Karen's Daily Blog

To welcome the new protist section of the microbe area of our Web site, I pulled up a stool in the Hydro Lab to talk to the University of Southern California’s Dr. Dave Caron and postdoctoral research associate Dr. Pete Countway, who are taking part in the Extreme 2008 cruise to study protists at the hydrothermal vents.

“Protists have been ignored for 30 years [of research at the hydrothermal vents],” says
Dave. At first, he says, the emphasis of research was on the newly discovered charismatic macrofauna (this phrase means cool bigger animals) at the events.

“There was a huge impetus to study the larger organisms. But microbes must be the source of everything.” he says. “In other environments, protists make life possible for metazoa, because they eat bacteria and are in turn eaten by copepods and larger organisms (the metazoa). So they pass energy and nutrients through food webs to higher tropic levels. But we don’t really know if they do this here. So you can’t ignore them!”

Pete says, “In the scientific community we don’t have a clue to the diversity of microorganisms on this planet. We just don’t know how many species there are. Part of what we’re doing and have been doing for ten to twenty years is play catch up. Microbiologists -- people who study everything that’s little and tiny -- have not had tools to characterize their subject until recently.”

Pete adds, “Microscopy has helped, the scanning electron microscope has helped, but what’s really breaking the field open is the use of genetic signatures as tags to identify microorganisms.”

The Caron Lab’s studies encompass the Antarctic, the Arctic, the Sargasso Sea in the North Atlantic, the Arabian Sea, 9º North’s water column, and the Pacific off of Southern California. In the Sargasso Sea, they have studied what’s living right near the surface, and 2,500 meters deep, just as they have done here at 9º North.

“If they’re different, how are they different, and why are they different?” Dave says. “There is a swirling controversy in our field over the answer, and people fall into two camps.”

One camp says that all microbial species could be everywhere, and that the organisms found in a particular environment are the ones the conditions in that environment select.  In this scenario, an environment is like a soccer team with 11 players. They represent the organisms that are found in the environment, he explains.

“But there’s an infinitely large bench, so players can be switched in and out,” Dave says. “If it gets rough, you can pull the big burly guys off the bench. If it gets hot, you can put in the leaner guys.” 

Which players are on the field depends on the conditions.

“In an environment,” Pete says, “there’s a switching that appears to take place based on conditions. There may be a limitless diversity of organisms that can arise.  They may already be there in very, very low abundance, but we don’t know. “

The other camp proposes that ecological functions would die out in response to conditions. Dave describes Australia, hundreds of thousands of years ago.

“You would find almost all marsupials, in the same ecological roles as placental mammals fill in other areas. There are marsupial flying squirrels in Australia, and placental flying squirrels in South America.  If you went into Australia and changed the conditions a hundred thousand years ago so that marsupials could no longer hack it, the functions those animals did would die out,” Dave says.

This is because if the conditions changed to cause marsupials to die out, there would be nothing else “on the bench” to take their place in the environment.

These split scenarios raise the question of what will happen if microbial organisms are pushed so hard (in terms of changes in the conditions in which they live in response, say, to global warming) that their functions drop. 

“If organisms are specially adapted to the conditions in certain locales on the planet, we will lose them as conditions change,” says Dave.

Here’s one especially exciting example of what the Caron lab is doing during the Extreme mission. The other night they found parasites invading some snail eggs the other night and eating the larva. People have looked at the vents for ten years and have seen the genetic signatures of a group of microbes called alveolates, but couldn’t figure out what microbe owned the DNA. Thanks to the Extreme 2008 cruise, the Caron lab may be the first to see these previously unknown, uncultured, unvisualized organisms. 

Dr. Dave Caron and Dr. Peter Countway.

In the past, biologists have classified animals based on appearance (the morphological approach) alone, working from the general to the specific in order to create groups and subgroups, and, eventually, to narrow down a species. Now, genetic sequencing (the molecular approach) allows them to know the specifics about an organism from the inside out.

