Tag Archives: Microbiology

ASM New Orleans: Here we come!

19 May

The American Society for Microbiology 

Some of you may already be aware of the rapidly approaching 111th General Meeting of the American Society of Microbiology (ASM) in New Orleans, May 21st through the 24th.  I’m pretty excited to say this will be my very first opportunity to attend the ASM meeting.  This may be a little surprising considering the fact that if you have any idea what this blog is all about, you know that Microbiology is what I do, it’s what I study, immerse myself in, and it’s what I love.

So why on earth haven’t I attended one of these meetings before?  It just so happens that my work (study, love, etc) also falls within the realm of soils, biogeochemistry, environment, and ecology, as well.  Accordingly, over the course of my professional life to date, I have only attended soils, environmental, and ecological professional meetings.  I have been advised by colleagues in the past that the ASM meetings are extremely large and primarily catered to medical/clinical and basic microbiology crowds and that I would actually glean the most useful knowledge (for my particular line of work) from the more applied meetings.

My Agenda at the ASM Meeting

This year I decided to find out for myself about the ASM General Meeting (and blog it thoroughly).  I’ve taken it as my personal mission to track down and report on as much environmental microbiology (and microbial ecology) at the meeting as I possibly can.  My cover will be as a lowly postdoc presenting a poster on my most recent work with fungi and Pb-contaminated soils.  Wish me luck!

In the meantime…

I’ve heard some talk about the new way of doing things at this year’s meeting and thought I’d look into it a little beforehand.

At the inaugural meeting of ASM  in 1899, at the time called the Society of American Bacteriologists, there were roughly 30 professionals in attendance (Miller, et al. 2010).  In recent years you can expect upwards of 10 to 15 thousand attendees in any given year with a very wide range of areas of expertise, a veritable smorgasbord of high-tech vendors, and people from all over the world, from students and undergraduates to postdocs and profs, even true, historical icons.  However, the clinical microbiology community still accounts for roughly 1/3 of the meeting’s attendance.  Obviously, there have been some big changes in the society and this year’s dynamic platform is an attempt to adjust the design and flow of the meeting to accommodate the new demographic, while still meeting the needs of the core.

This year a new mission statement for the meeting was adopted by the Society: “The ASM General Meeting showcases the central role of microbes in the biosphere by communicating today’s cutting edge science in the diverse areas influenced by microbes.” (Miller, et al. 2010) Which actually sounds quite promising, if you ask me.

Apparently, one of the most dramatic changes to the general meeting involves the number and nature of session and includes a parallel meeting, specifically tailored to the needs of the clinical microbiology community entitled “Medical Microbiology Track.”  Not exactly my cup of tea, but to each his own.

Each morning there will be only 4 concurrent sessions focused on topics of broad interest, which is a reduction in the number of session since years past.  The goal is to “showcase” inspirational interdisciplinary science with minimal overlap and maximum appeal.

That all sounds well and good, (actually it sounds pretty fantastic and exciting to the incorrigible science dork), but we’ll have to see how it all plays out in the real world.

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ResearchBlogging.orgMiller JF, McFall-Ngai M, & Casadevall A (2010). A New Design for the ASM General Meeting. mBio, 1 (5) PMID: 21151775

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Shall we dance?…

29 Sep

This post was chosen as an Editor's Selection for ResearchBlogging.org… says the rhizobial bacteria to the leguminous plant root.  In response, the plant warmly embraces her partner, literally wrapping herself fully around the bacteria, and so the intricate and highly choreographed ballet begins.

Image of a root hair embracing it's bacterial consort, by Euan James, via Life Sciences at the University of Dundee.

But how can a minuscule little bacterium communicate to a “higher plant” in a way to elicit such an overwhelming positive response?  A response which catalyzes this fundamental and truly amazing partnership, on which the world as we know it has depended for millenia?

