THE DIVERSITY OF CULTIVABLE HYDROCARBON-DEGRADING BACTERIA ISOLATED FROM CRUDE OIL CONTAMINATED SOIL AND SLUDGE FROM ARZEW REFINERY IN ALGERIA

AUTHORS

ABSTRACT

The use of autochtonious bacterial strains is a valuable bioremediation strategy for cleaning the environment from hydrocarbon pollutants. The isolation, selection and identification of hydrocarbon-degrading bacteria is therefore crucial for obtaining the most promising strains for decontaminate a specific site. In this study, two different media, a minimal medium supplemented with petroleum and with oil refinery sludge as sole carbon source, were used for the isolation of native hydrocarbon-degrading bacterial strains from crude oil contaminated soils and oil refinery sludges which allowed isolation of fifty-eight strains.The evalution of diversity of twenty-two bacterials isolates reveled a dominance of the phylum Proteobacteria (20/22 strains), with a unique class of Alphaproteobacteria, the two remaining strains belong to the phylum Actinobacteria. Partial 16S rRNA gene sequencing performed on isolates showed high level of identity with known sequences. Strains were affiliated to Sinorhizobium, Promicromonospora, Novosphingobium, Georgenia, Ancylobacter, Roseomonas, Hansschlegelia and Tistrella genera. Research for the genes that encoding for degradation enzymes in isolated genera genome data deposited in Genbank reveled the presence of degradation gene in three species Sinorhizobium meliloti, Novosphingobium panipatenseand Tistrella mobilis.

KEYWORDS

INTRODUCTION

Petroleum hydrocarbons are the most common environmental pollutants, their release into the environnement, whether accidentally or due to human activities poses a great hazard to terrestrial and marine ecosystems (Holliger et al., 1997). The oil industry including, transport, storage, processing or use generates a significant quantity of sludge during the petroleum-refining process and as the installations are cleaned (Cerqueira et al., 2011). The sludges that result from this treatment process have a high content of petroleum derived hydrocarbons, mainly alkanes and paraffins of 1–40 carbon atoms, along with cycloalkanes and aromatic compounds (Overcash and Pal, 1979). The soil contamination by petroleum hydrocarbons which are known to belong to the family of carcinogens and neurotoxic organic pollutants (Abioye, 2011) causes a significant decline in its quality and such soils become unusable (Gojgic-Cvijovic et al., 2012). Algeria, whose national economy depends on petroleum exploitation, is not an exception to this pollution problem. The Arzew refinery, considered as one of the biggest and most profitable in the North Africa, the third of the country, possesses a high crude oil processing capacity, the various by-products stemming from the refining allow to satisfy fuel, lubricants, asphalt needs of the local population and also to export the surplus products (Naphta and Fuel). However, it is also accompanied by the annual discharge of an important quantity of sludge during the storage tank cleaning operations, which engenders hydrocarbon soil pollution.  This is why, the need to clean up crude oil contaminated site is necessary. Bioremediation is an economically and environmentally-friendly procedure based on the metabolic capacities of microorganisms to degrade contaminants biochemically (Huang et al., 2013). Bacteria in particular are considered to be the dominant agents of hydrocarbon degradation in the environment (Röling et al., 2002). Biodegradation using autochthonous bacterial strains is a valuable bioremediation strategy, these indigenous microbes are more likely to survive and proliferate when reintroduced into the site (Silva et al., 2009; Madueño et al., 2011; Fukuhara et al., 2013; Shankar et al., 2014). The aim of the present work is to isolate autochnonous bacterial strains from polluted soil and oil sludge samples in Arzew refinery. The distribution of genes coding for twenty three enzymes degrading hydrocarbon will be also analyzed from hydrocarbon degrading genera genome data deposited in GenBank and compared to the isolated genera in this study.

MATERIALS AND METHODS

Site description and sampling

 Oil polluted soil and oil sludge samples were collected from the Arzew refinery (35°49’21.29″N 0°18’37.58″O) in Northern Algeria (Sonatrach, Algerian Petroleum Company). Two soil samples were taken from the surrounding of the storage tank of crude oil at different period (soil A and soil B on 12.02.2015 and 26.02.2015 respectively). Each sample was a mixture of five sub-samples. A scoop was used to remove organic particles from the soil surface. Soil was collected at 0 to 20cm of depth randomly, air dried and sieved (2mm) and stored in a dry place at room temperature (~28°C). Two oil sludge samples were taken from the quagmire of the Arzew refinery, sampling were performed at two different dates (sludge C and sludge D on 12.02.2015 and 26.02.2015 respectively) and from 0 to 20cm depth. The physicochemical parameters of these soil and sludge samples were analyzed including water content (WC), total nitrogen (N_tot) was determined by Kjeldahl digestion, while total phosphorus (P_tot) using phosphor molybdic acid, total organic carbon (OC_tot) was determined according to Walkley-Black and total petroleum hydrocarbons (TPH) were determined by extracting the samples in methylene chloride, then analyzing the extracts by capillary gas chromatography with flame ionization detection. Oil used in this experiment was provided by the staff of the Arzew refinery and stored in the dark at ambient temperature throughout the study. Before use, oil was sterilized using 0.2μm membrane filter. 

