Monday, May 11, 2015

Concluding Impressions

The time has come. The elevator is empty, Jason is stowed, and the lab is slowly being separated into boxes. The screens show a quiet deck and the wake of the ship as we steam towards Auckland.

The end of a cruise is a bittersweet time – everyone looks forward to their return home (and to solid ground), but the family gained while on board is something to be missed. We have created both intellectual and personal relationships with everyone, whether during van shifts, meal times, or simple down time. We return to port for one last celebration of time between shipmates, between new friends and old colleagues, and of the science that brought us all together.

Jason team and science watch the semi-final ping pong match

Niya dilutes metal samples to create vials for SiO2 samples from the fluids gained at each vent. “It was a great learning experience,” she said. “This was my first cruise, and I didn’t know how things worked. I loved being in the control van and actually seeing the vents in real time. I hadn’t appreciated how small the vent sites really were. Jason gives off this tiny halo of light, and you realize just how much you could be missing. We learned that on this cruise with the Eccentric Gardens site – it was on the edge of the map, and no one had ever found it before. It was great seeing the critters at each vent and learning what they were, writing down ‘galatheids’ and other names I’d never heard of before.” She grinned. 
Neya finishing her analysis
Others had similar opinions. For many it was their first cruise, and expectations varied across the board. “I didn’t expect to be so seasick,” Alex jokes, and the rest of the lab laughs. “Nonetheless, it was a very interesting experience. For example, doing PCR without a PCR box in such rocky conditions, but still getting good results. It was interesting to see all the work that goes into piloting Jason, and I’d definitely come back, but it’ll be good to stand on steady ground again.”

When asked, everyone agreed that they would come back in a heartbeat. It is such a wonderful experience and we all learned so much. It isn’t until you’re on a research cruise that you realize just how much work goes into sampling, collecting, and processing. In the end, however, it’s all worth it. When it comes to the best part of the cruise? That varies:

·      Being in the control van and seeing things many only read about

·      Finding the new vent sites

·      Getting good samples!

Alex setting up one last qPCR experiment
·      Seeing unique structures and finding the microbial communities that live within them

·      The teamwork, meeting new people, and playing (and losing) board games in the downtime

·      Watching pilots attempt to collect chimneys far bigger than expected

The one thing no one agreed upon was the favorite site. From Toilet Bowl to Mothership to ABE and back, the opinions varied - and rightly so. Every site we visited had a special significance to someone and provided a sample that could potentially give science a new insight into hydrothermal vents and their microbes, chemistry, and communities.

It has been an unforgettable experience. Someday we will return to sample again, but for now this cruise – and this blog – have ended. Thank you to all science members, pilots, engineers, and ship crew. We couldn’t have done this without you.

The "Mothership" flange complex at Tui Malila

Saturday, May 9, 2015

Tubeworms seen at Mariner

Towards the end of our dive at Mariner, we spotted some tubeworms.  The most obvious invertebrates in the Lau Basin are snails (Ifremeria and Alvinichoncha) and mussels, shrimp and crabs. So seeing tubeworms is quite unusual. We did see some in our research cruise to this area in 2006, but never at Mariner.  A very healthy community was spotted this time on a huge hydrothermal pillar near our "toilet bowl" sampling area. Crabs were happily munching away on a tube or 2 about 2 cm (200mm, ~ 1 inch) long.   There were thick communities of this tiny little tubeworm. They appear to be Arcovestia ivanovi, found in the Lau and Manus hydrothermal basin areas.

Tubeworms have an interesting lifestyle.  The have no mouth or digestive system like other worms. They are essentially a sack (trophosome) of bacteria or endosymbionts, and a plume (the red structure) that captures hydrogen sulfide, carbon dioxide and oxygen.  These gases are transported from the plume to the trophosome, where they are food (energy and carbon sources) for the bacteria. The chemolithoautotrophic bacteria oxidize the sulfide, and use the energy in that redox reaction to fix carbon dioxide into organic carbon. The tubeworm is then sustained by the endosymbionts organic carbon.  Sulfide levels are quite low at Mariner relative to other deep-sea vent sites where tubeworms thrive, so it is indeed curious that we found them here.

