Aislamiento Degradadoras_TRATABILIDAD_Chaerun y Col (2004)

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    Bioremediation of coastal areas 5 years after the Nakhodka oil

    spill in the Sea of Japan: isolation and characterization of

    hydrocarbon-degrading bacteria

    S. Khodijah Chaeruna,*, Kazue Tazakib, Ryuji Asadab, Kazuhiro Kogurec

    aGraduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, JapanbDepartment of Earth Sciences, Faculty of Science, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan

    cOcean Research Institute, University of Tokyo, Minamidai, Nakano, Tokyo 164-8639, Japan

    Received 3 December 2003; accepted 24 February 2004

    Available online 23 April 2004

    Abstract

    Five years after the 1997 Nakhodkaoil spill in the Sea of Japan, seven bacterial strains capable of utilizing the heavy oil spilled from the

    NakhodkaRussian oil tanker were isolated from three coastal areas (namely Katano Seashore of Fukui Prefecture, Osawa and Atake seashores

    of Ishikawa Prefecture) and the NakhodkaRussian oil tanker after a 5-year bioremediation process. All bacterial strains isolated could utilize

    long-chain-length alkanes efficiently, but not aromatic, and all of them were able to grow well on heavy oil. Using 16S rDNA sequencing,

    most of the strains were affiliated toPseudomonas aeruginosa.Comparing between the year 1997 (at the beginning of bioremediation process)

    and the year 2001 (after 5 years of bioremediation), there was no significant change in morphology and size of hydrocarbon-degrading bacteria

    during the 5-year bioremediation. Scanning and transmission electron microscopic observations revealed that a large number of hydrocarbon-

    degrading bacteria still existed in the sites consisting of a variety of morphological forms of bacteria, such as coccus ( Streptococcusand

    Staphylococcus) and bacillus (Streptobacillus). On the application of bioremediation processes on the laboratory-scale, laboratory microcosm

    experiments (containing seawater, beach sand, and heavy oil) under aerobic condition by two different treatments (i.e., placed the insidebuilding and the outside building) were established for bioremediation of heavy oil to investigate the significance of the role of hydrocarbon-

    degrading bacteria on them. There was no significant bacterial activity differentiation in the two treatments, and removal of heavy oil by

    hydrocarbon-degrading bacteria in the outside building was slightly greater than that in the inside building. The values of pH, Eh, EC, and

    dissolved oxygen (DO) in two treatments indicated that the bioremediation process took place under aerobic conditions (DO: 16 mg/l; Eh:

    12300 mV) and neutral-alkaline conditions (pH 6.48) with NaCl concentrations of 315% (ECs of 45200 mS/cm).

    D 2004 Elsevier Ltd. All rights reserved.

    Keywords: Nakhodka Russian oil tanker; Bioremediation; Heavy oil; Hydrocarbon-degrading bacteria; Pseudomonas aeruginosa

    1. Introduction

    During the past few decades the incidence and threat of

    oil pollution has resulted in extensive research. The anthro-

    pogenic origins (particularly via leak of coastal oil refiner-

    ies) of petroleum have led to interest in their distribution and

    fate in the environment, mainly the marine environment.

    Tanker accidents are major causes of oil pollution of marine

    environments. One of the recent examples of such accidents

    is that of theNakhodkaRussian oil tanker which discharged

    approximately 6240 kl of C-heavy oil into the Japan Sea on

    January 2, 1997. The heavy oil spill led to a serious impact

    to the surrounding environment, particularly the heavy oil

    pollution of the shoreline of Mikuni, Fukui Prefecture to

    Noto Peninsula, Ishikawa Prefecture(Tazaki, 2003).

    Petroleum hydrocarbon can be degraded by microorgan-

    isms such as bacteria, fungi, yeast, and microalgae (e.g.,

    Atlas, 1981; Leahy and Colwell, 1990). Numerous studies

    have been conducted on microbial consortia and enrichment

    (e.g., Atlas, 1981), and most bacterial petroleum hydrocar-

    bon degraders have been isolated from heavily contaminat-

    ed coastal areas under this study (Itagaki and Ishida, 1999;

    Kasai et al., 2001;Tazaki, 2003). However, no data exist on

    0160-4120/$ - see front matterD 2004 Elsevier Ltd. All rights reserved.

    doi:10.1016/j.envint.2004.02.007

    * Corresponding author. Tel.: +81-76-264-5732; fax: +81-76-264-

    5746.

    E-mail addresses: [email protected],

    [email protected] (S.K. Chaerun).

    www.elsevier.com/locate/envint

    Environment International 30 (2004) 911 922

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    the findings of the superior hydrocarbon indigenous

    degraders of bacterial isolates in degrading the Nakhodka

    oil spill. Also, there was no preservation of those isolates as

    pure bacterial cultures that can be used for more detailed

    investigations on the degradation processes of the Nakhodka

    oil spill. For these reasons, the isolation and characterization

    of pure bacterial strains indigenous to the Nakhodkaoil spillwere carried out to obtain the superior pure bacterial strains

    in degrading the Nakhodka oil spill, being further used for

    future studies. Since some attempts to demonstrate the

    potential for bioaugmentation, a technique used in bioreme-

    diation by adding microorganisms to sites contaminated

    with oil, in soils have resulted in successes and failures

    (Vogel, 1996), biostimulation of the indigenous bacteria that

    break down oil pollutants is considered a priority. The

    isolation of bacteria was undertaken mainly after 5 years

    of bioremediation with a reason: the strains isolated may

    have adapted to the toxicity of the Nakhodkaoil spill, so that

    they will be capable of utilizing heavy oil as substrate if

    compared with that was undertaken at the beginning of

    bioremediation process (e.g., year 1997).

