Amycolicicoccus subflavus gen. nov., sp. nov., an actinomycete isolated from a saline soil contaminated by crude oil

Abstract

Two novel actinomycetes, designated DQS3-9A1T and DQS3-9A2, were isolated from a saline soil contaminated with crude oil in the Shengli Oilfield in China. On the basis of 16S rRNA gene sequence analysis, the two strains were most closely related to Mycobacterium species (92.7–94.9 % similarities), and formed a distinct lineage in the suborder Corynebacterineae. In addition, the major sugars in the cell wall, arabinose and galactose, supported the affiliation of strain DQS3-9A1T with members of the family Mycobacteriaceae. However, strain DQS3-9A1T did not contain mycolic acids and MK-8 (85.5 %) was the major menaquinone for both isolates. The major cellular fatty acids for strain DQS3-9A1T were C16 : 0 (20.5 %), 10-methyl C17 : 0 (19.3 %), 10-methyl C18 : 0 (16.1 %), summed feature 3 (11.4 %), C15 : 0 (11.3 %), C17 : 0 (5.0 %) and C17 : 1 ω8c (5.0 %). The polar lipids of strain DQS3-9A1T consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphatidylinositol and an unknown glucosamine-containing phospholipid. These chemotaxonomic data indicated that strain DQS3-9A1T differs from the present members of the suborder Corynebacterineae. Therefore, the creation of Amycolicicoccus subflavus gen. nov., sp. nov. is proposed, with DQS3-9A1T (=DSM 45089T=CGMCC 4.3532T) as the type strain.

The Genome of the Moderate Halophile Amycolicicoccus subflavus DQS3-9A1T Reveals Four Alkane Hydroxylation Systems and Provides Some Clues on the Genetic Basis for Its Adaptation to a Petroleum Environment

“…The bacterium has a lower abundance of genes in COG categories of cell duplication (L), intracellular trafficking, secretion, and vesicular transport (U), cell wall/membrane/envelope biogenesis (M), cell motility-related genes (N), as well as genes for carbohydrate transport and metabolism (G), compared with those in bacterial genomes released. The loss of redundant genes in carbohydrate metabolism did not influence the bacterium’s life functions, which was confirmed by the fact that the strain could utilize various carbohydrates, including D-fructose and D-glucose, as the sole carbon source [15]. This characteristic gene composition is very similar with that of Polymorphum gilvum SL003B-26A1 T [37], which was also isolated from a crude oil-related environment [38].…”

“…The strain A. subflavus DQS3-9A1 T was isolated from oil “mud,” which was sedimented from oil produced water at Daqing Oilfield, China [15]. The concentration of total dissolved salts in the oil produced water was around 8,000 mg/liter, and the temperatures of the reservoir working strata and the produced water were both 45°C.…”

“…To test growth with different NaCl concentrations, cells were grown in modified artificial seawater (ASW) medium [15] (5 g peptone, 1 g yeast extract, 4 g Na 2 SO 4 , 0.68 g KCl, 0.1 g KBr, 0.025 g H 3 BO 3 , 5.4 g MgCl 2 ·H 2 O, 1.5 g CaCl 2 ·2H 2 O, 0.024 g SrCl 2 ·6H 2 O, 0.2 g NaHCO 3 , 0.04 g Na 2 HPO 4 , 0.5 g NH 4 Cl, and 0.002 g NaF per liter of deionized water, pH 8.0), with NaCl added at the indicated concentration when necessary. The cell growth was determined by detecting OD 600 with time.…”

“…Recently, we isolated a moderate halophile Amycolicicoccus subflavus DQS3-9A1 T with the ability to degrade crude oil and grow in 1–12% (wt/vol) NaCl [15]. The genome sequence suggested that the strain harbored alkB homologous genes and a complete n -alkane metabolism pathway [16].…”

Recent studies in microbial degradation of petroleum hydrocarbons in hypersaline environments

“…The organism degraded crude oil and diesel as the source of carbon in the presence of 0–12% NaCl. Wang et al (2010) have isolated a moderate halophilic actinomycete, Amycolicicoccus subflavus DQS3-9A1 T from oily sludge at Daqing Oilfield, China with the ability to degrade crude oil in the presence of 1–12% NaCl. Later, Nie et al (2013) studied the genetic capability of the DQS3-9A1 T to metabolize a range of short-chain and long-chain n -alkanes such as propane and C 10 –C 36 alkanes, respectively, as the sole carbon sources in the presence of 1–12% NaCl.…”