Notice the crabs eating the tubes

SinD Lopper

We dive down with a bright yellow light
Chief Sci says when you gonna sample it right
Oh Anna dear we're not decision-making ones
And microbes, they want to have fun
Oh microbes just want to have fun

Jimmy sits in the middle of the row
He yells out we're gonna do this thing right
Oh Jimmy dear you know you're Jason pilot one
 But microbes, they want to have fun
Oh microbes just want to have

That's all they really want
Some fun
When the science is all done
Microbes - they want to have fun
Oh microbes just want to have fun

Some say all you need is CTD
But we say you need more creativity
We want to be the ones to bring them up in the sun
Oh microbes they want to have fun
Oh microbes just want to have

That's all they really want
Some fun
When the science is all done
Microbes - they want to have fun
Oh microbes just want to have fun, 
They want to have fun,
They want to have fun....

Science isn't all technobabble and pipetting. Sometimes we have to get creative in our sampling methods, and at sea, that's where engineers come in. See our post on its origins from a previous cruise here:   After Anna-Louise challenged our scientists to come up with something that, unlike the strong arms of Jason, wouldn't crush fragile chimney and beehive structures, creativity came to life.

We began with the FST3000, whose tin bottom was tragically too weak to cut through the chimneys all the way. After some experimenting, Jimmy came up with a new contraption - the SinD Lopper. Made out of a coffee can with the bottom removed, the SinD Lopper acts as a guillotine, sending a metal bottom slicing across the chimney and beehives to remove them from their bases. Not only is this less forceful than Jason's grip, the reduced surface area allows the chimney structures to stay more or less intact for transfer to Jason's deck. It is still undergoing beta testing, but SinD Lopper is so far doing better than we could have imagined, and we look forward to exploring future realms of the deep with the new invention!
Contributed by Morgan Haldeman 

Friday, May 8, 2015

Back in the water!

We're back at Mariner, at >1900 m as of noon today!  Yesterday, with the the weather situation, Stephane L'Haridon made use of the time to run a different experiment... he explains below...

Ocean covered 70 % of the Earth's surface, and the microbial diversity of the oceans is still not well understood.    The number of microbes in the sea has been estimated around 1029 cells, the number of microbial species is still under debate but estimates suggest the presence of at least 106 different microbial species in the ocean. Finding out who these species were, was greatly aided by the technical revolution that started in the 1980s in the field of molecular biology.  Microbiologists were able to identify microorganisms without first needing to cultivate them based on the sequence of the small-subunit ribosomal RNA (16S rRNA) gene. Recently, a new generation of DNA sequencers have been developed that allows us to sequence full genomes of uncultured microbes and has led to the development of “Omics-based” approaches to microbiology. Most of the organisms detected by this approach have never been described, even after 120 years of trying to get them to grow. These microbes and are the so called “uncultivable” species; less than half of the known phyla of microorganisms have a cultured representative, and more than 99% of all microbes remain “uncultivable”. It is these microbes that we are trying to grow from samples collected on this expedition.

Stephane, Brett, and Bud watch the CTD computer display

Mainly two strategies are employed to isolate pure strains, after a first step of enrichment, microbiologists isolated colonies by streaking on medium solidified by a gelling agent or they performed serial dilution in liquid medium until they obtained a pure culture.
Claude Zobell, who was a pioneer in the study of marine microbes, developed the marine agar 2116 medium (Marine Broth Medium) in1941. This nutrient-rich medium has allowed the isolation of many heterotrophic bacteria belonging principally to a fairly limited number of genera, including Vibrio, Pseudomonas, Oceanospirillum, Aeromonas, Deleya, Flavobacterium, Alteromonas, and Marinomonas. Nutrient rich-media at the step of enrichment on liquid or solid medium favor the growth of faster-growing bacteria, referred to as “r”-strategists at the expense of slow growing bacteria,”K”-strategists, the latter represent the relevant microorganisms in the pelagic environment. Mimicking the natural sea water that microbes thrive in, is a challenge for microbiologists. The Marine Broth 2216 medium has 170- fold more dissolved organic carbon than natural sea water which clearly inhibits the growth of oligotrophs (microbes that live on a very little 'food') which represent the majority of the microbes in the ocean.  Only recently, in 1993, did D. K. Button and colleagues used the natural sea water with small inocula for isolating marine bacteria. This concept of natural sea water as medium and low concentration of cells as inocula was improved in the Giovannoni laboratory at Oregon State University (USA) two decades later by using high throughtput cultivation (HTC). The HTC permits the isolation of members of the Sar11 group of microbes, one of the most dominant groups of microbes in the ocean.
CTD profile showing sensors such as oxygen, depth, temperature

