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Coffee Fermentation

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42
Coffee Fermentation

Rosane Freitas Schwan, Cristina Ferreira Silva, and Luis Roberto Batista Batista

Contents
42.1 Introduction................................................................................................................................... 677
42.2 Coffea Arabica and C. canephora................................................................................................ 678
42.3 Postharvest Processing of Coffee Fruits and Beverage Quality................................................... 678
42.3.1 Dry or Natural Process..................................................................................................... 678
42.3.2 Wet Process...................................................................................................................... 680
42.3.3 Semidry Process............................................................................................................... 681
42.3.4 Storage of Green Beans.................................................................................................... 681
42.4 Microorganisms Present in Coffee Fruits..................................................................................... 682
42.4.1 Bacteria............................................................................................................................. 682
42.4.2 Yeasts................................................................................................................................ 683
42.4.3 Filamentous Fungi............................................................................................................ 683
42.4.3.1 Ochratoxin A–Producing Toxigenic Fungi....................................................... 684
42.5 Microbiota of Wet Processed, Depulped, and Washed Coffee..................................................... 684
42.5.1 Bacteria............................................................................................................................. 685
42.5.2 Yeasts................................................................................................................................ 685
42.6 Final Considerations..................................................................................................................... 686
References............................................................................................................................................... 687

42.1  Introduction
Originally, coffee was grown in the Kaffa region in Ethiopia; later, in the early 17th century, the Dutch
spread it throughout Europe. Coffee reached North America in the beginning of the 17th century and
South and Central America in 1825. The habit of drinking coffee was developed in Arab culture, and the
coffee beverage was known only for its properties as a stimulant. Coffee fruit was consumed raw and fed
to herds as a stimulant while they were traveling. In 1000 AD, the Arabs began to prepare an infusion of
coffee cherries, boiling them in water. The roasting process was developed only in the 14th century, and
coffee finally became similar to today’s beverage (ABIC 2010).
As a beverage, coffee is characterized as energizing and nonalcoholic, with potential beneficial effects
on human health; it mainly acts as an antioxidant (Andueza et al. 2004). There are different types of
coffee beverages characterized by different nuances in terms of body, aroma, acidity, and astringency.
One hundred species are associated with the genus Coffea, but only two species are agroeconomically
important, Coffea arabica and Coffea canephora. Coffea dewevrei, C. congensis, C. eugenioides C.
kapakata, C. salvatrix, C. stenophyla, C. liberica, C. racemosa, and others are primarily used in genetic
crosses. Coffea arabica, known as Arabica in the coffee market, makes up 70% of total production vol-
ume, and C. canephora (Robusta coffee) is responsible for the remaining 30%. Currently, Brazil is the
largest producer of arabica coffees, followed by Colombia, Paraguay, Venezuela, Indonesia, Ethiopia,
India, Mexico, and 40 other countries. The United States, Brazil, and the European countries are the
major consumer markets.

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42.2  Coffea Arabica and C. canephora

Coffea arabica was first described by Linnaeus in 1753. Its fruits are round, smooth, slightly bitter, and
chocolaty in color, with a smooth crust and an intense aroma. Brazil is the leading producer and exporter
of Coffea arabica (ABIC 2010) and the second largest consumer. There are currently 11 varieties most
frequently planted in producing countries. These varieties are the result of breeding projects intended to
achieve early maturity, a size suitable for mechanical harvesting, rust resistance, high-density planting,
and improved beverage quality (Fazuoli 1999).
The Coffea canephora species, also known as Robust or Conillon coffee, is stronger and more pro-
ductive than Arabica coffee, but its flavor is less popular with consumers, and it is mainly used in the
formulation of blends and espressos. Indonesia is the largest producer of this coffee, followed by Brazil,
Vietnam, the Ivory Coast, and Uganda (Ferreira Júnior and Mitchell 2007).
The two species Coffea arabica and C. canephora feature differing levels of caffeine, chlorogenic
acids, sucrose, and amines (putrescine) (Andueza et al. 2004; Casal et al. 2004, Martin et al. 2001,
Gonzalez et al. 2001). Table 1 summarizes the different compounds and their compositions in Arabica
and Robusta coffee.