Count and isolation of hydrocarbon-degrading bacteria

Hydrocarbon-degrading bacteria were isolated from oil sludge and oil contaminated soil samples by using the Bushnell Hass (BH) Mineral Salts (BHMS) medium (Bushnell and Hass, 1941). This medium contains all nutrients except the carbon source. The medium composition is as follows: MgSO₄.7H₂O (0.2 g/L), K2HPO4 (1.0 g/L), KH₂PO₄ (1.0 g/L), FeCl₃ (0.05 g/L), NH₄NO₃ (1.0 g/L) and CaCl₂ (0.02g/L) at pH 7.2, agar (20 g/L) was added for BH agar. The source of carbon and energy was provided either by the addition of sludge in BHMS medium before autoclaving or by adding sterilized oil in the BHMS medium after autoclaving.The hydrocarbon degrading-bacteria cultured from the contaminated soil (A and B) and oil sludge (C and D) samples were quantified by mixing 1g of sample with 9mL of sterile physiological serum (9‰ NaCl) for 2min at high speed. From this soil suspension, successive 1/10 dilutions were made (10ˉ³, 10ˉ⁴, 10ˉ⁵). An aliquot (0.1mL) of each diluted soil suspension was spread on BHMS agar plate with the addition of sludge as carbon source and on BHMS agar plate with 100µl of oil. The plates were incubated at 29˚C for 1 week. Bacterial hydrocarbon-degrading likely grown over incubation period. Colonies were then counted and the number was expressed as UFC / g of sample, bacterial counts were carried out in triplicate. Colonies presenting different morphological appearance were then sub-cultured, purified and conserved for molecular identification.Three mediums were used for strains subculture: Nutrient agar, Tryptic Soy Agar (TSA) medium and diluted 1/10 TSA medium (Biomeriu, France). The isolated strains were then conserved in their appropriated growth medium supplemented with 50% v/v glycerol solution at -80°C. For day-to-day experimentation strains were maintained on their growth medium slants at 4°C in refrigerator and sub-cultured at an interval of 30 days.

DNA Extraction

DNA from bacterial cells was extracted using NucleoSpin® 96 tissue-vacuum processing (Genomic DNA from tissue and cells, MACHEREY-NAGEL, Hoerdt, France), the strains were cultured for 72h at 29°C in 150µl of Nutrient Broth (NB) or TSA medium depending on their growth requirements, then 50 ml of bacteria cultures were transferred in 150ml of medium (Nutrient Broth or TSA) and were incubated until the appearance of a bacterial disorder, the cultures were then centrifuged at 4000rpm/min ; 4 °C for 30min, the obtained bacterial pellets were frozen at -80°C. Lysis was achieved with the NucleoSpin® 96 tissue method by incubation of the bacterial pellets in a solution containing Sodium Dodecyl Sulfate (SDS) and proteinase K. Appropriate conditions for binding of DNA to the silica membrane in the NucleoSpin® 96 tissue columns were created by addition of large amounts of chaotropic salt and ethanol to the lysate. The binding process was reversible and specific to nucleic acids. Contaminations were removed by washing with two different buffers. Pure genomic DNA was finally eluted under low ionic strength conditions in a slightly alkaline elution buffer and wasstored at −20 °C until 16S ribosomal RNA (rRNA) gene amplification.

PCR amplification of bacterial 16S rRNA genes

Bacterial 16S rRNA genes were amplified from all DNA samples using the bacterial specific primers pA (5’AGA GTT TGA TCC TGG CTC AG3’) and pH (5’AAG GAG GTG ATC CAG CCG CA3’) (Edwards and al. 1989). Amplification reaction was performed using Platinum® PCR SuperMix 96 (Invitrogen, France), each plate well contains anti-Taq DNA polymerase antibody, Mg++, deoxyribonucleotide triphosphates (dNTP), and recombinant Taq DNA Polymerase and each 22.5µl volume of Platinum® PCR SuperMix well was supplied at 1.1X concentration to allow approximately 10% of the final reaction volume to be used for the addition of 1µl of each primer and 2µl of DNA solution (10 to 50ng). The PCR amplification program was conducted as follows: Incubate at 94°C for 5min to activate the enzyme, and then perform 30 cycles of PCR. Denature 94°C for 15s, Anneal 55°C for 30s, Extend 72°C for 1min 30s then hold at 10°C. Amplified DNA was verified in 1% agarose gel electrophoresis.

Sequencing and phylogenetic analysis

 PCR products were sequenced by GATC Biotech AG (Constance, Allemagne); 20 μl of PCR products were sent to sequence. The sequences were corrected by the SeqMan Pro softwwere (http://www.dnastar.com) before alignment and analysis of the 16S rRNA gene sequences using CLUSTAL X software (version 2.0) (http://www.clustal.org). Taxonomic affiliation was done by analyzing similarities using Blast on NCBI (Altschul et al., 1990). A phylogenetic dendrogram was constructed by the Neighbor Joining Method and tree topology as evaluated by performing boot-strap using Mega 6.06.

Distribution of genes encoding for hydrocarbon degrading enzymes

Twenty-seven proteins sequences listed in Table 4 were selected as reference sequence of hydrocarbon dergradation and investigated for their different encoding genes. The conserved proteomic domains were checked in total sequenced gonome database from GenBank for nine genera (Sinorhizobium, Promicromonospora, Novosphingobium, Georgenia, Starkeya, Roseomonas, Ancylobacter and Hansschlegelia). These specific genes were highlited for genera level.

