However, in the deep Gulf of Mexico the  devastation was hidden 2 kilometers below in the dark depths of the ocean .  

Investigations of the site began just months after the oil spill using a remote operated vehicle. Dramatic losses of deep-sea biodiversity in the immediate aftermath of the spill were documented by Louisiana State University researchers.  Additional surveys continued for one year until the summer of 2011. Meanwhile, ship-board collection of sesdiments monitored the slow recovery of life, noting a 40-90% reduction in diversity, on the deep-sea floor until 2014

…after which monitoring stopped. 

In 2017, Clifton Nunnally and I with a team of scientists revisited the DWH wreckage and Macondo wellhead site for the first time since monitoring ceased in 2011.  Video captured a deep sea unrecovered after 7 years.  Showing a seafloor, marred by wreckage, physical upheaval and sediments covered in black, oily marine snow unrecognizable from the healthy habitats in the deep Gulf of Mexico.

Near the wreckage and wellhead, many of the animal characteristic of other areas of the deep Gulf of Mexico, including sea cucumbers, Giant Isopods, glass sponges, and whip corals, were absent.  What remained was a homogenous wasteland in contrast to the rich heterogeneity of life seen in healthy deep sea.  

Conspicuously absent were the sessile animals that typically cling to any type of hard structure in an otherwise soft, muddy habitat.  Hard substrate in the deep sea is a valuable commodity but at the Deepwater Horizon site metal and other hard substrates were devoid of typical deep-sea colonizers.

Sea floor communities at the impact site were also characterized by high densities of decapod shrimp and crabs.  Crabs showed clearly visible physical defects and sluggish behavior compared to the healthy crabs outside of the impacted zone of the Deepwater Horizon wellhead.  

We hypothesize these crustaceans are drawn to the site because degrading hydrocarbons may serve as luring sexual hormone mimics. Once these crustaceans reach the site they may become too unhealthy to leave in a La Brea Tarpit scenario.

The scope of impacts may extend beyond the impacted sites with the potential for impacts to pelagic food webs and commercially important species.

Our Recommendations:

1. Longer funding cycles are needed to assess the recovery of deep-sea ecosystems.
2. Increased commitment to fund pre-impact baseline surveys.
3. Stronger, more explicit policy to support future monitoring efforts.

Overall, deep-sea ecosystem health, 7 years post spill, is recovering slowly and lingering effects may be extreme. 

In an ecosystem that measures longevity in centuries and millennia the impact of 4 million barrels of oil constitutes a crisis of epic proportions. 

The post Slow Road to Recovery after the Deepwater Horizon oil spill for Deep-Sea Communities first appeared on Deep Sea News.

From the darkness emerges a boot. An old leather, steel-toed, work boot. It shouldn’t be there resting on the seafloor nearly two kilometers deep. I’m speachless. Even knowin this was going to be one of the toughest dives of my career, I’m still not prepared.

Seven years prior in 2010, Marla Valentine and Mark Benfield were the first scientist to visit the deep-sea floor after the Deepwater Horizon accident. On 20 April 2010, and continuing for 87 days, approximately 4 million barrels spilled from the Macondo Wellhead making it the largest accidental marine oil spill in history. Just months after the oil spill, Valentine and Benfield conducted video observations with a remotely operated vehicle (ROV) of the deep-sea impact. Overall, they found a deep-sea floor ravaged by the spill. Much of the diversity was lost and the seafloor littered with the carcasses of pyrosomes, salps, sea cucumbers, sea pens, and glass sponges.

Researchers continued to find severe impacts on deep-sea life. The numerical declines were staggering within the first few months; forams (↓80–93%), copepods (↓64%), meiofauna (↓38%), macrofauna (↓54%) and megafauna (↓40%). One year later, the impacts on diversity were still evident and correlated with increases in total petroleum hydrocarbons (TPH), polycyclic aromatic hydrocarbons (PAH), and barium in deep-sea sediments. In 2014, PAH was still 15.5 and TPH 11.4 times higher in the impact zone versus the non-impact zone, and the impact zones still exhibited depressed diversity. Continued research on corals found the majority of colonies still had not recovered by 2017. However, studies examining the impacts of the DWH oil spill on most deep-sea life ended in 2014.

This gap in knowledge on the lingering impacts of one of the largest oil spills of all time is why I sit here in this cold, dark, ROV control room staring at a work boot in the abyss. A year prior, I had reached out to Mark Benfield about replicating his ROV methods and locations. I am here seven years after his study beginning to replicate his first video transect.

