The Potential of Phylogenetically Diverse Culturable Actinobacteria from Litopenaeus vannamei Pond Sediment as Extracellular Proteolytic and Lipolytic Enzyme Producers
Main Article Content
Abstract
Enzymes are catalysts that can increase the reaction time of a biochemical process. Hydrolytic enzymes have a pivotal role in degrading organic waste in both terrestrial and aquatic environments. The aims of this study were (1) to investigate the ability of actinobacteria isolated from Litopenaeus vannamei pond sediment to produce proteolytic and lipolytic enzymes, (2) to identify promising candidates using 16S rRNA gene amplification, and (3) to construct a phylogenetic tree based on the 16S rRNA genes. A skim milk agar medium was used in the preliminary experiment of the proteolytic assay, and a Tween 20/80 medium was used in the lipolytic assay. Fifteen and 20 (out of 40) actinobacterial isolates showed great potential for proteolytic and lipolytic activities, respectively. Furthermore, four actinobacteria isolates produced both enzyme types with proteolytic and lipolytic index scores of 1–6.5. The most promising candidates were SA 2.2 (IM8), SC 2.1 (IM6), SD 1.5 (IM6) and SE 1.1 (IM8). BLAST homology results showed a high similarity between the actinobacteria isolates and Streptomyces verucosisporus, S. mangrovicola, S. barkulensis and Nocardiopsis lucentensis, respectively. Therefore, actinobacteria from Litopenaeus vannamei pond sediment are high-potential proteolytic and lipolytic enzyme producers.
Article Details
This work is licensed under a Creative Commons Attribution 4.0 International License.
References
Akhwale J K, Göker M, Rohde M, Schumann P, Boga H I and Klenk H P. (2016). Nocardiopsis mwathae sp. nov., isolated from the haloalkaline Lake Elmenteita in the African Rift Valley. Antonie Van Leeuwenhoek 109: 421–430. https://doi.org/10.1007/s10482-016-0647-z
Al-Dhabi N A, Esmail G A, Duraipandiyan V and Arasu M V. (2019). Chemical profiling of Streptomyces sp. Al-Dhabi-2 recovered from an extreme environment in Saudi Arabia as a novel drug source for medical and industrial applications. Saudi Journal of Biological Science 26: 758–766. https://doi.org/10.1016/j.sjbs.2019.03.009
Al-Dhabi N A, Esmail G A, Ghilan A M and Arasu M V. (2020). Isolation and screening of Streptomyces sp. Al-Dhabi-49 from the environment of Saudi Arabia with concomitant production of lipase and protease in submerged fermentation. Saudi Journal of Biological Science 27(1): 474–479. https://doi.org/10.1016/j.sjbs.2019.11.011
Armaida E and Khotimah S. (2016). Karakterisasi actinomycetes yang berasosiasi dengan porifera (Axinella spp.) dari perairan Pulau Lemukutan Kalimantan Barat. Protobiont 5(1): 68–73.