In the framework of the European Program, MaCuMBA, coordinated by Dr Lucas Stal, in which we are one of  the 23 partners, we are developing new approaches, new devices to cultivate the “uncultivable” microbes by applying innovative methods, and the use of automated high throughput procedures. To isolate new key players microbes from  the Tongan sea water, we deployed a CTD cast  to a depth of 500meters and collected samples from 5, 95, 200, 300 and 500 meters depth. To perform the HTC method, after sterilizing some of the seawater we collected, I added nitrogen, phosphate, carbon and vitamin sources at very low concentrations. I then put the medium into the 96 wells of the microplate, and added about 2 cells from the samples we collected to each well. It’s a challenge for microbiologist to try to work under sterile conditions on a vessel without a PSM (Microbial sterile cabinet)! Only 7 hours after the recovery of water sampling, 34 microplates containing the cultures were incubated at room temperature (20°C). 
My microtiter plates cultures incubating at room temperature

After patiently waiting, in two months, when I am back in France and in my laboratory, I will check to see if anything grew in these 96 X 34 little wells. From past experience, there will be lots of novel bacteria happily living in these culture wells!

Contributed by Stephane L'Haridon

Thursday, May 7, 2015

Growing ELSC heat-loving microbes

In addition to our geochemical and metagenomic research aims on this expedition, we also seek to isolate novel microbial species.  To achieve this, we use data from our geochemical and metagenomic experiments to direct traditional cultivation-dependent microbiological techniques.  Studying an isolated microorganism in culture allows us to test a range of physiological conditions and can help elucidate the microbe's metabolism beyond what one might learn from genomics alone.

Growing and isolating select microorganisms is very difficult and often proves impossible.  Scientists estimate less than 2% of environmental microbes may be easily isolated and cultured in a laboratory setting.  While some bacteria thrive easily –and grow like “weeds” – on media rich in nutrients, others require atypical growth nutrients.  Interspecies microbial relationships that involve one microbe providing a vital growth factor for another may exist –making it impossible for one species to grow without the other present.

There are billions of microbes colonizing hydrothermal deep-sea vent chimneys waiting to be isolated (see photo below).  Working with the Jason II team, great care is taken to preserve the integrity of chimneys as they are sampled and brought to the surface for study.  Once on board and processed, microbial biofilms on the  outer layer of the chimney are harvested by scraping and used in enrichment and isolation experiments.

Scanning electron micrograph of microbial biofilm on a hydrothermal vent chimeny
On this cruise one group we're targeting is the isolation of a thermoacidophilic deep-sea hydrothermal vent-dwelling Euryarchaeota (Aciduliprofundum species). In this case we use an acidic culture media and incubate it at temperatures between 60 ºC and 90ºC.  We hope these conditions will promote growth of these thermoacidophiles, but if it does grow, it won't be the only microbe.
enrichment cultures to extinction.  This is to say – we dilute cultures in series until the dilution is sufficient to reduce enrichment cultures down to a single species.