The answer is simple, these bacteria developed special signaling molecules called nodulation (Nod) factors to communicate with certain plants.  These nodulation factors are diffusible signals, which mimic plant hormones, and stimulate very specific developmental processes within the plant during the initiation of the symbiotic relationship (Oldroyd & Downie, 2008).  They provide the choreography of the dance.

By simply altering the length and degree of saturation (think, saturated vs. unsaturated fats) of the nodulation factors, bacteria can target very specific plants.  This species-specific tuning of the nodulation signals allows an individual bacterium to “speak to” the host it prefers and form a relationship with, for example, a soybean plant rather than an alfalfa plant.

Once the plant recognizes the nodulation factor of the rhizobial bacteria, infection occurs through root hair cells which curl around and entrap the attached bacteria.  The bacteria, in turn, begin to break down the plant cell walls which entrap them, and subsequently initiate the formation of a tube-like structure called the intracellular infection thread or IIT (Ivanov, et al. 2010).

Intracellular infection threads containing fluroescently labeled rhizobial bacteria.  (By Dan Gage)

Intracellular infection threads (IIT) containing fluroescently labeled rhizobial bacteria. (By Dan Gage)

The IIT serves as a biological inoculation needle, so to speak, penetrating the root primordial cells and releasing bacteria into the cytoplasm of the plant.  At this point, the plant cells form a protective membrane around the mass of bacterial cells, where the bacteria differentiate into their nitrogen-fixing stage.  This special intercellular plant membrane, also called the peribacteroid membrane (PBM), allows nutrient exchange and helps protect the bacteria from oxygen, which would destroy the nitrogenase enzyme crucial to the process of gaseous N2 fixation (the process which is central to the nitrogen cycle, controls nitrogen availability, and consequently supports life on this earth).

At every point in this intricate dance, the bacteria and plant are engaged in a complex dialogue; this constant communication prevents activation of the plant defensive systems and the final formation of a functional symbiotic relationship (i.e. an active root nodule).  It’s a beautiful and fascinating process on which we rely, and should duly appreciate.

So, when, in my previous post, I mentioned the fact that it perturbs me when people dismiss the role bacteria play in symbiotic nitrogen fixation, I hope you can see that saying “plants fix nitrogen” for me, is comparable to saying Da Vinci’s paintbrush was responsible for the Mona Lisa, or that Einstein’s pen introduced the Theory of Relativity.  It just doesn’t give credit where credit is due.

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ResearchBlogging.orgIvanov, S., Fedorova, E., & Bisseling, T. (2010). Intracellular plant microbe associations: secretory pathways and the formation of perimicrobial compartments. Current Opinion in Plant Biology, 13 (4), 372-377 DOI: 10.1016/j.pbi.2010.04.005

Oldroyd, G., & Downie, J. (2008). Coordinating Nodule Morphogenesis with Rhizobial Infection in Legumes. Annual Review of Plant Biology, 59 (1), 519-546 DOI: 10.1146/annurev.arplant.59.032607.092839

Helper Microbes and Heavy Metals…

3 Sep
Marine bacteria exhibiting "helper" facilitated growth.

Series of Petri plates with marine bacteria exhibiting "helper" facilitated growth of previously uncultured organisms.

Last week, the American Society for Microbiology posted a story that caught my eye which highlighted the most recent work of Kim Lewis and his collaborators published in Chemistry and Biology in March (see citation below).  It caught my eye due to the term “siderophores” in the title.  You may be wondering why a strange Greek term like that would be of any interest to a soil microbiologist like me, so let me share my fascination for these weird and wonderful molecules and how they may be changing approaches in microbiology.

First, let’s define the word siderophore in simple language. 

