Oil-eating bacteria are often the unsung heroes when it comes to oil spill response. We spoke with Heriot Watt Associate Professor Tony Gutierrez about his recent work cracking the genetic code of these intriguing organisms
Dr. Tony Gutierrez’ freezer is an interesting place. Deep in the bowels of the his laboratory at Heriot Watt University, under lock and key, are samples of bacteria from locations across the world’s seas and oceans, many of which could hold the key to new surfactants, biopolymers and even how best to respond to future oil spills.
Some samples are particularly infamous. When the Deepwater Horizon rig explosion occurred at the Macondo prospect 2010, an estimated 4.1 million barrels of crude gushed into the Gulf of Mexico over 87 days. During that time, particular bacteria attuned to digesting hydrocarbons bloomed spectacularly, allowing researchers and the authorities to monitor their progress as they undertook a major clean-up operation.
Gutierrez is one of the leading experts on such oil-degrading bacteria. In 2010, he was working on postdoctoral research at the University of North Carolina, Chapel Hill, under a Marie Curie fellowship, and access to the Gulf of Mexico via research cruises meant he could conduct detailed microbiological research contaminated samples collected from sea surface oil slicks and in deep waters. “When the oil spill happened, colleagues at the University called me and said that this was a big spill, and that this was a huge opportunity to do some really cool work and to investigate the microbiological response.”
As a microbial ecologist specialising in the marine environment, Gutierrez’ expertise lie in using sophisticated molecular biology techniques – DNA stable isotope probing and metagenomic tools, for example – to identify and study important roles that bacteria play in marine environments. In doing do, he has been able to discover new species and families of bacteria, and in work outlined in one of his most recent papers, crack the genetic code of the species that played a key role in the biodegradation during the Deepwater Horizon spill.
Oceans of organisms
The bacteria Gutierrez and his associates have investigated, which eat oil, all occur naturally and are found throughout the world’s oceans, and at all depths. “If there’s no oil in a particular environment these organisms are in very low abundance – less than one cell per litre of seawater,” he explains. “But when oil enters this environment these organisms will bloom and thrive, whilst other bacteria may die due to the toxic effects of the oil or they may survive by breaking down by-products from the breakdown of the oil. There are many different species of oil-degrading bacteria, but some have evolved over time to eat oil with a ravenous appetite.”
Some bacteria he describes as “generalists” – they can eat oil in addition to other food substances. But others consume the hydrocarbons in crude oil almost exclusively, eschewing any other potential food sources. “Their genetic capability has not evolved, or it has lost the ability to use sugars and other simple-to-degrade carbon sources, but if you give them oil they will thrive on it, it’s remarkable” he says.
That means that these particular organisms can play a vital role in clean-up operations. While response teams can work to localise the oil on the water’s surface or separate it from seawater to salvage it, “a lot of the oil that enters the ocean either stays there, or it is degraded and ultimately removed by the activities of these bacteria.”
This is the process that occurred during Deepwater Horizon. “Essentially the Gulf of Mexico was like a culture flask for us,” he says. “We went, sampled it and were able to analyse what was actually happening almost in real time over a period of almost 3 months that the oil continued to gush into the Gulf of Mexico.”
Several years later, and having accepted his current role as Associate Professor at Scotland’s Heriot Watt University in Edinburgh, Gutierrez revisited some of the samples taken from the Gulf. With his colleague Brett Baker, an expert in genome reconstruction at the University of Texas, and postdoctoral researcher Nina Dombrowski at the Baker Lab, he proposed sequencing the genome of these particular oil-eating bacteria to discover more about the genetic pathways that allow them to degrade the various hydrocarbons in the Macondo oil that gushed into the Gulf.
Crude oil, of course, contains many different chemical hydrocarbons, from long saturated chains through to the more toxic polycyclic aromatic hydrocarbons (PAHs) and then heavier asphaltenes and resins. Through genetic sequencing, the researchers were able to identify pathways used by some of the key bacteria to break down oil during the spill, and in the case of some strains, to successfully reconstruct almost complete genomes.
“What was interesting is that with some bacteria, like Marinobacter, we found complete pathways for the breakdown of long-chain saturated hydrocarbons. For others, like Alcanivorax, we did not identify complete pathways for the breakdown of PAHs – they had snippets of genes within a complete pathway. This suggested to us that these bacteria are not able to break down the toxic PAHs completely, but they played an important part together with the rest of the oil-degrading bacterial community in degrading these toxic hydrocarbons,” Gutierrez explained.