There is no question, Dave says, that eventually we’ll have a system that works something like (Star Trek’s) Mr. Spock’s tricorder: you take the wing of a butterfly, put it in the machine, sequence the genes, and get back what species the butterfly is. This is the idea of the Barcode of Life, a brand-new classification system based on genetics.

Pete adds, “We used to say, does it have six legs? Now we’ll say, does it have GCCA or GCCT at this place in the genetic code. Bacteriologists have had a head start on this, because they’ve never had morphological characteristics to fall back on. They may say, ‘Okay, so there’s 98 percent similarity between one thing and another, so we’ll call them the same kind of thing.’”

“What level of gene sequence similarity should we accept as indicative of the same species?” asks Dave. We humans have more than 99 percent similarity to chimps, but we are different species. What is different, and what is the same?

Well, what difference does it make, I ask, with microbes, about which we know so little, to try to find similarities between them and others?” The answer, Caron and Countway say, is in understanding community diversity -- knowing who all the players on the bench are.

Dave says, “If environmental conditions change, are there players on the bench doing similar ecological roles but can tolerate different conditions so that the game can continue unabated? Understanding community function is the center of all the work that we’re doing -- at the vents and elsewhere.”

Today's Extreme Blogger:
Lisa Zeigler

Hello Everyone!  Lisa Zeigler here from the J. Craig Venter Institute (JCVI) (www.jcvi.org).  I am part of the viral team analyzing the microbial and viral fractions associated with deep-sea hydrothermal vents.  From JCVI we have Doug Fadrosh and myself, and we are both from the Environmental Genomics department working under Dr. Shannon J. Williamson. Our group is part of the larger team onboard which consists of Dr. Eric Wommack, Dr. Craig Cary, Dr. Shawn Polson, and Dr. Bekki Helton (all from the University of Delaware). 

While at sea ,we use the LVWS (large volume water sampler) to filter seawater near vents in what is called the diffuse flow area. These waters are usually between 20-55°C and are also known as “shimmering waters” that are seen percolating through the cracks and biology that surround the large vent structures. 

At JCVI there is a wide variety of research being conducted just within the Environmental Genomics department; our group under Dr. Williamson is interested in using metagenomic analyses, which take genetic material directly from environmental samples (i.e., via the LVWS), to gain a better understanding of the viral communities that inhabit these environments.

 

From the LVWS, we are able to recover different size classes of microbes from filters, as well as 210L of 0.22um-filtered seawater. This seawater contains what we refer to as the viral fraction. Once the instrument is recovered onboard the Atlantis, the viral fraction is concentrated using tangential flow filtration down to about 1L. After much more processing back on shore, genomic DNA is isolated and libraries are made to sequence, so we can analyze the genetic potential of the vents.

Having the opportunity to go to sea, as an oceanographer, is essential and rewarding. It is a passion of mine to study the microbial life that inhabit the oceans in order to better understand their role in life at sea and even on land. Many researchers study a variety of aspects regarding marine microbial life and I feel so fortunate to be beginning a career among these people that I have admired for so long. I came from a small town (Pasco, Washington), to work at Scripps Institution of Oceanography (San Diego, California) so I could learn and become more involved in oceanographic research.

Life at sea is almost indescribable for me. From my first cruise until now I have loved every minute of it. It can be full of long grueling days with lots of frustrations in order to get sampling devices working properly and recovering what is needed to go back to the lab. However, every sample gained is a reward and well worth any troubles. In addition to working on your own project, it is a time to learn more about the other scientists on board, either their aspirations for current research projects or even on a more personal level.

I have been fortunate to gain lasting friendships from the many research cruises that I have been a part of. In addition, the crew on the Atlantis is extremely helpful and friendly. The crew welcomes scientists into their home while we are on board and seem to always do it graciously.

Well, for our team, we are ready for the transit to Guaymas, Mexico, where our next LVWS deployment will take place.

