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ScienceDirect
Bacterial diversity in oil-polluted marine coastal
sediments
Alejandro Acosta-González1 and Silvia Marqués2
Marine environments harbour a persistent microbial seed
which can be shaped by changes of the environmental
conditions such as contamination by petroleum
components. Oil spills, together with small but continuous
discharges of oil from transportation and recreational
activities, are important sources of hydrocarbon pollution
within the marine realm. Consequently, prokaryotic
communities have become well pre-adapted toward oil
pollution, and many microorganisms that are exposed to its
presence develop an active degradative response. The
natural attenuation of oil pollutants, as has been
demonstrated in many sites, is modulated according to the
intrinsic environmental properties such as the availability of
terminal electron acceptors and elemental nutrients, together
with the degree of pollution and the type of hydrocarbon
fractions present. Whilst dynamics in the bacterial
communities in the aerobic zones of coastal sediments are
well characterized and the key players in hydrocarbon
biodegradation have been identified, the subtidal ecology of
the anaerobic community is still not well understood.
However, current data suggest common patterns of
response in these ecosystems.
Addresses
1
Grupo de Investigación en Bioprospección (GIBP), Facultad de
Ingenierı́a, Universidad de La Sabana, Autopista Norte km 7, Chı́a,
Cundinamarca, Colombia
2
Consejo Superior de Investigaciones Cientı́ficas, Estación
Experimental del Zaidı́n, Department of Environmental Protection,
Profesor Albareda 1, E-18008 Granada, Spain
Corresponding author: Marqués, Silvia (silvia@eez.csic.es)
Current Opinion in Biotechnology 2016, 38:24–32
This review comes from a themed issue on Environmental
biotechnology
Edited by Bernardo González and Regina-Michaela Wittich
For a complete overview see the Issue and the Editorial
Available online 7th January 2016
http://dx.doi.org/10.1016/j.copbio.2015.12.010
0958-1669/# 2015 Elsevier Ltd. All rights reserved.
Introduction
Continental shelves, which represent 15% of the total
volume of marine sediments [1], are areas constantly
exposed to pollution caused by human activities, and
are particularly threatened by oil spills. Three zones,
Current Opinion in Biotechnology 2016, 38:24–32
with specific geochemical and ecological characteristics,
can be distinguished within these habitats: (i) the supra-
tidal zone, above the high tide shoreline, where sediment
deposits are exposed to subaerial conditions most of the
time; (ii) the intertidal zone (littoral) that comprises
the area covered by the highest tide and is exposed
during the lowest tide, and which includes wetlands
(i.e., sandy, silty, and muddy sediments) and rocky cliffs;
and (iii) the subtidal zone that remains permanently
submerged (Figure 1). Studies on the microbial ecology
of sediments have mainly focused on muddy sediments
because of their high organic matter (OM) content, which
is at least 10-fold higher than the OM in sandy sediments,
and of the higher cell density inherent to the surface of
the sediment’s smallest particles [2]. However, black
tides mainly impact sandy sediments, which cover
>50% of coastal sediments worldwide (<200 m water
depth) [3]. Many decades ago, pioneering works on
microbial physiology established the role of microorgan-
isms in carbon, nitrogen, sulphur, and iron cycles within
coastal environments, and described the nexus to geo-
chemical profiles throughout the sediment depth (from a
thin superficial oxic layer, through an oxygen/redox
‘transition’ zone, to a deep anoxic zone, see Figure 1)
[4]. Initial taxonomic studies were limited by the impos-
sibility of cultivating the majority of prokaryotes but this
was partially solved recently, when the emergence of
powerful sequencing technologies provided the possibil-
ity to address the bacterial uncultured fraction in depth
[5]. The massive spill resulting from the blowout of
the Deepwater Horizon (DWH) platform generated a
number of significant ‘omics-based’ studies, which have
recently been reviewed [6]. Research initially focused
on the water column, where the microbial response to the
spill was thoroughly described [7,8]. Nevertheless,
these techniques have not been extensively applied to
polluted marine sediments, which remained insufficient-
ly studied. However, the information gathered during
recent years, largely thanks to metagenomic (16S rRNA
and shotgun) and metatranscriptomics approaches, pro-
vides the first clues for understanding the response of
such complex bacterial communities to the presence of
hydrocarbon pollution. Linking changes in microbial
diversity to biodegradation should be an important
goal in this research, providing new biotechnological
opportunities for the efficient recovery of polluted coast-
al areas [9].