If after all of these steps we're lucky enough to get our new isolate, we still have the challenge of maintaining it, getting a good stock, and preserving it for future characterization studies or to share with other labs. In Dr. Reysenbach's lab at Portland State University we have been lucky to get tricky thermophilic microbes to grow and thrive. We're a part of the Center for Life in Extreme Environments and maintain an Extremophile Culture Collection – think of it as a library (or zoo) of interesting microbes, many of them yet to be fully characterized!
Jessica checking some of the cultures with her shrunken head friends

Contributed by Jessica Hardwicke (undergrad student at PSU)

Tuesday, May 5, 2015

The Importance of Coffee

Winds are meant to ease over the next day or so... and hopefully we'll get to dive again. In the meantime we have time for a cup of coffee. 
Jeff and Sean's morning Jo'
Jeff and Sean take their coffee very seriously. Somewhere packed among the crates of scientific equipment is an espresso machine. By the time we leave Auckland, ten bags of coffee beans are set to accompany us. We have also managed to pick up a few New Zealand-themed espresso cups, rainbow-colored sheep and kiwis. Should the espresso machine break due to some unforeseen tragedy, a rarely used French press stands ready to fill the gap.
Sean jokes about how they made sure to calibrate the thermocouple (a fancy thermometer) on the espresso machine before leaving Jeff's lab in Woods Hole. Thermocouples are something close to Jeff and Sean's scientific work as well, as is the handling of hot, pressurized fluids. Besides the espresso machine, the center-point of their laboratory is a set of isobaric gas-tight fluid samplers (IGTs) with thermocouples attached to the nozzles . These highly specialized and custom-built pieces of equipment are able to collect hydrothermal fluids at the bottom of the ocean and return them, at seafloor pressure, to the surface. Keeping the fluid pressurized is essential for measuring dissolved gases that are an important part of the fluid’s chemistry. However, releasing these fluids without losing the gases and measuring them accurately enough to be useful is also tricky, and requires an elaborate, mobile chemical laboratory. It is also important to keep the IGTs well serviced in order for them to function properly. Like a two-man pit crew, Jeff and Sean routinely assemble and disassemble the equipment. With IGTs going in and fluid samples coming out of the water at all times of day, the espresso machine sure gets a workout.   Contributed Guy Evans

Jeff and Sean’s collection of espresso cups (upper right) and coffee beans (lower left). IGT samplers 5 and 6 ready for servicing (above center) and being serviced (right).

Monday, May 4, 2015

Geomicrobiology in the Taupō Volcanic Zone (TVZ)

The wind speeds are up, and the swell --big!

Extending SSE from the Lau basin, and part of the "Ring of Fire", we encounter New Zealand. Here, plate tectonic movement, and consequently spreading and fracturing in the Earth's crust, manifests as geothermal springs. Just prior to our research expedition to Lau, several of us visited this geothermal area and sampled some hot springs in collaboration with our colleagues at GNS Science to find and grow a very unusual microbial group; a parasitic/symbiotic group of Archaea called the Nanoarchaeota.

Just three hours south of Auckland within a geothermally active area known as the Taupō Volcanic Zone (TVZ) is the town Taupō-nui-a-Tia. Translated from the Māori language as "The great cloak of Tia", both the town and lake are named after Tia, the Māori chief who discovered the area.   Some hotsprings in the TVZ are a gentle 25°C with neutral pH and others boil to the surface, more acidic than battery-acid. 

Carlo and Karen, on our research expedition, are members of the GNS Extremophiles laboratory,  and are actively studying the geomicrobiology of the New Zealand hot springs. They have helped collect microbiological and geochemical samples for the “1000 Springs Project”; a comprehensive bio-inventory of the microbial diversity of New Zealand’s geothermal ecosystems. To date the Extremophiles laboratory has collected over 42,000 geochemical data points with corresponding microbial community information for each hot-spring. All this information is publicly available in an impressive user friendly and educational website:

