grow until the end of the fermentation up to 16 hr. Most of these lactic acid bacterias have
the ability as biopreservatif agents and can produce antimicrobial and antifungal compounds
expecially bacteriocin (Cahyaningsih, 2006; Usmiati and Richana, 2011; Yang et al., 2012;
Fauziah et al., 2013; Indriati et al., 2014; Leong et al., 2014; Khiriyah et al., 2014; Kusmarwati et
al., 2014; Shindy, 2014).
Yeast were predominant microorganisms during coffee fermentation period. The major
yeast genera have already in previous studies of coffee fermentation by the wet process were
Candida, Pichia, Debaryomyces, Kluyveromyces and Saccharomyces such as Pichia kluyvery, P.
fermentans, Hanseniaspora uvarum, P. kudriavzevii, Issatchenkia orientalis, Clavispora
lusitaniae and P. guilliermondii were most common yeast (Hamadi et al., 2014; Nasanit and
Satayamut, 2015; Feng et al., 2016). Most of these yeasts have the ability to produce pectinolytic
enzymes and organic compounds. S. cereviseae UFLACN727, P. guilliermondii UFLACN731 and
C. parapsilosis UFLACN448 have the ability to produce pectin lyase (PL) and 1,2-propanediol,
hexanoic acid, decanoic acid, nonanoic acid and ethyl acetate isolates are promising candidates as
coffee starter cultures (Silva et al., 2013). S. cereviseae CAT1, P. anomala, P. kudriavzevii,
Issatchenkia orientalis, Clavispora lusitaniae and P. guilliermondii potential for bioethanol
production from wet coffee processing waste (Menezes et al., 2013; Hamadi et al., 2014; Sisbudi
and Fauzi, 2015; Woldesenbet et al., 2016). Some yeast species such as S. cereviseae mixed with
L. rhamnosus NRRL B-442 resulted in the inhibition of the growth of fungi (A. flavus producer of
aflatoxin) when inoculated into fermented food (Sheikh-Ali et al., 2015). Inoculation of S.
cerevisiae UFLA YCN727, S. cerevisiae UFLA YCN724, Candida parapsilosis UFLA YCN448
and P. guillermondii UFLA YCN731 in a semi-dry coffee have been recently reported to be able
to produce a special aroma of caramel flavor in coffee that was not detected in control
(Evalingelista et al., 2014)
The microflora was consumed sugar on mucilage layer, and the first consume the substrate
that is easily metabolized, such as a monosaccharide before hydrolyzing a polysaccharide. The
quantity of microflora in the sampling of coffee bean increased from the start until last of
fermentation, because much sugar on mucilage layer can consume by microflora until last of
fermentation period. These result are in opposition to the quantity of microflora in the sampling of
liquid fermented coffee, at the start of the fermentation, much sugar is probably in liquid fermented
coffee bean after depulped coffee until the fermentation up to 8 hr but decreased after 8 hr of
fermentation. It is probably the reason that the quantity of microflora in the sampling of liquid
fermented coffee bean increased gradually from the start of fermentation and reached their maxima
up to 8 hr and decreased dramatically after 8 hr of fermentation.
Fungi was no detected microorganisms in the wet fermentation process in Kintamani,
Bangli, Bali. However, it has been reported to be diverse in the wet fermentation process in Brazil
and Thailand, expecially Penicillium and Aspergillus was most common genus in the current study
and there have been reports of their pectinolytic activity (Silva et al., 2008; Nasanit et al., 2015).
It was probably due to water activity and the growth of other microbial groups e.g. bacteria, lactic
acid bacteria and yeasts very high. These microflora significantly can produce metabolites makes
acidity increases and pH decreases which inhibits the growth of fungi (Silva et al., 2008; Silva et
al., 2013; Feng et al., 2016; Nasanit and Satayamut, 2015). These differences found in the number
and diversity of fungi in the coffee beans could be related with the long period of fermentation and
drying (15-25 days) (Silva et al., 2008) and was the period fermentation for arabica coffee
processing in Kintamani, Bangli just 16 hr. However, some species fungi of Penicillium and
Aspergillus detected were be able to produce mycotoxins such as ochratoxin A, aflatoxin B1,
citrinin, which can affect consumer health because mutagenic, carcinogen, nephrotoxic and
pathogen (Ostry et al., 2013; Sheikh-Ali et al., 2014; Aaraj et al., 2015; Hsuuw et al., 2013; Klaric
et al., 2013; Kumar et al., 2014; Carvajal-Moreno, 2015; Gan et al., 2015; Madrigal-Bujaidar et
al., 2015; Park et al., 2015; Bovdisova et al., 2016).Therefore, this matter needs to be considered
in coffee production. Fortunately, these were not found in this study. Therefore, to limit coffee
defects, coffee fermentation has to be controlled because the humidity and chemical composition
of the coffee beans, environmental conditions and crop and product manajement can influence
development of fungi and their metabolic activity (Silva et al., 2008).

Conclusion
Aerobic microorganisms, bacteria, lactic acid bacteria and yeast in the two sampling of
coffee bean and liquid fermented coffee bean were detected during the fermentation process of
coffee arabica by the wet method in Kintamani, Bangli, Bali. The predominant microflora were
bacteria, lactic acid bacteria and yeast. The microflora during coffee fermentation found in this
study can produce metabolites makes acidity increases and pH decreases which is interesting for
inhibit fungi’s growth, because in this studi fungi was no detected during coffee fermentation. It
was probably due to water activity and the growth of other microbial groups e.g. bacteria, lactic
acid bacteria and yeasts very high.

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