RESULTS AND DISCUSSION

Soils and sludges characteristics, counts of culturable hydrocarbon-degrading bacteria

The physico-chemical analysis of crude oil polluted soil and oil refinery sludge samples (Table 1) revealed the following C: N: P ratio: Polluted soil A (1 :1.2 : 2.5), Polluted soil B (1 : 1.25 : 3.35), Oil refinery sludge C (3.17 : 1 : 1.23), Oil refinery D (1.3 : 1 : 2.6), while for bioremediation operations, US EPA recommended a ratio of 100:10:1 in soil for appropriate nutrients to stimulate microorganism growth (U.S. EPA, 2002). This study reported that biostimulation (i.e., addition of nutrients N and P) strategies are essential to enhance bioremediation of the crude oil contaminated soil and oil refinery sludge collected from Arzew rafinery. Enumeration of culturable bacteria in soil and sludge samples (Table 2) demonstrated that significant hydrocarbon degrading bacteria populations were present in all samples. A number from 0.74×10⁵ to 1.8×10⁵ CFU/g are counted in the sludge medium and from 0.82×10⁵ to 2.02×10⁵ CFU/g in the petroleum medium. The same concentration was found in the soil contaminated with crude petroleum oil in Jordan (Saadoun, 2002).

Table 1 Physicochemical features of soil and sludge samples

WC water content, N_tottotal nitrogen, P_tot total phosphorus, OC_tot total organic carbon, TPH total petroleum hydrocarbon

Table 2 Counts of hydrocarbons-degrading bacteria on oil refinery sludge and petroleum medium

Identification of hydrocarbon-degrading bacterial isolates

Fifty-eight bacterial strains were isolated from polluted soil and oil refinery sludge on petroleum and oil refinery sludge medium, cultures were maintained at 29°C for 1 week. Based on phenotypic characteristics (colony morphology, pigmentation, growth properties), 22 strains were selected for 16S rRNA gene sequencing. The comparison of obtained sequences by BLAST in Genbank showed that the majority of these strains (20/22) belonged to the phylum Proteobacteria (Table 3), with a unique class of Alphaproteobacteria; the two remaining strains belonged to the phylum Actinobacteria. Many studies on the bacterial diversity in a hydrocarbon-contaminated soil, whether by culture-based methods or molecular methods, proved the dominance of Proteobacteria in hydrocarbonscontaminated soils (Saul et al., 2005; Uhlik et al., 2012; Zhang et al., 2012; Mao et al., 2012). The genus Rhizobium (9 strains) was dominating among Alphaproteobacteria; with a singlespecies Sinorhizobium meliloti (showed 100% 16S rRNA of gene sequence similarity). Other representatives of this class were related to the genera Novosphingobium (4 strains) with two species Novosphingobium naphthalenivorans (99% of similarity) and Novosphingobium panipatense (99% of similarity), Tistrella (4 strains), Roseomonas (1), Hansschlegelia (1) and Ancylobacter (1). The Actinobacteria comprised two genera Promicromonospora (1) and Georgenia (1). Zhang et al., (2012) revealed a bacterial diversity close to the identified strains in this study, dominated by the phylum Proteobacteria with a majority of strains belonging to the genus Rhizobium in addition to both genera Roseomonas and Tistrella. The construction of a phylogenetic tree by the neighbor-joining method permitted grouping the isolates into 8 clusters (Figure 1).

The first cluster was close to Sinorhizobium meliloti, including SA1, SA12, SA13, SA14, SA15 and SA17 strains isolated from oil polluted soil A and SB4, SB5 and SB6 strains isolated from oil polluted soil B. Rhizobia survival under hydrocarbon contamination and the interaction of these bacteria with pollutant was reported by several authors (Andreoni et al.,2004 ; Keum et al., 2006; Poonthrigpun et al., 2006 ; Wang et al., 2007),  Sinorhizobium meliloti species had been isolated from hydrocarbon contaminated soil (Ahmadet al., 1997;Muratova, 2014 ; Abou-Shanab, 2016 ) and had shown their ability to degrade various forms of hydrocarbon such as aromatic compounds (Frassinetti et al., 1998) and PCB (Poly Chlororinated Biphenyl) (Wang et al., 2016). Interestingly, the ability for N-fixation of the genus Rhizobium and their presence in the rhizosphere of oil-contaminated soils could play a major role in phytoremediation (Jurelevicius et al., 2010; Xu et al., 2010)thanks to their legumessymbiotic interaction (Johnson et al., 2004; Suominen et al., 2000). The second cluster comprised one strain SB15 isolated from oil polluted soil B and it was close to Hansschlegelia zhihuaiae. The genus Hansschlegelia is a member of family Methylocystaceae (Ivanova et al., 2010) that belonged to the order Rhizobiales, within the class Alphaproteobacteria. This family was classified as type II methanotrophs, which was able to utilize methane and its derivatives as carbon sources through the serine pathway. Many of these methanotrophic bacteria performed important environmental functions as they were a link in the global carbon cycle, acted as nitrogen fixers, and have the ability to degrade a variety of organic contaminants (Gulledge et al., 2001). Hansschlegelia zhihuaiae was isolated from a polluted-soil sample (Wen et al., 2011), and known for its degradation ability of a variety of sulfonylurea herbicides (Hang et al., 2012), whereas there are no reports for their ability to survive in hydrocarbon polluted soils. This is the first time where Hansschlegelia zhihuaiae shows ability to survive in oil polluted soil. The third cluster included one strain SB7 isolated from oil polluted soil B and it was close to Starkeya koreensi (Blast in NCBI), this species was isolated from rice straw (Im et al., 2006), however another species Starkeya novella was isolated from agricultural soil and employed a mixotrophic growth strategy, Starkeya novella was a facultative sulfur oxidizing chemolithoautotroph, but is also capable of utilizing various carbon compounds, including methanol, for growth as well as atleast 39 reduced carbon sources including sugars, amino sugars, amino acids, and organic acids (Starkey, 1935; Chandra and Shethna, 1977; Kelly et al., 2000; Kappler et al., 2012). Since Starkeya novella used a wide range of carbon compounds for its metabolism, this could explain its presence in soils polluted by hydrocarbons. Phylogenetically, strain SB7 was related with Ancylobacter dichloromethanicus species, this strain was isolated from the polluted soil and was utilized dichloromethane, methanol, formate and formaldehyde along with a variety of polycarbon compounds (Firsova et al., 2009). The fourth cluster grouped four strains ORSA6, ORSA7, SA9 and ORSA5 isolated from oil contaminated soil A and oil refinery sludge A and were close to two species Novosphingobium naphthalenivorans and Novosphingobium panipatense, respectively. Several aromatic-degrading strains of Novosphingobium such as Novosphingobium aromaticivorans, Novosphingobium naphthalenivorans, Novosphingobium pentaromaticivorans, Novosphingobium panipatenseand Novosphingobium naphthaehad been reported (Kertesz and Kawasaki, 2010; Gupta, 2009; Suzuki and Hiraishi, 2007; Lyu, 2014; Chaudhary and Kim, 2016).