Two main strategies have been used to address the
microbial response to oil pollution: in situ studies at
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 Bacterial diversity in polluted coastal sediments Acosta-González and Marqués 25

Figure 1

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NO3 N2 O2 H2O O2 H2O
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FeOOH Fe+2
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SO4 HS- FeOOH Fe+2 MnO2 Mn+2

SO4 HS- FeOOH Fe+2

CO2 CH4 SO4 HS-

CO2 CH4

Supratidal zone
Intertidal zone
Subtidal zone

Current Opinion in Biotechnology

Redox processes present in marine coastal sediments. Schematic representation of redox processes present in marine coastal sediments. The
depth profiles show the stratification of different zones depending on the availability of terminal electrons acceptors (inherent to each site). A well-
defined succession of respiratory metabolisms is evidenced and explained by the tendency of these compounds to accept electrons:
microorganisms consume the oxygen that penetrates the surface influenced by the type of matrix (sand, mud, etc.), mixing effect by waves (few
millimetres/centimetres in the case of subtidal sediments) or bioturbation. Once the oxygen consumption exceeds its supply, anoxic conditions are
established below the zone of oxygen-influence. Nitrate, manganese and iron are used for anaerobic respiration if present. Sulphate reduction is
dominant at depths where other terminal electrons acceptors are depleted. In the case of subtidal sediments, sulphate reduction becomes
dominant as sulphate is not a limiting factor in marine environments. Aerobic and anoxic processes are stimulated if biodegradable OM is
available for oxidation, converting the use of each terminal electron acceptor as the driving force for microbes to use a specific metabolism. These
redox zones formed in the coastal sediments can be visualized by eye inspection especially if a carbon input (such as oil) is present: (i) an upper
oxidized brown layer that can range between a few millimetres to several centimetres; (ii) an anoxic but oxidized transition zone where nitrate,
manganese and/or iron oxides are reduced; and (iii) finally, a dark grey to black reduced sulphidic zone, in which sulphate reduction
predominates. However, in many cases more than one terminal electron acceptor can be used in the same redox zone. Methanogenesis develops
in the sediment depending on the interaction between methanogens and sulphate reducers, generally described as mutually exclusive. In parallel,
both biotic (chemolithotrophs) and abiotic processes can oxidize the inorganic compounds reduced by chemoorganotrophs, thus recycling
elements in the sediments.

the polluted sites, and simulation experiments in
microcosms and mesocosms under controlled laboratory
conditions. The results from hydrocarbon-polluted
coastal sediments of the recent years will be revised
here, with the exception of wetland sediments, which
have recently been addressed in an excellent review
[10].