    InNakhodkaheavy oil spill along seashores in the Sea of

    Japan (from Mikuni, Fukui Prefecture to Noto Peninsula,

    Ishikawa Prefecture, Japan), a careful bioremediational study

    has been performed by our group since 1997. After a 5-year

    bioremediation process, the isolation of indigenous bacterial

    strains was conducted in three coastal areas (namely Katano

    seashore of Fukui Prefecture, Atake and Osawa seashores of

    Ishikawa Prefecture), and theNakhodka Russian oil tanker.

    Investigation of the role of these bacteria in the bioremedi-

    ation of heavy oil polluted sites, particularly coastal areas,

    was carried out as well. Bacterial strains capable of growingon heavy oil were isolated from the above four locations by

    using enrichment and isolation techniques. Additionally, the

    bacteria were isolated not only from seawater, but also from

    beach sands polluted by heavy oil for over 5 years, namely at

    the top layer (030 cm) about 34 m outside the shoreline,

    and at the top layer (060 cm) about 56 m outside the

    shoreline at Atake seashore, Ishikawa Prefecture, Japan.

    Thirty-nine hydrocarbon-utilizing bacterial strains capable

    of growing on and utilizing heavy oil as a sole carbon and

    energy source were isolated from coastal areas. Of the 39

    bacterial strains tested, only 7 bacterial strains could grow

    very well on heavy oil (unpublished data).

    Accordingly, the primary objective of this study was to

    isolate bacterial strains capable of utilizing hydrocarbons

    indigenous to the Nakhodka oil spill-polluted coastal areas

    in order to obtain the most superior hydrocarbon degrader,

    being further used for investigating the environmental factors

    influencing the bioremediation of theNakhodka oil spill. This

    paper described the results of efforts of isolation and charac-

    terization of the seven aerobic, halotolerant hydrocarbon-

    degrading indigenous bacterial strains from seashores of

    Mikuni, Fukui Prefecture to Noto Peninsula, Ishikawa Pre-

    fecture (mainly from Wajima seashore, Ishikawa Prefecture

    and Katano seashore, Fukui Prefecture) 5 years after the

    Nakhodka Russian oil tanker spill in the Sea of Japan in

    relation to bioremediation process. The strains could use

    alkanes and heavy oil (from the Nakhodka oil spill) aerobi-

    cally as their sole carbon sources but not aromatics, and all of

    them were able to grow well on heavy oil. The microbial

    activity of hydrocarbon-degrading bacteria between year

    1997 (after the Nakhodka oil spill) and year 2001 (after 5years of bioremediation processes) were evaluated. In addi-

    tion, ex situ bioremediation process in laboratory microcosms

    (containing seawater, beach sand, and heavy oil) under

    aerobic condition by two different treatments, viz. treatments

    outside building and inside building, was also investigated.

    2. Materials and methods

    2.1. Field sites and sample collection

    The sampling sites are located in the Sea of Japan, i.e.,

    from Mikuni, Fukui Prefecture to Noto Peninsula, Ishikawa

    Prefecture, Japan (Fig. 1). Field sampling was performed

    three times. Samples of heavy oil, seawater, and sand were

    collected from Nakhodka tanker on February 21, 1997, on

    December 10, 1999 from Katano seashore in Fukui Prefec-

    ture, and on November 21, 2001 from Osawa and Atake at

    Wajima seashore in Ishikawa Prefecture, Japan (Fig. 2).At

    the Atake seashore, sands were sampled at two previous

    heavily oil-polluted fields, that is, from the top layer (030

    Fig. 1. Location of the sampling sites in the Sea of Japan. The arrow

    indicates sites in which the photographs (Fig. 2)were taken.

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    cm) about 34 m outside the shoreline and from the top

    layer (060 cm) about 56 m outside the shoreline. These

    were undertaken to investigate the difference of microbial

    activity of hydrocarbon-degrading bacteria, and also as

    controlled sampling in the isolation of hydrocarbon-degrad-

    ing bacteria. In addition, heavy oil samples were collected at

    three differently polluted field sites namely on inshore,

    nearshore, and away from outside shorelines. All samples

    were stored at 4 jC until required for analysis. Fieldparameters including seawater temperature, pH, dissolved

    oxygen (DO), electrode potential versus the standard hy-

    drogen electrode (Eh), and electrical conductivity (EC) were

    measured in situ using a portable meter.

    2.2. Chemical analyses of seawater, heavy oil, and sand

    Chemical composition of seawater and sand was analyzed

    using the energy-dispersive X-ray fluorescence (ED-XRF)

    analyzer. The seawater was furthermore used for ZOBELL

    medium in isolating hydrocarbon-degrading bacteria. Ele-

    mental composition of the seawater and sand is given in

    Tables 1 and 2. The chemical composition of heavy oil in

    N (nitrogen), C (carbon), and S (sulfur) was estimated by

    using the NCS analyzer, in order to determine the biodeg-

    radation of hydrocarbons. Additionally, the initial compo-

    sition of heavy oil spilled from the Nakhodka Russian oil

    tanker was analyzed by CHNS chemical analyzer

    (FISONS) (Table 3).

    2.3. Isolation, purification and enumeration of hydrocarbon

    degrading bacteria

    Bacteria were isolated from seawater, heavy oil, and sand

    samples from three coastal areas contaminated with the

    Nakhodkaoil spill, namely Katano seashoreFukui Prefec-

    ture, Osawa and Atake seashoresIshikawa Prefecture, and

    Table 1Elemental composition of seawater used for ZOBELL medium analyzed by

    ED-XRF

    Element wt.%

    Na 8.27

    Mg 1.49

    Si 0.26

    S 2.94

    Cl 79.94

    K 2.99

    Ca 3.57

    Co 0.05

    Br 0.42

    Sr 0.06

    Table 2

    Average elemental composition (wt.%) of beach sands collected from

    Katano seashore and Atake seashore analyzed by ED-XRF

    Element Katano seashore Atake seashore

    Mg 0.34 0.55

    Al 6.55 9.62

    Si 73.16 59.19

    K 8.77 11.42

    Ca 2.45 7.00

    Ti 0.77 1.27

    Mn 0.15 0.13

    Fe 7.73 10.61

    Sr 0.07 0.21

    Samples of beach sands were collected from Katano seashore on December

    10, 1999, and from Atake seashore on November 21, 2003. The beach sand

    is mainly composed of quartz (SiO2), feldspars (AlSi), and very few clay

    minerals.