Table 3  Origin, isolation medium and genotypic characteristics of isolated strains

Figure 1 Phylogenetic tree based on 16SrRNA gene sequence (>900nt) analysis of new and reference strains. Neighbor-joinin method integrating Kimura-2distance was used. Data are bootstrap values issued from 1000 repetitions

The fifth cluster was close to Tistrella mobilis and included four strains, ORSB4, ORSB6, ORSB5 and ORSB2 isolated from oil refinery sludge B. The genus Tistrella was isolated from soil samples contaminated with polycyclic aromatic hydrocarbon (PAH)-containing waste from oil refinery field in Shanghai, China and can increase the speed of phenanthrene degradation (Zhao et al., 2008), the species Tistrella bauzanensis was isolated from soil containing high levels of heavy oil (Zhang et al., 2011)howeverthe species Tistrella mobilis was isolated only from wastewater, sea water and  surface sediment collected from deep sea contaminated by hydrocarbons and proved its efficiency in this pollutants degradation (Shi et al., 2002 ; Cuiand Shao, 2009). The sixth cluster comprised one strain SB11 isolated from oil polluted soil B and it was close to Roseomonas ludipueritiae. The genus Roseomonas of the familly Acetobacteraceae belonging to phylum Proteobacteria, was first described by Rihs et al. (1993) associated with bacteraemia and other humain infections. Recently, a new strain Roseomonas nepalensiswas isolated from oil-contaminated soil of Nepal, during a study of oil-utilizing bacteria (Chaudhary and Kim, 2017). The seventh cluster included one strain SA16 isolated from oil polluted soil A and it was close to Georgenia ferrireducens.Franzetti et al.(2011) isolated Georgenia ferrireducens as bacteria able to produce biological emulsifiers from a polycyclic aromatic hydrocarbons (PAHs) contaminated soil. The eighth and last cluster comprised one strain SA3 isolated from oil polluted soil A and it was close to Promicromonospora aerolata.it was reported that Promicromonospora aerolatas pecies was isolated from air (Busse et al., 2003).  However, several species belonging to the genus Promicromonospora were isolated from soil; recently, two genera isolated from soil were added: Promicromonospora soli (Zhang et al., 2017) and Promicromonospora kermanensis (Mohammadipanah et al., 2017), however, there was no reports in their ability to survive in hydrocarbon polluted soils.

Distribution of genes coding for dgradation enzymes in isolated genera

Haut du formulaire

Different genes encoding for hydrocarbons degradation were investigated through Genbank (tBLASTn) databases. Many studies dealing with total genome sequencing revealed the presence of these genes of interest (Table 4), but without proving their real ability to degrade hydrocarbons in vitro (Sinorhizobium americanum, S. saheli, Promicromonospora kroppenstedtii, Starkeya novella, Ancylobacter sp., Methylosinus trichosporium, , Methylopila sp., Ancylobacter rudongensis, Roseomonas stagnii, R. gilardi, and R. aerilata); Only seven species did degrade hydrocarbons and possessed these genes of interest : Sinorhizobium meliloti which was reported as PAH-degrading (Ahmad et al., 1997) and harbored several putative genes of degradation (Galibert et al., 2001); Novosphingobium aromaticivorans (Fredrickson et al., 1991 , 1995; Romine et al., 1999) ; N. naphthalenivorans  (Suzuki and Hiraishi, 2007); N. panipatense (Gupta et al., 2009) ; Methylosinus sp. (Bowman et al., 1993); Georgenia sp. (Al-Awadhi et al.,2007); Tistrella mobilis (Cui et al., 2009). Finally ; Hansschlegelia zhihuaiaedid degrade hydrocarbon in this study but no work did reveal the gens of degradation.