Within minutes of reaching the seafloor with the ROV, every scientist on the vessel staring at monitors showing live video from remote seafloor knew something was wrong. As Mark Benfield, Clif Nunnally, and I report in a new open-access article, the deep sea was not recovering at the impact site.  The seafloor was unrecognizable from the healthy habitats in the deep Gulf of Mexico, marred by wreckage, physical upheaval and sediments covered in black, oily marine snow.

Near the wreckage and wellhead, many of the animals characteristic of other areas of the deep Gulf of Mexico, including sea cucumbers, Giant Isopods, glass sponges, and whip corals, were absent.  What we observed was a homogenous wasteland, in great contrast to the rich heterogeneity of life seen in a healthy deep sea.

Conspicuously absent were the sessile animals that typically cling to any type of hard structure in an otherwise soft, muddy habitat.  Hard substrate in the deep sea is a valuable commodity but at the Deepwater Horizon site metal and other hard substrates were devoid of typically deep-sea colonizers.

The seafloor at impact site was characterized by high numbers of shrimps and crabs.  Crabs showed clearly visible physical abnormalities and sluggish behavior compared to the healthy crabs we had observed elsewhere.  We believe these crustaceans are drawn to the site because degrading hydrocarbons serve as luring sexual hormone mimics. Once these crustaceans reach the site they may become too unhealthy to leave much like those prehistoric mammals and the Le Brea tarpits.

The ROV dive began with a boot belonging to one of the workers on the Deepwater Horizon rig. The dive ended at the wellhead, now capped with a memorial to those workers who lost their lives. A dive bookended with reminders of the human tragedy of the oil spill. The narrative that unfolded between these was an environmental catastrophe. In an ecosystem that measures longevity in centuries and millennia the impact of 4 million barrels of oil continues to constitutes a crisis of epic proportions.

Valentine, Marla M., and Mark C. Benfield. “Characterization of epibenthic and demersal megafauna at Mississippi Canyon 252 shortly after the Deepwater Horizon Oil Spill.” Marine Pollution Bulletin 77.1-2 (2013): 196-209.

McClain, Craig R., Clifton Nunnally, and Mark C. Benfield. “Persistent and substantial impacts of the Deepwater Horizon oil spill on deep-sea megafauna.” Royal Society Open Science 6.8 (2019): 191164.

The post The lingering and extreme impacts of the Deepwater Horizon oil spill on the deep sea first appeared on Deep Sea News.

“Even though this is a BRITISH Petroleum spill, it’s AMERICA’S Ocean”

The post Nicholas Cage is making a movie about the Deepwater Horizon Oil Spill first appeared on Deep Sea News.

Check out this stunningly, beautiful recap of where we are now and the questions still remaining. This video, featured by onEarth Magazine, was concocted by the one and only Perrin Ireland (@experrinment). Having seen Perrin create exquisite works of science art live, I speak from experience when I say she is nothing short of spectacular.

The post Day 1,825 first appeared on Deep Sea News.

Just near 6 million liters of oil spilled out of Macondo well in 2010, about 6 supertankers worth of oil. The ramifications of the oil spill are still being documented and far reaching but included aberrant protein expression in fish gills, altered bacterial communities, and a whole suite nastiness in dolphins. At three different sites deep-sea corals appear to be impacted (study 1, study 2). Corals were covered with brown flocculent material and showed telltale signs of stress including excess mucus, enlargement of the skeletal elements (sclerites), and tissue loss. But new work suggests that it was not the oil that leads to unhealthy and dying corals rather dispersant.

Nearly 7 million liters of oil dispersants were applied during the cleanup efforts, 3 million of these in the deep sea directly near the wellhead. Yet little is known how oil and the dispersant, and the mixture of the two, impacts deep-sea corals. New work by Danielle DeLeo and colleagues sets out to address this in three different coral species. The group collected individual corals from the deep Gulf of Mexico using remote operated vehicles. On board corals were exposed to crude oil (collected from Macondo during the spill, dispersant (Corexit 9500A), a mixture of the two, and a seawater control.

All three deep-sea coral species examined showed more severe declines in health in response to dispersant alone and the oil-dispersant mixtures than the oil-only treatments. To restate, the dispersant was more toxic than the oil. Dispersants are known to disrupt the normal function of cell and organelle membranes. This means molecules are not transported normally across the membranes and cells cannot osmoregulate. Dispersant mixed with oil increases polycyclic aromatic hydrocarbons that organisms break down into toxic forms. Basically, the dispersant, as designed, increased the proportion of crude oil compounds that were biologically available.

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The post Given the choice, corals would prefer oil to dispersant first appeared on Deep Sea News.