    Fig. 2. Samples of heavy oil and sand were collected from each sampling site. (A) The Nakhodka tanker (on February 21, 1997), (B) Katano seashore (on

    December 10, 1999), (C) Osawa seashore (on November 21, 2001), and (D) Atake seashore (on November 21, 2001).

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    Nakhodka tanker by selective enrichment by using the

    Bushnell Hass Mineral Salts (BHMS) medium comprising

    heavy oil 1% (v/v). Bacteria were maintained on either liquid

    or solid mineral salts medium as the sole carbon source. The

    medium supplemented with 2% NaCl was used for the

    growth of marine bacteria. BHMS contained (per liter of

    distilled water) 0.2 g of MgSO47H2O, 0.02 g of CaCl2, 1 g

    of KH2PO4, 1 g of K2HPO4, 1 g of NH4NO3, 2 drops of

    FeCl360%. The pH was adjusted to 77.8 (neutral-alkaline

    condition). The bacteria were isolated by using an enrich-

    ment culture and a single-colony isolation technique. Sea-

    water, heavy oil, and sand samples collected from seashores

    in the Sea of Japan were inoculated to BHMS medium

    supplemented with 2% NaCl, and incubated on a rotary

    shaker (125 rpm) at room temperature. When the growth of

    bacteria was detected in the medium, a sample of culture

    medium was spread on ZOBELL agar plates supplemented

    with 1% (v/v) heavy oil as a substrate and incubated for 2

    weeks at 25 jC. Colonies appearing on the plate were

    isolated by a single colony isolation procedure, which was

    repeated several times. The final isolate (each strain) waspreserved in ZOBELL agar medium. Enumeration of the

    number of viable cells in bacterial culture was determined by

    a serial dilution-agar plating procedure.

    2.4. Characterization of hydrocarbon degrading bacteria

    All the colonies obtained on ZOBELL agar were purified

    several times on the same medium. Pure strains were

    conserved on ZOBELL agar/glycerol (v/v) at 20 jC.

    Growth of bacterial isolates on individual hydrocarbons

    and heavy oil (from the Nakhodka oil spill) was tested in

    a tube containing 10 ml of BHMS medium supplemented

    with 2% NaCl and 1 g/l of hydrocarbon. Hydrocarbons were

    sterilized by filtration (membrane filter 0.2 Am). Solid

    hydrocarbons (octadecane, eicosane, octacosane, and aro-

    matic compounds) were added directly to BHMS medium

    before autoclaving. Test tubes were agitated for 15 days at

    room temperature. Growth was then evaluated by compa-

    rison of optical density (OD600) against sterile control.

    2.5. 16S rDNA sequencing analysis

    Sequence analyses of 16S ribosomal DNA (16S rDNA)

    were performed on the isolates by amplifying the 16S rRNA

    genes by PCR using the bacterial universal primers 27f and

    1492r (Lane, 1991). The PCR mixture contained 1 Al of

    template DNA, 2.5 Al of 10 reaction buffer, 2 Al of 2.5

    mM of deoxynucleoside triphosphate (dNTPs), 0.5 Al of 10

    pmol of each primers, and 0.25Al of 2.5 U of Z-Taq DNA

    polymerase (TaKaRa Bio, Shiga, Japan) in a final volume of

    25 Al. DNA amplification was performed in a model PTC-100 Thermal cycler (MJ Research, Watertown, MA, USA)

    with following profile: 30 cycles of 96 jC for 1 s, 55 jC for

    10 s, and 72 jC for 20 s. The PCR products purified with

    EXOSAP-IT kit (USB, USA) were sequenced directly using

    an ABI PRISM BigDye Terminator cycle sequencing ready

    reaction kit (Applied Biosystems, USA). After purification

    of sequencing products by ethanol precipitation, they were

    run on an ABI 3100 Genetic Analyser (Applied Biosys-

    tems). The most closely related sequences were found using

    the BLAST programs(Altschul et al., 1997).

    2.6. Experimental growth of bacterial strains in an

    enrichment liquid medium

    Four selected strains were tested for the ability to grow

    in an enrichment liquid medium. The laboratory experi-

    ment was designed in a batch reactor under aerobic

    condition by shaking on orbital shaker (rotation speed

    of 150 rpm) at room temperature (25 jC) for 185 h. A

    series of 500-ml Erlenmeyer flasks were used for this

    experiment. Each flask contained 200 ml of 8 g/l of

    nutrient broth containing beef extract and peptone (i.e.,

    organic compound with very high nutrient content), 1 g/

    l of yeast extract (as co-substrate), 0.85% (w/v) of NaCl

    were inoculated by 10% (v/v) inocula of strain A1(Nakhodka), strain A3 (Katano), strain A4 (Osawa), strain

    A5 (Atake), respectively. Flasks with killed cells were

    used for controls. All treatments were performed in

    triplicate, and samples were compared to the killed

    controls. The growth kinetic of these strains was deter-

    mined in cultures (200 ml, 150 rpm, 25 jC) containing

    enrichment medium. Samples were removed periodically

    to assess the concentration of the biomass (dry weight), as

    calculated from the absorbance (optical density at 600

    nm) of washed cells. Values for specific growth rates

    (designated l) were obtained by fitting data by using

    linear regression analysis, whereas the cell density was

    measured by using a spectrophotometer UV (APEL Mod-

    el PD-303). The initial substrate concentration was

    detected as mg/l chemical oxygen demand (COD) for

    each treatment (APHA, 1998).