42.3  Postharvest Processing of Coffee Fruits and Beverage Quality

The fruit consists of the peduncle, crown, exocarp (epicarp or crust), mesocarp (mucilage or pulp), endo-
carp (parchment), spermoderm (testa or outer coat), endosperm (albumen), and embryos with two coty-
ledons. The coffee bean used for beverage preparation is the endosperm. To obtain green beans, coffee
fruits are subjected to three different types of postharvest processing. Figures 42.1, 42.2, and 42.3 shows
the three processes—dry, semidry, and wet, respectively—and their different stages. The choice of pro-
cessing type is subject to the uniformity of fruit maturation, the local weather conditions at harvest time,
and the availability of water at the production site. Yield is not a deciding factor because each different
Convert to
metric? process produces equivalent yield. On average, from a 550-lb batch of cherry fruits, 100 lb of processed
grains are obtained, which will decrease another 16% in weight after roasting (Hicks 2001).

42.3.1  Dry or Natural Process

In general, Robust and Arabic coffees grown in Brazil, Ethiopia, Haiti, Indonesia, and Paraguay are
processed using the dry or natural method. This kind of process creates so-called natural or nonwashed
coffees. During this process, the intact coffee fruits dry in terraces or platforms of concrete, asphalt, or
packed dirt. The process involves few steps and entails low equipment demand (Figure 42.1). The fruit
harvesting process, performed via manual stripping, yields fruit lots at different stages of maturation

TABLE 42.1
Chemical Compounds and Their Respective Concentrations Present in Coffee Beans Used
as Chemical Markers to Differentiate Between Coffea arabica and Coffea canephora
Chemical Markers (Dry Weight) Coffea arabica Coffea canephora
Sucrose 9.3 5.45
Putrescine-free (μg/g) 47.9 11.1
Linoleic acid (%) 6.1 3.7
Oleic acid (%) 8.3 12.3
Chlorogenic acids 4.1 11.3
Caffeine (%) 1–2 >3
β-Tocopherol (μg/g) 58.46 13.1

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Coffee Fermentation 679

Fruit of coffee

Mechanical harvest Harvesting manually

Washing fruits for separations

of different fractions

Fermentation and drying

Hulling

Storage of green beans

FIGURE 42.1  Main steps involved in dry or natural coffee fermentation.

Coffee fruits

Selective manual harvest

Mechanical pulping

Fermentation and drying

Hulling

Green beans

FIGURE 42.2  Main steps involved in wet coffee fermentation.

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680 Handbook of Plant-Based Fermented Food and Beverage Technology

Fruits of coffee

Selective manual harvest

Mechanical pulping
Waste skin and pulp

Dry fermentacion Wet fermentacion

Fermentation and drying

Hulling

Storage of green beans

FIGURE 42.3  Main steps involved in semidry coffee fermentation.

(green, yellow green, cherry, dried). These types of fruit are separated by density during the fruit-wash-
ing phase. The fruits in the same maturity stage are placed on the threshing floor and remain there for
about 15–20 days, depending on weather conditions. The fruits are raked daily so that they will dry
evenly, and this process continues until they reach 11% and 12% humidity. This produces the so-called
green beans, which are stored in burlap sacks until marketing.
Several physicochemical, microbiological, agricultural, cultural, and processing- and storage-related
conditions can influence the final quality of the beverage. Natural coffees are more full-bodied and less
acidic than coffees processed using the wet method. The drying and storage of coffee fruit is important
to preserving the sensory and sanitary quality. Sanitary quality is preserved by reducing the water con-
tent and thus preventing colonization by toxigenic fungi during postprocessing. The drying temperature
also affects cell integrity. When the cells of the grains are broken, occur leakage of cellular material, and
quality decreases (Borem et al. 2008). Natural fruits cannot be stored above 40°C (Sfredo et al. 2005)
if they are to retain maximum quality, and the maximum possible storage time is 90 days (Coradi et al.
2007).