• Fukushima radiation leak
• Starfish wasting disease
• the Deepwater Horizon oil spill
• California oarfish “mortality event”
• Hurricane/Superstorm Sandy
• the “great Pacific garbage patch”
• the current Atlantic dolphin UME
• the collapse of various fisheries, exemplified by the Long Island Sound lobster fishery

So what’s wrong with debating these fascinating topics?  Well nothing, as long as the discussions are based on reason, information and, frankly, reality.  Also nothing, as long as there actually IS a debate, which isn’t always the case.   Here are some examples of the sort of reasoning that we have seen in comments, emails and tweets about the above examples:

• Starfish wasting disease. Starfish are melting. Radiation leaked into the ocean at Fukushima. Therefore Fukushima caused the starfish melting.
• Hurricane/Superstorm Sandy.  Hurricane Sandy happened. Then dolphins began dying on the Atlantic coast. Therefore Sandy caused the Atlantic dolphin UME.
• The “great Pacific garbage patch”.  There’s a giant patch of garbage out there.  If we could just sort of scoop it up, that would be good.  Someone should invent something to do that.
• The Long Island Sound lobster fishery. “They” sprayed insecticides in the tri-state area to control mosquito populations.  Around the same time, lobsters died.  Therefore insecticide spraying killed lobsters.

Among these sorts of comments and communications dwell many types of formal and informal logical fallacies, that is, flawed reasoning.  A common one is Arguing from Ignorance which is not meant as an insult, but is defined as “assuming that a claim is true because it has not been proven false”; this can be seen as a facet of Arguing from Silence, where a cause is assumed based on absence of evidence.  For example, the LIS lobster fishers made an erroneous connection between insecticide spraying and lobster mortality back in 1999 because there wasn’t another explanation at the time and it seemed reasonable (to them). A big problem is that you can make this sort of logical fallacy in the blink of an eye – it’s basically intellectual laziness – whereas the sorts of controlled and rigorous studies required to build a good theory for any environmental disaster can take a really long time.  In other words, fallacy is instantaneous but truth works at the speed of science, which is, unfortunately, often pretty gastropodal.  Not enough time has yet elapsed to reveal the true cause(s) of the starfish melting syndrome, for example, but in the case of the LIS lobsters, science showed pretty unequivocally that the mortality resulted from a multifactorial suite of environmental problems, particularly chronically elevated temperatures and persistent hypoxia, probably exacerbated by some fishery-related factors.  Pesticides didn’t enter into it.  And yet, if you ask the average Joe on the street in Hicksville, they are more than likely to say that the pesticides killed the lobsters in ’99, because that message – wrong as it was – was widely disseminated in the heat of the crisis, whereas the truth came out quietly in scientific papers and agency reports years later when the crash had long since faded from The News.

A related problem is that in the time between when people first propose a fallacious cause, and when the true cause is revealed through reason and research, the fallacious one can become ingrained like an Alabama tick.  Once people get an idea in their head, even if it’s wrong, getting them to let go of it can be bloody hard.  Indeed, there’s a term for this; it’s called “the Backfire Effect”: when confronting someone with data contrary to their position in an argument, counter-intuitively results in their digging their heels in even more.  In this phenomenon, the media has to accept a sizable chunk of responsibility because, as the lobster example shows, the deadline-driven world of media agencies is more aligned with the rapid pace of the logical fallacy than with the slow and deliberate pace of scientific research.  Many media outlets are often quite happy to give airtime to ideas that haven’t yet been critically evaluated, especially if there isn’t much other information to report (yet) about a given crisis.  I’m pretty sure some folks I know are going to totally jump down my throat for saying that.  They will doubtless point out that journalists are the defenders of the One Truth, but this is my editorial soapbox, so go ahead fellas.  Besides, John Stewart calls CNN out for this sort of stuff practically every night, and if it’s good enough for him…

Perhaps the most common flawed thinking we see in the comments and back channels of #DeepSN is the false correlation, or causality inferred from coincidence; formally, this is called post hoc ergo propter hoc.  This was the fallacy that Jenny McCarthy committed when she decided that the MMR vaccine had caused her sons autism, simply because the latter followed the former closely in time.  Well yeah, 100% of car accident victims ate breakfast that day too, but you don’t see people ditching their cheerios do you?  McCarthy’s willingness to shout her ignorance from the rooftops (and Oprah’s couch) has done untold damage to the public health, especially as it now turns out that her son didn’t have autism anyway.  The point is, logically flawed thinking of this kind is not trivial or a private deficiency; it can cause real harm to the thinker and to others. The recent kerfuffle on Chris Mah’s excellent post debunking a link between the Fukushima disaster and the starfish melting syndrome on the US Pacific coast is a perfect example of post hoc thinking.  Fukushima happened -> Starfish wasting happened -> therefore Fukushima caused starfish wasting.  As Chris pointed out, though, starfish wasting started before the Fukushima event, so even before any research has been done on the true cause of the syndrome, we can comfortably discount Fukushima radiation as the primary contributor.  If, as an academic exercise you apply post hoc thinking in light of Chris’s point, flipping the first two premises in the above syllogism, you could just as easily argue that Starfish wasting caused the Fukushima event!  That’s obviously absurd on its face and just serves to reveal the fallacy for what it is.  It may be more plausible that the radiation caused the starfish melting rather than the other way around, but that doesn’t make it any less fallacious.  Another aspect of the post hoc phenomenon is that it doesn’t seem to happen in the good direction, only the bad.  Fukushima must have caused the starfish melting syndrome, but no one is jumping up and down saying that the record numbers of whales in California waters this year are a pleasant and unexpected side effect of Fukushima, even though it’s happening at the exact same time as the starfish problem.

