Article

Deep-Sea Oil Plume Enriches Indigenous Oil-Degrading Bacteria

MS 70A-3317, One Cyclotron Road, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Science (Impact Factor: 33.61). 10/2010; 330(6001):204-8. DOI: 10.1126/science.1195979
Source: PubMed

ABSTRACT

The biological effects and expected fate of the vast amount of oil in the Gulf of Mexico from the Deepwater Horizon blowout
are unknown owing to the depth and magnitude of this event. Here, we report that the dispersed hydrocarbon plume stimulated
deep-sea indigenous γ-Proteobacteria that are closely related to known petroleum degraders. Hydrocarbon-degrading genes coincided
with the concentration of various oil contaminants. Changes in hydrocarbon composition with distance from the source and incubation
experiments with environmental isolates demonstrated faster-than-expected hydrocarbon biodegradation rates at 5°C. Based on
these results, the potential exists for intrinsic bioremediation of the oil plume in the deep-water column without substantial
oxygen drawdown.

Download full-text

Full-text

Available from: Yvette Piceno
  • Source
    • "However, the ability of the microbial community to degrade petroleum hydrocarbons is poorly known in cold and brackish marine systems such as the Baltic Sea. In the water body of the ocean, Gammaproteobacteria are most often responsible for the degradation process of petroleum hydrocarbons for instance in the Gulf of Mexico (Hazen et al. 2010, Gutierrez et al. 2013), the North Sea (Brakstad and Lodeng 2005) and in the Mediterranean (Cappello et al. 2007). On the other hand, in the Baltic Sea, the dominant bacterial phyla responsible for the degradation of oil seem to differ along the salinity gradient: in lower salinity Betaproteobacteria and Actinobacteria are enriched (Reunamo et al. 2013), while in the higher salinity Alpha– and Gammaproteobacteria take over (Viggor et al. 2013). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Abstract Mineral concretions or nodules are found from the Oceans, lakes and in soils. Their element content has been studied well due to possible commercial use, but interest in their bacterial communities has risen due to environmental implications. Iron–manganese (Fe–Mn) concretions cover vast bottom areas in the Gulf of Bothnia and the Gulf of Finland (GoF). These mineral precipitates sequester several times higher amounts of Fe, Mn, phosphorus (P) and arsenic (As) than the surrounding sediment. Despite their large occurrence, the environmental significance of the concretion bottoms has been a somewhat understudied issue. The aim of the present study was to investigate the bacterial community structure, and possible microbial contributions to the formation and decay of concretions in the Baltic Sea. The further aim was to study how concretions respond to different environmental stresses, such as anoxia and crude–oil contamination, which the concretions may encounter in GoF bottoms. The methods used were determination of solid and dissolved Fe, Mn, P and As during microcosm incubations under oxidising or reducing conditions, also with crude oil and 14C–naphthalene added. Bacterial community structure was studied by cloning and sequencing taxonomic marker gene (partial 16S rRNA gene), and quantification of polycyclic aromatic hydrocarbon degradation (PAH–RHDα) gene copy number. Morphologically and taxonomically diverse bacteria colonise both the pitted surface and the porous interior of spherical concretions. Half of the population was affiliated to uncultured Proteobacteria, and one third was unclassified bacteria. Concretion bacteria populations appeared typical for this habitat. Bacteria may significantly affect the formation of the concretions in the GoF, because known Mn–oxidising bacteria were enriched in Mn2+–containing liquid and semi–solid media. The Fe2+–oxygen gradient favoured the enrichment of species which are known to reduce Fe and to degrade petroleum hydrocarbons. Concretions released Fe and Mn during anoxic conditions only if they were supplied with labile carbon source, indicating bacterial metal reduction. The dissolution of Mn was the highest, but the release of P and As followed Fe. The release rates (µmol m-2 d-1) from the concretions were within the range of the previously estimated fluxes out of the GoF sediment. Still, the concretions released only minor proportions (0.1–0.4%) of their total Fe, Mn, P and As content during a prolonged anoxic period. Concretions and sediment had a very similar capacity to remove petroleum compounds and mineralise naphthalene under oxic as well as anoxic conditions, and over one half of the added crude oil disappeared from the microcosms. Copy numbers of PAH–degradation