Citation: Prartono, T.; Dwinovantyo, A.; Syafrizal, S.; Syakti, A.D. Potential Use of Deep-Sea Sediment Bacteria for Oil Spill Biodegradation: A Laboratory Simulation. Microorganisms 2022, 10, 1616. https://doi.org/10.3390/ microorganisms10081616 Academic Editor: Yangguo Zhao Received: 5 July 2022 Accepted: 7 August 2022 Published: 10 August 2022 Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affil- iations. Copyright: © 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). microorganisms Article Potential Use of Deep-Sea Sediment Bacteria for Oil Spill Biodegradation: A Laboratory Simulation Tri Prartono 1, *, Angga Dwinovantyo 2, * , Syafrizal Syafrizal 3 and Agung Dhamar Syakti 4 1 Department of Marine Science and Technology, Faculty of Fisheries and Marine Sciences, IPB University, Jl. Agatis IPB Dramaga Campus, Bogor 16680, Indonesia 2 Research Center for Oceanography, The National Research and Innovation Agency (BRIN) of the Republic of Indonesia, Jl. Pasir Putih Raya No. 1, Jakarta 14430, Indonesia 3 Laboratory of Chemical Properties of Oil and Product Test, Research and Development Centre for Oil and Gas Technology (LEMIGAS), Ministry of Energy and Mineral Resources of the Republic of Indonesia, Jl. Ciledug Raya Kavling 109, Jakarta 12230, Indonesia 4 Marine Sciences Department, Marine Science and Fisheries Faculty, Raja Ali Haji Maritime University, Jl. Politeknik Senggarang, Tanjungpinang 29100, Indonesia * Correspondence: tripr@apps.ipb.ac.id (T.P.); angga.dwinovantyo@brin.go.id (A.D.) Abstract: Deep-sea sedimentary hydrocarbonoclastic bacteria are still not widely used in the biore- mediation field, especially for crude oil spill biodegradation. This study utilized a mixed culture of Raoultella sp., Enterobacter sp., and Pseudomonas sp. isolated from deep-sea sediment to determine the abilities of bacteria to degrade petroleum hydrocarbons while incorporating environmental variations in a microcosm study. The oil biodegradation extent was determined by measuring the remaining oil and grease in the sample vials. The highest percentage of biodegradation was 88.6%, with a constant degradation rate of 0.399 day –1 . GC-MS analysis showed that the most degradable compound in the oil samples was paraffin. This study also observed that microbial degradation was optimized within three days of exposure and that degradation ability decreased at 35 ◦ C. The salinity variation effects were insignificant. Based on all analyses, deep-sea sediment bacteria have great potential in oil spill biodegradation in a microcosm scale. Keywords: bioremediation; deep-sea sedimentary bacteria; GC-MS; microcosm; oil degradation 1. Introduction Oil spills are a severe cause of marine environmental pollution that result from in- tentional or accidental activities such as tanker accidents during marine oil transporta- tion, offshore oil exploration and exploitation, and oil and fuel run-off from the land [1]. Once spilled into the marine environment, petroleum hydrocarbons and their products are subject to various natural processes such as evaporation, emulsification, dispersion, photo-oxidation, biodegradation, and sedimentation [2]. In many cases, oil accumulation in an environment occurs faster than its recovery from a spill. Consequently, applying appropriate technology is necessary to remediate oil spill pollution [3]. Although much of an oil spill can easily be dispersed in the water column, a portion may also settle in deep-sea sediments [4]. This happens through adsorption to suspended solids that subsequently sink into the underlying sediments in many cases. Sedimentation of spilled oil also occurs when oil reacts with oil dispersants to produce denser oil. The dispersed oil can then be deposited into bottom sediments via oil-plume settling [5]. Most previous work on oil spill biodegradation has been conducted using hydrocarbon- degrading bacteria from the water column and coastal sediments [6–9]. Some studies also suggest that deep-sea sediment bacteria have been recognized as capable of hydrocarbon degradation [10]. In deep-sea sediment, bacterial communities respond to hydrocarbon pollution through aerobic processes in surface sediments and anaerobic processes in sub- surface sediments. Microorganisms 2022, 10, 1616. https://doi.org/10.3390/microorganisms10081616 https://www.mdpi.com/journal/microorganisms