42.3.2  Wet Process

Wet processing gives rise to pulped, peeled, and demucilated coffees, depending on the processing pro-
cedure used. Countries such as Colombia, Kenya, countries in Central America and Hawaii perform this
type of processing. The steps involved are represented in Figure 42.2 and include the following:

1. Selective harvesting of fruits at the maximum maturity stage (cherry)

2. Mechanical depulping (demucilation)
3. Fermentation in tanks of water and subsequent drying

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Coffee Fermentation 681

Roasted green beans will yield beverages that are softer, less viscous, and more acidic (Selmaret al.
2002) than natural coffees. The disadvantage of wet processing is the high consumption of water used to
pulp, ferment, and wash beans after fermentation.
The washed coffee beans have a chemical composition different from that of nonwashed beans
because the type of processing influences the metabolism of the seeds (Knopp et al. 2006). However,
environmental factors and genetic factors related to treatment, agricultural practices, soil and climatic
conditions, and technical procedures and postharvest fermentation time can influence the quality of the
washed coffee beverage. This is because environmental factors such as shading and altitude influence the
formation of aroma precursors such as proteins, amino acids, sucrose, triacylglycerols, chlorogenic acid,
and caffeine, as suggested by Vaast et al. (2006). The end of fermentation is determined by the producers
based on their tactile perceptions of the fruit. When the fruits are slippery, there is evidence of the pres-
ence of mucilage, indicating that fermentation should continue. However, tactile detection may fail, and
as a result, Jackels and Jackels (2005) propose the periodic measurement of pH value as an alternative.
When this parameter reaches a value of 4.6, this is indicative of the total release of mucilage and thus
the end of fermentation.

42.3.3  Semidry Process

The semidry process is a variation on wet processing. It is an intermediate process between dry and wet
processing (Figure 42.3) and results in what are called pulped natural coffees (Duarte et al. 2010). Some
studies have focused on the chemical properties of coffee beans under semidry processing and the cor-
relation between those properties and beverage quality (Duarte et al. 2010; Tarzia et al. 2010). No study
has yet presented conclusive evidence of the level of influence of this process on the final quality of the
beverage. However, it is possible to say that the qualities of coffee beverages made from pulped natural
coffee lie somewhere between those obtained using dry and wet processing. The green beans produced
via semidry processing are usually used in espresso blends (Duarte et al. 2010).
The concentration of aroma precursor compounds such as caffeine, trigonelline, sucrose, and chloro-
genic acids can positively or negatively affect flavor. Chlorogenic acids are reported to be responsible
for bitterness, and the concentration of these compounds in pulped natural coffees is lower than when
wet processing is used. Trigonelline provides a pleasant flavor and is present in lower concentrations in
semidry processing than in wet processed grains. Sucrose is the precursor to volatile compounds and
corresponds, in dry weight, to 7.5 g/100 g. Aldehydes and carboxylic acids are desirable in high concen-
trations, as they are responsible for the production of furan. The concentration of sucrose is higher in
semidry processing than in wet processing (Selmar et al. 2008).

42.3.4  Storage of Green Beans

After they are processed, the coffee fruits are hulled and stored until they are put on the market. After
processing, the factors that affect the preservation of beverage quality are the physical storage conditions
and the storage time (Coradi et al. 2007; Borem et al. 2008). Because the grains are stored for up to three
years, they should be stored under constant temperature and relative humidity (RH) conditions to prevent
the rehydration of the grain and postharvest reactions. The coffee bean embryos remain viable during
processing but die after long periods of storage (usually after 6 months). After the death of the embryo,
enzymes such as polyphenol oxidase and laccase can remain viable if the grain presents moisture above
20%; these would be inappropriate storage conditions and would allow the rehydration of the grains.
The action of PPOs and laccase would cause the oxidation of phenolic compounds and decrease quality
(Selmar et al. 2008).
In dry, semidry, and wet coffee processing in Brazil, storage temperatures above 40°C have damaged
the cells of the grains, causing the leakage of intracellular material and decreasing beverage quality
(Borem et al. 2008; Coradi et al. 2007). Selmar et al. (2008) suggest that the green beans must be stored
(RH 63% and 22°C) with parchment because, regardless of the type of processing, the grains are of bet-
ter quality when they are not hulled.

