Isolation and identification of caffeine-degrading bacteria from soil, coffee pulp waste and excreted coffee bean in Luwak feces

Abstract

Abstract. Iswanto T, Shovitri M, Altway A, Widjaja T, Kusumawati DI, Lisdiyanti P. 2019. Isolation and identification of caffeine-degrading bacteria from soil, coffee pulp waste and excreted coffee bean in Luwak feces. Biodiversitas 20: 1580-1587. The present study deals with the isolation and identification of caffeine-degrading bacteria obtained from the caffeine contaminated environment or caffeinated wastes. These bacteria are useful for various biotechnological applications especially in increasing the potential utilization of caffeinated wastes and producing the high-value chemicals. The suspected caffeine-degrading bacteria have been isolated from the soil of coffee plantation area, coffee pulp waste, and the excreted coffee bean in fresh feces of Luwak (Paradoxurus hermaphroditus or Asian Palm Civet) by growing them on the caffeinated agar medium (CAM) containing basal salt medium (M9) and caffeine as a sole source of carbon and nitrogen. CAM-supplemented with 1.5 to 10 g L-1 of caffeine has been used for screening of the potential bacteria which able to grow in high caffeine concentration. Molecular identification based on 16S rRNA gene sequence was performed to identify the selected bacteria. The result revealed that there were 11 and 3 strains of 12 selected bacteria which could grow on the CAM-supplemented with caffeine up to 7 and 10 g L-1, respectively. Based on 16S rRNA gene sequence and phylogenetic analysis, those bacteria were from 5 Gram-negative species, namely Pseudomonas japonica (4/12), Methylobacterium populi (5/12), Raoultella ornithinolytica (1/12), Klebsiella quasipneumoniae (1/12), and Stenotrophomonas chelatiphaga (1/12). Further investigations to determine their metabolic pathway, enzyme, and growth kinetics in the caffeinated medium may provide insights into its possible utilization for scientific or other applications.

Structure and Dynamics of the Gut Bacterial Community Across the Developmental Stages of the Coffee Berry Borer, Hypothenemus hampei

“…Recently, it was shown that CBB-associated P. fulva and other four Pseudomona species contains a full gene complement for caffeine metabolism, while other additional sixteen bacteria species contain partial gene complements for the same process (Vega et al, 2021). Caffeine degradation capability has been shown for other strains of Stenotrophomonas, Serratia, Acinetobacter, Klebsiella, Rhodococcus, and Methylobacterium as well (Madyastha and Sridhar, 1998;Yamaoka and Mazzafera, 1998;Iswanto et al, 2019). Bacteria in the genus Pseudomonas were shown to be highly abundant (21-25%) in CBB females from coffee plots in Puerto Rico (Mariño et al, 2018) but not in our study (1.1% in the CBB female sample).…”

Cellulolytic and mannanolytic aerobic bacteria isolated from Buffalo rumen (Bubalus babalis) and its potency to degrade fiber in palm kernel meal

“…Klebsiella quasipneumoniae and Acinetobacter baumannii have been identified as member of Proteobacteria. Klebsiella quasipneumoniae had been successfully isolated from excreted coffee beans in Luwak feces (Iswanto et al 2019). Some species of Klebsiella has been reported to have cellulolytic and hemicellulolytic activity including K. pneumonia from digestive tract of Bombix morii (Anand et al 2010), K. ozeanae (Kalaiselvi and Jayalakshmi 2013), K. oxytoca, K. variicola (Dantur et al 2015).…”

Coffee Microbiota and Its Potential Use in Sustainable Crop Management. A Review

“…This strategy was successfully employed to demonstrate the ability of some biocontrol agents to inhibit the development of some of the major coffee diseases such as the CLR caused by the fungal pathogen H. vastatrix (Shiomi et al, 2006;Bettiol et al, 2007;Silva et al, 2008Silva et al, , 2012Daivasikamani and Rajanaika, 2009;Haddad et al, 2013) or the coffee wilt disease (CWD) also known as tracheomycosis caused by the fungal pathogen Gibberella xylarioides (Muleta et al, 2007;Mulaw et al, 2010Mulaw et al, , 2013Tiru et al, 2013). This methodology was also used to reveal the microorganisms biocontrol potential toward numerous other phytopathogens including Alternaria alternata, A. solani, Ambrosiella macrospora, Botrytis cinereal, Colletotrichum gloeosporioides, C. coffeicola, Fusarium oxysporum, F. solani, F. verticillioides, Glomerella sp., Macrophomina phaseolina, Myrothecium roridum, Pestalotia longisetula, Phoma sp., Phytophthora capsici, P. meadii, Pythium aphanidermatum, Rhizoctonia solani, and Sclerotinia sclerotiorum (Nair et al, 2002;Mulaw et al, 2013;Bongiorno et al, 2016;Kejela et al, 2016;Monteiro et al, 2017;Ranjini and Raja, 2019;Hoang et al, 2020;Duong et al, 2021) but also some pests such as the coffee berry borer Hypothenemus hampei (Vega et al, 2008), the root knot nematode Meloidogyne incognita (Mekete et al, 2009;Hoang et al, 2020), the burrowing nematode Radopholus duriophilus, and the root lesion nematode Pratylenchus coffeae (Duong et al, 2021), as well as some toxigenic fungi including Aspergillus carbonarius, A. flavus, A. niger, A. ochraceus, and A. westerdijkiae (Masoud and Kaltoft, 2006;Ramos et al, 2010;Djossou et al, 2011;Leong et al, 2014;De Melo Pereira et al, 2015a;De Almeida et al, 2019).…”

“…However, these strategies are difficult to implement because of caffeine, tannin, and polyphenol contents that make the wastes toxic. For these reasons, microorganisms have also been studied for their potential utilization in detoxifying the coffee wastes and were therefore screened for their capacity to degrade the caffeine and tannins (Aquiahuatl et al, 1988;Roussos et al, 1995;Brand et al, 2000;Mazzafera, 2002;Nayak et al, 2012). Finally, microorganisms have also been explored for some industrial applications such as the production of enzymes with by-products such as amylases (Murthy et al, 2009), pectinases (Antier et al, 1993;Boccas et al, 1994;Sakiyama et al, 2001;Serrat et al, 2002;Masoud and Jespersen, 2006), proteases (Rodarte et al, 2011), and xylanases (Murthy and Naidu, 2012).…”