It’s from the original Greek meaning “iron carrier” and describes a small molecule specifically designed to address the biological iron requirement.  While you and I might be able to eat our Flintstones and therefore don’t need to worry about iron, the vast majority of life on earth has to figure out a way around the fact that biological systems require the soluble Fe2+ (ferrous iron), but iron for the most part exists in the environment as the highly insoluble Fe3+ (ferric iron).  Why?  Because life evolved when the earth was anaerobic (meaning there was virtually no oxygen); there was an overabundance of iron all over the place in the ferrous form.  Gradually life took over the face of the planet, turning out atmosphere aerobic, and all that oxygen essentially ‘spoiled’ the iron-rich crust of the earth, oxidizing the iron into the ferric form, which is essentially insoluble and not bioavailable. 

Long-story short, we’ve all developed some strategy to deal with this problem.  Humans use transferrin in our bloodstream to bind iron, while bacteria, fungi, and some plants use what we call siderophores.  These small molecules grab onto ferric iron in the environment and chelate it, forming soluble iron complexes, making it available for biological purposes.  For a really gre,at in-depth review of siderophores, look here.

Curiouser and curiouser…

What has intrigued me for years about siderophores is a uniquely discriminating selectivity.  I know that may sound redundant, but what I’m trying to say is that certain microbial siderophores are extremely specific to iron and actually can scavenge iron from metamorphic rocks, oxides, hydroxides, you name it they can leach it out, to the point that they even have biotechnological applications in mining activities.  At the same time, other microbial siderophores may be able to pick up any positively charged metal or micronutrient in the environment.  This includes all the common heavy-metal contaminants that I deal with on a daily basis, from lead and cadmium, to arsenic and uranium.  Certain siderophores can chelate these toxic metals and bind them in such a way as to allow them to precipitate out of solution, making them no longer a toxic threat to the organism.  Even more fascinating is that the same siderophore, under different conditions, might bind a scarce essential nutrient so the microbe can take it up and continue living normally.  There has also been evidence recently to support that microbial siderophores may be involved in quorum sensing (microbial cross-talk) and biofilm formation, but the new work by Kim Lewis and his colleagues brings it all to a new level.

The “great plate county anomaly”

For years, microbiologists have been working on new ways to culture (or, grow in the lab) environmental microorganisms and attempts to overcome the “great plate count anomaly” have included a multitude of creative approaches.  All my microbiologist-readers will be intimately familiar with that little problem, but for those of you out there who aren’t … the “great plate count anomaly” describes the fact that no matter how many microbes we can see under a microscrope or detect DNA for in any given sample (soil, marine sediment, water, mucosa, etc), we can only successfully get around 0.1 – 1% to grow on Petri plates in the lab.  This severely limits what we can find out about how these organisms function out in the real world and has stalled many aspects of microbial ecology.

The authors were able to definitively prove the siderophores produced by some “helper” microbes actually allowed the growth of other, previously uncultured, bacteria on Petri plates in the lab.  They were able to identify cooperative pairs of organisms, in which one organism was identified as the helper and secreted siderophores into the media, and the other organism was only capable of growth when exposed to the siderophores of the helper.  They tried an array of synthetic (store-bought) siderophores, which worked in some cases but others did not. They also tried to supplement with high quantities of bioavailable iron, which also, worked in some cases (allowed the growth of previously uncultured microorganisms), and in others did not. This means the helpers likely have very specific relationships with the organisms that rely on their siderophores, with a great degree of discrimination, despite the fact the pairs of organisms were not closely related, not even in the same genus.  It may also mean that the function of the siderophore in the media may not have anything to do with iron in some cases.  By using these helper organisms the authors were actually able to culture as much as 40% of the total community, which is a vast improvement of the typical <1% we see from most environmental samples.

As a scientist who has literally watched this phenomena unfold on my own Petri plates, but had no clear explanation at the time, I am truly enthralled by this new discovery.  It raises some very interesting questions with regard to the microbial ecology of this helper-pair system, in addition to opening doors with regard to antimicrobial therapies and basic culture techniques.     