    2.7. Laboratory microcosm experiment of bioremediation

    process

    Laboratory microcosm experiments were undertaken to

    investigate the role of hydrocarbon-degrading bacteria in

    bioremediation processing of heavy oil since 1997. Labo-

    ratory microcosms contained seawater, heavy oil, and beach

    Table 3

    The initial composition of heavy oil spilled from theNakhodkaRussian oil

    tanker analyzed by CHNS chemical analyzer (FISONS)

    Chemical composition of heavy oil wt.%

    Carbon 62.2

    Hydrogen 10.1

    Nitrogen 0.246

    Sulfur < 0.1Oxygen 27.4

    Sampei et al., 2003.

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    sand. The two different treatments were established by

    placing microcosms outside building and inside building.

    At the outside building, it can be assigned that not only

    heavy oil is as a sole energy source but also another energy

    source is sunlight that is directly used by phototrophs. For

    chemical and physical parameters, pH, Eh, EC, and DO,

    respectively, were measured during the sampling to observethe bioremediation process taking place. Laboratory exper-

    iment at the inside building was conducted at room tem-

    pe ra ture (2 2 25 jC). At the outside building, the

    experimental temperature was not maintained depending

    on the seasons (i.e., winter, spring, summer, and autumn).

    However, the temperature measurement of both treatments

    was not conducted. The chemical composition of heavy oil

    in N, C, and S to determine biodegradation of hydrocarbon

    was estimated by using NCS analyzer. Additionally, micro-

    biological parameters were measured to investigate micro-

    bial activity of hydrocarbon-degrading bacteria during the

    process observed by scanning electron microscope (SEM;

    JEOL JSM-5200LV) and transmission electron microscope

    (TEM; JEOL JEM-2000EX).

    2.8. Light, scanning and transmission electron microscopy

    For light microscopy, bacterial cells were wet mounted on

    glass slides, stained with 4V,6-diamidino-2-phenylindole

    (DAPI), then observed under epifluorescence microscope

    (Nikon NTF2A). For scanning electron microscopy, bacterial

    cells were fixed with 2.5% (v/v) glutaraldehyde in phosphate

    buffer at room temperature for 1 h, washed in the same buffer,

    post-fixed in 1% (w/v) osmium tetroxide (OsO4) at room

    temperature for 1 h, dehydrated in a graded ethanol series (50,75, 95, and 100%), mounted on carbon-coated copper stubs,

    and viewed on a JEOL JSM-5200LV scanning electron

    microscope. Samples for transmission electron microscopy

    were fixed and dehydrated as described above, mounted on

    copper specimen grids, and viewed using a JEOL JEM-

    2000EX transmission electron microscope.

    3. Results

    3.1. Physical analysis of seawater

    Physical analysis was performed to provide a detailed

    description of sampling site condition. The physical charac-

    teristics of seawater are listed inTable 4.These showed that

    seawater temperatures ranged between 14.0 and 16.5 jC; pH

    from 7.9 to 8.6; dissolved oxygen from 4.8 to 11.1 mg/l; EC

    from10.4 to 48.6 mS/cm, and Eh between 20 and 118 mV.

    3.2. Isolation of hydrocarbon-utilizing bacteria from

    various coastal areas

    Thirty-nine strains of hydrocarbon-utilizing marine bac-

    teria were isolated from heavy oil, seawater, and sand

    samples obtained at three coastal sites in the Sea of Japan

    and the Nakhodka tanker (data not shown). When grown

    aerobically in BHMS medium (pH 77.8), the isolates gave

    cell yields ranging from 106 to 107 cells/ml. The strains

    grew well not only in BHMS medium but also in ZOBELL

    agar medium with the high NaCl concentration (Table 1). It

    seems clear that any bacterial strains proliferating well in the

    NaCl-supplied medium could withstand high concentrations

    of salt (NaCl).

    Isolation by agar dilution series was then successfully

    attempted. Two strains originated from Nakhodka tanker,

    three strains originated from Osawa seashore, two strains

    originated from Katano seashore, and 32 strains originated

    from Atake seashore, namely 9 strains resulted from sea-

    water and heavy oil samples, 9 strains and 14 strains

    resulted from sand samples from the top layer (030 cm)

    and (060 cm), respectively. All bacterial strains were able

    to consume either heavy oil or peptone and yeast extract as asole source of carbon as well as octadecane for their growth

    with the different generation time. Our experimental results

    on carbon source utilization thus suggested that the 39

    isolates were hydrocarbon-degrading bacterial strains. How-

    ever, of the 39 bacterial strains isolated, only 7 bacterial

    strains could grow well on heavy oil when grown aerobi-

    cally in BHMS medium supplemented with 2% NaCl and

    1% (v/v) heavy oil as substrate. They were coded: A1, A2,

    A3, A4, A5, A6, and A7(Table 5).Strains A1 and A2 were

    isolated from the Nakhodka oil tanker, strain A3 was

    isolated from Katano seashore, strain A4 was isolated from

    Osawa seashore, and strains A5, A6, and A7 were isolated

    from Atake seashore.

    3.3. Phylogenetic analyses of the bacterial isolates

    In order to identify the bacterial isolates, their 16S rDNA

    genes were amplified and sequenced. Strain A1 was affil-

    iated to Pseudomonas aeruginosa (99% similarity), strain

    A2 to Bacillus cereus (99%) or Bacillus thuringiensis

    (99%), strain A3 to P. aeruginosa (98%), strain A4 to P.

    aeruginosa (99%), strain A5 to P. aeruginosa (98%), strain

    A6 to P. aeruginosa (99%), and strain A7 to Paracoccus

    seriniphilus (97%) orParacoccus marcusii(97%)(Table 5).