One last example of flawed thinking that inhibits reasoned debate about ocean science issues is false pattern recognition, or simply “leaping to conclusions”.  The 2013 case of “oarfish mortality” is a great example.  Last year precisely two oarfish washed up in California, within a couple of weeks of each other.  Oarfish are rare, so when two of them washed up in quick succession, many folks were quick to assume that the two events were related and that we were at the start of an oarfish mortality event.  Of course, it was just a statistical anomaly; a rare event that nonetheless happens inevitably if you wait long enough.  TV and radio media are some of the worst offenders when it comes to leaping to conclusions this way (print media outlets tend to be a bit more rigorous).  One of the ways they justify this is through posing a question.  Rather than framing the piece as “Oarfish mass mortality underway”, which would require fact checking, they go with “Are we at the start of an oarfish mortality event?” and support it with a few quotes from bystanders asked to wax hypothetical about their experiences.  By framing the story as a question or hypothetical in this way, journalists abdicate somewhat the responsibility to substantiate the claims made.  It may appear to editors to be a harmless practice that stimulates conversation around an interesting topic, but it often causes a significant amount of work for those who make it their business to try to inject a bit of science into the public conversation.  This is especially the case when the truth (statistical anomaly) is a lot less interesting than the alternative, that 30ft oarfish are going to start washing up all over the place!

There are a whole slew of other related phenomena collectively called “cognitive biases” (of which the Backfire Effect is one example), that come into play during heated debates about events like Sandy, Deepwater Horizon and Fukushima.  I am not even going to scratch the surface on those here, because this post is long enough already and we hope to have some experts on these phenomena comment here soon. In the meantime, perhaps one way we can help move the conversations in more helpful directions would be a checklist that people can consult to check their logic.  After all, awareness of a problem is half the solution, amIright?  Scientists often have some form of this kind of thinking ingrained as a part of their training, but not always, so it can’t hurt for all of us to think consciously about our thinking, me included.   To that end, I offer the following, non-comprehensive list of things to consider before you hit “Reply” on that cleverly crafted response.  If you have additional suggestions I invite you to add them in the comments.

• Am I seeing a pattern that could just be a statistical rarity, and leaping to a conclusion?
• Am I connecting two events causally, because they occurred close together in space or time?
• Am I inferring a cause in the absence of evidence for any other explanation?
• Am I thinking inductively “It must have been such and such…”
• Am I framing the issue as a false dichotomy (debating only two possible causes, when there may be many others).  In other words, am I framing the issue as an argument with two sides, rather than a lively discussion about complex issues?
• Am I attacking my “opponent” and/or his/her credentials, rather than his/her argument?
• Am I arguing something simply because other/many people believe it to be true?
• Am I ignoring data because I don’t want to lose face by conceding that I may be wrong?
• Am I cherry picking data that support my position (a cognitive bias)

Deep Sea News seeks to raise awareness through scrutiny, not negativity.  By that we mean that we try our best to stick to the facts and then deliver them in our usual style of “reverent irreverence“.  For those who favour the ad hominem attack: we’re not paid to blog and we don’t all work at the same place (in fact, we all work at different places, all educational or non-profit).   We’re just 7 scientists who love what we do and want to share that passion with everyone else.  We relish vigorous discussion about the subject we all love, marine science, so with a bit of luck and a bit of effort, I hope we can improve the conversation by keeping it reasoned and scientific, so that DSN stays fun and informative, and doesn’t become a hive for trolls and a battlefield for flame wars.

The post No, but in all seriousness… first appeared on Deep Sea News.

The authors used chemical analysis to look for signatures of DWH oil, while simultaneously counting and identifying species of meiofauna (microscopic animals such as nematode worms, copepod crustaceans, etc.) and macrofauna (slightly larger, but still small animals such as polychaete worms). In this way, the presence of oil compounds could be compared with the number of deep-sea species present and the abundance of different organisms.