But, I have to wonder, why?  What’s the purpose of this highly complex and specific signaling and nutrient acquisition cross-talk?  How would it benefit the microbial community as a whole?  Is this cooperation and microbial co-evolution at its best, right before our eyes?  Things I’ll be pondering over the weekend…

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ResearchBlogging.orgD’Onofrio A, Crawford JM, Stewart EJ, Witt K, Gavrish E, Epstein S, Clardy J, & Lewis K (2010). Siderophores from neighboring organisms promote the growth of uncultured bacteria. Chemistry & biology, 17 (3), 254-64 PMID: 20338517

Friday Fun – Microbial Art

23 Jul
Intricate chiral patterns formed by Paenibacillus dendritiformis grown on minimal media in a Petri dish as it searches for food.

Intricate chiral patterns formed by a single bacterial colony as it searches for food.

While roaming the great wide web for the newest microbial topic that would stir intrigue, wonder, and appreciation for the microbial world in the hearts of my readers, I stumbled across the Microbial Art Gallery and just had to share it and some fantastic images. 

The gallery is a collection of unique artwork created using living bacteria, fungi, and protists in ways you might never have imagined possible.

Not only are these tiny creatures infinitely useful, helpful, even necessary to our very existence, but they are beautiful and creative in their own right. 

Some of my favorites in the gallery (reproduced here with kind permission of Dr. Eshel Ben-Jacob) are actual images of Petri-dish cultures of Paenibacillus dendritiformis, a bacterium that has engineered these complex chiral structures through self-organization survival strategies. 

Intricate chiral patterns formed by Paenibacillus dendritiformis grown on minimal media in a Petri dish as it searches for food.

More chiral patterns formed by Paenibacillus dendritiformis grown on minimal media.

This involves cooperation and advanced communication between the cells (and results in a very pretty picture).

As Dr. Ben-Jacob and his co-authors so aptly put it, “Collectively, bacteria can glean information from the environment and from other organisms, interpret the information in a ‘meaningful’ way, develop common knowledge and learn from past experience.  The colony behaves much like a multicellular organism.”

I guess I’m just not quite sure why we’re still calling them “lower” life forms anymore.

 

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Ben-Jacob, E., Becker, I., Shapira, Y., and H. Levine. (2004).  Bacterial linguistic communication and social intelligence.  TRENDS in Microbiology, 12(8): 366-372. 

doi:10.1016/j.tim.2004.06.006 

 

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.

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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

Toxic Tradeoff: An Oil-Dispersant Story

12 Jul

I’ve been interested in the discussions on oil dispersants being used in the BP gulf disaster recently, specifically from the microbial break-down perspective.  Theoretically, dispersing the oil should give it greater surface area, allowing more rapid chemical and biological degradation rates. Speedy biodegradation seems like a good thing.   However, I just discovered an article published this spring in the International Journal of Environmental Research   which gave me pause to think on the whole issue in a way I hadn’t before. 

The article’s author (Dr. A. Otitoloju – a research scientist in the department of Zoology at the University of Lagos, Nigeria ) evaluated crude oil break-down under natural, versus dispersant-controlled settings and the findings seem especially meaningful in light on the current situation in the gulf. First, I should mention that this subject area is much more toxicology than microbiology and therefore my knowledge base is limited.  So it was particularly interesting for me to find out from this article that, “most of the dispersants that have been initially introduced into the market were found to either to be very toxic on their own or enhance the toxicity of the spilled oil on the receiving habitat or exposed organism when deployed to control oil spills.”  Of course this isn’t news to everybody and BP’s use of the toxic COREXIT ® has been the subject of some heated debate already  mostly due to the fact that there are  other dispersants tested by the EPA  found to be less toxic and more effective.

Perhaps it isn’t surprising then that this research article by Otitoloju found increased toxicity of the oil-dispersant mixture to the test organisms, African catfish.  But what is interesting is that over the 28 days of the study, the level of toxicity did not decrease but actually increased over time.  Overall, the dispersant mixture was about twice as deadly to the fish as was the uncontrolled oil, mostly likely due to increased exposure (if the oil is in dense clods or balls, or floating on the surface of the water, the fish can’t get as easily coated with and absorb the oil  as it can when the oil has been chemically dispersed thoughout the water column).