    Table 4

    Physical characteristics of seawater for each sampling site

    Sampling site Sample

    source

    pH Eh

    (mV)

    EC

    (mS/cm)

    DO

    (mg/l)

    WT

    (jC)

    Osawa seashore seawater 7.9 20 10.4 11.1 16

    Atake seashore seawater 8.6 75 48.6 9.6 16.5

    seawater +

    heavy oil

    8.3 118 19 4.8 14

    Eh: electrode potential versus standard hydrogen electrode; EC: electronic

    conductivity; DO: dissolved oxygen; WT: water temperature. The

    measurement of DO was performed on the oil water phase. These

    parameters were measured in November 2001. In theNakhodkatanker and

    Katano seashore, these parameters were not measured. Only samples of

    heavy oil and sand were collected.

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    3.4. Growth on hydrocarbons as the sole carbon source

    Result of bacterial growth on pure hydrocarbons and

    heavy oil is given in Table 6. The seven bacterial strains

    were able to grow well on aliphatic hydrocarbons such as

    tetradecane (C14), hexadecane (C16), octodecane (C18), and

    eicosane (C20) as well as on heavy oil (from the Nakhodkaoil

    spill). Also, they grew poorly on hexane (C6), octane (C8),

    octacosane (C28), paraffin, pristane (branched C19), and

    cyclohexane. However, these bacterial strains did not appear

    to utilize aromatic hydrocarbons as carbon source, except that

    Table 6

    Growth and ability of strains isolated to use different organic compounds as

    carbon source

    Organic

    compounds

    Strain A1 A2 A3 A4 A5 A6 A7

    Alkanes Hexane (C6) + + + + + + +

    Octane (C8) + + + + + + +

    Tetradecane (C14) + + + + + + + + + + + + + +

    Hexadecane (C16) + + + + + + + + + + + + + +

    Octadecane (C18) + + + + + + + + + + + + + + +

    Eicosane (C20) + + + + + + + + + + + +

    Octacosane (C28) + + + + + + +

    Paraffin + + + + + + +

    Pristane

    (branched C19)

    + + + + + + +

    Cyclohexane + + + + + + + +

    Aromatics Toluene (1 ring) +

    Biphenyl (2 rings)

    Naphthalene

    (2 rings)

    Phenanthrene

    (3 rings)

    +

    Fluoranthene

    (4 rings)

    +

    Heavy oil the Nakhodka

    oil spill

    + + + + + + + + + + + + + + + + + +

    + = low growth; + + = medium growth; +++ = strong growth; = no

    growth.

    Table 5

    Strains isolated able to grow well on and use heavy oil as carbon source

    No. Sampling site Sample

    source

    Strain Species Sequence

    similarity

    (%)

    1 Nakhodka tanker heavy oil A1 Pseudomonas

    aeruginosa

    99

    A2 Bacillusthuringiensis or

    Bacillus cereus

    99

    2 Katano seashore sand+

    heavy oil

    A3 Pseudomonas

    aeruginosa

    98

    3 Osawa seashore heavy oil A4 Pseudomonas

    aeruginosa

    99

    4 Atake seashore heavy oil A5 Pseudomonas

    aeruginosa

    98

    (outside seashore)

    (inshore) seawater +

    heavy oil

    A6 Pseudomonas

    aeruginosa

    99

    (sand of 30 cm

    deep at 3rd layer)

    sand A7 Paracoccus

    seriniphilus

    Paracoccus

    marcusii

    97

    The name of strains was a result of 16S rDNA sequencing analysis.

    Fig. 3. Epifluorescence photomicrograph (A) and scanning electron

    micrograph (B) of strain A3 (Katano) at the exponential phase after 44h of incubation grown in an enrichment liquid medium containing 8 g/l of

    nutrient broth and 1 g/l of yeast extract, and 0.85% (w/v) of NaCl.

    Fig. 4. Growth curve in density of four bacterial strains of A1 (Nakhodka),

    A3 (Katano), A4 (Osawa), and A5 (Atake) in an enrichment liquid medium.

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    strain A5 grew poorly on phenantherene and fluoranthene,

    and strain A6 utilized toluene poorly. Of the seven bacterial

    strains tested in utilizing various hydrocarbons, strain A5 was

    the most superior hydrocarbon degrader, therefore being

    studied in more detail and used for future studies, especially

    in investigations on the environmental factors influencing the

    bioremediation of theNakhodkaoil spill.

    3.5. Bacterial growth and growth kinetics in an enrichment

    liquid medium

    Growth of strains A1 (Nakhodka), A3 (Katano), A4

    (Osawa), and A5 (Atake) on enriched liquid medium was

    tested(Figs. 3 and 4). These strains grew well in enriched

    liquid media containing 8 g/l of nutrient broth, 1 g/l of

    yeast extract (as co-substrate), 0.85% (w/v) of NaCl, as

    the sole source of carbon, nitrogen, and energy. When

    growth was not limited by growth factor(s), i.e., at

    enrichment culture, a classical growth response consisting

    of an exponential phase followed by a stationary phasewas observed. All strains were capable of utilizing con-

    centrations as great as 3030 mg/l COD without an appre-

    ciable lag phase. This concentration was the initial

    substrate concentration detected as COD (mg/l) for each

    treatment. On the other hand, it was apparent that it was

    difficult for all bacterial strains to reach an optical density

    Fig. 5. Growth curve in biomass and determination of specific growth rate of four bacterial strains of A1 (Nakhodka), A3 (Katano), A4 (Osawa), and A5

    (Atake) in an enrichment liquid medium.

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    at 600 nm (OD600) of R 1, indicating the low cell yield of

    growth on this substrate (Fig. 4).

