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Hiring a Lab Technician

7 Feb

I’m a Fatboy Slim fan, and when I decided to write today’s post, “Praise You” started playing in my head.  Besides the fact that I need to update my music taste, it reminded me that I want to thank all my faithful followers out there for waiting around for me to post again.

It’s been ages (2 years to the day) since I’ve posted and I salute you both.

Many things have changed since I was blogging last… I’m now the proud SciMom to two little rugrats, and a tenure-track faculty member at Wazzu.  [I feel somehow obligated to assert the obvious fact here that all opinions given in this blog are my own and have absolutely nothing to do with my university.]

That’s right folks, 2 virtual petri dishes that crawl and drool and snot all over the place, AND all the responsibilities of a brand-new, wet-behind-the-ears ass prof (assistant professor, for those of you confused about the abbreviation); I’m just a glutton for punishment.

This has given me a new-found sense of juxtaposition: freedom, weighed down by grant-writing; imagination, mired in the realities of funding priorities; and an awesome new job, potentially debunked at tenure-review time.

I, therefore, chose to attempt to squeeze into my painstakingly time-managed work-day schedule some time for fun-writing (aka, blogging).  The shape and form and overall thrust of this blog will largely remain the same – Microbes do, in fact, still rule the world, and I will continue to extoll their virtues.  However, I hope to also cover science and science events more broadly and may even share the odd job posting. (a clear transition into…)

With my very first blog as a new tenure-track faculty, I will shamelessly let you all know that I need to hire a lab technician.  I need someone with experience in soil microbiology and molecular biology, cultivation-dependent and independent techniques.  The pay is not particularly great to start and I can’t cover relocation costs, but the boss is usually pretty cool and she’s super enthusiastic about what she does.   And you should know that Eastern Washington/northern Idaho is not the big city, but rather the outdoor-enthusiast’s playland.  So, for the full job description and details, contact her directly.


Fungi that eat lead

19 Nov

This post was chosen as an Editor's Selection for ResearchBlogging.orgBioavailability = solubility (for the most part)

To discuss heavy metals (lead, nickel, mercury, cadmium, silver, copper, and so on) and how they can be detrimental to the environment or toxic to people, plants, or animals, we have to first posses a vague understanding of bioavailability and bioaccessibility.  These terms describe whether or not the substance in question can cross an organism’s cellular membrane, which allows the organism’s internal system access to the substance.

This might sound a little confusing at first, but if the toxin can’t get inside the organism, it can’t do damage (i.e. if the small child didn’t eat the paint flakes, he wouldn’t suffer from lead poisoning).  Whether or not a toxic heavy-metal can enter into the cells of a plant, microbe, and even a human, depends on the solubility of that metal, and the solubility of any given metal will change according to what it’s chemically bound with. For an entertaining visual demonstration of chemical bonding, I thought you might enjoy this video …

But seriously, bioavailability…

The child eating lead based paint is actually a good illustration of what I’m trying to convey here.  The lead typically found in lead based paint is lead carbonate or lead chromate, which means the lead is chemically bound with carbon and oxygen, or chromium and oxygen.  Humans cannot absorb that type of lead through our skin and therefore it isn’t toxic unless ingested, in which case our digestive processes dissolve the different lead-compounds and we absorb the lead into our systems.

However, lead nitrate is another story altogether.  In lead nitrate, the lead is bound with nitrogen and oxygen and is extremely toxic because it is highly soluble in water; we can absorb it through our skin fairly easily, so we don’t have to eat it for it to become bioaccessible.

Most of the time, bioaccessabilty and bioavailability, relate directly back to the solubility of a substance.  If it’s not soluble, it’s not bioavailable, and vice versa.  The more bioavailable a toxin is, the more dangerous it is, to us and the environment at large.

But what about the microbes…?

With all that in mind, I find it particularly interesting to know that various microorganisms found in the soils, sediments, and waters of contaminated sites (mines, smelters, spill sites, etc.) have been discovered over the last 50 years capable of converting insoluble metal compounds (such as lead carbonate) into more soluble forms.   These microbes are able to convert metals from relatively inert forms into readily available (often bioavailable) forms and have received much attention for their biotechnological applications, such as dissolving useful metals from metal ores (termed “bioleaching”).