Ayuningrum D, Kristiana R, Nisa A A, Radjasa S K, Muchlissin S I, Radjasa O K, Sabdono A and Trianto A. (2019). Bacteria associated with Tunicate, Polycarpa aurata, from Lease Sea, Maluku, Indonesia exhibiting anti-multidrug resistant bacteria. Biodiversitas 20(4): 956964. https://doi.org/10.13057/biodiv/d200404
Ayuningrum D, Sabdaningsih A and Jati O E. (2021). Screening of actinobacteria-producing amylolytic enzyme in sediment from Litopenaeus vannamei (Boone, 1931) ponds in Rembang District, Central Java, Indonesia. Biodiversitas 22(4): 1819–1828. https://doi.org/10.13057/biodiv/d220427
Babu D T, Archana K, Kavhiprath B, Solomon S, Jayanath G, Singh I S and Philip R. (2018). Marine actinomycetes as bioremediators in Penaeus monodon rearing system. Fish and Shellfish Immunology 75: 231–242. https://doi.org/10.1016/j.fsi.2018.01.037
Balagurunathan R, Radhakrishnan M, Shanmugasundaram T, Gopikrishnan V and Jerrine J. (2020) Evaluation of actinobacteria for aquaculture applications. In Protocols in actinobacterial research: Springer protocols handbooks. New York, NY: Springer. https://doi.org/10.1007/978-1-0716-0728-2_11
Beg Q K and Gupta R. (2003). Purification and characterization of an oxidation-stable, thiol-dependent serine alkaline protease from Bacillus mojavensis. Enzyme and Microbial Technology 32: 294–304. https://doi.org/10.1016/S0141-0229(02)00293-4
Bernal M F, Campa-Cordova A I, Saucedo P E, Gonzales M C, Marrero M R and MazonSuastegui J M. (2015). Isolation and in vitro selection of actinomycetes strains as potential probiotics for aquaculture. Veterinary World 8(2): 170–176. https://doi.org/10.14202/vetworld.2015.170-176
Bredholt H, Fjærvik E, Johnsen G and Zotchev S B. (2008). Actinomycetes from sediments in the Trondheim Fjord, Norway: Diversity and biological activity. Marine Drugs 6(1): 12–24. https://doi.org/10.3390/md6010012
Chandra P, Enespa, Singh R and Arora P K. (2020) Microbial lipases and their industrial applications: A comprehensive review. Microbial Cell Factories 19: 169. https://doi.org/10.1186/s12934-020-01428-8
Chen M, Xu P, Zeng G, Yang C, Huang D and Zhang J. (2015). Bioremediation of soils contaminated with polycyclic aromatic hydrocarbons, petroleum, pesticides, chlorophenols and heavy metals by composting: Applications, microbes and future research needs. Biotechnology Advances 1(33): 745–755. https://doi.org/10.1016/j.biotechadv.2015.05.003
Chevrette M G, Carlos-Shanley C, Louie K B, Bowen B P, Northen T R and Currie C R. (2019). Taxonomic and metabolic incongruence in the ancient genus Streptomyces. Frontiers in Microbiology 10: 2170. https://doi.org/10.3389/fmicb.2019.02170
De Azeredo L A I, De Lima M B, Coelho R R R and Freire D M G. (2006). A low-cost fermentation medium for thermophilic protease production by Streptomyces sp. 594 using feather meal and corn steep liquor. Current Microbiology 53: 335–339. https://doi.org/10.1007/s00284-006-0163-x
Durham D R, Stewart D B and Stellwag E J. (1987). Novel alkaline and heat stable serine proteases from alkalaphilic Bacillus sp. strain GX6638. Journal of Bacterialogy 169(6): 2762–2768. https://doi.org/10.1128/jb.169.6.2762-2768.1987
Ghorbel S, Kammoun M, Soltana H, Nasri M and Hmidet N. (2014). Streptomyces flavogriseus HS1: Isolation and characterization of extracellular proteases and their compatibility with laundry detergents. Biomed Research International 2014: 345980. https://doi.org/10.1155/2014/345980
Goodfellow M, Kampfer P, Busse H, Trujillo ME, Suzuki K, Ludwig W and Whitman W B. (2012). Bergey’s manual of systematic bacteriology, 2nd ed. Vol. 5: The Actinobacteria. New York: Springer. https://doi.org/10.1007/978-0-387-68233-4
Gupta R, Beg Q K and Lorenz P. (2002). Bacterial alkaline proteases: Molecular approaches and industrial applications. Applied Microbiology and Biotechnology 59(1):15–32. https://doi.org/10.1007/s00253-002-0975-y
Gupta R and Ramnani P. (2006) Microbial keratinases and their prospective applications: An overview. Applied Microbiology and Biotechnology 70(1): 21–33. https://doi.org/10.1007/s00253-005-0239-8
Hamdani S, Asstiyani N, Astriany D, Singgih M and Ibrahim S. (2019). Isolation and identification of proteolytic bacteria from pig sludge and protease activity determination. IOP Conference Series: Earth and Environmental Science 230: 012095. https://doi.org/10.1088/1755-1315/230/1/012095