CONCLUSION

In conclusion a high diversity of hydrocarbon-degrading bacteria were found in crude oil polluted soil and oil refinery sludge from Arzew refinery, cultured-method allowed to obtain different species known for their degradative capability and to demonstrate species never known for hydrocarbon degradation. A limited number of genes coding for degradation enzymes were revealed in these genera Promicromonospora, Georgenia, Starkeya, Ancylobacter and Methylocystaceae family. However, as a perspective it is interesting to look for these genes of interest in the isolated species belonging in these genera or complete sequencing of the genome.

Table 4 Distribution of genes coding for degradation enzymes in isolated genera genome data deposited in Genbank

REFERENCES

Abioye, O. P. 2011. Biological remediation of hydrocarbon and heavy metals contaminated soil. In Soil Contamination. InTech. https://doi.org/10.5772/24938

Abou-Shanab, R. A. I., Eraky, M., Haddad, A. M., Abdel-Gaffar, A. B., Salem, A. M. 2016. Characterization of Crude Oil Degrading Bacteria Isolated from Contaminated Soils Surrounding Gas Stations. Bulletin of environmental contamination and toxicology, 97(5), 684-688. https://dx.doi.org/10.1007/s00128-016-1924-2

Ahmad, D., Mehmannavaz, R., Damaj, M. 1997. Isolation and characterization of symbiotic N2-fixing Rhizobium meliloti from soils contaminated with aromatic and chloroaromatic hydrocarbons: PAHs and PCBs. International biodeterioration & biodegradation, 39(1), 33-43. https://dx.doi.org/10.1016/S0964-8305(96)00065-0

Al-Awadhi, H., Sulaiman, R. H., Mahmoud, H. M., Radwan, S. S. 2007. Alkaliphilic and halophilic hydrocarbon-utilizing bacteria from Kuwaiti coasts of the Arabian Gulf. Applied microbiology and biotechnology, 77(1), 183-186. https://dx.doi.org/10.1007/s00253-007-1127-1 

Altschul, S. F., Gish, W., Miller, W., Myers, E. W., Lipman, D. J. 1990. Basic local alignment search tool. Journal of molecular biology, 215(3), 403-410. https://dx.doi.org/10.1016/S0022-2836(05)80360-2

Andreoni, V., Cavalca, L., Rao, M. A., Nocerino, G., Bernasconi, S., Dell’Amico, E., … Gianfreda, L. 2004. Bacterial communities and enzyme activities of PAHs polluted soils. Chemosphere, 57(5), 401-412. https://dx.doi.org/10.1016/j.chemosphere.2004.06.013

Bowman, J. P., Sly, L. I., Nichols, P. D., Hayward, A. C. 1993. Revised taxonomy of the methanotrophs: description of Methylobacter gen. nov., emendation of Methylococcus, validation of Methylosinus and Methylocystis species, and a proposal that the family Methylococcaceae includes only the group I methanotrophs. International Journal of Systematic and Evolutionary Microbiology, 43(4), 735-753. https://dx.doi.org/10.1099/00207713-43-4-735

Bushnell, L. D., Haas, H. F. 1941. The utilization of certain hydrocarbons by microorganisms. Journal of Bacteriology, 41(5), 653.

Busse, H. J., Zlamala, C., Buczolits, S., Lubitz, W., Kämpfer, P., Takeuchi, M. 2003. Promicromonospora vindobonensis sp. nov. and Promicromonospora aerolata sp. nov., isolated from the air in the medieval ‘Virgilkapelle’in Vienna. International journal of systematic and evolutionary microbiology, 53(5), 1503-1507. https://dx.doi.org/10.1099/ijs.0.02522-0

Cerqueira, V. S., Hollenbach, E. B., Maboni, F., Vainstein, M. H., Camargo, F. A., Maria do Carmo, R. P., Bento, F. M. 2011. Biodegradation potential of oily sludge by pure and mixed bacterial cultures. Bioresource technology, 102(23), 11003-11010. https://dx.doi.org/10.1016/j.biortech.2011.09.074

Chandra T. S., Shethna Y. I. 1977. Oxalate, formate, formamide, and methanol metabolism in Thiobacillus novellus. J. Bacteriol. 131, 389–398

Chaudhary, D. K., Kim, J. 2016. Novosphingobium naphthae sp. nov., from oil-contaminated soil. International journal of systematic and evolutionary microbiology, 66(8), 3170-3176. https://dx.doi.org/10.1099/ijsem.0.001164

Chaudhary, D. K., Kim, J. 2017. Roseomonas nepalensis sp. nov., isolated from oil-contaminated soil. International journal of systematic and evolutionary microbiology, 67(4), 981-987. https://dx.doi.org/10.1099/ijsem.0.001727

Cui, Z., Shao, Z. 2009. Predominant strains of polycyclic aromatic hydrocarbon-degrading consortia from deep sea of the Middle Atlantic Ridge. Wei sheng wu xue bao= Acta microbiologica Sinica, 49(7), 902-909.