In fact, in 1995, Geoffrey Gadd and his colleagues at the University of Dundee (Dundee, U.K.) developed a particularly useful method to screen soil fungi for their potential ability to solubilize heavy metals in the lab (Gadd et al, 1995).  They were able to incorporate any one of a variety of insoluble metal compounds into the agar of a Petri dish and measure the rate at which the fungus could dissolve the metals.  They tested the method using aluminum, cobalt, manganese and zinc and found many fungi from a common “garden soil” sample were able to dissolve insoluble zinc and cobalt just as quickly as they could grow and expand across the Petri dish.

A common fungus dissolves the highly insoluble lead carbonate as it grows across a Petri dish.

In my own experiments recently, I’ve tested this method and have a nice photo of a fairly common fungus (Aspergillus niger) literally dissolving lead carbonate, just like the lead carbonate found in lead-based paints. (photo at right)

This may initially seem like a bad thing… soil organisms turning relatively insoluble and inert metals into the more soluble, and consequently more bioavailable, forms.  But learning about the natural process and understanding how it all works actually affords science a new and developing tool in the ongoing struggle against contamination.  We can apply our knowledge to clean up efforts and remediation work on contaminated sites, and even biotechnology for lower-impact mining techniques.

Of course, we have a long way to go with the organisms I’m working on right now, but along the way they help us understand which contamination sites can cause the most dangerous types of human exposure and why.  It all comes back to how the toxins interact with the microbes in the soil!

So, back to the lab I go this afternoon to see how my other fungi are breaking down lead (or not) and converting metals from insoluble forms to the bioavailable forms (after I watch that chemical bonding video one more time for laughs!)

ResearchBlogging.orgSayer, J., Raggett, S., & Gadd, G. (1995). Solubilization of insoluble metal compounds by soil fungi: development of a screening method for solubilizing ability and metal tolerance Mycological Research, 99 (8), 987-993 DOI: 10.1016/S0953-7562(09)80762-4

Too Cool for School – Psychrophilic oil-degrading microbes to the rescue!

26 Aug

This post was chosen as an Editor's Selection for

Two days ago, an article was released by Science on their Sciencexpress website with some of the first data coming out of the Gulf with regard to the microbial ecology of the deep-sea in response to the massive quantities of oil released by the Macondo well. This is one of those moments when I embrace how truly nerdy I really am and I actually get a little flutter of excitement from reading the peer-reviewed literature.

In case you aren’t yet familiar with the deep-sea oil plumes resulting from the BP oil spill, you can find descriptions of the phenomena here and here

Essentially, what happened is that the well was pumping oil into the deep ocean, then BP started pumping Corexit 9500 down near the burst wellhead, and the result (beyond the oil slicks and tar balls at the surface) is a massive plume of “dispersed” oil between 1,099 and 1,219 m (3,600 – 4,000 f) below the ocean surface.  This plume runs more than 6 miles out away from the wellhead.  This makes for an unprecedented oil-spill situation, for which we have no similar data on record and a wellspring of opportunity to find out about deep-sea microbial ecology. 

So, what’s happening with the microbes down there? 

Terry Hazen and his colleagues discovered that not only are there much greater numbers of microorganisms in the plume than in the surrounding waters, but also that the organisms of the plume are unique with regard to anything we’ve ever seen before. 

A scanning electron micrograph of the dominant bacteria found within the oil plume: Oceanospirillales.

They were able to identify over 900 species of bacteria in the plume, 16 of which were greatly enriched compared to the surrounding water without oil contamination.  In fact, 90% of all the bacterial sequences they were able to recover from the plume belonged to a single organism, most closely related to the genus Oceanospirillales.  These organisms only made up 5% of the sequences in the non-plume samples.  What makes this really interesting is that we have no known cultured representative of this genus, but it’s lipid profile (the fats the microbes use to build their cell membranes and walls) is similar to Antarctic hydrocarbon-degrading marine organisms.    Keep in mind, the average temperature of the plume waters is around 4.7° C, or 40°F, which makes these little guys pyschrophiles.