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682 Handbook of Plant-Based Fermented Food and Beverage Technology

42.4  Microorganisms Present in Coffee Fruits

Natural or dry processing is mainly used in Brazil, Ethiopia, Haiti, Indonesia, and Paraguay, where there
is a low rainfall density during the fruit harvest. Studies focusing on microbial diversity in coffee fruits
at different stages of maturity and during the overall drying process have been carried out by Silva et
al. (2000, 2008a,b) and Vaughn (1958). These populations are diverse and include bacteria, yeasts, and
filamentous fungi, all of which predominate in the fruits as they undergo constant physical and chemical
changes. These changes are due to seed metabolism and to the gradual loss of water that occurs on the
threshing floor. The drying period corresponds to the fruit fermentation period, in which the pulp and
mucilage break down.
The species able to colonize the fruit must also be able to withstand the physicochemical changes
that will occur (in pH, sugar content, and moisture), which will secrete pectinases on pectin pulp and
mucilage. The depolymerization of pectin is the carbon source for microorganisms after the initial intake
of simple sugars. This process is promoted by the 20-day period, during which the fruits remain on the
threshing floor, with microbial growth sustained by pectin depolymerization. At the beginning of fer-
mentation, the high water activity (approximately 0.9) facilitates the development and action of bacteria
on the coffee fruit that are gradually replaced by yeasts and filamentous fungi at the end of the process
(aw 0.7). The largest bacterial population in the early stages of fermentation was recorded by Vaughn
(1958), Silva et al. (2000, 2008a), and the largest population in samples of fresh coffee pulp was reported
by Gaime-Perraud et al. (1993).

42.4.1  Bacteria
In natural coffee, some authors (Table 42.2) have identified the presence of Gram-negative and Gram-
positive bacteria; in the first days of fermentation, the average population found is 106 –109 CFU/g. Along
with the high bacteria count in natural coffee fruit, there is also a great deal of species diversity, some
native to the fruit, and so originating from the soil, agricultural tools, air, and water (Silva et al. 2008a).
Thus, some species present in the fruit may not be part of the fermentation process.
All species identified in coffee fruits at different stages of natural maturation and processing are listed
in the studies by Silva et al. (2000, 2008a,b). Among these species are Tatumella ptyseos, Pseudomonas
putrefaciens, P. mirabilis, Enterobacter aerogenes, Acinetobacter, and B. subtills (Silva et al. 2000,
2008a), and Paenibacillus amylolyticus (Sakiyama et al. 2001), which is an endophytic species that
presents pectin lyase activity and is therefore co-responsible for the fermentation of natural coffee, along
with some yeast species.

TABLE 42.2
Bacteria Species Identified During the Period of Natural (Dry) Fermentation Coffee Fruits
Reference Country Bacteria
Silva et al. (2000, 2008b) Brazil Gram-positive: Bacillus cereus, B. subtilis, B. macerans, B.
Sakiyama et al. (2001) megaterium, B. stearothermophilus, B. laterosporus,
Vaughn (1958) Cellulomonas. Arthrobacter, Microbacterium, Brochothrix,
Dermabacter, Lactobacillus, Acinetobacter sp., B. polymyxa,
Kurthia, Paenibacillus amylolyticus
Gram-negative: Aeromonas, Enterobacter agglomerans,
Pseudomonas, Serratia rubidea, S. plymutica, Hafnia, Tatumella
ptyseos, Flavobacteriu, Klebsiella, Chromobacterium,
Pasteurella, Acinetobacter, Cedecea, Citrobacter, Shigella,
Providencia mirabilis
De Bruyne et al. (2007) Ethiopia Leuconostoc
Van Pee and Castelein (1972) Congo Erwinia dissolvens, Hafnia, Enterobacter aerogenes, E. cloacae,
Klebsiella

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Coffee Fermentation 683

The presence of organic acid from fermentation metabolism (acetic, lactic, butyric, and propionic
acids) confirms the microbial action in the fermentation process for natural coffees. In a study by Silva et
al. (2008a), the production of organic acids from microbial metabolism and seed via high-performance
liquid chromatography was assessed. In that study, it was observed that butyric acid is not detected in
any of the samples analyzed. The presence of this acid in coffee beans generally gives an unpleasant
flavor to the beverage and thus leads to quality loss. Acetic acid is detected mainly in the pulp and in
parts of the mucilage. Acetic acid production is an aerobic metabolic process that can be of bacterial ori-
gin or the product of the oxidation of yeast-produced alcohol. The bacteria present on the surface of the
coffee cherries synthesize the acid that can migrate to the pulp and mucilage and can interfere with the
organoleptic quality of the beans. The negative influence of bacteria on the quality of the coffee beverage
is linked to the species present and not to population density. In natural coffee, ruit rated very soft (i.e.,
as having optimal sensory quality), the bacterial population can represent up to 80% of total microbiota
during this process.