Aaaand, there’s no questioning these results. Here’s a map of sample sites, where color indicates impact (red = highest impact, with a high chemical signature of oil, low species diversity, and high nematode:copepod ratios, which is a biological indicator of oil pollution):

Now we zoom in and focus on the area surrounding the wellhead:

Since you can’t sample everywhere in the deep-sea, the authors also used their dataset to model the predicted benthic footprint over a wider area. Remember, red is bad:

And again, zooming into the area directly around the wellhead. Shazaam:

In addition to confirming the impact around the wellhead, this modeling approach picks up on shallow water impacts (orange patches off Louisiana, likely driven by surface transport of oil slicks), as well as a predicted area of moderate impact extending 17km to the southwest of the wellhead (remember that deepwater oil plume? Yeah, it seems to have affected animals living in the mud below it).

Note that the red “severely impacted” deep-sea area is 24.4 square kilometers, and the moderately impacted yellow area is 148 sq km (in total, that’s more than TWO Manhattans impacted by oil. Imagine New York City covered in sticky crude twice over…).

When you think about the size of the deep-sea impact, the road to recovery also seems quite grim. We’re talking possibly decades to return to business as normal:

Full recovery at impacted stations will require degradation or burial of DWH-derived contaminants in combination with naturally slow successional processes….Recovery of soft-bottom benthos after previous shallow-water oil spills has been documented to take years to decades [39,40]. In the deep-sea, temperature is uniformly around 4°C, and TOC [total organic carbon] and nutrient concentrations are low, so it is likely that [oil] hydrocarbons in sediments will degrade more slowly than in the water column or at the surface. Also, metabolic rates of benthos in the deep-sea are very slow and turnover times are very long [41,42]. Given deep- sea conditions, it is possible that recovery of deep-sea soft-bottom habitat and the associated communities in the vicinity of the DWH blowout will take decades or longer.

Reference:

Montagna PA, Baguley JG, Cooksey C, Hartwell I, Hyde LJ, Hyland JL, et al. (2013) Deep-Sea Benthic Footprint of the Deepwater Horizon Blowout. PLoS ONE, 8(8):e70540.

The post The Deep-sea footprint of Deepwater Horizon first appeared on Deep Sea News.

In September an oil sheen about four miles long had appeared in the Gulf of Mexico near the Deep Water Horizon well site.  The sheen was originally spotted on a satellite image from BP.  That oil from the sheen matches the oil from Deep Water Horizon site.

On December 15, remotely operated vehicles were sent to the Deepwater Horizon wreckage and the surrounding area.

“No apparent source of the surface sheen has been discovered by this effort,” said Capt. Duke Walker, Federal On-Scene Coordinator for Deepwater Horizon. “Next steps are being considered as we await the lab results of the surface and subsurface samples and more detailed analysis of the video shot during the mission.”

But of unfortunately, “The sheen is not feasible to recover” said Walker, but “does not pose a risk to the shoreline” Shoreline? What about the open ocean ecosystem?

Video of the ROV inspections can be found at the following links:

Well Heads

http://cgvi.uscg.mil/media/main.php?g2_itemId=1861633

Wreckage

http://cgvi.uscg.mil/media/main.php?g2_itemId=1861630

Riser Pipe

http://cgvi.uscg.mil/media/main.php?g2_itemId=1861396

Containment Dome

http://cgvi.uscg.mil/media/main.php?g2_itemId=1861393

The post Mystery Sheen Near Deep Water Horizon Site first appeared on Deep Sea News.

Past studies investigating effects of oil spills on salt marshes indicate that negative impacts on plants can be overcome by vegetation regrowth into disturbed areas once the oil has been degraded (8, 28–30). This finding suggests that marshes are intrinsically resilient to (i.e., able to recover from) oil-induced perturbation, especially in warmer climates such as the Gulf of Mexico, where oil degradation and plant growth rates may be high. (Silliman et al. 2012)

The finding’s aren’t surprising. Oil killed stuff. But even after 2 years, there’s been more speculation than published research and I think its important to highlight ongoing efforts to characterize the exact ways in which oil wreaked havoc on the Gulf ecosystem.