genes increased, indicating biological degradation potential of PAHs by the concretion bacterial community. Both concretions and sediment had rich and clearly different bacterial communities prior to and also past the exposure to crude oil. Only 9% of the OTUs were shared between the initial concretions and the sediment. Concretion bacterial sequences were affiliated to bacterial groups previously found from concretions and metal rich environments (ecotypes) even after the crude–oil exposure, whereas sediment bacterial sequences were similar to those originating from sediments and oil–contaminated sites. Tiivistelmä Konkretiot (myös nk. nodulit) ovat mineraalisaostumia, joita esiintyy merien ja järvien pohjilla sekä maassa. Konkretioiden alkuainekoostumusta on tutkittu paljon niistä mahdollisesti saatavan raaka–aineen takia. Kiinnostus konkretioiden mikrobiyhteisöjä kohtaan on myös kasvanut arvioitaessa konkretioiden merkitystä ympäristössään. Rauta–mangaanikonkretioita (Fe–Mn) löytyy laajoilta alueilta Pohjan– ja Suomenlahden pohjilta, joissa niihin on saostunut huomattavasti suurempia määriä rautaa, mangaania, fosforia (P) ja arseenia (As) kuin ympäröivään sedimenttiin. Laajuudestaan huolimatta konkretiopohjien merkitystä ympäristölleen on tutkittu vähän. Tämän työn tarkoitus oli tutkia konkretioiden bakteeriyhteisöjen rakennetta ja mikrobien vaikutusta konkretioiden muodostumiseen ja hajoamiseen Itämeressä. Tutkittiin myös kuinka erilaiset ympäristön stressitekijät, kuten hapettomuus ja raakaöljyllä saastuminen, voivat vaikuttaa konkretiopohjiin Suomenlahdella. Konkretioista määritettiin niiden Fe, Mn, P ja As pitoisuudet. Mitattiin myös kuinka paljon ja miten nopeasti määritetyt aineet liukenivat konkretioista eri koeolosuhteissa. Konkretionäytteitä inkuboitiin mikrokosmoksissa hapellisissa ja hapettomissa olosuhteissa, myös raakaöljyn ja radioisotoopilla leimatun 14C–naftaliinin kanssa. Bakteeriyhteisöjä tutkittiin kloonaamalla ja sekvensoimalla bakteereille spesifejä 16S rRNA geenejä, joiden vastaavuutta verrattiin sekvensseihin kansainvälisissä tietokannoissa. Bakteerien geneettistä potentiaalia hajottaa polyaromaattisia hiilivetyjä (PAH) tutkittiin mittaamalla PAH–RHDα geenin lukumäärää kvantitatiivisella PCR–menetelmällä. Monimuotoinen bakteerilajisto elää pallomaisten konkretioiden röpelöisellä pinnalla ja huokoisessa sisuksessa. Puolet lajistosta voitiin luokitella kuuluvaksi Proteobakteereihin mutta kolmasosa bakteerilajeista oli tuntemattomia. Konkretioiden bakteeriyhteisö ilmeni olevan tälle habitaatille tyypillinen (ekotyyppi). Lähimmät vastaavuudet sekvenssitietokannassa olivat peräisin konkretioista tai muista metalleja sisältävistä ympäristöistä. Bakteerit voivat merkittävästi vaikuttaa konkretioiden muodostumiseen Suomenlahdella. Koeolosuhteissa konkretioista peräisin olevat bakteerit hapettivat mangaania ja osallistuivat raudan hapettumiseen. Hapettavissa olosuhteissa rikastuneisiin bakteereihin kuului muun muassa tunnettuja mangaania hapettavia lajeja ja rautaa pelkistäviä lajeja. Hapettomissa olosuhteissa konkretioista vapautui rautaa ja mangaania merkittäviä määriä vain silloin kun metalleja pelkistäville konkretiobakteereille oli tarjolla lisätty hiilen lähde. Mangaania liukeni eniten mutta fosforin ja arseenin vapautuminen oli riippuvaista raudan liukenemisesta konkretioista. Metallien liukenemisnopeudet (µmol m-2 d-1) konkretioista olivat samaa suuruusluokkaa kuin aikaisemmin arvioidut nopeudet Suomenlahden sedimenteistä. Siitä huolimatta, ainoastaan alle prosentti (0.1–0.4%) konkretioiden sisältämästä raudasta, mangaanista, fosforista ja arseenista vapautui usean hapettoman koeviikon aikana. Konkretiot saattavat siis pidättää näitä aineita paremmin kuin ympäröivä sedimentti kausittaisten hapettomien jaksojen ajan Suomenlahdella. Konkretioilla ja niitä ympäröivillä sedimenteillä oli samantasoinen kyky poistaa raakaöljyä ja hajottaa naftaleenia hapellisissa ja hapettomissa olosuhteissa. Vähintään puolet lisätystä raakaöljystä katosi mikrokosmoksista biohajoamisen ja osin kemiallisen hajoamisen/ sitoutumisen takia. PAH–RHDα geenin lukumäärää kasvoi, mikä viittasi konkretiobakteerien mahdolliseen kykyyn hajottaa PAH–yhdisteitä. Konkretioiden ja niitä ympäröivien sedimenttien bakteeriyhteisöt poikkesivat toisistaan aluksi ja jopa raakaöljyaltistuksen jälkeen. Vain noin 9% taksoneista oli konkretioissa ja sedimentissä samoja. Raakaöljylle altistaminen ei vähentänyt bakteeriyhteisöjen monimuotoisuutta tai johtanut tunnettujen öljynhajottajalajien rikastumiseen. Sedimenttiä sisältävissä mikrokosmoksissa bakteerisekvenssien lähimmät vastaavuudet löytyivät sedimenteistä ja öljyllä saastuneista paikoista. Konkretioiden ominaisuudet ovat suunnanneet bakteeriyhteisöjen muodostumista tälle mikrohabitaatille tyypilliseksi.