The authors also discovered that the number of genes involved in hydrocarbon degradation were significantly increased in the oil plume samples over the non-plume samples and that these genes were significantly correlated with the constituents of the oil (isoproplybenzene, naphthalene, etc).  So, not only do we have a huge enrichment of previously undescribed organisms within the oil plume, but these new organisms contains a large number of the genes we know to be required for oil degradation.  Additionally, scientists aren’t observing the fatal drop in oxygen tensions that had been expected with this level of microbial hydrocarbon break-down.  Don’t misunderstand me here, there was a drop, but not to the levels that could kill off other marine life and result in a much-expanded dead-zone.  These data could suggest that these organisms are employing metabolic pathways of hydrocarbon degradation that are also (at least in part) previously undescribed.    How cool is that?! 

This confirms that not only do a variety of hydrocarbon degrading bacterial populations exist in the newly created deep-sea oil plume, but also, as the authors state “that the microbial communities appear to be undergoing rapid dynamic adaptation in response to oil contamination.” They speculate that the episodic oil leaks from natural and anthropogenic sources have allowed these deep-sea microbial communities the opportunity to develop these pathways over a long period of time, so they were poised to respond.  I’ve posted before about the “priming effect” of soil microbial community exposure to a toxin and how it can speed recovery, but now we’re getting to see it in action in the gulf!

The authors also note the “potential for intrinsic bioremediation” and in this case no known microbial inoculants could have worked as well as nature herself.

Overall,  a very nicely done article, out quickly and written concisely.  Nice job to the folks at the Lawrence Berkeley National Lab!  Looking forward to seeing more about this fascinating topic.

ResearchBlogging.orgHazen, T., Dubinsky, E., DeSantis, T., Andersen, G., Piceno, Y., Singh, N., Jansson, J., Probst, A., Borglin, S., Fortney, J., Stringfellow, W., Bill, M., Conrad, M., Tom, L., Chavarria, K., Alusi, T., Lamendella, R., Joyner, D., Spier, C., Baelum, J., Auer, M., Zemla, M., Chakraborty, R., Sonnenthal, E., D’haeseleer, P., Holman, H., Osman, S., Lu, Z., Van Nostrand, J., Deng, Y., Zhou, J., & Mason, O. (2010). Deep-Sea Oil Plume Enriches Indigenous Oil-Degrading Bacteria Science DOI: 10.1126/science.1195979

As the oil moves inland…

26 Jul

I’ve spent most of my July posts on oil (hydrocarbon) break-down and bioremediation in the sea environment.  When dealing with an open-ocean oil spill, we have a few things on our side with regard to oil biodegradation, including the natural mixing of the ocean currents, which not only dilutes the toxins in the oil, but also refreshes the oxygen levels vital to break-down processes.  But eventually we have to face the inevitable movement of oil onto the shores and into the more terrestrial environs of the coastal communities, which then makes this a soil and sediment contamination problem.   

So, to explore this issue of oil biodegradation in soils, I have a good old-fashioned compare and contrast between two very interesting research articles today.  The first (Wang, et al.) uses a laboratory experiment to test how well two different soil microbial communities break down a variety of the persistent organic pollutant (POPs) in oil, while the authors of the second article (Short, et al.) returned to Prince Williams Sound 16 years after the Exxon Valdez spill to conduct a field-study to check the beaches for remaining oil.

First, the good news.

Generally speaking, natural soil communities which have a history of prior exposure to a specific toxin will be better adapted to rapidly break it down than those soil communities that haven’t been exposed before.  For instance, let’s say we have two corn fields of the exact same soil type right next to one another.  On one field the grower applied Roundup (a.k.a.  glyphosate) for weed control – we’ll call this farmer “Pete”.  His neighbor (farmer “John”) understands the consequences of pesticide use, so he utilized non-toxic weed-prevention techniques and didn’t apply Roundup to his fields. 