    The growth of strains A1 (Nakhodka), A3 (Katano), A4

    (Osawa), and A5 (Atake) in liquid culture followed the first-

    order reaction (Fig. 5) with the following growth kinetic

    parameter: for strain A1 (Nakhodka), l = 0.063 h 1; strain

    A3 (Katano),l =0.01h 1

    ; strain A4 (Osawa),l =0.014h 1

    ;and strain A5 (Atake), l = 0.0164 h 1. The values of the

    growth kinetic parameters, l, can be determined so as to

    fit the calculated profiles with corresponding experimental

    ones by the least squares method, as in the case of nutrient

    broth as substrate. An example of the good coincidence

    between the experimental and calculated profiles is shown

    in Fig. 5 with the regression coefficient: R2 = 0.9249 (for

    strain A1 (Nakhodka)). The values of specific growth rate

    increased with the following sequences as: (strain A4

    (Katano) < strain A4 (Osawa) < strain A5 (Atake) < strain

    A1 (Nakhodka)), indicating that strain A1 (Nakhodka) had

    the highest capability in using this substrate for its growth

    than those of three strains. This also proved that strain A1(Nakhodka) was capable of growing quickly by using this

    substrate where transport of the substrate through the cell

    wall might be a rate-determining factor.

    3.6. Bioremediation process on the laboratory scale

    associated with in situ bioremediation

    3.6.1. Analysis of physical characteristics of seawater

    Comparison of physical characteristics between inside

    and outside building at laboratory microcosm assays for

    bioremediation processes during 5 years of bioremediation

    is given in Fig. 6. The graphs showed that seawater pH

    ranged between 6.4 and 7.8 having the tendency to

    neutral-alkaline condition; DO ranged from 0.6 to 5.5

    mg/l; Eh ranged from 50 to 300 mV; and EC ranged

    between 45 to 180 mS/cm. During the sampling at all

    treatments, there were no significant changes in pH,

    whereas EC increased rapidly. Conversely, Eh decreased

    sharply for all treatments, while DO concentrations indi-

    cated that bioremediation processes took place under

    aerobic conditions. On the other hand, at inside building

    treatment, at the second measurement (October 20, 1997)

    DO concentration decreased abruptly to anaerobic condi-

    tion (0.6 mg/l).

    Fig. 6. The values of pH, Eh, EC, and DO in laboratory microcosm

    experiments (i.e., the inside and outside building treatments) during the

    5-year bioremediation.

    Table 7

    Chemical composition of heavy oil in N, C, S (wt.%) for each sampling site

    analyzed by NCS analyzer

    Sampling site Sample source N (%) C (%) S (%)

    Nakhodka tanker seawater + h eavy oil n.d. 87.2 1.44

    Laboratory assay

    (inside building)

    seawater + heavy oil n.d. 59.68 1.83

    Laboratory assay(outside building)

    seawater + heavy oil n.d. 0.054 1.61

    Osawa seashore heavy oil 0.19 83.08 1.12

    Atake seshore heavy oil

    (outside seashore)

    n.d. 83.4 1.38

    heavy oil (inshore) n.d. 24.43 0.18

    heavy oil (nearshore) 0.22 82.9 1.2

    seawater + heavy oil n.d. 0.1 2.44

    seawater n.d. 0.03 2.27

    Atake seashore sand (1st layer) n.d. 0.14 0.01

    (sand of 30 cm sand (2nd layer) n.d. 0.1 n.d.

    in depth) sand (3rd layer) n.d. 0.14 0.01

    Atake seashore sand (1st layer) n.d. 0.2 n.d.

    (sand of 60 cm sand (2nd layer) n.d. 0.16 n.d.

    in depth) sand (3rd layer) n.d. 0.26 0.004

    sand (4th layer) n.d. 0.08 n.d.

    sand (5th layer) n.d. 0.06 n.d.

    N: nitrogen; C: carbon; S: sulfur; n.d.: not detected.

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    3.6.2. NCS analysis of heavy oil contents

    The chemical compositions of heavy oil for each sample

    after 5 years of bioremediation (year 2001) detected in N, C,

    and S are summarized in Table 7. The unit of contents is

    shown in percentage of weight. These compositions de-

    scribed not only bioremediation process on the laboratory

    scale (ex situ bioremediation) but also in situ bioremediationprocesses in comparison. The contents of C ranged from

    59.68 to 87.20 wt.% (for Nakhodka tanker, laboratory

    microcosm assay of inside building, Osawa seashore, and

    Atake seashore), 24.43 wt.% C (for heavy oil inshore in

    Atake seashore), 0.10 wt.% C (for seawater with heavy oil

    slick), 0.03 wt.% C (for seawater without heavy oil slick),

    and 0.06 0.20 wt.% C (for sand at different depths).

    Compared with the content of C, the contents of N and S

    were relatively low, that is, 00.22 wt.% N, and 02.44

    wt.% S. TheNakhodkatanker site was highest in proportion

    to the C content of those of other sites (i.e., 87.20 wt.%),

    while the lowest one was obtained from a seawater sample

    without heavy oil in Atake seashore (i.e., 0.03 wt.%). These

    provided that the biodegradation rate of heavy oil atNakhodka tanker site was relatively low if compared with

    those of other sites. Compared with inside building treat-

    ment, outside building treatment had a relatively high

    biodegradation rate of heavy oil shown by the low C content

    (0.054 wt.%). In Atake seashore, the biodegradation rate of

    heavy oil climbed slightly where it reached a peak on the

    inshore and gradually dropped into the nearshore and outside

    Fig. 7. Comparison of scanning (A1 2, B1 2) and transmission (A3, B3) electron micrographs of hydrocarbon-utilizing bacteria inhabiting heavy oil during

    bioremediation process between the year 1997 and the year 2001 at Wajima seashores, Noto Peninsula, Ishikawa Prefecture, Japan. Note: A1 3, the year 1997;

    B13, the year 2001.