However, it was clear that microbial growth was enhanced (more than 7-fold) and breakdown of the oil was more rapid when the dispersant was used.  So while the dispersant-oil mixture was clearly toxic to the fish (and likely other vertebrates), it enhanced degradation of the oil by microbial populations.  Worth noting, though, are the facts that:

1.) Even without dispersant added, the oil did begin to break down over the course of the 28-day study and gradually decreased in overall toxicity to the fish; and,

2.) Inreased microbial breakdown may be short-lived, according to an article in the ScienceInsider which discusses dispersant interference with natural microbial processes in marine systems.

Now, in thinking about how this pertains to the Gulf of Mexico, where almost 2 million gallons of dispersant have been applied already (and more every day), how will this play out in the long-run?  The dispersant makes the oil less obvious floating on the surface of the water and reduces the appearances of “tar-balls” on beaches, but increases bioavailability and exposure of the wildlife significantly, resulting in higher levels of toxicity, despite [temporarily]  increased microbial degradation rates.

So what exactly is the trade-off? 

Dispersant use equates more dead fish, coral, and so on, in the short-term, but with more rapid disappearance of the oil from the waters and coastline in the long-run (see also the article by M. Torrice cited below).

Degradation rates might be even more critical when we consider hurricane season could bring substantial quantities of oil inland. Maybe a dispersant is a necessary evil.  But in that case it seems only right to use the least toxic, most effective dispersant available, which certainly isn’t COREXIT ®.

(For more toxicity info, see the EPA’s Toxicity Testing of Dispersants for the Gulf, last updated June 30th)

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Otitoloju, A.A. (2010) Evaluation of crude oil degradation under a no-control and dispersant-control settings, based on biological and physical techniques International Journal of Enivronmental Research, 4(2): 353-360.

Torrice, M. (2010) Cleaning up the Gulf oil spill.  Chemical & Engineering News, 88(20): 36-37.

The Newest Bacterium: Part 3, Finalé

6 Jul

How did the Venter research group synthesize a genome for transplant? 

The first thing I really wanted to know in reading the original research article in Science (May 20th, 2010) was, how did the authors of this ground-breaking piece of science manage to synthesize an entire bacterial genome? 

And the answer is: they didn’t, not exactly. 

If you’d like to see for yourself, the actual materials and methods used in the Science article were not contained within the article itself.  They are, however, available here as “Supplementary Materials.” 

But if you’d rather not sit down with your molecular microbiology text book and dictionary to go through their 29 pages of methods, let me explain as briefly as possible…

As I mentioned in the previous post on this (Part 2), Venter’s group of scientists at the J. Craig Venter Institute (JCVI) had already worked with these Mycoplasmas for quite some time and had sequenced at least one entire genome.  In doing so, as well as a series of experiments in which they could delete one gene at a time and see what happened to the bacterium, they managed to figure out precisely which genes were necessary for survival in the lab and which were not.

At that point they simply ordered the genome sequence, in little pieces, from a company called Blue Heron  that commercially manufactures DNA in the form of oligonucleotides (a.k.a. oligos); an oligo is a small piece of DNA arranged according to your (consumer) specifications. 

There are a variety of companies in existence all over the world that will put together oligonucleotides for any researcher or institution; you only have to tell the company what order you want the bases in (A, T, C, and G).  Venter and the scientists at the JCVI simply ordered the known sequence of the genome of M. mycoides from Blue Heron in pieces each about 1,080 bases long, and made sure that the pieces all had overlapping, matching sequence at the ends. 

So, the Venter group also wanted to make sure that their soon-to-be creation would not only function properly, but could be identified, patented, and its movement tracked.  Therefore, in writing this synthetic genome, they included some “watermark” non-coding sequences.  These are bits of genetic material that don’t actually get used in the daily life-functions of the bacterium; they are just there, taking up space, allowing recognition and quality assurance by the scientists working with the organism.  In these watermark sequences the scientists spelled out their own names, a few choice quotes, and even a webpage, all in the genetic code of this organism (more info on the code at another interesting blog).