Now, let’s just say I came out to each of these fields in the middle of the summer and took soil samples.  Back in the lab I would find that the microbial communities of Pete’s fields would be able to break down glyphosate, while the microbial communities of farmer John’s fields, which had never received an application of Roundup, could not.  This has to do with rapid rates of adaptation and microbial gene transfer (and is also the basis for antibiotic resistance – which I’ll get to in another post later on).  In general, we’ve assumed this rule of thumb to be true with most contaminants, but the article by Wang, et al., asserts that this may not be the case for hydrocarbon pollutants such as crude oil.

They set up a series of “bioreactors” (fancy way to say 250 mL flasks) to which they added a mixture of the same toxins that are found in crude oil and added soil as a source of microbes (a.k.a. inoculum).  They used two different soils to test the concept I mentioned above: 1.) a “pristine” agricultural soil which had never been exposed to hydrocarbons before; or 2.) a soil which had been continuously contaminated with oil for many years.   They placed these flasks on a shaker and tracked the number of bacteria and fungi, as well as the break-down of the toxins over the course of 180 days. 

Not surprisingly, the numbers of bacteria and fungi correspondingly increased as the toxins were rapidly degraded, and the ole rule of thumb may require some modification; the soils with a history of contamination degraded the toxins more rapidly than the other soils (in fact, by the end of their 180 day study, the previously contaminated soil microbiota had broken down the oil toxins almost 100%!)  But, what was more interesting, was how quickly the “pristine” soils were also capable of breaking down the hydrocarbon toxins.  This suggests that the ability to degrade oil may be widespread in soils.  Meaning, regardless of the soil’s history, the microbes within it may be capable of rapidly adapting to oil contamination and act to break it down.  Unless, of course, their “pristine” soils weren’t as untainted as the researchers thought.  But either way, good news in the Gulf, for sure.

The not so good news.

But here we reach the age-old debate over the utility of small-sale laboratory incubations in predicting what will happen in an ecosystem.  The authors of the article by Short, et al., set out to rebuff all the lab studies that predict the natural soil communities should be great at breaking down oil by revisiting the site of a real-life oil spill and see where things stand 16 years later. 

The problems with the “microcosm” and “bioreactor” type studies have a lot to do with oxygen and exposure (although there are other issues, but not enough time to get into all of them). With a soil/oil/microbe mixture on a shaker in the lab, oxygen is constantly allowed to diffuse in where it’s needed.  But, out in the real world, once the oil percolates into the porous beaches and down into the soil, the oxygen which is absolutely crucial to microbial and chemical break-down processes becomes much more limited, if not down-right sparse. 

Apparently the oil loss rate (break-down rate) in Prince William Sound (PWS) in the first 3 years after the spill was around 68% per year, which made everybody think all the oil would be gone in the next few years.  But as the oil percolated deeper into the sand, soil, and sediments (between 1992 and 2001), the loss rate dropped to around 20% per year.  After 2001 it dropped even further to under 5% per year. 

However, the authors don’t actually attribute the slow-down entirely to low oxygen levels, but also to low nitrogen levels in the water and soils of the area, as well as low temperatures, and emulsification.  Basically, the oil was whipped into a nasty “mousse” in some places which increased the viscosity of the oil (it was whipped into a gummy mess).  This decreased the surface area where microbes could attack, and some of the oil in that state worked it’s way down into the soil where it sits to this day.  The results of the study suggest that subsurface oil may persist for decades, even where there is oxygen available.  Bad news for the Gulf.

So, what’s the take-home message?

The microbes of the sandy beaches, sediments and soils of the Gulf have had prior exposure to oil, albeit at much lower levels.  This means that those organisms should be “primed” and able to break down the hydrocarbons and toxins in the oil.  But it’s anybody’s ballgame as to how quickly we’ll see it happen.

The limiting factors to biodegradation will be: 1.) oxygen;  2.) nutrients;  and 3.) surface area of the oil.  The surface area of the oil was taken care of (at least in part) with millions of gallons of dispersant, resulting in less emulsification that what was seen in PWS.  So, speeding the break-down of the oil on the surface before it can leach down into the soil profile or sediments where oxygen is depleted will be very important. 