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    seashore designated by declining the C contents (83.40,

    82.90, and 24.40 wt.%, respectively). Whereas C content

    of sands at all depths elucidated that there was no significant

    difference between them, indicated by the low contents if

    compared with those of other samples. It thus seems that

    there was a sharp decrease in the content of carbon inshore in

    Atake seashore. A strong positive correlation exists herebetween the amount of organic matter (i.e., carbon content)

    and the abundance of hydrocarbon-degrading bacteria. Ken-

    nish (1995)reported that the abundance of bacteria peaks in

    the estuaries and coastal waters and gradually declines into

    offshore areas and the open ocean.

    3.6.3. Comparison of microbial activity of hydrocarbon-

    degrading bacteria between year 1997 and year 2001

    The enumeration of bacterial cell number, SEM and

    TEM observations were undertaken to investigate the mi-

    crobial activity of hydrocarbon-degrading bacteria in heavy

    oil samples collected from Wajima seashores, Noto Penin-

    sula, Ishikawa Prefecture, Japan. The population size of

    hydrocarbon-degrading bacteria in 2001 (after 5 years of

    bioremediation) was in the range of 104106 cells ml 1,

    while the population size in 1997 (at the beginning of

    bioremediation process) was in the range of 105106 cells

    ml 1 (Kasai et al., 2001). There was the similarity in

    population size of hydrocarbon-degrading bacteria between

    year 1997 and year 2001. The bacteria showed the popula-

    tion size of greater than 105 bacteria ml 1 indicating a

    relative abundance of hydrocarbon-utilizing bacteria repre-

    senting a population density of greater than 103 cells ml 1.

    Furthermore, SEM and TEM observations revealed that

    there was no significant change in morphology and size ofhydrocarbon-degrading bacteria during the 5-year bioreme-

    diation process (comparison between year 1997 and year

    2001). Hydrocarbon-degrading bacteria occurred in two

    basic shapes, namely cocci (spherical) and bacilli (rod-

    shaped), and one unusual shape namely filamentous (Fig.

    7). Bacteria sizes at all sampling sites were in the range of

    2 7 Am in length and 0.51 Am in width for rod-shaped

    bacteria, and 0.3 1.5Am in diameter for spherical bacteria,

    illustrating similarities from 1997 to 2001. Thus, the find-

    ings revealed that after 5 years of bioremediation, a large

    number of hydrocarbon-degrading bacteria still existed in

    the sites, consisting of a variety of morphological form of

    bacteria such as coccus (StreptococcusandStaphylococcus),

    bacillus (Streptobacillus), and filamentous (Bitton, 1994;

    Tortora et al., 1994; Chaerun and Tazaki, 2003). The

    bacterial cells tended to remain together in a cluster, that

    is, cocci (spherical) or bacilli (rod-shaped) occurred in long

    chains (Fig. 7A1). One rod-shaped bacterium appeared to

    harbor numerous hair-like appendages (assumed to be

    fimbriae or flagella) distributed over the surface of the cell

    (Fig. 7A3). Some cocci and bacilli formed a slime layer of

    cells(Fig. 7B2),while others occurred in three-dimensional

    cubes or irregular grape-shaped or irregular star-shaped

    clusters (figure not shown).

    4. Discussion

    The capacity of bacteria, especially P. aeruginosa, to

    metabolize aerobically heavy oil or aliphatic hydrocarbons

    is well known since a long time. In this study, for the first

    time to our knowledge, bacteria that are able to grow on

    heavy oil as a carbon source and electron donor were isolatedfrom marine coastal areas polluted by NakhodkaRussian oil

    tanker spill in the Sea of Japan (mainly from Wajima

    seashore, Ishikawa Prefecture, Japan). Aerobic culture con-

    ditions were chosen to select for an oxygen-dependent

    degradation. In addition, aerobic growth of the isolated

    bacteria on heavy oil demonstrated the presence of heavy

    oil-degrading capacities in oxygen-respiring bacteria. Of the

    seven bacterial strains isolated, most of them were affiliated

    toP. aeruginosa.The discovery of a majority ofPseudomo-

    nas is not surprising based on their frequency in the

    hydrocarbon-contaminated sites(Rosenberg, 1992; Janiyani

    et al., 1993). The seven bacterial isolates were able to grow

    well on n-alkane hydrocarbons and heavy oil. However,

    these bacteria did not appear to use aromatic hydrocarbons as

    carbon source. Microorganisms capable of degrading PAHs

    are often isolated from environments with a history of

    contamination by PAHs (Herbes and Schwall, 1978; Heit-

    kamp and Cerniglia, 1988; Kastner et al., 1994; Trzesicka-

    Mlynarz and Ward, 1995). Bacteria degrading alkanes com-

    monly do not degrade PAHs (Foght et al., 1990), although

    metabolic pathway for both types of compounds is not

    incompatible (Whyte et al., 1997). The incapacity of our

    bacterial isolates to use PAHs as sole carbon source was not

    surprising, since the strains were isolated from seashores

    contaminated with the Nakhodka oil spill which consistedmainly of aliphatic hydrocarbons. That is, n-alkanes of C9

    C30, in which n-eicosane (n-C20H42) was the most abundant

    compound, while the contents of aromatic compounds were

    low(Itagaki and Ishida, 1999; Tazaki, 2003).