Inferno crater
During our stay we visited Waimangu, New Zealand’s youngest geothermal field.  Waimangu was created in 1886 following the eruption of Mt. Tarawera- An eruption that also created Lake Rotomohana and flooded the fabled ‘Pink and White terraces’.   Inferno crater is particularly impressive.  This turquoise feature oscillates between 35°C and 80°C every 30 days, a fluctuation the resident microbes need to adapt to!  At low temperatures, microbial communities are dominated by non-spore forming Bacteria while at high temperatures, heat-loving Archaea dominate. 
Waiotapu (Māori for “sacred waters”) is located 52 km north of Taupō in the Okataina Volcanic Centre.  This geothermal area is high in concentrations of sulfur, arsenic and antimony, and produce colorful minerals such as orpiment  (As2S3) and stibnite (Sb2S3).  Two of New Zealand’s most impressive geothermal hot-springs, the neon-green “Devil's Bath” and bright orange “Champagne Pool”are in this area.
Champagne pool
"Devils bath"

 Contributions from Guy Evans, Jessica Hardwicke and Carlo Carere


Keeping up Moral

The weather forecast has been accurate and the seas are still too rough to launch Jason. As we wait for better weather to arrive, we are keeping busy by processing samples that were collected during our dives to Mariner and ABE vents. Our cultures are growing in the incubators and our gas samples have been measured, but life on board the ship isn't all work.

Carlo and Nick in training for the big tournament

Caption contest starring Styro Foam trying on a survival suit
Ping pong has a long and storied history among seagoing scientists and there is no greater honor than winning the expedition ping pong tournament. While ping pong is an official game of the Olympics, playing ping pong on a heaving ship requires the skill and coordination of a gaming master. Our great tournament has begun with tournament underdog John defeating his lab predecessor Gilbert in the first round. Board games are also popular on the cruise, and another pastime is the nightly Settlers of Catan game which has been dominated by Carlo thus far on the cruise. Finally, a “caption this picture” contest has emerged on our common whiteboard where the funniest caption wins the author fame and glory (and more!). All of these activities help keep moral high on the ship while we wait out the weather and hopefully we'll be diving again by the end of the week.

Contributed by Rick Davis

Sunday, May 3, 2015

The Pressure Effects....

Today' weather forecast: "Big high pressure (1033 mb) near North Is, NZ to drift slowly to the E with little change in strength during the next 2-3 days. This high may begin to weaken slowly during the middle of... Appears worst conditions may develop during Mon and continue..."

Pressure also has a big impact in the deep ocean. The bottom of the ocean is an inhospitable place. It is dark, cold, and under extreme pressures. Imagine you are swimming in a pool that is ten feet deep, or just about three meters. You dive to the bottom to pick up a pool toy or a penny and your ears pop. You feel the pressure on your body and on your head. Now imagine increasing that pressure over 100 times. With every ten meters of seawater, add one atmosphere of pressure. Now imagine traveling to 1000m, or 100x10m. Since we already exist at 1bar of pressure, the total pressure would be about 101bar.
Jason can dive to depths of 6000 meters. The ROV is specially reinforced to deal with the extreme pressures at depth so that it doesn’t implode, or compress explosively. The areas we work in the Lau Basin are at depths of 1700 to 2600m, but the pressures are no less damaging. 

Styrofoam cups and heads before their descent to our deep-sea research sites.
To demonstrate the pressures at depth, we sent down several Styrofoam heads that Allie, Joy, Francis and Piper illustrated, and cups that middle school teachers attending a science (STEM) workshop at the University of Nevada illustrated.   The cups and heads dropped to depths between 1900m and 2400m. Simply dropping to the bottom of the ocean allowed the pressures of nearly 200bars, or around 2500 pounds per square inch, to do its work.
The cups, once a full 10oz and over 3 inches tall, shrank down to around 2 to 3oz and around 2 inches tall. We stuffed wads of paper inside to allow them to keep their shape, but that did not necessarily ensure they were perfectly round at the end. Instead, they crumpled as the pressure increased, crushing them on one side or another depending on which way they were oriented. 

The extreme left scale bar was 1 inch. This illustrates nicely how much the cup shrunk!

Styrofoam is made of foam called polystyrene, which is full of air pockets. When put under pressure the air is squeezed out, but the foam retains its shape. This is why Styrofoam makes such a good example of pressure at depth – it does not warp the material past recognition, but it shrinks to a size that seems unrealistic to our 1bar atmosphere. 