42.4.2  Yeasts
The yeast population in natural coffee is usually lower than the bacterial population, presenting aver-
age values of 104 CFU/g; it becomes predominant with the reduction of water activity during the drying
period and is detected in fruits with aw of 0.6. Pichia, Candida, and Arxula are the most commonly
found genera in fermented and dried fruits (Silva et al. 2000, 2008a). The species identified by Silva et
al. (2000, 2008a) on the surface of coffee fruits included Arxula adeninivorans, Blastobotrys prolifer-
ans, Candida auringiensis, C. glucosophila, C. incommunis, C. membranifaciens, C. paludigena, C.
schatarii, C. saitoana, Candida fermentati, C. vartiovaarae, Citeromyces matritensis, Debaryomyces
polymorphus, D. hansenii, Geotrichum fermentans, Pichia guilliermondii, Pichia acaciae, P. anom-
ala, P. burtonii, P. ciferii, P. jadinii, P. lynferdii, P. ofunaensis, P. sydowiorium, P. subpelliculosa,
Saccharomyces cerevisiae, Saccharomycopsis fermentans, S. fibuligera, Schizosaccharomyces cpombe,
Sporopachydermia cereana, Stephanoascus smithiae, Trichosporonoides oedocephales, and Williopsis
saturnus var. sargentensis.
The involvement of yeast species in the fermentation process and bacterial action can be assumed
based on their potential to produce pectin lyase and polygalacturonases. Of the identified species,
Debaryomyces hansenii, Pichia sydowiorium, Sthephanoascus smithiae, and Arxula adeninivorans are
those that have the capacity for pectin lyase production and that therefore cause degradation of the pulp
and mucilage of natural coffee fruit (fermentation) via pectinolytic bacteria). The role of yeast may be
related not just to the fermentation process but also to the control of filamentous fungi growth. Isolates
belonging to the genera Debaryomyces and Pichia have demonstrated the ability to inhibit the growth of
toxigenic fungi and may therefore have the potential for biological control (Ramos et al. 2010).

42.4.3  Filamentous Fungi

Studies of natural coffee microbial populations always emphasize filamentous fungi isolation and iden-
tification, but the microorganisms present during the fermentation and drying period are predominantly
bacteria and yeasts. Therefore, the presence of filamentous fungi is not involved in the fermentation
process; these are detected in the last days of fermentation and during storage. Various levels of fun-
gal and toxin levels detected in processed dry beans can be found in studies by Batista et al. (2009),
Batista and Chalfoun (2007), Silva et al. (2003), De Moraes and Luchese (2003), Chalfoun and Batista
(2007), and Taniwaki et al. (2003).
The incidence of fungi in coffee fruits and beans is associated with a decrease in the sensory quality
of the final coffee beverage, probably due to the production of metabolites such as superior acids. One
exception is the presence of Cladosporium cladosporioides, which is usually found in high-quality bev-
erages (Pereira et al. 2005; Chalfoun et al. 2007).
The species of filamentous fungi isolated in natural coffee are Alternaria, Aspergillus flavus, A. niger,
A. tamarii, A. ochraceus, A. wentii, A. versicolor, A. glaucus group Cladosporium herbarum, Fusarium
stilboides, Penicillium chrysogenum, P. viridicatum, P. islandicum (Mislivec et al. 1983—countries of

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684 Handbook of Plant-Based Fermented Food and Beverage Technology