Jaeger K E, Ransac S, Dijkstra B W, Colson C, Van Heuvel M and Misset O. (1994). Bacterial lipases. FEMS Microbiology Reviews 15(1): 29–63. https://doi.org/10.1111/j.1574-6976.1994.tb00121.x
Jaeger K E and Reetz M T. (1998). Microbial lipases form versatile tools for biotechnology. Trends in Biotechnology 16(9): 396–403. https://doi.org/10.1016/S0167-7799(98)01195-0
Klausen C, Nicolaisen M H, Strobel B W, Warnecke F, Nielsen J L and Jørgensen N O G. (2005). Abundance of actinobacteria and production of geosmin and 2-methylisoborneol in Danish streams and fish ponds. FEMS Microbiology Ecology 52(2): 265–278. https://doi.org/10.1016/j.femsec.2004.11.015
Krishnappa L, Monteferrante C G, Neef J, Dreisbach A and van Dijl J M. (2014). Degradation of extracytoplasmic catalysts for protein folding in Bacillus subtilis. Applied and Environmental Microbiology 80: 1463–1468. https://doi.org/10.1128/aem.02799-2713
Kumar S, Stecher G, Li M, Knyaz C and Tamura K. (2018). MEGA X: Molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution 35(6): 1547–1549. https://doi.org/10.1093/molbev/msy096
Ludwig W, Euzeby J P and Whitman W B. (2015). Taxonomic outline of the phylum Actinobacteria. In W B Whitman (Ed.), Bergey’s manual of systematics of archaea and bacteria. Hoboken, NJ: John Wiley and Sons. https://doi.org/10.1002/9781118960608.bm00030
Macrae A R. (1983). Lipase-catalyzed interesterification of oils and fats. Journal of the American Oil Chemists' Society 60: 291–294. https://doi.org/10.1007/BF02543502
Mahajan R, Chaudhari G and Chopadaa M. (2016). Report on biotechnological applications of proteolytic enzymes from lattices of euphorbian plants. Journal of Applied Biotechnology Reports 2: 333–337. https://doi.org/10.21276/ijlssr.2016.2.4.7
Manikkam R, Imchen M, Kaari M, Vignesh A, Gopikrishnan V, Shanmugasundaram T, Joseph J, Balagurunathan R and Kumavath R. (2020). Metagenomic Insights unveil the dominance of undescribed actinobacteria in pond ecosystem of an Indian shrine. Meta Gene 23: 100639. https://doi.org/10.1016/j.mgene.2019.100639
Manisha and Yadav S K. (2017). Technological advances and applications of hydrolytic enzymes for valorization of lignocellulosic biomass. Bioresource Technology 245(Pt B): 1727–1739. https://doi.org/10.1016/j.biortech.2017.05.066
Meyer J. (1976). Nocardiopsis, a new genus of the order Actinomycetales. International Journal of Systematic and Evolutionary Microbiology 26(4): 487–493. https://doi.org/10.1099/00207713-26-4-487
Mohamedin A. (1999). Isolation, identification and some cultural conditions of a protease producing thermophilic Streptomyces strain grown on chicken feather as a substrate. International Biodeterioration & Biodegradation 43: 13–21. https://www.infona.pl/resource/bwmeta1.element.elsevier-26895658-838c-3c20-8b3c3145a6d1bbc8
Mukesh D, Rajan R, Lawrence L, Priyadarshini S, Chittybabu S and Kalaichelvan P. (2012). Distaining and de-hairing capability of partially purified Bacillus subtilis protease from optimized fermentation medium. Asian Journal of Experimental Biological Sciences 3: 613–620.
Mukhtar S, Zaheer A, Aiysha D, Malik K A and Mehnaz S. (2017). Actinomycetes: A source of industrially important enzymes. Journal of Proteomics and Bioinformatics 10: 12. https://doi.org/10.4172/0974-276X.1000456
Nei M and Kumar S. (2000). Molecular evolution and phylogenetics. New York: Oxford University Press. Palsaniya P, Mishra R, Beejawat N, Sethi S and Gupta B L. (2012). Optimization of alkaline protease production from bacteria isolated from soil. Journal of Microbiology and Biotechnology Research 2(6): 858–865. http://scholarsresearchlibrary.com/archive.html
Pastor M D, Lorda G S and Balatti A. (2001). Protease obtention using Bacillus subtilis 3411 and amaranth seed meal medium at different aeration rates. Brazilian Journal of Microbiology 32: 6–9. https://doi.org/10.1590/S1517-83822001000100002
Patang. (2016). Pengembangan udang windu melalui penerapan pembantutan, probiotik dan pengendalian lingkungan. Paper presented at Orasi Ilmiah Pengukuhan Guru Besar, Sidang Terbuka Luar Biasa Senat Universitas Negeri Makassar, Makassar, 27 December.