Firsova, J., Doronina, N., Lang, E., Spröer, C., Vuilleumier, S., Trotsenko, Y. 2009. Ancylobacter dichloromethanicus sp. nov. a new aerobic facultatively methylotrophic bacterium utilizing dichloromethane. Systematic and applied microbiology, 32(4), 227-232. https://dx.doi.org/10.1016/j.syapm.2009.02.002

Franzetti, A., Gandolfi, I., Bertolini, V., Raimondi, C., Piscitello, M., Papacchini, M., Bestetti, G. 2011. Phylogenetic characterization of bioemulsifier-producing bacteria. International biodeterioration & biodegradation, 65(7), 1095-1099. https://dx.doi.org/10.1016/j.ibiod.2011.01.014

Frassinetti, S., Setti, L., Corti, A., Farrinelli, P., Montevecchi, P., Vallini, G. 1998. Biodegradation of dibenzothiophene by a nodulating isolate of Rhizobium meliloti. Canadian journal of microbiology, 44(3), 289-297. https://dx.doi.org/10.1139/w97-155

Fredrickson, J. K., Balkwill, D. L., Drake, G. R., Romine, M. F., Ringelberg, D. B., White, D. C. 1995. Aromatic-degrading Sphingomonas isolates from the deep subsurface. Applied and environmental microbiology, 61(5), 1917-1922.

Fredrickson, J. K., Brockman, F. J., Workman, D. J., Li, S. W., Stevens, T. O. 1991. Isolation and characterization of a subsurface bacterium capable of growth on toluene, naphthalene, and other aromatic compounds. Applied and environmental microbiology, 57(3), 796-803.

Fukuhara, Y., Horii, S., Matsuno, T., Matsumiya, Y., Mukai, M., Kubo, M. 2013. Distribution of hydrocarbon-degrading bacteria in the soil environment and their contribution to bioremediation. Applied biochemistry and biotechnology, 170(2), 329-339. https://dx.doi.org/10.1007/s12010-013-0170-x

Galibert, F., Finan, T. M., Long, S. R., Pühler, A., Abola, P., Ampe, F., … Bothe, G. 2001. The composite genome of the legume symbiont Sinorhizobium meliloti. Science, 293(5530), 668-672. https://dx.doi.org/10.1126/science.1060966

Gojgic-Cvijovic, G. D., Milic, J. S., Solevic, T. M., Beskoski, V. P., Ilic, M. V., Djokic, L. S., … Vrvic, M. M. 2012. Biodegradation of petroleum sludge and petroleum polluted soil by a bacterial consortium: a laboratory study. Biodegradation, 23(1), 1-14. https://dx.doi.org/10.1007/s10532-011-9481-1

Gulledge, J., Ahmad, A., Steudler, P. A., Pomerantz, W. J., Cavanaugh, C. M. 2001. Family-and genus-level 16S rRNA-targeted oligonucleotide probes for ecological studies of methanotrophic bacteria. Applied and environmental microbiology, 67(10), 4726-4733. http://dx.doi.org/10.1128/AEM.67.10.4726-4733.2001

Gupta, S. K., Lal, D., Lal, R. 2009. Novosphingobium panipatense sp. nov. and Novosphingobium mathurense sp. nov., from oil-contaminated soil. International journal of systematic and evolutionary microbiology, 59(1), 156-161. https://dx.doi.org/10.1099/ijs.0.65743-0

Hang, B. J., Hong, Q., Xie, X. T., Huang, X., Wang, C. H., He, J., Li, S. P. 2012. SulE, a sulfonylurea herbicide de-esterification esterase from Hansschlegelia zhihuaiae S113. Applied and environmental microbiology, 78(6), 1962-1968. https://dx.doi.org/10.1128/AEM.07440-11

Holliger, C., Gaspard, S., Glod, G., Heijman, C., Schumacher, W., Schwarzenbach, R. P., Vazquez, F. 1997. Contaminated environments in the subsurface and bioremediation: organic contaminants. FEMS Microbiology Reviews, 20(3‐4), 517-523. https://dx.doi.org/10.1111/j.1574-6976.1997.tb00334.x

Huang, Y., Zeng, Y., Yu, Z., Zhang, J., Feng, H., Lin, X. 2013. In silico and experimental methods revealed highly diverse bacteria with quorum sensing and aromatics biodegradation systems–a potential broad application on bioremediation. Bioresource technology, 148, 311-316. https://dx.doi.org/10.1016/j.biortech.2013.08.155

Im, W. T., Aslam, Z., Lee, M., Ten, L. N., Yang, D. C., Lee, S. T. 2006. Starkeya koreensis sp. nov., isolated from rice straw. International journal of systematic and evolutionary microbiology, 56(10), 2409-2414. https://dx.doi.org/10.1099/ijs.0.64093-0

Ivanova, E., Doronina, N., Trotsenko, Y. 2010. Hansschlegelia plantiphila gen. nov., sp. nov. List of New Names and New Combinations Previously Effectively, but not Validly, Published. Validation List, (133), 1009-1010.  https://dx.doi.org/10.1099/ijs.0.024562-0

Johnson, D. L., Maguire, K. L., Anderson, D. R., McGrath, S. P. 2004. Enhanced dissipation of chrysene in planted soil: the impact of a rhizobial inoculum. Soil biology and biochemistry, 36(1), 33-38. https://dx.doi.org/10.1016/j.soilbio.2003.07.004