 This extreme pressure at deep-sea vents also allows the very hot hydrothermal fluid to remain in a liquid state in most cases, except when the temperature is so high the fluid will boil as we saw in the Mariner blog post.  Many of the deep-sea invertebrates; snails, mussels, shrimp, crabs, do not have gas-filled organelles, such as humans or other land-dwellers, which would be compressed under pressure, and so these creatures are not nearly as affected by pressure as we are.

the normal head
the shrunken head
The bacteria we bring up to our lab are not necessarily barophiles (piezophiles), or pressure-loving, but they do thrive under those conditions nonetheless. Even the fluid samples we bring up show evidence of pressure – there are no bubbles emerging from the vents, but when we remove the fluid from its pressure-tight sampler (the IGT see "hot water" post), it may erupt with bubbles as the gases escape the solution.

Much of the deep ocean is as yet unexplored. And how pressure affects life in this deep ocean biosphere will no doubt lead to a new understanding of the extent of life on Earth.

Contributed Morgan Haldeman, Nick Rhoades and John Kelley.  

Friday, May 1, 2015

Rough Seas Ahead

Despite the best planning, problems arise while at sea. The ship can have a malfunction, Jason needs to be repaired, scientists forget an important chemical back home in the lab. These are problems that we can usually fix or work around to get the job done and continue with our exploration of the Lau Basin. Unfortunately, one factor that we cannot plan for and have no control over is the weather at sea. Our ship, the R/V Roger Revelle has no problem in rough seas, however the ROV Jason II needs relatively calm seas to be safely launched and recovered. This is because Jason must be craned from the side of the ship and high wind and waves will make the ROV swing on the crane, which is dangerous because Jason weighs over 4000 kg out of the water which is about three times heavier than an average automobile. 
Rough seas prevent Jason from diving

Weather conditions such as wave height are monitored in the computer lab.
We are currently experiencing 20 knot winds and an average wave height of 3.5 meters. The weather forecast calls for more wind in the next couple of days so our dives are likely to be on hold for at least that long. Luckily we have lots of good samples from ABE and Mariner Vent Sites and we are still busy at work measuring the water chemistry and grow microorganisms from these samples. There is always plenty to do when out at sea, even when Jason is sitting on the deck.

Contributed by Rick Davis

Thursday, April 30, 2015

Taming wild microbes

Karen Houghton checking growth  of acidophiles in her culture tubes
On the surface of Earth, most biological communities are fueled by organisms that use light energy to convert inorganic carbon (CO2) into organic compounds (i.e. biomass) in a process known as photosynthesis. This is what plants do. In deep-sea hydrothermal environments, there is no sunlight so instead these communities are supported by chemosynthesis – a process by which microorganisms use chemical energy to convert CO2 into biomass. The chemical energy for chemosynthesis comes in the form of reduced chemical compounds (H2, Fe2+, H2S, CH4) that are relatively abundant in hydrothermal fluids. Organisms that perform chemosynthesis are known as chemolithoautotrophs.  Both aerobic microorganisms, which require oxygen (O2) to grow and anaerobic microorganisms, which use alternative electron acceptors (NO3-, S0, SO3-2), are found in hydrothermal environments.  Within the Lau Basin and other deep-sea vent fields, microbial communities are heavily influenced by steep chemical, pH and temperature gradients.  For this reason, microbiologists on board the Revelle hope to isolate several novel acid-loving (acidophiles), high-temperature (thermophile) species on this expedition.

90 degree Celsius oven filled with enrichment cultures from samples collected at ABE and Mariner
The isolation of chemolithoautotrophs is driven by the principles of growth selection.  In practice, synthetic media is prepared that mimics the conditions in the deep-sea but only the necessary energy (e.g. reduced inorganic chemical), carbon (e.g. CO2) and electron acceptors (O2 or NO3-, S0, SO3-2) required for a specific type of chemosynthetic metabolism are supplied.  By restricting alternative metabolisms and by exposure to stringent pH and temperatures, microorganisms with desirable traits out-compete undesirable species and become enriched.  Over time, with the application of sufficiently selective growth conditions, it is possible to remove all undesired microorganisms; resulting in a “pure” isolate.