But how did they assemble the pieces of DNA into a genome?

Two words:   slave   labor 

Only, not the way you might be thinking.  They used a common yeast (Saccharomyces cerevisiae; a.k.a. “bakers’ yeast” or “brewers’ yeast”) to put all the pieces together for them.  This particular yeast was the first fully sequenced eukaryotic (eukaryote = cells with a true nucleus, i.e. plants, animals, us, not bacteria) organism and is particularly easy to grow. 

Since its genome was sequenced more than ten years ago and it’s the “model organism” for eukaryotic cell function, we know a lot about it, how it works, but more specifically, how it’s DNA repair and synthesis mechanisms function. 

Dr. Venter and his team of scientists made use of this knowledge in the way they designed the pieces of the bacterial genome that they were interested in transplanting.  There were specific recognition sites allowing the natural machinery of the yeast cell to stitch them all together in a specific order.  They had to go through three rounds of yeast-facilitated patch-work-quilting to get the whole genome, starting with the small pieces they ordered from Blue Heron, then gradually making larger and larger pieces until one of their yeasts finally contained the entire “synthetic” Mycoplasma mycoides genome (plus watermark sequences).

My 2¢ on the whole thing…

The researchers at JCVI actually published another paper in Nucleic Acids Research only about 3 months earlier describing this entire process, entitled “Cloning whole bacterial genomes in yeast.”  They do a nice job of explaining that microbial gene cloning  has been done for years in microbiology laboratories all over the world for a variety of reasons.  Now, just read that last sentence again slowly and let it really sink in. Then think about this: In 1973, Stanley Cohen and Herbert Boyer actually created the first recombinant DNA (cloned) organism and we’ve been using this technology ever since. (Cloning technology development timeline)

This paper in Science which has caused all this hubbub simply pushed a common method a bit further, from just one gene or a few genes, into the ability to manipulate a very small bacterial genome.  One major driver to this type of research (amongst others) has been the difficulty in not being able to grow most microbes in the lab for detailed study. (The uncultured microbial majority)

If you can’t grow it in the lab, you know fairly little about the organism or what it does out in nature.  We can sequence the same microbe, but still we aren’t certain how that genetic code amounts to functionality in the environment.  The primary advantage to the JCVI’s newest technique over the cloning that we’ve been doing previously is that we can use much larger pieces of DNA, longer gene sequences, and this means more information

The limitations of this technique are obvious when we consider the fact that the transplanted genome was in fact that of Mycoplasma mycoides (with a few additions and deletions).  Not only was the genome specific to that organism, but all the constraints to making this experiment work will be equally as specific.  Try a different genus and the whole ballgame has changed. 

That said, I do acknowledge the fact that these two organisms and the M. mycoides genome may serve as a useful platform or starting place.  I would imagine next steps will be to put together sets of genes from a host of different organisms to create hybrids with the M. mycoides sequence, or some other very simplified genome. In this case, the donors of the genes tacked on to the base genome wouldn’t have to be limited to microbial species,  many genes and gene fragments have already been patented  amid some more recent controversy (roughly 20% of the human genome, in fact).  Each new hybrid, of course, would be patentable in its own right and you can easily see how lucrative this line of research will soon be.

Did I say I’d be brief?

So, in short, the research group at JCVI combined several techniques commonly used in the various fields of microbiology and transplanted the piecemeal genome of one organism into a closely related organism where it began to function rather normally as the first organism.  An interesting and noteworthy piece of science, it is not, in my opinion, the “creation of life” that merits the fear and awe with which the world reacted (at least not yet).

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 Gibson, D.G. et al. (2010) Creation of a bacterial cell controlled by a chemically synthesized genome.  Science, 329 (5987): 52-56.  DOI: 10.1126/science.1190719