Coastal marine sediments are heterogeneous
and sustain highly diverse bacterial
communities
Recent estimates reveal that coastal sediments harbour
the highest values of microbial abundance [11] and
diversity (alpha and beta indexes) within the marine
realms [12], which is due in part to the stratification of

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26 Environmental biotechnology
the redox gradient and the availability of nutrients that
shape these communities [13]. Taxa–area and distance–
decay relationships for bacteria have been shown to be
higher in marine sediments than in global ecosystems
[14]. Furthermore, the composition of the bacterial
community in coastal sediments shows a high dissimilari-
ty between sites, reflecting the heterogeneity of these
environments, which is locally preserved due to limited
physical mixing. Studies comparing global diversity with-
in coastal sediments are scarce, but a dominance of
Proteobacteria, especially the Gamma and Delta classes,
is evident in marine sediments. A global analysis of
available datasets of marine sequences distinguished
coastal from deep-sea sediments by their higher propor-
tion of Clostridia and Bacilli and a reduced presence of
Acidobacteria and Planctomycetaceae [12]. In coastal sands,
physical mixing by waves and seasonal variation deter-
mine the dynamics of community structures, where few
bacterial groups constitute the dominant populations and
the so-called ‘rare biosphere’ varies significantly with
parameters associated to nutritional stress [15]. Additional
factors, such as the presence of viruses, protist predators
and the vegetation of sediments, contribute to shape the
bacterial communities [16]. Different studies on recent
oil spills reveal that the functional diversity and the
potential for the biodegradation of pollutants of the
microbial community in coastal marine ecosystems
are significant, explaining the ability of huge populations
of microbes to survive the toxicity of certain constituents
and degrade oil components [17].
Effect of crude oil on supratidal and intertidal
sediment community structure
In beach sands and in general in supratidal sediments the
oxygen influence zone is broader than in subtidal sedi-
ments and the prevailing type of metabolism is aerobic. In
these environments the microbial response to the pres-
ence of hydrocarbons essentially follows similar trends to
those described for planktonic communities in the water
column, as evidenced by the thorough analysis of multi-
ple sites affected by the DWH blowout (reviewed in King
et al. [6]). One advantage of the studies on DWH
affected ecosystems was the availability of pre-spill sam-
ples that allowed comparison of the community structure
both before and after the accident. Differences in com-
munity composition between beach sands sampled at
geographically separated sites were high when compared
to the planktonic counterpart [18,19], as previously
described for the polluted beaches of the southern Gulf
of Mexico [20]. However, the patterns of the benthic
community shift in sand affected by the spill resembled
the bacterial succession (at a high taxonomic level) de-
scribed for planktonic communities in the plume
(reviewed in [21]). The primary work by Kostka
et al. [22] analyzing beach sediments affected by the
DWH spill described a significant increase in microbial
abundance in oil contaminated sand, dominated by an
Current Opinion in Biotechnology 2016, 38:24–32
active community of Gammaproteobacteria, especially by
members of known hydrocarbonoclastic groups such as
Alcanivorax and Marinobacter. Similar trends were ob-
served in mesocosm experiments [23] and in the long-
term analyses of different sandy beaches [19]. Results of
an in-depth petroleomic analysis could link the microbial
blooming to the degradation of fractions of oil deposited
on the beach [24], while metatranscriptomics detected a
significant increase in the expression of genes related to
oil component degradation which could be affiliated to
the Alphaproteobacteria and Gammaproteobacteria [25]. As
for the planktonic community, there was a succession of
microbial groups over time, where the Oceanospirillales
dominated in the early stages and were gradually replaced
by Rhodobacteraceae (Alphaproteobacteria) and Bacillus.
Oceanospirillales and Rhodobacteraceae were also among
the most abundant taxa detected in beach sand and rocks
after the Prestige oil spill (reviewed in [26]). However, in
the DWH-affected benthic communities, Alcanivorax
appeared to be more competitive for hydrocarbon degra-
dation than their planktonic counterparts [6]. The suc-
cessional pattern of diversity analyzed during one year
corroborated previous findings, showing an initial de-
crease in community diversity (the first four months after
exposure), which recovered thereafter [27]. The initial
alkane degrading populations were later replaced by
members of the genus Treponema and the class Alphapro-
teobacteria, probably involved later-on in the degradation
of polycyclic aromatic hydrocarbons (PAHs). However,
the functional diversity, as determined from the alkB
gene sequences retrieved from metagenomic data, in-
creased during the first months after exposure and was
maintained thereafter, to finally decrease to initial levels
one year after the oil had reached the shore. These
findings were explained in terms of community general-
ists (copiotrophic) being less affected by disturbances
caused by crude oil, which was probably due to the higher
sensitivity of the specialist population (oligotrophic) to its
toxic components and/or to their limited capacities for
hydrocarbon degradation [27]. Altogether, this would
suggest that rather than selecting specific taxa, the pre-
ferred strategy for bacterial-based remediation protocols
in marine sediments should seek to maintain high levels
of bacterial diversity [28].
Surface sediments in the intertidal area are character-
ized by the presence of a burrowing macrofauna that
results in the bioturbation of the upper layers of the
sediment, with important consequences on microbial
metabolism. In mesocosm experiments, the presence
of the burrowing organism Hediste diversicolor affected
the structure of the bacterial community, thereby
increasing the abundance of Gammaproteobacteria,
which are generally related to aerobic and/or facultative
metabolism. The difference between bioturbated and
non-bioturbated sediments was also evident in the
presence of crude oil, although no differences in oil
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 Bacterial diversity in polluted coastal sediments Acosta-González and Marqués 27
removal were observed between the two conditions
[29,30].
Bacterial community structure in
hydrocarbon-polluted subtidal sediments
Whilst both in the water column and in beach sand
cumulative evidence clearly suggests a common pattern
in the microbial shift after a spill incident, thus allowing
the identification of the key players linked to the aerobic
biodegradation of the main hydrocarbon constituents of
oil, such a clear picture is not yet available for anoxic
hydrocarbon-polluted sediments. Unlike the sea water
column, subtidal sediments encompass a characteristic
steady redox gradient throughout the depth profile that
defines the predominant respiratory metabolism at each
level, as schematized in Figure 1. To obtain a reliable
picture of the community distribution in these ecosys-
tems, it is important to preserve the sediment structure
during the sampling process. Unfortunately, most studies
analyzing the effect of hydrocarbon pollution on subtidal
sediments have disregarded the differential bacterial
distribution throughout the depth profile and sediment
samples have generally been analyzed in bulk or only the
uppermost centimetres have been considered. Further-
more, in many cases the sediment depth of the sampled
material is not detailed and numerous analyses targeting
sediment ecology are restricted to aerobic metabolism.
Nevertheless, general inferences can be drawn about the
overall structure of the subtidal communities in the
presence of hydrocarbons.
As for unaffected sediments, the phylum Proteobacteria
is found to be the prevailing group in most hydrocar-
bon-polluted subtidal sediments. It constituted more
than 70% of 200 retrieved 16S rRNA sequences from
seabed sediments of Livorno harbour (Italy), dominat-
ed by the Gammaproteobacteria and Deltaproteobacteria
subclasses, followed by Bacteroidetes [31]. A similar
picture was obtained from sediments from a chronically
oil-polluted retention basin in the Berre lagoon, domi-
nated by the Proteobacteria and Bacteroidetes phyla [32],
and from sediments affected by the Prestige oil spill on
the northern Spanish coast [33]. In all cases, the
concentration of hydrocarbons seemed to play a role
in shaping the bacterial community, which also selected
for those groups which were resistant to the toxicity of
oil components.
Recently, a multi-omics and biodegradation analysis of
sediment samples taken from a series of chronically
polluted sites along the Mediterranean coastline showed
that each site hosted a distinct bacterial community
dominated by members of the Proteobacteria, composed
of strains other than the specialized hydrocarbonoclastic
bacteria generally found after acute pollution [34], as it
had been observed in other chronically polluted sites
[32,33]. The only exception was a micro-tidal lagoon in
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Northern Morocco dominated by Flavobacteria where
Proteobacteria were almost absent. In the Mediterranean
survey, none of the retrieved taxons was common to all
the sampled sites [34], which is consistent with the
general idea that the coastal subsurface hosts highly
diversified bacterial assemblages [16]. However, a posi-
tive correlation could be established between the tem-
perature and the community composition of the site
[34], as it was previously described for other ecosystems
[35], and irrespective of the level of pollution. Further-
more, as inferred from metagenomic data, the tempera-
ture also shaped the biodegradation potential of the
community. The predicted degradation pathways ex-
trapolated from the global analysis suggested that all
communities had the potential to metabolize a high
number of hydrocarbon pollutants, which for half of
them could be experimentally validated in enrichment
cultures [34].
The bacterial community response to the hydrocarbon
input was also addressed using microcosms setups
established from coastal sediment samples. In nutrient-
amended microcosms established from hydrocarbon-
polluted harbour surface sediments, the temperature
was also shown to be a determining factor controlling
bacterial abundance, community structure and biodegra-
dation, by increasing the bacterial diversity under aerobic
conditions while decreasing it under anoxic conditions
[28]. In a 1000 kg sediment mesocosm, Genovese
et al. [36] found that if the sediments remained undis-
turbed and anoxic conditions were established, the addi-
tion of high loads of fuel oil resulted in a drastic loss of
diversity concomitant with the enrichment of members of
the Deltaproteobacteria, dominated by a clone previously
found in sediments affected by the Prestige spills [33] and
by known alkane-degrading and PAH-degrading anae-
robes [37,38]. It is a recurrent observation that most 16S
rRNA gene sequences of uncultured organisms retrieved
from oil polluted sediments are closely related to organ-
isms detected in similar polluted sites, which suggests a
common trend in the structuring of communities in the
presence of oil. The enrichment of members of the
Deltaproteobacteria is consistent with sulphate reduction
being the prevailing respiratory metabolism in marine
sediments which agrees with the observation that the
abundance of sulphate-reducing Deltaproteobacteria also
increased in deep-sea sediments near the DWH Macondo
wellhead [39] (reviewed in [21]). Deltaproteobacteria
also constituted the prevailing group in the anoxic layer
of subtidal sediments affected by the Prestige spill, domi-
nated by the Desulfobacteraceae [33]. Interestingly,
specialized clades of Desulfobacteraceae belonging to the
Desulfosarcina/Desulfococcus group were recently identified
as responsible for the initial steps in anaerobic short-chain
and long-chain alkane degradation in marine seeps [40].
The possible role of Deltaproteobacteria in the degradation
of hydrocarbons was directly addressed with estuarine
Current Opinion in Biotechnology 2016, 38:24–32
28 Environmental biotechnology
sediment samples incubated under sulphate-reducing
conditions [41]. The presence of crude oil stimulated
sulphate reduction, as previously observed in Mediterra-
nean mesocosms amended with crude oil [42], and may be
linked to alkane degradation [41]. Remarkably, the sul-
phate reducing bacteria enriched in the presence of crude
oil were different from the conventional groups previous-
ly associated to hydrocarbon degradation (Supplementary
Table 1), as determined from 16S rRNA gene clone
libraries. The medium-term incubation of five months
enriched the cultures in Gammaproteobacteria, mostly
related to the genus Marinobacter, and in clones related
to uncultured Peptostreptococcaceae within the Clostridiales
(Firmicutes), while after long-term incubations, when the
sulphate was depleted, the community shifted toward the
enrichment of members of the Chloroflexi, together with
Deltaproteobacteria closely related to clones previously
detected in oil-polluted sediments affected by the Prestige
oil spill [33,41]. Similarly, Rocchetti et al. [43] were
unable to detect known hydrocarbonoclastic strains in
microcosms of harbour sediment amended with acetate
and lactate to stimulate biodegradation. The analysis of a
limited number of 16S rRNA gene library clones identi-
fied members of the Alphaproteobacteria as important
players in hydrocarbon degradation under anoxic condi-
tions.
A number of studies specifically focused the upper
layer (0–5 cm) of subtidal sediments, where generally
the prevailing metabolism is aerobic. The role of tem-
perature in structuring the microbial community was
again evidenced. The alkB gene sequences retrieved
from surface sediments of a chronically polluted sub-
antarctic coastal environment were closely related to
genes of microorganisms from cold marine sediments
and soils exposed to low temperatures [44]. Interest-
ingly, the addition of crude oil to these sediments in
microcosm experiments enriched bacterial communi-
ties not previously associated with hydrocarbon degra-
dation, belonging to Gammaproteobacteria (Spongiibacter)
and Alphaproteobacteria (Maribius and Robiginitomacu-
lum). In surface sediments collected in the northern
Adriatic Sea the bacterial diversity was highest at sites
with moderate pollution and decreased as the pollution
level increased [45]. As for similar aerobic samples,
Proteobacteria (Gamma and Alpha), Firmicutes and Bac-
teroidetes were the prevailing groups, whilst most of the
retrieved alkB sequences could be affiliated to
the genus Alcanivorax. Contamination levels (including
PAHs) were also shown to negatively influence bacte-
rial richness in chemically polluted surface sediments of
the Italian Adriatic coast, although in this case Delta-
proteobacteria and Gammaproteobacteria were the most
abundant classes in the community. The analysis of
microcosm setups from a series of sediments collected
at different sites in the Gulf of Mexico showed
distinct bacterial communities at each site, confirming
Current Opinion in Biotechnology 2016, 38:24–32
the plasticity of bacterial assemblages in coastal sedi-
ments [46]. However, all of them responded to the
addition of crude oil with a transient increase in bacte-
rial diversity, where the phyla Proteobacteria, Firmicutes
and Bacteroidetes were the major players in restructuring
the community, further supporting the idea that gen-
eralists are initially favoured after a profound distur-
bance of the ecosystem. Similarly, a study targeting the
Archaea nitrifying community in coastal sediments of
the northern Gulf of Mexico showed that the arrival of
crude oil from the DWH spill produced a transient shift
in the ammonia oxidizing Archaea (AOA) community as
determined with an amoA gene microarray, concomitant
with an increase in the diversity of this group [47]. The
degradative potential of hydrocarbon oxidizing bacteria
associated to denitrification in subtidal sediments was
shown to be even higher than the aerobic metabolism
in the upper sediment layers, although it remained one
order of magnitude lower than the predominant sul-
phate reducing metabolism at deeper layers [33].
Thus, the nitrogen input from terrestrial sources can
greatly impact the redox conditions in coastal sedi-
ments and the biodegradative response [48].
Functional coherence is maintained despite
shifts in bacterial communities
Metagenomics has proved a valuable approach for de-
scribing the main functional traits in an ecosystem’s
metabolic network in environments as diverse as the
human gut, seawater, or agricultural soils, which can be
clearly distinguished by their metagenomic profile [49].
However, evidence suggests that this approach is not as
valuable as expected for capturing the functional changes
in a bacterial community when the environmental
conditions are modified. Unexpectedly, the bacterial
communities in a given ecosystem seems to have evolved
to preserve a common gene complement which consti-
tutes more than 95% of the metagenome (the so-called
core metagenome), so that only slight changes are ob-
served in the broad functional profile of a community
exposed to an external input, despite huge changes in the
bacterial community structure [50]. As a result of this
genomic ‘coherence’, a higher resolution analysis of the
metagenomic data is required to identify the relevant
changes, which are generally circumscribed to auxiliary
functions such as transport systems and transcriptional
factors, or to highly specific functions. The same seems to
be true for coastal sediment ecosystems, where exposure
to crude oil was shown to produce a complete shift in the
community structure but generated only very minor
changes in the metagenomic profile (A. Acosta-González,
PhD thesis, University of Granada, 2013; [23]). However,
a detailed insight into those genes known to be specifi-
cally related to hydrocarbon degradation revealed an
increase in the number and diversity of retrieved
sequences after crude oil treatment. A similar but more
pronounced increase in hydrocarbon degradation genes,
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 Bacterial diversity in polluted coastal sediments Acosta-González and Marqués 29
especially those related to anaerobic alkane degradation
in Deltaproteobacteria, was observed in oil-polluted
marshes after the DWH spill [51]. Similarly, the com-
parison of the metagenome of samples taken during the
first year after the DWH spill detected the differences
mainly in the hydrocarbon degradation-related sequences
and in the abundance of transport-function and specific-
function genes related to nutrient scavenging, whilst the
abundance of genes for general functions remained stable
[27]. In the metagenomic survey of the Mediterranean’s
chronically polluted sites, hydrocarbon degradation
sequences constituted less than 1% of all potential pro-
tein-coding sequences but allowed the identification of
major catabolic features common to all polluted sites
[34]. Nevertheless, more empirical work is needed to
confirm this trend in marine sediments.
Bacterial diversity in bioremediation
strategies
Ideally, the diversity analysis of oil-polluted sediments
aimed at establishing common community traits should
provide valuable tools to assess both the presence and the
type of pollution, and the potential for intrinsic bioreme-
diation, as the ultimate fate of hydrocarbons in the
environment. The structure of the bacterial community
has been prospected as an index of hydrocarbon exposure
in sediments [52], and the presence, abundance and
diversity of hydrocarbon degradation genes has been
used as an indication of biodegradation capacities in
the autochthonous community, both in aerobic and anox-
ic sediments [53–55]. The abundance of hydrocarbon
degradation-related genes suggests a high potential for
intrinsic oil remediation, even in coastal sediments with
no recent history of contamination [23]. Additionally,
biostimulation experiments have shown that the addition
of OM to crude-oil amended sediment microcosms
significantly increased the mineralization rates for
hydrocarbons and enriched particular groups of the Gam-
maproteobacteria and Alphaproteobacteria [56].
Chemical dispersants generally used in clean-up strate-
gies after a spill can result in the suppression of hydro-
carbon oxidation [57]. A promising approach to
enhanced bioremediation through biostimulation is
the concomitant production of biosurfactants by marine
hydrocarbon-degrading consortia (primarily composed
of Gammaproteobacteria species related to Alcanivorax,
Halomonas and Marinomonas), and single cultures of
Alcanivorax borkumensis SK2 and Paracoccus marcusii
[58]. This latter strain, isolated from coastal sediments,
was especially suitable for bioremediation strategies due
to its capacity to remain trapped within the oil phase,
thus avoiding the potential dilution of the biosurfactant
into the seawater. Air-sparging has also been tested in
the remediation of a simulated spill in sediment meso-
cosm set-ups [36]. This treatment produced a transient
increase in strains related to the genera Alcanivorax,
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Cycloclasticus and Marinobacter, which resulted in a sig-
nificant reduction of the toxicity of the polluted sedi-
ments. However, the economical sustainability of such
protocols should be carefully evaluated.
Bacterial diversity can also be exploited in innovative
approaches to sediment bioremediation, such as the use
of electrodes made of conductive material, which were
inserted into the sediment to stimulate hydrocarbon
oxidation by means of creating an electrochemical con-
nection between the anoxic polluted sediments and the
aerobic overlaying water. A significant increase in biodeg-
radation rates can be obtained with this approach, al-
though the role of the electrode-associated microbial
community involved in the process remains to be deter-
mined [59].
As compared to terrestrial environments such as soil and
aquifers, the cultivable diversity of marine hydrocarbon
oxidizers is low. However, a substantial number of hy-
drocarbon degrading strains have been obtained from
various polluted coastal sediments (Supplementary
Table 1). Although the phylogeny of the isolated marine
hydrocarbon oxidizers belongs to the four main phyla that
microbiologists have traditionally cultivated, marine gen-
era are definitely different to described soil or aquifer
genera. Whilst the isolation of anaerobic hydrocarbon
degraders has been reported to be more difficult than
for other anaerobes, the description of new anaerobic
degradation pathways for compounds such as naphtha-
lene, 2-methylnaphthalene and alkanes has been possible
due to the cultivation of several marine strains with
anaerobic degradative capacities [60–62]. Furthermore,
several popular aerobic hydrocarbon degrading strains
(i.e., Alcanivorax borkumensis SK2, Cycloclasticus pugetii
PS-1, Vibrio cyclotrophicus P-2P44 and Marinobacter hydro-
carbonoclasticus SP17) are actually facultative anaerobes
able to reduce nitrate (Supplementary Table 1), but their
anaerobic metabolisms associated to oil degradation has
not been verified. Finally, in many cases, species with
degradative capacities can only be cultivated as consortia
[63].