In our lab on the Revelle, microbiologists are working hard to isolate high temperature, acid-loving hydrogen-oxidizers and methane oxidizing species; in addition to heterotrophic bacteria capable of eating organic compounds (amino acids, peptides, chitin).  In the weeks to come, both microbial community and metagenomic data will be used to refine the selective media used in isolations.    

Contributed by Carlo Carere and Gilbert Flores

Mariner vent field

We have been working at the Mariner vent field for the past 48 hours or so. For some of us this is one of our favorite places on the bottom of the ocean. Because this deep-sea vent field is very close to the island arc volcanoes, the hydrothermal vent fluids are greatly influenced by very acidic fluids released by the magma chamber below the seafloor.  These acidic fluids mix with the seawater-derived hydrothermal fluids to create highly acidic hydrothermal fluids that leach metals from the oceanic crust, such copper.  Because these fluids are more acidic (~pH 2.5) than the vent fluids to the North (e.g. ABE and previously Kilo Moana) they contain much higher concentrations of metals like copper, zinc and iron. When these fluids form hydrothermal chimneys, they are quite tall spindly structures, venting high temperatures fluids over 360 degrees C. We also found some fluids that were boiling,which causes phase separation and results in rather unusual fluid chemistry.
Copper and iron rich hydrothermal chimneys at Mariner
The bright white areas at the right, that look a little like white flames are fluids that are being emitted and are boiling.
The microbial biofilm on the "Toilet bowl" rock
The 'Toilet bowl' structure
 From a microbial perspective, Mariner is also very interesting. Samples from here, collected in 2005, resulted in the first truly acid and heat-loving ('thermoacidophile') microbe from deep-sea vents. But also the microbial communities associated with these hydrothermal chimneys are dramatically different from those in the North.  One area that has yielded DNA sequences of heat-loving microbes never before found at deep-sea vents is where a structure we call the 'toilet bowl' is located.  So this vent field has great potential for discovery of new microbes and providing deeper insights into the diversity and extent of life on Earth.
Samples are placed in 'bioboxes' on the Jason.  Note sample still 'smoking'

Wednesday, April 29, 2015

Genomes from Smokers

We’ve got samples! Now comes the really fun part-- discovering new microbes and finding out how they survive and grow in such extreme environments. We are examining these communities using two different approaches. Many of the microbiologists on board are developing new culturing techniques to get novel Bacteria and Archaea to grow as isolated cultures in a lab. Another approach is to look at the communities using molecular techniques to determine the ecology and biochemical mechanisms of microbes in the environment. One of the most exciting developments in environmental microbiology is the ability to perform genomic analysis of environmental samples, known as metagenomics.
Hydrothermal vent chimneys about to be sampled

Metagenomic analysis of a sample should give us information about who is living at these vents as well as how they survive there, but the process is long and difficult. The method begins with extracting and purifying total DNA from sulfide chimneys. Once we break open the cells, we need to purify the DNA to remove any traces of metals or cell debris which inhibit our future sequencing steps. This purified DNA consists of a mixture of genomes from each microorganism that is living in the sample. We then sequence the fragments using a next-generation sequencer that gives us hundreds of millions of fragments of DNA sequences. We then rebuild the genomes from these small fragments using powerful computer algorithms so we can study them in more detail. Once these genomes are reconstructed, it will help us understand how the genomes of these microbes differ between the different deep-sea vents sites here in the Lau Basin, and help guide our culturing efforts in new directions to try and get these microbes to grow in a test tube. We’ll follow this post with more information about how we grow microbes on the ship. 

Contributed by Rick Davis

Inside view of a hydrothermal sulfide chimney sample from ABE. The yellowish mineral is
chalcopyrite, a copper, sulfide, iron mineral CuFeS2