Central and South America, Asia, and Africa), Aspergillus flavus, A. fumigatus, A. niger, A. parasiti-
cus, A. sydowii, A. tamarii, A. terreus, Cladosporium cladosporioides, C. herbarum, C. macrocarpum,
Fusarium oxysporum, Penicillium albidum, P. brevicompactum, P. chrysogenum, P. citrinum, P. cyclo-
pium, P. funiculosum, P. jensenii (Abdel-Hafez and El Maghraby 1992—Egypt), Aspergillus fumiga-
tus, A. niger, Fusarium graminearum, Penicillium granulatum (Liardon et al. 1992—Brazil), Mucor,
Cercospora, Phoma, Penicillium (Alves and Castro 1998—Brazil), A. carbonarius, A. niger, A. ochra-
ceus, Penicillium sp. (Taniwaki et al. 2003—Brazil), A. ochraceus, Aspergillus section Nigri, Rhizopus
(Pardo et al. 2004—Angola, Bolivia, Brazil, Costa Rica, Ecuador, Ethiopia, Guatemala, India, Indonesia,
Ivory Coast, Java, Nicaragua, Uganda, and Vietnam), A. tubingensis, A. carbonarius, A. ochraceus, A.
sulphureus, A. tamari, A. niger, A. flavus (Magnani et al. 2005—Brazil), Cladosporium cladosporioi-
des (Chalfoun et al. 2007—Brazil), A. ochraceus, A. flavus, A. sulphureus, A. niger, A. versicolor, A.
sydowii, A. ostianus, A. melleus, A. dimorphicus, A. sclerotiorum, A. auricomus, A. foetidius, Eurotium
amstelodami, and E. chevalieri (Batista et al. 2001, 2007, 2009—Brazil), A. flavus, A. niger, A. ochra-
ceus, A. tamari, A. sydowii, A. foetidius, A. dimorphicus, Fusarium lateritium, F. solani, F. illudens, F.
stilboides, F. semitectum, P. brevicompactum, P. crustosum, P. roqueforti, P. citrinum, Cladosporium
cladosporioides, Paecelomyces sp. (Silva et al. 2000, 2008a,b—Brazil).

42.4.3.1  Ochratoxin A–Producing Toxigenic Fungi

The toxigenic potential of a fungus is defined as the ability of a strain to produce toxic metabolites.
Mycotoxins are characterized as secondary metabolites and are produced between the late exponential
phase and early stationary phase of fungal growth; they are therefore not related to the biological role
of microorganisms (Bars and Bars 2000). The conditions that enable the production of mycotoxins by a
potentially toxigenic strain are more limited than those that permit the growth of fungi. Many strains of
a species that is considered toxigenic may not possess this property. In potentially toxigenic species, the
production of toxins can vary by up to 1000 times (Bars and Bars 2000).
Ochratoxin A present in coffee samples has mainly been attributed to the presence of species of
the genus Aspergillus belonging to section Circumdati and section Nigri (Urban et al. 2001; Batista et
al. 2003). Ochratoxin A is a secondary metabolite that is mainly produced by fungi belonging to the
genera Aspergillus, Petromyces, Neopetromyces, and Penicillium (Frisvad and Samson 2000), but the
genus Aspergillus is undoubtedly one of the most important for coffee. Among the species of the genus
Aspergillus belonging to section Circumdati, the leading producer of ochratoxin A is A. ochraceus, but
other species belonging to this section and producing ochratoxin A have been found in coffee fruit and
Missing spe-
cies here. beans, including A. elegans, A. auricomus, A. ostianus, A. petrakii, A., and A. sclerotiorum sulphureus
(Batista et al. 2003). Frisvad et al. (2004) and Sartori et al. (2006) indicated that A. westerdijkiae can
also contribute to the presence of ochratoxin A in coffee beans in Brazil. Studies have revealed that A.
carbonarius is more common and represents the major source of ochratoxin A in section Nigri, whereas
A. niger is rarely the producer (Heenan et al. 1998). Others studies indicate that other species including
A. steynii, A. westerdijkiae, A. lactofeatus, and A. slerotioniger (Frisvad et al. 2004; Samson et al. 2004)
can also be producers of ochratoxin A in coffee. In the genus Penicillium, the only species considered
producers of ochratoxin A are Penicillium verrucosum and P. nordicum (Larsen et al. 2001).
Both the environmental conditions of the geographic area and the types of grains influence the popula-
tion of fungi and mycotoxin production. The study of the economic importance of Aspergillus species
using polyphasic taxonomy is an innovative strategy that assists in characterizing the biodiversity of spe-
cies and evaluating the risk of ochratoxin A contamination in coffee beans.

42.5  Microbiota of Wet Processed, Depulped, and Washed Coffee

The mechanical removal of pulp that occurs in wet processing allows mucilage to remain adhered to
coffee beans. This mucilage is the substrate used by bacteria and yeast during fermentation. During
fermentation, the precursors of flavor-enhancing compounds are naturally excreted by the fermentative
microbiota present in coffee fruits (Gonzalez-Rios et al. 2007).