Patel G B, Rakholiya P, Shindal T, Varjani S, Tabhani N M and Shah K R. (2021). Lipolytic Nocardiopsis for reduction of pollution load in textile industry effluent and SWISS model for structural study of lipase. Bioresource Technology 341: 125673. https://doi.org/10.1016/j.biortech.2021.125673
Pearson W R. (2013). An introduction to sequence similarity (“homology”) searching. In Current Protocol in Bioinformatics. John Wiley and Sons, Unit 3.1. https://doi.org/10.1002/0471250953.bi0301s42
Ramnath L, Sithole B and Govinden R. (2017). Identification of lipolytic enzymes isolated from bacteria indigenous to Eucalyptus wood species for application in the pulping industry. Biotechnology Reports 15: 114–124. https://doi.org/10.1016/j.btre.2017.07.004
Sathishkumar R, Ananthan G and Arun J. (2015). Production, purification and characterization of alkaline protease by ascidian associated Bacillus subtilis GA CAS8 using agricultural wastes. Biocatalysis and Agricultural Biotechnology 4(2): 214–220. https://doi.org/10.1016/j.bcab.2014.12.003
Shijila Rani A S, Babu S, Anbukumaran A, Prakash P, Veeramani S and Ambikapathy V. (2022) Isolation of actinobacteria from shrimp. In D. Dharumadurai (ed.). Methods in actinobacteriology. New York, NY: Springer. https://doi.org/10.1007/978-1-0716-1728-1_6
Sun F, Hu Y, Chen Q, Kong B and Qian L. (2019). Purification and biochemical characteristics of the extracellular protease from Pediococcus pentosaceus isolated from Harbin dry sausages. Meat Science 156: 156–165. https://doi.org/10.1016/j.meatsci.2019.05.030
Suwoyo H S, Tahe S and Fahrur M. (2015). Karakterisasi limbah sedimen tambak udang vaname (Litopenaeus vannamei) super intensif dengan kepadatan berbeda. Prosiding Forum Inovasi Teknologi Akuakultur 2015: 1015–1026.
Tennalli G, Udapudi B and Naik P. (2012). Isolation of proteolytic bacteria and characterization of their proteolytic activity. International Journal of Advances in Engineering, Science and Technology 2(3): 185–192.
Ugur A, Sarac N, Boran R, Ayaz B, Ceylan O and Okmen G. (2014). New lipase for biodiesel production: Partial purification and characterization of LipSB 25-4. ISRN Biochemistry 2014: 289749. https://doi.org/10.1155/2014/289749
Vijayaraghavan P, Lazarus S and Vincent S G. (2014). De-hairing protease production by an isolated Bacillus cereus strain AT under solid-state fermentation using cow dung: Biosynthesis and properties. Saudi Journal of Biological Science 21(1): 27– 34. https://doi.org/10.1016/j.sjbs.2013.04.010
Vishnupriya B, Sundaramoorthi C, Kalaivani M and Selvam K. (2010). Production of lipase from Streptomyces griseus and evaluation of bioparameters. International Journal of ChemTech Research 2(3): 1380–1383.
Weisburg W G, Barns S M, Pelletier D A and Lane D J. (1991). 16S Ribosomal DNA amplification for phylogenetic study. Journal of Bacteriology 173(2): 7.
Willerding A L, Oliveira L A, Moreira F W, Germano M G and Chagas Jr. F. (2011). Lipase activity among bacteria isolated from amazonian soils. Enzyme 2011. https://doi.org/10.4061/2011/720194
Yassin A F, Sproer C, Hupfer H, Siering C and Klenk H P. (2009). Nocardiopsis potens sp. nov., isolated from household waste. International Journal of Systematic and Evolutionary Microbiology 59(11): 2729–2733. https://doi.org/10.1099/ijs.0.011288-0