Biostimulation (fertilization) with nutrients such as nitrogen could theoretically achieve a more rapid degradation by providing limiting nutrients to the hydrocarbon-degrading microbes.  I feel like I’ve said that before… weird.


Wang, C., Wang, F., Wang, T., Bian, Y., Yang, X., and X. Jiang.  (2010). PAHs biodegradation potential of indigenous consortia from agricultural soil and contaminated soil in two-liquid-phase bioreactor (TLPB).  Journal of Hazardous Materials, 176: 41-47.  doi:10.1016/j.jhazmat.2009.10.123

Short, J.W. et al. (2007).  Slightly weathered Exxon Valdez oil persists in Gulf of Alaska beach sediments after 16 years.  Environmental Science & Technology, 41: 1245-1250. doi:10.1021/es0620033

Yet another post on crude-oil bioremediation

19 Jul

On Friday, members of the the American Society for Microbiology (ASM) received our bi-monthly e-mail from the new President of our organization, Dr. Bonnie Bassler, in which she addressed the very two subjects I’ve been so interested in the last few months: the article in Science on the “synthetic cell”, and the oil spill disaster in the gulf. 

With regard to the JCVI “synthetic cell,” the official position statement of the organization is remarkably in-line with my own opinions as I’ve state in previous posts, albeit slightly more vague and probably a bit more polite.

As for the Deep Water Horizon debacle, she sent out a link to a video that I had not yet seen, which was recorded at this year’s annual ASM meeting in May (which I unfortunately missed due to my efforts to complete my dissertation right about then).  The video is roughly  a half-hour long interview of Dr. Jay Grimes of the University of Southern Mississippi and Dr. Ronald Atlas of the University of Louisville, two true experts in the field of marine biology and hydrocarbon bioremediation. 

The video is terribly slow and a bit boring (may as well skip the first 7 minutes, for sure), but they eventually cover some great information all about the state of the science when it comes to oil bioremediation… so check it out if you have a half-hour to kill watching scientists sit around discussing the gulf oil spill.  In the meantime, I found an interesting and relevant article I thought you all might like to know about which examines the efficacy and effects of crude oil bioremediation in marine systems.

Getting terms straight, again.

Before I launch into the paper, I want to make sure we’re all clear on the terms I’ll be using (and have used) a great deal.  First, the broad term that covers the use of any living organism (plant, fungus, bacterium, earthworm, what-have-you) to clean up some toxic problem is “bioremediation.”  There are hundreds of different ways to achieve bioremediation, including “natural attenuation” (essentially allowing mother-nature to do her thing, without further intervention) as well as the two methods that the authors of these papers examined and that I’ve mentioned in previous posts: biostimulation and bioaugmentation

Lots of syllables for some fairly straight-forward concepts:  biostimuation is as simple as fertilizing.  The idea is to stimulate the growth of the native microbial populations;  find out what they are lacking and give it to them (like the veggie garden).  In the case of microbes that eat oil and gas (which are essentially carbon), those microbes need nitrogen, phosphorus, potassium, and sometimes micronutrients (like vitamins and minerals for humans).  Bioaugmentation just as simply, means to add (or augment) beneficial microbes.  There are a number of different approaches to this idea, in terms of precisely which microbes to add, in what quantities (i.e., did you get the microbes from the site and just grow them in the lab to greater numbers, or did you genetically engineer organisms from someplace else?).  The issue is that the number of microbes naturally equipped to deal with the problem may not be great enough to break it down at the speed we think is best, so if we can add some players to the game we can more rapidly attain the goal.

How do these strategies effect the natives?

The article for the day (McKew, et al) addresses the issue of how the use of bioremediation technologies  impacts the indigenous populations of hydrocarbon-eating microbes, for which the authors actually use the term “hydrocarbonoclastic bacteria” (don’t bother trying to pronounce it because they abbreviate it as HCB for most of the paper).  For the most part, studies in the past have focused on how quickly the oil is degraded after applying bioremediation, but we know little about the dynamics of the native microbial populations.