These data provide evidence of salt-marsh community die-off in the near-shore portion of the Louisiana shoreline after the BP-DWH oil spill because of high concentrations of oil at the edge of the marsh. Specifically, these findings suggest that the veg- etation at the marsh edge, by reaching above the highest high- tide line in the microtidal environment of the Gulf of Mexico, blocked and confined incoming oil to the shoreline region of the marsh. This shoreline containment of the oil may have protected inland marsh but led to extensive mortality of marsh plants lo- cated from the marsh edge to 5–10 m inland and to sublethal plant impacts on plants 10–20 m from the shoreline, where plant oiling was less severe….These data also suggest that the mechanism of the lethal effects of oil are more likely derived from interference with respiration and photosynthesis than from direct toxicity because plant death only occurred at high levels of oil coverage. (Silliman et al. 2012)

Silliman et al. found that this oil-induced plan death effectively speed up the rate of erosion in Louisiana marsh ecosystems. Oiled sites eroded twice as fast as reference (non-oiled) sites, for a full year (October 2010-October 2011) before leveling back off again.

Our results suggest that there are reasons for both optimism and concern about the impact of this oil spill on Mississippi deltaic marshes of Louisiana. On one hand, our results reveal that marsh vegetation displays remarkable resilience to oil spills by concentrating and confining the effects of oil to the marsh edge, recovering fully in noneroded areas after ∼1.5 y, and suppressing, through this recolonization, further accelerated erosion rates along the shoreline. The lack of oil on the marsh surface or on grasses at distances greater than 15 m from the shoreline at any site (Fig. 1A) suggests that incoming oil sheens were contained and prevented from moving into interior marshes by a baffling wall of live and dying salt-marsh grasses, a process that in itself increases the resistance of the extensive marsh ecosystem to oil spill. However, this resistance comes at a high cost for the impacted areas because marsh grass die-off and subsequent sediment exposure to waves resulted in a more than doubling of the rate of erosion of the intertidal platform, leading to permanent marsh ecosystem loss. (Silliman et al. 2012)

Louisiana’s salt marshes play a critical ecological roles, acting as storm buffers and breeding grounds that underpin the entire Gulf seafood industry. But they have been in trouble for a looooong time. The BP oil spill added extra stress to these already-stressed ecosystems–yet another anthropogenic impact promoting further ecosystem decline.

Reference

Silliman BR, van de Koppel J, McCoy MW, Diller J, Kasozi GN, Earl K, et al. Degradation and resilience in Louisiana salt marshes after the BP-Deepwater Horizon oil spill. Proc Natl Acad Sci USA. 2012 Jun. 25.

The post Gulf oil spill suffocated marsh grasses, enhanced erosion first appeared on Deep Sea News.

When all the shiz went down in the Gulf of Mexico, yours truly and collaborators had their nose to the grind, madly running around collecting samples and spending late nights in the lab listening to the hum of PCR machines. We were awarded an NSF RAPID grant in August 2010 to use parallel taxonomic and high-throughput sequencing approaches to characterize the impacts of the Deepwater Horizon oil spill on microscopic eukaryote communities inhabiting marine sediments. In English: we used both DNA and old skool microscopy to compare species living on beaches before and after the oil spill. This grant funded some hardcore sampling trips (September 2010, where I went on a boat and drove 1700+ miles along the Gulf Coast in one week, and March 2011 when we returned to sample sites a year after the oil spill) and a kickass undergraduate workshop about the “Bioinformatics of Biodiversity” which may or may not have involved YouTube Karaoke sessions and a randomly acquired cowboy hat.

So today, I’m pleased to announce that the first (of hopefully many) papers from this project has officially been published in PLoS One. For our first manuscript, we focused on a set of pre- and post-spill samples collected around Dapuhin Island, Alabama in May and September 2010, respectively. Our pre-spill samples represented our baseline, collected by our collaborator Ken Halanych at Auburn University days after the oil started gushing (his team quickly drove down to the coast before any of it had come close to the shore). Post-spill samples were collected 4 months later, after sheets of sticky crude were pitched ashore during a summertime of heavy beach oiling and BP’s cleanup efforts doggedly wiped away the blackness. We also included another post-spill sample site from Grand Isle, Louisiana, where I suspected that the the state of the beach would produce some intriguing data.

Before I describe our results, I’ll show you what the beaches looked like at the time of post-spill sampling. In September 2010, Dauphin Island was pretty serene: quiet, yes, because tourists were eschewing the region, but the shoreline itself showed little evidence of the BP fiasco. If you looked closely (which I certainly did), you could find little splotches of oil, an isolated tarball, or a buried “dirty” layer of sand. But if you had spent the past year on a media blackout, never heard of Deepwater Horizon, you would think that the Alabama coast looked pretty ordinary.

Grand Isle was a scene from another planet. A far cry from the parallel, reestablished tranquility on other Gulf shores. Grand Isle was a beach that was clearly impacted at the time of sampling. In fact, I specifically made a 6-hour detour to this site after hearing local news reports lamenting those tarnished Louisiana shores. Upon my arrival, I found the beach to be so impacted that I was hardly allowed near the sea. The ranger on duty turned me away at the local park. Fluorescent orange mesh blocked my attempts to cross the dunes. When I finally found a gap that led me to water, I made haste for fear of being chased away. There was heavy machinery humming up and down the shore (the park ranger noted that beach access was restricted for safety concerns), and piles of oiled sand awaiting a mechanical cleanse.