Conclusions
Oil spill accidents have shown a tendency to decrease in
recent decades. However, accidents such as the DWH
blowout, the worst accident in the history of the industrial
era, and the continuous input of many other pollutants
into the coastal environment lead to the demand to
continue the research on the role of microorganisms in
the natural and the induced attenuation of pollutants. A
great deal of effort should be devoted to understanding
the role of microorganisms in the restoration of an eco-
system where the world’s population is concentrated
(about 40% of the world’s population inhabits areas within
100 km of the coastline, with a consequent important
influence on the sediment ecosystem) [64].
Current Opinion in Biotechnology 2016, 38:24–32
30 Environmental biotechnology
Whilst the key players in the aerobic biodegradation of
the main hydrocarbon constituents of oil after a spill
incident have been identified in the water column
and beach sand, future research should focus on anoxic
polluted sediments. Although the hitherto available in-
formation is still limited, current data suggest that, as for
the aerobic ecosystems, anoxic sediments affected by
hydrocarbon input will be enriched in specific bacterial
taxa involved in anaerobic hydrocarbon biodegradation.
Evidence clearly indicates that sediment environments
are more variable and complex than their overlaying water
body, and will thus require greater efforts to better
understand the functioning of their microbial communi-
ties, including the insufficiently studied effect of the
presence of protists, of the bacterivorous meiofauna
and of viruses that may affect bacterial populations and
the efficiency of hydrocarbon degradation [65]. The po-
tential for an efficient biodegradation depends on geo-
chemical conditions (mainly the availability of terminal
electron acceptors) but is also dependent on nutrient
availability and temperature. Unfortunately, the difficul-
ties of isolating hydrocarbon degrading anaerobes from
marine samples complicate a clear identification of the
relevant strains involved in the response toward the input
of crude oil in these ecosystems. Linking the microbial
diversity to the efficiency of biodegradation would pro-
vide new biotechnologically relevant opportunities to
improve the success of bioremediation processes by de-
termining the best conditions for biostimulation for the
degraders. The application of available ‘omics’ tools for
characterizing the microbial response against external oil
input into marine environments will allow scientists to
understand the structure and dynamics of specific bacte-
rial communities responding to oil spills over time. Future
work should improve the analysis of community struc-
tures by examining the lowest taxonomical categories.
Furthermore, preserving the sediment structure during
the sampling process would help to compare sites and
unify the resulting data. Finally, analyses should take into
account that marine sediments harbour other pollutants
(organic and inorganic) that affect biodegradation rates
and that crude oil contamination is generally accompa-
nied by various chemical pollutants that will also lead to
specific microbial responses.
Acknowledgements
This work was supported by the European Regional Development Fund
FEDER and grants from the Junta de Andalucı́a (P08-CVI03591), from the
Spanish Ministry of Economy and Competitiveness (BIO2014-54361-R),
and from the European Union’s 7th Framework Program under Grant
Agreement 312139. Alejandro Acosta-González is recipient of an ‘Es
Tiempo de volver 2015–2016’ postdoctoral fellowship from Colciencias and
La Sabana University (Bogotá, Colombia).
Appendix A. Supplementary data
Supplementary material related to this article can be
found, in the online version, at http://dx.doi.org/10.
1016/j.copbio.2015.12.010.
Current Opinion in Biotechnology 2016, 38:24–32
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