So, to address this issue, the authors took natural seawater from estuaries surrounding oil refineries in the UK and added weathered crude oil.  Then they looked at how different treatments of nutrients, emulsifiers, and two species of known oil-degrading bacteria (Alcanivorax borkumensis and Thalassolituus oleivorans) would effect not only oil degradation rates, but also the natural microbial communitites in the sea water.

Result#1: Emulsifiers enhanced hydrocarbon degradation only when nutrients are not limiting.  When they added emulsifiers, the native HCB populations gew rapidly and had greater access to the carbon, but could only utilize it if they had all the additional nutrients they needed.  In other words, the scientists could add emulsifier (or dispersant) all day long, but it would not increase the break-down of the oil without the addition of the necessary nutrients as well.  Not an unexpected result when we consider the wealth of previous literature on the subject.

Result #2:  Addition of A. borkumensis enhanced degradation of specific components of the oil (polycyclic aromatic hydrocarbons – PAHs).  This is particularly interesting when we consider the fact that this species does not actually break down PAHs, but rather produces a natural emulsifier (also called a biosurfactant).  This species effectively made the oil more bioavailable to the native HCB species and allowed more rapid degradation.

Result #3: Addition of T. oleivorans actually reduced the numbers of native HCB and of A. borkumensis.  Apparently, competition between the different HCB species is fierce, andT. oleivorans  can produce metabolites that inhibit the growth of other organisms.  Chemical warfare in microbes is a common occurance, but in this case it actually excluded a number of different beneficial microbes – not such a good thing.

Result #4:  Combined treatments of bioaugmentation (addition of microbes) and biostimulation (addition of nutrients) were no more effective at enhancing degradation than simple biostimulation alone.  Addition of nutrients stimulated indigenous populations of Cycloclasticus, a native HCB, and overall oil break-down was the same as the treatments where HCB were added.  However, in the first five days of the experiment, there were higher rates of degradation in the experiments with A. borkumensis.

Conclusions:  Biostimulation is a no-brainer.  It could be aided by bioaugmentation of certain bacterial species very early on after an oil spill, but species interactions are extremely important and can not be overlooked in planning bioaugmentation strategies.  The authors put it succintly,

“For bioaugmentation to be successful the addition of appropriate bacteria, with consideration to both the environment and pollutant, is of paramount importance.”

… not to mention the effects on the native HCB. 

Of course, the authors only looked at vials of water (a.k.a. microcosms) which don’t exactly reflect the real ecosystem, for a variety of reasons.  One of the biggest hurdles to bioaumentation of open water is simple dilution effects.  Can we really add enough organisms to that amount of open sea to make a difference? 

Overall, a nice paper than demonstrates the utility of biostimulation and just the tip of the iceberg in terms of issues to overcome for successful bioaugmentation.


McKew, B. et al. (2007)  Efficacy of intervention strategies for bioremediation of crude oil in marine systems and effects of indigenous hydrocarbonoclastic bacteria.  Environmental Microbiology, 9(6):1562-1571. doi:10.1111/j.1462-2920.2007.01277.x

Bioremediation with Beeswax

13 Jul

Two years ago, I showed this video in a class I was teaching on Environmental Microbiology and I still love it… it’s a fantastic example of biostimulation that I just had to share when I saw a story on  the possible application of PRP in clean-up efforts in the Gulf

A NASA partnership in the early 1990’s created a fine powder out of beeswax, called PRP, which can be spread over petroleum or oil to absorb (or encapsulate) the oil at the same time providing essential nutrients (nitrogen, phosphorus, and potassium) to the oil-eating microbes and speeding up the break-down process. 

Gotta love the History Channel!

Exxon Valdez: Lessons in Bioremediation

7 Jul

 With the oil-spill disaster in the Gulf of Mexico on everyone’s minds, I thought this was a great video reminding us how effective the natural microbial communities were in cleaning up after the Exxon Valdez spill.  (Not to mention, I also get a little kick out of the hair-styles, clothes, and lab safety goggles of the late 80’s).

via MicrobeWorld