At each site we collected replicate sediment cores for DNA work (frozen immediately on dry ice) and taxonomic analysis (archived in 4% formalin, which is better for preserving morphology). The sequencing itself was a piece of cake (although the bioinformatics, not so much). I carried out standard environmental DNA protocols at the Hubbard Center for Genome Studies at the University of New Hampshire, where I was previously working as a postdoc under Kelley Thomas (senior author on our paper). First we separated the microbial eukaryote species from the sediment by suspending them in water and concentrating these organisms on a 45um sieve. Next we broke open all the cells using a beadbeather: think “Will it Blend” with ball bearings and soft tissue. Nothing stays intact. Finally, we used the Polymerase Chain Reaction (PCR) to broadly amplify two different regions of the 18S rRNA gene from the entire biological community present at each sample site. PCR amplicons were sent off for 454 sequencing, and we waited. In the meantime, Jo Sharma at UTSA was spending long hours at the microscope carrying out taxonomic identifications for nematodes at each site being sequenced.

I’ll pause for a moment here to offer more context. When I say we are studying “microbial eukaryote” species, I’m talking about puny things with a body size <1mm. You know, the ones no one cares about. And the ones I happen to be obsessed with (they’re so much more interesting than dolphins). We’re talking about taxonomic groups like meiofaunal metazoans (e.g. Nematoda, Platyhelminthes, Gastrotricha and Kinorhyncha, etc.), microbial representatives of fungi and deep protist lineages (Alveolata, Rhizaria, Amoebozoa, algal taxa in the Chlorophyta and Rhodophyta, etc.), and eggs and juvenile stages of some larger metazoan species. The reason why we chose to focus on these groups is precisely because they tend to be ignored. Most of the awesome genomic investigations only look at Bacteria and Archaea. But small eukaryotes are equally ubiquitous as their non-nucleated counterparts, and in marine ecosystems they play key roles as decomposers, predators, producers and parasites–yet we know little about their biology, ecology and diversity. By describing species changes in the Gulf of Mexico, we wanted to infer something about the potential for large-scale or long-term repercussions for Gulf ecosystems.

Sorry to keep you waiting–lets get down to the juicy stuff. Our results were pretty dramatic. After analyzing 1.2 million DNA sequences alongside nematode taxonomy, we found shockingly significant shifts in microbial communities between pre- and post-spill sites.

The first thing we saw was a stark shift in the diversity and abundance of taxa between pre- and post-spill sites. Pre-spill sites showed a typical marine community: dominated by nematodes, but containing a mishmash of other taxa such as arthropods, polychaetes, protists, algae, and fungi. Post-spill sites, in contrast, were almost exclusively dominated by a few species of fungi, with a spattering of some other metazoan species.

After looking at the charts summarizing the overall taxonomic assemblages, we moved on to ecological analyses such as Unifrac. We built a phylogenetic tree with our DNA sequences, computed some metrics about the branching topology, and got an overarching indication of how similar our samples sites were at the community level (e.g. for all species sequenced at each site).

We also did something similar with taxonomic data, using the Bray-Curtis similarity metric to analyze the list of visually-identified nematode species which were present (or not) across our sample sites.

Both our DNA and taxonomic analyses were relaying the same story: our samples clustered together according to pre- and post-spill time points: the before/after communities at the SAME site weren’t closely related to each other. Principal Coordinates Analysis (PCoA, Unifrac figure B, above) also underlined biodiversity distinctions across pre-spill sites. Even though pre-spill sites were characterized by nematode dominance, it wasn’t the same group of nematode species present at every site. In contrast, post-spill sites converged towards a similar community structure–these trends were likely driven by oil-associated fungal taxa that were common across post-spill sites.

You’ll also note that we observed a few outlier sites; Ryan Court (a sandy beach in front of residential property, on the Gulf coast of Dauphin Island) and Dauphin Bay (an inlet on the opposite site of the island, facing the Alabama mainland). Although we did observe community shifts in these post-spill samples, the shifts weren’t characterized by the typical fungal dominance seen at other sites. We think this has something to do with the geography and human-mediated cleanup efforts. To protect residents, Ryan Court had waterborne barriers going up and down during the heaviest oiling–this might have mitigated the worst effects in the sediment perhaps, preventing a shift to fungal dominance. Oil also might not have penetrated the inland Dauphin Bay site very well, since it was inherently sheltered by its location and some nearby marshland on Dauphin Island.