    Full-text · Thesis · Nov 2015
  • Source
    • "Since we had not used the metatranscriptomic data for clustering, the extensive mapping of the transcriptome reads to DWH O. desum confirms the link between its abundance in this dataset and its activity in the environment. The 1,375 nt 16S rRNA gene from DWH O. desum matched the uncultured Oceanospirillales bacterium clones from proximal and distal stations published by Hazen et al. (2010) with over 99% sequence identity. The first cultured organism matched to O. desum 16s rRNA by BLAST against the NCBI's refseq genomic database was Oleispira antarctica strain RB-8 (Oceanospirillales; Oceanospirillaceae) at 92% identity, and the O. desum 23S rRNA gene matched that of Oleispira antarctica at 93% identity. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Advances in high-throughput sequencing and ‘omics technologies are revolutionizing studies of naturally occurring microbial communities. Comprehensive investigations of microbial lifestyles require the ability to interactively organize and visualize genetic information and to incorporate subtle differences that enable greater resolution of complex data. Here we introduce anvi’o, an advanced analysis and visualization platform that offers automated and human-guided characterization of microbial genomes in metagenomic assemblies, with interactive interfaces that can link ‘omics data from multiple sources into a single, intuitive display. Its extensible visualization approach distills multiple dimensions of information about each contig, offering a dynamic and unified work environment for data exploration, manipulation, and reporting. Using anvi’o, we re-analyzed publicly available datasets and explored temporal genomic changes within naturally occurring microbial populations through de novo characterization of single nucleotide variations, and linked cultivar and single-cell genomes with metagenomic and metatranscriptomic data. Anvi’o is an open-source platform that empowers researchers without extensive bioinformatics skills to perform and communicate in-depth analyses on large ‘omics datasets.
    Full-text · Article · Oct 2015 · PeerJ
  • Source
    • "Petroleum hydrocarbons released under high-pressure undergo a series of interconnected physical and chemical processes that affect their fate and transport in the deep sea (Camilli et al., 2010; Kessler et al., 2011; Reddy et al., 2012). Following the direct injection of disperant (Corexit 9527A and 9500A) to the Macondo well head at a depth of 1544 meters (Hazen et al., 2010), a large oil plume persisted for months centered at approximately 1100 meters (m) depth, without substantial biodegradation (Camilli et al., 2010). Oil spewing from the wellhead encountered turbulent mixing and was emulsified as a result of its reduced buoyancy at depth and the application of dispersant (Fodrie & Heck Jr., 2011). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Cold-water corals serve as important foundation species by building complex habitat within deep-sea benthic communities. Little is known about the stress response of these foundation species yet they are increasingly exposed to anthropogenic disturbance as human industrial presence expands further into the deep sea. A recent prominent example is the Deepwater Horizon oil-spill disaster and ensuing clean-up efforts that employed chemical dispersants. This study examined the effects of bulk oil-water mixtures, water-accommodated oil fractions, the dispersant Corexit9500A®, and the combination of hydrocarbons and dispersants on three species of corals living near the spill site in the Gulf of Mexico between 500–1100 m depths: Paramuricea sp. B3, Callogorgia delta and Leiopathes glaberrima. Following short-term toxicological assays (0–96 h), all three coral species examined showed more severe health declines in response to dispersant alone (2.3–3.4 fold) and the oil-dispersant mixtures (1.1–4.4 fold) than in the oil-only treatments. Higher concentrations of dispersant alone and the oil-dispersant mixtures resulted in more severe health declines. C. delta exhibited somewhat less severe health declines than the other two species in response to oil and oil/dispersant mixture treatments, likely related to its increased abundance near natural hydrocarbon seeps. These experiments provide direct evidence for the toxicity of both oil and dispersant on deep-water corals, which should be taken into consideration in the development of strategies for intervention in future oil spills.
    Full-text · Article · Apr 2015 · Deep Sea Research Part II Topical Studies in Oceanography
Show more