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Coffee Fermentation 685

The microbial diversity of coffee beans in wet processing is lower than in dry processing due to
fermentation conditions like reduced fermentation time (48 hours), faster decreases in pH, and pulp
removal. The microbiota includes few species of bacteria and yeast and have been no reports of fila-
mentous fungi involved in the fermentation process. The greatest microbial diversity in washed coffee
fruits can be recognized using molecular techniques that allow the detection of culturable and uncultur-
able microorganisms. The molecular identification of microorganisms associated with coffee has been
performed by Vilela et al. (2010) for semidry processing and Masoud et al. (2004) for wet processing. In
semidry processing, microbial succession occurs, bacteria dominated at the beginning of the process, but
after 72 hours, bacteria and yeasts populations reach similar values (average 106 CFU/g), and the yeast
dominate after 192 hours of fermentation (Vilela et al. 2010). This process is similar to the process of
ecological succession described in Silva et al. (2008a), who observed that filamentous fungi were rarely
found in semidry processes.

42.5.1  Bacteria
Studies dating back to the 1920s have isolated bacteria, fungi, and yeasts from coffee fruits, but do not make
inferences about the involvement of microorganisms in mucilage degradation. Currently, there is still doubt
about the apparent involvement of bacteria in coffee fruit fermentation, and since 2002, no results that address
this issue have been published. An early study on the action of microorganisms present in coffee fermentation
was published in 1946 by Pederson and Breed (1946) using samples of coffee from Colombia and Mexico.
These authors isolated cocci and microaerophilic bacteria such as Leuconostoc mesenteroides, Lactobacillus
plantarum, Lactobacillus brevis, and Streptococcus faecalis as facilitating the lysis of mucilage but not its
detachment. Agate and Bhat (1966) isolate and identify Streptococcus, Pseudomonas, Flavobacterium, and
Proteus from depulped coffees in India and state that these bacteria are not pectinolytic and are therefore not
involved in the process of fermentation of depulped fruits.
Avallone et al. (1999, 2001, 2002) have isolated bacteria from wet processed fruits and detect the
Gram-negative bacteria Erwinia and Klebsiella in a culture containing pectin, isolated from the coffee.
They were characterized by low pectinolytic capacity and produced pectate lyase. The authors support
the hypothesis that the presence of bacteria is facilitated by the consumption of simple sugars because
the production of pectate lyase keeps these bacteria from affecting the fruit mucilage; the bacteria that
produce polygalacturonase are rarely identified as Lactobacillus brevis. Microorganisms that facilitate
the degradation of mucilage must be capable of secreting pectin lyase and polygalacturonase due to the
methylated structure of pectin.
In semidry processing, 15 species, including Acinetobacter, Bacillus cereus, B. macerans, B. megate-
rium, B. subtilis, Enterobacter agglomerans, Erwinia herbicola, Escherichia coli, Klebsiella pneumoniae,
Lactobacillus brevis, L. plantarum, Lactococcus lactis, Leuconostoc mesenteroides, and Serratia (Vilela et
al. 2010), have been identified using traditional and molecular methods. Some of these species have also been
identified in coffee cherries, possibly due to natural, common aspects of these two processes.

42.5.2  Yeasts
The population of yeasts in depulped coffees is greater than that of bacteria at the beginning of the fer-
mentation period, with a density close to 104 CFU/g that increases during fermentation, reaching a value
of 107 CFU/g (Masoud et al. 2004).
Of the studies that have been published on the isolation and the role of microorganisms in the fermen-
tation of depulped coffee, only the research by Avallone et al. (2001, 2002) has not inferred the degra-
dation of mucilage to be a product of the action of bacteria and/or yeast, which are responsible for the
production of ethanol in overfermented coffees. However, pectinolytic yeasts have been isolated during
the wet processing of coffee (Masoud and Jespersen 2006; Agate and Bhat 1966; Daivasikamani and
Kannan 1986; Van Pee and Castelein 1971) in both Robust and Arabic coffees.
Agate and Bhat (1966) observed that the yeasts found in Robust coffee beans from India are predomi-
nant over the population of bacteria. The yeasts Kluyveromyces, Saccharomyces sp., Saccharomyces
marxianus [Kluyveromyces marxianus (EC Hansen) van der Walt (1971)], S. bayanus, S. cerevisiae