For me, the most convincing evidence of oil impacts was the data from Grand Isle. That 5-hour drive (and accompanying True Blood soundtrack) was the best sampling decision I made. Although I was pretty scared of Vampires when I was driving back through Louisiana that night. The beach was unarguably facing heavy oil impacts when I took samples. DNA analysis showed that the fungal-dominated post-spill assemblage in LA contained the same taxa as the Shellfish Lab, Dauphin Island community. Same putative species (Operational Taxonomic Units, a.k.a. OTUs), found 250 miles apart. To the casual observer, the scene at Dauphin Island didn’t look anything like Grand Isle. But thanks to the deep insight afforded by high-throughput sequencing, we were able to capture a snapshot of post-spill microbial assemblages that was highly indicative of environmental disturbance.

So we started looking closer at the data. Looking within phylogenetic tree topologies, I manually examined what taxa were most closely related to our fungal OTUs. Evolutionary relationships seemed to hint that post-spill fungi could survive using environmental hydrocarbons as an energy source:

Two distinct fungal community structures were recovered at post-spill sites: one assemblage dominated by Cladosporium OTUs (recovered at Shellfish Lab and Grand Isle), showing a close relationship to C. cladosporioides sequences in phylogenetic topologies, and a second assemblage dominated by OTUs in the fungal genus Alternaria (Belleair Blvd and Bayfront Park).  Fungal taxon dominance may be dictated by the physical marine environment; Alternaria OTUs dominated in brackish Mobile Bay, while Cladosporium was recovered in higher-salinity sediments on the outer shores of Dauphin Island.  These highly dominant post-spill OTUs appear as rare taxa in diverse pre-spill fungal assemblages, suggesting that oil-induced environmental stress may have favoured the rise of resilient, opportunistic species (able to capitalize on the large input of new resources).  Although the diversity and ecological role of marine fungi is not well understood, previous evidence suggests that observed fungal assemblages denote a signature of crude oil in Gulf sediments. Cladosporium contains ubiquitous, opportunistic species that can extensively utilize hydrocarbon compounds and thrive in hostile, polluted conditions that appear to be intolerable for other marine fungi [9,10].  Compared to many other fungi, marine Altenaria demonstrate increased activity of lignocellulose-degrading enzymes [11] that have been implicated in breakdown of industrial toxins [12,13].  In addition to these dominant OTUs, we recovered a variety of fungi at post-spill sites (including OTUs phylogenetically related to Apergillus, Acremonium, Acarospora, Rhodocollybia, and Rhizopus) that rarely comprised a significant component of pre-spill fungal communities. A number of these marine groups have also been shown to metabolize hydrocarbon compounds [14,15]. (Bik et al. 2012)

This paper has been a long time coming, and I’ve been dying to blog about it for the better part of a year. We went through the rounds and rejections at several top-tier journals before a lengthy review process at PLoS ONE, so I’m now pleased that these results are finally seeing the light of day. Our work in the Gulf of Mexico is still ongoing — unfortunately this was one study that raised a hell of a lot more questions than answers. We’ve continued to collect post-spill samples at regular intervals (including the samples I collected one-year after the original pre-spill samples). We want to figure out if the community shifts we saw in this study were really due to oil (as suggested by the dominance of oil-associated fungal taxa), mechanical beach cleanup efforts (which may have physically damaged and killed fragile microbial species), or whether they might be influenced by seasonal and temporal variation in the Gulf region (a topic where there isn’t much existing data). Another motivation is to study the longevity of these patterns–additional sampling time points will allow us to track the post-spill recovery, or lack thereof, of microbial eukaryote communities. Will assemblages begin to resemble pre-spill communities again, or will these beaches remain depauperate and/or be replenished with a different set of fauna? The post-spill fungi are cool and intriguing too. Were they thriving in oiled beach sands, or just weakly persisting after other species were killed off? Transcriptomics (studying gene expression by sequencing mRNA) will help us to answer this question and determine the species that were alive and kicking at the time of sampling. We’re also going to use random, shotgun sequencing to look deeply into the genomes of sparsely-populated, fungal-dominated beaches at sites such as Grand Isle: if post-spill species are eating hydrocarbon compounds, perhaps their genetic machinery will give an indication of the metabolic pathways that enable them to use oil as an energy source.

So really, this first paper is just a prelude. The main act will be as grand as Beethoven’s 5th.

Reference: Bik, H.M., Halanych, K.M., Sharma, J. & Thomas, W.K. (2012) Dramatic shifts in benthic microbial eukaryote communities following the Deepwater Horizon oil spill, PLoS ONE http://dx.plos.org/10.1371/journal.pone.0038550

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