Jurelevicius, D., Korenblum, E., Casella, R., Vital, R. L., Seldin, L. 2010. Polyphasic analysis of the bacterial community in the rhizosphere and roots of Cyperus rotundus L. grown in a petroleum-contaminated soil. J Microbiol Biotechnol, 20(5), 862-870. https://dx.doi.org/10.4014/jmb.0910.10012

Kappler, U., Davenport, K., Beatson, S., Lucas, S., Lapidus, A., Copeland, A., … Tice, H. 2012. Complete genome sequence of the facultatively chemolithoautotrophic and methylotrophic alpha proteobacterium Starkeya novella type strain (ATCC 8093 T). Standards in genomic sciences, 7(1), 44. https://dx.doi.org/10.4056/sigs.3006378

Kelly, D. P., McDonald, I. R., Wood, A. P. 2000. Proposal for the reclassification of Thiobacillus novellus as Starkeya novella gen. nov., comb. nov., in the alpha-subclass of the Proteobacteria. International journal of systematic and evolutionary microbiology, 50(5), 1797-1802. https://dx.doi.org/10.1099/00207713-50-5-1797

Kertesz, M. A., Kawasaki, A. 2010. Hydrocarbon-degrading sphingomonads: Sphingomonas, sphingobium, novosphingobium, and sphingopyxis. In Handbook of hydrocarbon and lipid microbiology (pp. 1693-1705). Springer Berlin Heidelberg. https://dx.doi.org/10.1007/978-3-540-77587-4_119

Keum, Y. S., Seo, J. S., Hu, Y., Li, Q. X. 2006. Degradation pathways of phenanthrene by Sinorhizobium sp. C4. Applied microbiology and biotechnology, 71(6), 935-941. https://dx.doi.org/10.1007/s00253-005-0219-z

Lyu, Y., Zheng, W., Zheng, T., Tian, Y. 2014. Biodegradation of polycyclic aromatic hydrocarbons by Novosphingobium pentaromativorans US6-1. PloS one, 9(7), e101438. https://dx.doi.org/10.1371/journal.pone.0101438

Madueño, L., Coppotelli, B. M., Alvarez, H. M., Morelli, I. S. 2011. Isolation and characterization of indigenous soil bacteria for bioaugmentation of PAH contaminated soil of semiarid Patagonia, Argentina. International biodeterioration & biodegradation, 65(2), 345-351. https://dx.doi.org/10.1016/j.ibiod.2010.12.008

Mao, J., Luo, Y., Teng, Y., Li, Z. 2012. Bioremediation of polycyclic aromatic hydrocarbon-contaminated soil by a bacterial consortium and associated microbial community changes. International Biodeterioration & Biodegradation, 70, 141-147. https://dx.doi.org/10.1016/j.ibiod.2012.03.002

Mohammadipanah, F., del Carmen Montero-Calasanz, M., Schumann, P., Spröer, C., Rohde, M., Klenk, H. P. 2017. Promicromonospora kermanensis sp. nov., an actinobacterium isolated from soil. International journal of systematic and evolutionary microbiology, 67(2), 262-267. https://dx.doi.org/10.1099/ijsem.0.001613

Muratova, A., Pozdnyakova, N., Makarov, O., Baboshin, M., Baskunov, B., Myasoedova, N., … Turkovskaya, O. 2014. Degradation of phenanthrene by the rhizobacterium Ensifer meliloti. Biodegradation, 25(6), 787-795. https://dx.doi.org/10.1007/s10532-014-9699-9

Overcash, M. R., Pal, D. 1979. Design of land treatment systems for industrial wastes-theory and practice. Ann Arbor Science Publishers Inc..

Poonthrigpun, S., Pattaragulwanit, K., Paengthai, S., Kriangkripipat, T., Juntongjin, K., Thaniyavarn, S., … Pinphanichakarn, P. 2006. Novel intermediates of acenaphthylene degradation by Rhizobium sp. strain CU-A1: evidence for naphthalene-1, 8-dicarboxylic acid metabolism. Applied and environmental microbiology, 72(9), 6034-6039. https://dx.doi.org/10.1128/AEM.00897-06

Rihs, J. D., Brenner, D. J., Weaver, R. E., Steigerwalt, A. G., Hollis, D. G., Yu, V. L. 1993. Roseomonas, a new genus associated with bacteremia and other human infections. Journal of clinical microbiology, 31(12), 3275-3283.

Röling, W. F., Milner, M. G., Jones, D. M., Lee, K., Daniel, F., Swannell, R. J., Head, I. M. 2002. Robust hydrocarbon degradation and dynamics of bacterial communities during nutrient-enhanced oil spill bioremediation. Applied and environmental microbiology, 68(11), 5537-5548. https://dx.doi.org/10.1128/AEM.68.11.5537-5548.2002

Romine, M. F., Fredrickson, J. K., Li, S. W. 1999. Induction of aromatic catabolic activity in Sphingomonas aromaticivorans strain F199. Journal of industrial microbiology & biotechnology, 23(4), 303-313. https://dx.doi.org/10.1038/sj.jim.2900750

Saadoun, I. 2002. Isolation and characterization of bacteria from crude petroleum oil contaminated soil and their potential to degrade diesel fuel. Journal of basic microbiology, 42(6), 420-428.