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var. ellipsoideus produce pectinases that degrade mucilage pectin. In that instance, it was impossible to
confirm the degradation of mucilage because the degradation of mucilage was not observed when the
depulped fruits were sterilized. Working with depulped coffees from the Congo, Van Pee and Castelein
(1971) have identified yeasts of the genus Candida, with C. guilliermondii var. membranaefaciens found
on the surface and mucilage of the grains; C. parapsilosis, Saccharomyces cerevisiae, Torulopsis famata
[Candida famata (Harrison) SA Meyer & Yarrow (Yarrow and Meyer 1978)], Saccharomyces marxianus
[Kluyveromyces marxianus (EC Hansen) van der Walt (1971)], Candida tropicalis, Rhodotorula muci-
laginosa, and Candida pelliculosa were found on the surface of grains.
The different types of pectinase produced by organisms can affect the degree of depolymerization of
the pectin components, which can then influence the selection of the dominant group of microorganisms
(Jones and Jones 1984). The depolymerization of pectin can be performed using the enzymes pectin
lyase, pectin methyl esterase, and polygalacturonase. Pectin from the fruit mucilage will be degraded via
pectin lyase and polygalacturonase.
The presence of Kluyveromyces marxianus in wastewater for fermentation tanks and of Pichia kluyv-
ery, P. anomala, Hanseniaspora uvarum with high pectinolytic capacity seems to enhance the action
of yeast during the fermentation process (Serrat et al. 2002; Masoud and Jespersen 2006). The latter
three species are capable of producing polygalacturonase in vitro under physicochemical conditions (pH
5.3–3.5 and 30°C) similar to those characteristic of the fermentation process. Thus, the authors conclude
that yeasts use mucilage pectin as a carbon source with simple sugars (glucose and fructose), inducing
polygalacturonase production.
Similarly, it has been observed that Pichia kluyvery, P. anomala, Hanseniaspora uvarum (Masoud
and Kaltoft 2006) have an inhibitory effect on the growth of Aspergillus ochraceus, a fungus that is
potentially toxigenic and is often isolated in coffee fruits and beans (Batista et al. 2009; Silva et al.
2008a,b). Thus, yeasts play a dual role during the processing of coffee fruits: they facilitate fermentation
and biological control.
Species identified in washed and natural coffee fruits have also been found in semidry processing
(Vilela et al. 2010). Pichia anomala have been shown to be similarly present in freshly harvested fruits
(104 CFU/g) and have persisted through the 216-hour-long fermentation process. The persistence of this
species may suggest the involvement of yeast in mucilage degradation. Other identified species include
Arxula sp., Candida ernobii, C. fukuyamaensis, C. membranifaciens, C. carpophila, Hanseniaspora
uvarum, Kloeckera, Kluyveromyces sp., Pichia caribbica, Rhodotorula mucilaginosa, Saccharomyces
bayanus, and Torulaspora delbrueckii.

42.6  Final Considerations

Coffee is among the most consumed nonalcoholic beverages worldwide, and its production has signifi-
cant financial ramifications in producing, exporting, and importing countries. The species Coffea ara-
bica and Coffea canephora are the most used due to their cultural and sensory characteristics. Various
chemical compounds are used to certify the coffee species used and the types of processing employed,
as the beans have an aggregate value that is directly dependent on their quality. After harvesting, the
fruits are processed via dry, semidry, and wet processing, which create different aromas and flavors, and
it is up to the consumer to choose the type of beverage that he or she best likes. During processing, the
fruits undergo a microbial fermentation process that is responsible for the spontaneous degradation of
pulp and fruit mucilage. The microbiota involved in the fermentation process includes several species
of bacteria, yeasts, and filamentous fungi. These seem not to participate in the fermentation process and
are usually related to decreased beverage quality, with the exception of the Cladosporium species. The
presence of filamentous fungi may create the risk of contamination by mycotoxins for fruits and coffee
beans. The adoption of good agricultural practices and the hazard analysis and critical control points
system will significantly reduce the risk of contamination by microorganisms and decrease the incidence
of conditions in which the deterioration of the fruits or coffee beans may occur, for instance, by reducing
ochratoxin A.

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