They also identified which bacteria appeared to work best at different depths. Unclassified members of the group called Oceanospirillales, they found, worked best at degrading alkanes in deep waters where a massive oil plume had formed at around 1,000-1,200 metres depth. Meanwhile, the reconstructed genomes of bacteria such as Rhodospiralles and Cycloclasticus were responsible for degrading the more toxic polycyclic aromatics.
“We knew that certain bacteria will respond…but we didn’t know how this was co-ordinated. By reconstructing the genomes of these bacteria we’ve discovered [that] the bacteria work as a community to degrade the oil,” he said. “That was interesting. The results show that you can’t just say one bacteria was a major factor.” In their paper, Dombrowski compared the bacteria to an orchestra playing different sequences of a larger piece of music; Gutierrez likened the process to a bee colony, each organism playing its part in a functional hive.
That is not to say that the process is perfect, nor is it justification for a complacent spill response. The waxier asphaltenes and resins remain very difficult to degrade, even for these bacteria, meaning that these substances frequently wash ashore, or may eventually be buried in the sediment on the sea floor.
As with tackling asphaltene and paraffin deposits in industrial settings, there is no easy solution for their removal after a spill. Gutierrez is less bullish on the possibility of introducing oil-eating bacteria as part of targeted attacks on these deposits, largely because the existing bacteria will always be better adapted: “Adding a microorganism in order to enhance degradation has been attempted in aquatic systems and on land before, and there have been times where this approach has been effective – but at the end of the day it is better to allow the indigenous microorganisms to do the job. They are already adapted to that environment, so it’s often a matter of trying to enhance their metabolic activities, such as by adding some nutrients, to speed up their biodegradation capabilities.”
Likewise, these bacteria are unlikely to offer any help in paraffin removal in a pipeline or refinery: “In cases like this, often prevention is better than the cure.”
Dispersants pose another problem. Although these chemicals can help to break up hydrocarbons into smaller droplets, thereby increasing the surface area of the oil for the bacteria to attack, dispersants can often be toxic to marine life, including to oil-degrading bacteria. Indeed, the use of some dispersants such as Corexit – as was used in the Gulf – has been criticised because, while effective, its long-term effects are relatively unknown.
Yet Gutierrez noted that: “Our findings suggest that some of the bacteria that responded to the spill in the Gulf may be able to degrade the dispersant Corexit, potentially rendering it ineffective after having done its job.” If so, that may go some way towards mitigating concerns over the long-term impact of such dispersants. However, that may be disputed: another recent study by Samantha Joye, a professor of marine sciences in the US’ University of Georgia reported that in lab tests, Corexit did not aid bacteria as much as may have been thought, and even impaired the growth of oil-eating Marinobacter bacteria.
The potential hazards of dispersants like Corexit highlight the need for greener options. “One thing the oil and gas industry should consider as part of oil-spill contingency plans is the use of bio-based eco-friendly dispersants. This is something we are working on in my research group,” Gutierrez added.
Gutierrez and his colleagues’ genome research now informs his latest work investigating potential bioremediation plans in the northeast Atlantic. Despite having been an area of oil and gas operations since the mid 1960s, there remains a distinct lack of information on the water column microbiology of the region – a “knowledge gap” identified in the preliminary assessment of the EU Marine Framework Directive. As oil exploration expands into deeper waters (>1,000m depth), such as in the Faroe Shetland Channel (FSC), Gutierrez explains: “My group has been working to produce a baseline of the water column microbiology for the FSC, including an understanding of the presence and activities of oil-degrading bacteria in this region.”
“We are compiling a spatial and temporal microbiological baseline for the FSC, which would be a first in UK waters,” he continued. “The FSC is an area with a very dynamic oceanography. In the advent of a deepwater oil spill in this area, a subsurface oil plume could form in the water column, similar to that which occurred during the Deepwater Horizon oil spill.”
As with the bacterial studies in the Gulf of Mexico, the group will also be investigating the use and effects of dispersants in the FSC, which could potentially be employed in the event of an oil spill in this region of the Atlantic, with a view to advising UK authorities on those which prove to be most effective and have the least toxicological effects on the natural ecosystem. Gutierrez is a Principal Investigator of a 4.8 million euro EU project to discover novel types of bio-surfactants (aka bio-dispersants) for commercial applications, and he aims to develop his network towards the discovery of natural bio-based dispersants for combatting oil spills and that will pose less of a concern to the environment compared to their synthetic counterparts.
When it comes to oil spills, prevention undoubtedly remains better than the cure. Yet it is encouraging to find that bacteria in the Gulf of Mexico, the FSC and across the world may yet provide new insight into how hydrocarbons are broken down in marine environments, and how best to tackle a spill if it does occur. Indeed, Gutierrez may yet have a few surprising discoveries lurking in his well-stocked freezer.