    The n-alkanes are the most biodegradable of the petroleum

    hydrocarbons and are attacked by more microbial species

    than aromatic or naphthenic compounds. However, normal

    alkanes in the C5 C10 range are inhibitory to many hydro-

    carbon degraders at high concentrations because as solvents

    they disrupt lipid membrane and the cycloalkanes (alicyclic

    hydrocarbons) are less degradable than their straight-chain

    parent, the alkanes, but more degradable than the polycyclic

    aromatics (PAHs)(Jeffrey, 1980; Trudgill, 1984).From some

    years, the biodegradation of alkanes correlated with denitri-

    fication, sulfate reduction, and metanogenesis has been

    described (Aeckersberg et al., 1991, 1998; Rueter et al.,

    1994; So and Young, 1999a,b). Moreover, aliphatic hydro-

    carbons are not fermentable, and only in the presence of O2,significant aliphatic hydrocarbon degradation occurs. The

    initial degradation of petroleum hydrocarbons often requires

    the action of oxygenase enzymes and so is dependent on the

    presence of molecular oxygen (Brock, 1970; Atlas, 1991).

    Aerobic conditions are therefore necessary for the initial

    breakdown of petroleum hydrocarbons and in subsequent

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    steps, nitrate or sulfate may serve as a terminal electron

    acceptor(Bartha, 1986),but oxygen is most commonly used.

    The DO values of laboratory microcosm experiments show-

    ing that the bioremediation processes mostly ensued under

    aerobic condition confirmed the bacterial role in the degra-

    dation of aliphatic hydrocarbons of the Nakhodka oil spill

    during the 5-year bioremediation(Fig. 6).It is most likely forthe indigenous bacteria to degrade and clean up sites con-

    taminated with petroleum hydrocarbons (mainly aliphatics)

    as long as there are no major limitations of bioavailability,

    oxygen, and temperature (Atlas, 1981; Leahy and Colwell,

    1990). Based on the composition of the oil and seawater

    (Tables 1, 3, and 7), their sulfur content may affect the

    oxidation rate of oil during the 5-year bioremediation.

    On the basis of bacterial growth in an enrichment liquid

    medium, for bioremediation or biodegradation processes to

    cleanup or remove pollutants or contaminants, it was required

    that growth yield was low, expressing the low specific growth

    rate (low biomass produced) and the high substrate-degrada-

    tion rate (high substrate consumed). Under the circumstances,

    we could not determine which strain was the best one in using

    this substrate, because the degradation rate of substrate was

    not observed (not measured). Furthermore, there is a close

    relationship between biomass produced and amount of sub-

    strate consumed that is a variable which depends on the

    balance between: (a) how much of the available growth-

    substrate is used for new biomass produced; and (b) how

    much of the substrate is consumed by the growing cells for

    energy to drive biosynthetic reactions (Shuler and Kargi,

    1992). Clearly, the greater the efficiency of energy generation

    or the less energy required for biomass production, then the

    less substrate has to be dissimilated for this purpose and themore substrate is available for biomass production.

    Furthermore, SEM and TEM observations of bacterial

    community of hydrocarbon-degrading bacteria suggest that

    the bacteria are interestingly well known for their metabolic

    diversity and the capability to degrade many biohazardous

    or persistent anthropogenic chemical compounds or various

    xenobiotic substances(Fig. 7).For both in situ and ex situ

    bioremediation process on the laboratory scale, bacteria

    were among the dominant microorganisms in these process-

    es during the 5-year bioremediation, indicating that the

    bacteria had the ability to survive for the relatively long

    periods even in the nutrient-poor environments (figure not

    shown). It was thus believed that under circumstances,

    bacteria may be ubiquitous in oligotrophic environments

    and essential to maintain the bioremediation process in the

    oligotrophic process as well. These results further support

    the view that bacteria can exist in and dominate some

    extreme environments.

    5. Conclusions

    After 5 years of bioremediation processes in the

    Nakhodka heavy oil spill along seashores in the Sea of

    Japan (from Mikuni, Fukui Prefecture to Noto Peninsula,

    Ishikawa Prefecture, Japan), the bacterial strains isolated

    show that they are able to utilize alkanes, but not aro-

    matics, with the exception of one strain (i.e., strain 5

    isolated from Atake seashore), which has the capability to

    use both aliphatic and aromatic compounds. Most of the

    bacterial isolates are affiliated to P. aeruginosa. It has alsobeen shown that bacteria are the most predominant micro-

    organism among other microorganisms in either in situ or

    ex situ bioremediation processes, indicating that bacteria

    are the main agents responsible for degradation of heavy

    oil and appear to be the prevalent hydrocarbon degraders

    in coastal areas. It is not surprising that hydrocarbono-

    clastic bacteria are present in the hydrocarbon-polluted

    sites.

    The bacterial strains isolated from the Nakhodkaoil spill-

    contaminated sites (at the beginning of bioremediation

    process) has been reported in the early literature; however,

    these cultures were not preserved and have not been further

    studied. Thus, the findings of bacterial isolates as pure

    bacterial cultures capable of utilizing the Nakhodkaoil spill

    and indigenous to the Nakhodkaoil spill-polluted areas here

    will be helpful and will be used for more detailed future

    investigations on the biodegradation processes, especially in

    studies on the environmental factors influencing the biore-

    mediation of theNakhodkaoil spill (being performed by our

    group).

    Acknowledgements

    The authors thank Darius Greenidge, PhD, for correctingthe manuscript. One of us (S.K.C) would like to thank

    Associate Professor Chiaki Imada, PhD, and Professor

    Naoto Urano, PhD (Tokyo University of Fisheries), for

    helpful and motivating discussions, and Professor Dr.

    Bernhard Schink (Konstanz University, Germany) for

    continuous support. We are also grateful for the cooperation

    and assistance of all students of the Tazaki laboratory. We

    greatly acknowledge the help of all students of the Kogure

    laboratory (University of Tokyo) for help with 16S rDNA

    sequencing analysis. We also thank anonymous reviewers

    for constructive comments. This study was funded by a

    grant from the Japanese Ministry of Education, Culture,Science and Technology to Dr. Kazue Tazaki.

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