Saul, D. J., Aislabie, J. M., Brown, C. E., Harris, L., Foght, J. M. 2005. Hydrocarbon contamination changes the bacterial diversity of soil from around Scott Base, Antarctica. FEMS Microbiology Ecology, 53(1), 141-155. https://dx.doi.org/10.1016/j.femsec.2004.11.007

Shankar, S., Kansrajh, C., Dinesh, M. G., Satyan, R. S., Kiruthika, S., Tharanipriya, A. 2014. Application of indigenous microbial consortia in bioremediation of oil-contaminated soils. International Journal of Environmental Science and Technology, 11(2), 367-376. https://dx.doi.org/10.1007/s13762-013-0366-1

Shi, B. H., Arunpairojana, V., Palakawong, S., Yokota, A. 2002. Tistrella mobilis gen. nov., sp. nov., a novel polyhydroxyalkanoate-producing bacterium belonging to α-Proteobacteria. The Journal of general and applied microbiology, 48(6), 335-343. https://dx.doi.org/10.2323/jgam.48.335

Silva, Í. S., dos Santos, E. D. C., de Menezes, C. R., de Faria, A. F., Franciscon, E., Grossman, M., Durrant, L. R. 2009. Bioremediation of a polyaromatic hydrocarbon contaminated soil by native soil microbiota and bioaugmentation with isolated microbial consortia. Bioresource Technology, 100(20), 4669-4675. https://dx.doi.org/10.1016/j.biortech.2009.03.079 

Starkey, R. L. 1935. Products of the oxidation of thiosulfate by bacteria in mineral media. The Journal of general physiology, 18(3), 325-349. https://dx.doi.org/10.1085/jgp.18.3.325

Suominen, L., Jussila, M. M., Mäkeläinen, K., Romantschuk, M., Lindström, K. 2000. Evaluation of the Galega–Rhizobiumgalegae system for the bioremediation of oil-contaminated soil. Environmental pollution, 107(2), 239-244. https://dx.doi.org/10.1016/S0269-7491(99)00143-8

Suzuki, S., Hiraishi, A. 2007. Novosphingobium naphthalenivorans sp. nov., a naphthalene-degrading bacterium isolated from polychlorinated-dioxin-contaminated environments. The Journal of general and applied microbiology, 53(4), 221-228. https://dx.doi.org/10.2323/jgam.53.221

S. Environmental Protection Agency. (2002). Application, Performance, and Costs of Biotreatment Technologies for Contaminated Soils, EPA/600/R-03/037, Battelle Contract No.68-C-00e185.

Uhlik, O., Wald, J., Strejcek, M., Musilova, L., Ridl, J., Hroudova, M., … Macek, T. 2012. Identification of bacteria utilizing biphenyl, benzoate, and naphthalene in long-term contaminated soil. PloS one, 7(7), e40653. https://dx.doi.org/10.1371/journal.pone.0040653

Wang, J., Xu, H., Guo, S. 2007. Isolation and characteristics of a microbial consortium for effectively degrading phenanthrene. Petroleum Science, 4(3), 68-75. https://dx.doi.org/10.1007/s12182-007-0012-y

Wang, X., Teng, Y., Luo, Y., Dick, R. P. 2016. Biodegradation of 3, 3′, 4, 4′-tetrachlorobiphenyl by Sinorhizobium meliloti NM. Bioresource technology, 201, 261-268. https://dx.doi.org/10.1016/j.biortech.2015.11.056

Wen, Y., Huang, X., Zhou, Y., Hong, Q., Li, S. 2011. Hansschlegelia zhihuaiae sp. nov., isolated from a polluted farmland soil. International journal of systematic and evolutionary microbiology, 61(5), 1114-1117. https://dx.doi.org/10.1099/ijs.0.021543-0

Xu, L., Teng, Y., Li, Z. G., Norton, J. M., Luo, Y. M. 2010. Enhanced removal of polychlorinated biphenyls from alfalfa rhizosphere soil in a field study: the impact of a rhizobial inoculum. Science of the total environment, 408(5), 1007-1013. https://dx.doi.org/10.1016/j.scitotenv.2009.11.031

Zhang, D. C., Liu, H. C., Zhou, Y. G., Schinner, F., Margesin, R. 2011. Tistrella bauzanensis sp. nov., isolated from soil. International journal of systematic and evolutionary microbiology, 61(9), 2227-2230. https://dx.doi.org/10.1099/ijs.0.026930-0

Zhang, D. C., Mörtelmaier, C., Margesin, R. 2012. Characterization of the bacterial archaeal diversity in hydrocarbon-contaminated soil. Science of the Total Environment, 421, 184-196. https://dx.doi.org/10.1016/j.scitotenv.2012.01.043

Zhao, H. P., Wang, L., Ren, J. R., Li, Z., Li, M., Gao, H. W. 2008. Isolation and characterization of phenanthrene-degrading strains Sphingomonas sp. ZP1 and Tistrella sp. ZP5. Journal of hazardous materials, 152(3), 1293-1300. https://dx.doi.org/10.1016/j.jhazmat.2007.08.008

Zheng, W., Li, D., Zhao, J., Liu, C., Zhao, Y., Xiang, W., Wang, X. 2017. Promicromonospora soli sp. nov., a novel actinomycete isolated from soil. International journal of systematic and evolutionary microbiology, 67(10), 3829-3833. https://dx.doi.org/10.1099/ijsem.0.002207