Best wishes,
Lisa Zeigler

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Dive Log

Alvin Dive 4475                        AT15-39                                    9° North, East Pacific Rise

Pilot: Bruce Strickrott           
Starboard Observer: Jamie Botelho
Port Observer: Julie Smith

15:42 GMT On the bottom, 200m from BioVent

BioVent
16:01 GMT Arrived at BioVent
16:17 GMT Placed HOBO #148 in smoker, about halfway up chimney, temp = 353°C
16:22 GMT Collected chimney sample.
16:33 GMT Located HOBO #111 & retrieved. It had a lot of sulfide around it, not in active vent.
16:49 GMT Headed to East Wall.

East Wall
17:17 GMT Arrived at East Wall.
17:27 GMT Sipper #1 & 2 taken at Prototrap #121.
                       X = 4556, Y = 78430, Z = 2509, Hd = 94, Sipper ICL* = 4.5°C
17:29 GMT Retrieved Prototrap #121, placed in ARTY chamber #3, flooded with RNA Later.
17:57 GMT Sipper #3 & 4 taken at White Slurp.
                       X = 4557, Y = 78429, Z = 2510, Hd = 79, Sipper ICL* = 4.3°C
17:38 GMT Dead Riftia & mussels collected into rear of large biobox.
            X = 4558, Y = 78430, Z = 2509, Hd = 105
17:57 GMT White slurp taken in dead Riftia/Mussel mung area.
                       May have left some sulfide from BioVent chimney at this site.
18:02 GMT Headed to Tica.

Tica
18:11 GMT Arrive at Tica.
18:22 GMT Sipper #5 & 6 taken at Prototrap #18.
                      X = 4602, Y = 78167, Z = 2509, Hd = 89, Sipper ICL* = 4.5°C
18:25 GMT Prototrap #18 retrieved and placed in small biobox (compartment on the inside relative to basket edge).
18:37 GMT Sipper #7 & 8 taken at Prototrap #120.
                       X = 4586, Y = 78178, Z = 2514, Hd = 145, Sipper ICL* = 7.4°C
18:38 GMT Prototrap #120 placed in ARTY chamber #2, flooded with RNA Later.
18:44 GMT Collected live Rifitia and Tevnia and placed in middle compartment of large biobox.
19:07 GMT Headed to P Vent.

P Vent
19:21 GMT Arrived at P Vent.
19:25 GMT Collected Prototrap #110 and placed in small biobox. (No tape for trap #110). Put in new tapes.
19:41 GMT Sipper #9 & 10 taken in Alvinella tube.
                      X = 4644, Y = 77953, Z = 2503, Hd = 125, Sipper ICL* = 41.9°C
19:43 GMT Alvinella with minimal tube material added to ARTY chamber #1, attempted to flood with RNA Later, but we ran out of RNA Later.
20:08 GMT Alvinella collected live and added to middle compartment of large biobox (with Riftia).
20:11 GMT Attempted to take red slurp at base of Alvinella, but could not see material being picked up.
                       X = 4644, Y = 77953, Z = 2503, Hd = 125
20:14 GMT Headed to Marker 28.

Marker 28
20:25 GMT Arrive at Marker 28
20:26 GMT Collected Prototrap #102 from bare basalt area, placed in forward compartment of large biobox
                       (outer compartment with respect to basket edge). This prototrap was a little damaged during the
                       collection.   X = 4665, Y = 77745, Z = 2505, Hd = 3
20:31 GMT Sipper #11 & 12 taken at Prototrap #101, among Riftia
             X = 4663, Y = 77745, Z = 2505, Hd = 326, Sipper ICL* = 7.0°C.
20:34 GMT Prototrap #101 placed in forward compartment of large biobox
                       (inner compartment relative to basket edge). Collected big piece of basalt.
20:57 Weights away.

*Sipper ICL tested before this dive and it is reading about 3°C too high.

So, the corrected temperatures are listed below: