Posts in category Microbial & Environmental Genomics

Amazon Expedition

Yesterday, JCVI expedition scientist Jeff Hoffman embarked from Manaus on a sampling expedition of the Amazon River and its tributaries, which contains 1/5th of the Earth’s river flow. In collaboration with scientists Dr. Guilherme Oliviera and Dr. Sara Cuadros from the Centro de Excelencia em Bioinformatica (CEBIO) of Belo Horizonte, Jeff is taking samples to characterize the genomes of microbes found along 2/3rds of the entire Amazon watershed, including inflowing rivers from Manaus to Macapa. Our collaborators at CEBIO will be sequencing the samples with a joint Brazil-USA effort on analysis. Long recognized for the biodiversity of visible organisms, the Amazon is understudied with regards to the diversity of microscopic organisms and this expedition will substantially increase our understanding of the biological diversity on Earth. This work continues, leverages, and complements previous and ongoing JCVI work characterizing the unexplored microbiomes of marine, estuarine, freshwater, and terrestrial environments around the world.

See a gallery of the expedition on Facebook. More pictures will be added throughout the trip.

The 2014 Summer Internship Application is Open and Announcing the Genomics Scholar Program

The 2014 Summer Internship Application is now open.   Last summer, we hosted 49 interns from a pool of 424 applicants. They presented their research in the First Annual Summer Internship Poster Sessions held in San Diego and Rockville. The posters were judged by a team of volunteer JCVI scientists and the poster sessions were open to all employees, interns and their guests to share what great work they all participated in this summer.

 

 

2013 Intern Poster Session

2013 Intern Poster Session

We are also excited to announce the new Genomics Scholar Program beginning this summer and also accepting applications.  The Genomic Scholar Program (GSP) is a targeted research experience program to community college students in Rockville. Our program incorporates multiple avenues of support for students through the research experience with the Principal Investigators as mentors, and supplemental professional development provided by the JCVI.  Additionally, selected students will have the opportunity to participate in undergraduate research conferences.

The GSP is supported by the National Institute of Diabetes and Digestive and Kidney Diseases of the National Institutes of Health under award number R25DK098111.

Sampling: US to the Azores

I’m off again on an ocean sampling voyage but this time instead of being onboard the JCVI’s Sorcerer II, I am onboard the R/V Endeavor as part of a multi-institution, international scientific sampling team that is headed from the US to the Azores.

On Thursday August 22 we left Morehead City, North Carolina for Ponta Delgada on Sao Miguel Island in the Azores.  The research vessel will take multiple samples along the 23 day transect.  Here is a rundown of the teams and the science we are conducting.

Crew leaving Morehead City, NC.

Crew leaving Morehead City, NC. From the left: Sarah Fawcett, Amandine Sabadel, Malcolm Woodward, and Bess Ward.

R/V Endeavor

R/V Endeavor

I will be filtering large volumes of seawater on 293mm filters for DNA sequencing, as well as smaller volumes onto smaller Sterivex filters for RNA sequencing and associated studies of gene expression within various microbial communities. This research expedition is funded by a grant from the National Science Foundation program in Dimensions of Biodiversity to Bess Ward at Princeton University and Andrew Allen at JCVI. The goal of our JCVI group is to extend findings from the Sorcerer II Global Ocean Sampling program, which documented massive genomic diversity and unusual physiological and biochemical capabilities within and between many lineages of marine microorganism. With samples collected on this research cruise, we will have the opportunity to document large-scale patterns in gene expression, and generate key hypotheses related to the most biochemically-active microbes across a major section of the upper 1000m of the North Atlantic. Data obtained from this study will be combined with similar data we collected last February and August on cruises out of Bermuda to the Bermuda Atlantic Time Series (BATS) stations in the in the sub-tropical Atlantic.

North Atlantic Transect, north of Sorcerer II transect to the Azores in 2009.

North Atlantic Transect, north of Sorcerer II transect to the Azores in 2009.

The Princeton team headed up by Bess Ward includes Sarah Fawcett, Nicolas Van Oostende, Jess Lueders-Dumont, Dario Marconi, and Keiran Swart. Their primary research involves using flow cytometry to physically capture, size fractionate and identify microbes living in the sunlit layer of the ocean. These microbes are directly responsible for assimilation of dissolved nitrate, which accumulates in the dark interior of the ocean. Specific identification of these microbes is an important research goal for microbial oceanography because the regulation and magnitude of global oceanic CO2 assimilation is driven explicitly by nitrate assimilation by photosynthetic microbes. Such microorganisms also produce a large fraction of the oxygen in the atmosphere. The Princeton group will perform nitrification experiments and measure levels of dissolved nitrate, ammonia and carbon by using stable and natural isotope tracers. The team will investigate the origins of dissolved inorganic nitrogen by measuring the natural abundance of the nitrogen isotopes.  Net tows will also be performed to collect the “bigger” planktonic organisms, such as zooplankton, within the ocean food chain.

Real time nutrient data down to nanomolar levels will be determined by Malcolm Woodward of Plymouth Marine Laboratory (PML) and Amandine Sabadel from the University of Otago in New Zealand.

As we motor to our first station, which we should reach on Monday September 2nd, we stop every morning at 5 am to perform a CTD cast to 1000 meters.  Based on biological and physical features, observable in real time via CTD sensors cabled to the shipboard computer,12 bottles, each containing 30 liters of sea water, are sealed at varied depths and the 360 liters is brought to the boats deck.  Once the CTD is on the deck, the different scientists scurry to gather their allocated amount of water from the CTD rosette and hurry back to their labs to do the appropriate work.

CTD Controls

CTD Controls

CTD Controls

CTD Controls

CTD1

CTD1

As of Wednesday August 28, 2013, we have done 7 transect CTD casts, all but one to 1000 meters.  Today we sampled on the Grand Banks and the water column depth was only 57 meters. For every cast I have collected RNA samples at 1000 meters, 250 meters, within the Deep Chlorophyll Max (DCM) (if no DCM is apparent, then just below the Chlorophyll max), a sample from within the Chlorophyll max and in the mixed layer (normally at 20 meters).

The weather has been great except for one 24 hour period when the swells grew to about 7 feet and the boat was really rolling back and forth.  The crew is great, the food is awesome, good thing they have a small gym or I don’t think most of us would fit in our clothes after a few weeks out here! The scientists are working well as a team and this should be a very exciting and beneficial science expedition.

CTD Profile

CTD Profile

Dry Lab

Dry Lab

 

Once we get to the our first station we will stay there for two days………….it will be a very intense two days, then a day motor to the second station followed by another crazy two days of sampling………….more on that next blog!

Thule, Greenland – Day One

Arrived at Thule, Greenland after a 5 hr flight from Copenhagen.  It was pretty interesting seeing a long line of people all getting on a flight that was headed to a part of the world that usually has less than 600 people there at any given time.  Arrival was pretty straightforward, no jetway, no customs, no LCD screens telling you where to pick up your bag.  Just a few military personnel checking your documents to ensure that you have the approval from the Danish government and USAF to be on base.  First impression getting off the plane…it’s cold.  Not as cold as I expected it to be but it was just 90 degrees F when I left home a few days ago.  Today’s high was 39 degrees F.  Standing in the sun it’s not so bad but when the wind starts blowing it turns into a recipe for chapped lips and windburn.  Oh and did I mention the massive mosquitos here?  Not much wildlife in this part of the world but the mosquitos outnumbers the vertebrates probably a million to one.  They are also VERY aggressive; they even swarmed the trucks while we were driving around the base.  We were shown our living quarters, which were very nice, kind of reminded me of living in the dorms during undergrad.  There are individual rooms and a shared bathroom on each floor.  We toured the various sites that our collaborator Slava Epstein already pointed out as good sampling sites that vary in vegetation and proximity to water.  The land here is quite desolate, not much green, mostly moss and small shrubs growing.  Traditional trees are nonexistent but “ground trees” are actually common.  They are trees that grow outward on the grass and not upward.  The rest resembles pictures taken by the mars rover.  As the day goes by I noticed the sun was circling and I came to the realization that the typical artic summer was happening right in front of me.  The sun literally circles and will not go down until around September.  It was quite odd, getting in bed at midnight and seeing the sun still in the sky.  Tomorrow will be more interesting since we will be going further away from base to sample additional areas. 

blog2

blog1

Thule, Greenland – Day Three

Day three started with me missing breakfast. It seems that folks around here only eat breakfast between 5am and 8am. Today was a very rough day for sampling.  About an hour drive to the area near the site, about a three-mile hike to one spot another half-mile hike to another spot followed by the three and a half mile hike back to the truck. We sampled “rich” soil and “rich” soil from a lake. These two sites were sampled and categorized as “rich” due to the abundance of vegetation around and near the sites. The area surrounding Thule is very desolate so I can imagine the plants have a hard enough time growing.  It would be very interesting to see what microbes are present in these two sites to allow such vegetation to grow; even more interesting to see how water affects the microbial population. Samples were frozen once we got back to the on site lab. A small portion was saturated with AllProtect to ensure preservation of RNA for transcriptomics analysis.

DSCF0619

DSCF0622

 

The day ended with a lecture from another NSF grant recipient to install a telescope on the Greenlandic ice cap. It was an interesting idea to coordinate radio imaging from other telescopes around the world to look at quantum singularities that were very far away. After speaking to some of the other scientists here I found out that our group, which includes myself and our collaborators Slava Epstein and Dawoon Jung, were the ONLY Microbiologists on the base. Everyone else was either a Geologist, Environmental Scientist, Astronomer, or Meteorologist. It was great to hear about everyone else’s projects.

Carl Woese 1928-2012

Editor’s Note: This post originally appeared on T. Taxus, December 31, 2012, by Jonathan Badger. Dr. Badger  is an Assistant Professor in the Microbial and Environmental Genomics Group at the J. Craig Venter Institute in La Jolla, CA. Reprinted by permission.

As you may have heard, Carl Woese died of pancreatic cancer yesterday at the age of 84. I had the honor of working with Carl in grad school at the University of Illinois where my advisor, Gary Olsen, ran a joint lab with Carl.

Carl Woese

Carl Woese. Photo courtesy IGB.

As the originator of the use of ribosomal RNA to distinguish and classify organisms (including obviously the Archaea), Carl both revolutionized evolutionary biology and created a method that is still very much in use today. Even in the latest metagenomic study of the oceans or of the human gut, a 16S rRNA diversity study is required as a control in addition to whatever additional markers or random sequencing is used.

One of the things that fascinated me about Carl is how he constantly reinvented himself and explored new fields of biology — his early work in the 1960s dealt with classical molecular biology and the genetic code (the origins of which continued to fascinate him for the rest of his life). He then transfered to the study of the ribosome and its structure, which in turn led to his study of 16S and its evolutionary implications. In the 1990s, when I worked with him, he was a pioneeering microbial genomicist and collaborated with TIGR to sequence the first two Archaeal genomes. And in his final years he focused on early evolution and the last common ancestor of life in the light of what genomics has taught us.

Carl also had his humorous and counter-cultural side. I remember him telling me how his lab in the 1960s heard about the rumor that compounds in banana peels were a legal narcotic and how they launched an unofficial research project to isolate these. His verdict was that there was nothing there and neither the peels nor anything in them could get you high — but he wanted to empirically test that. Also, when reading about a supposed “Qi master” who claimed to be able to influence mutation rates with his mind, he invited him to the lab to give a demonstation — which naturally failed to show any effect under controlled conditions — but he wanted to see if the guy could really do it.

Genomics, metagenomics, and evolutionary biology has lost one of its greats — but his legacy lives on.

The Hill School: Day 2

The day started early Tuesday with first period.  Thirty eager students arrived on the bus to determine the results of the amplification of the DNA they extracted the day before.  The PCR ran overnight, copying part of a conserved gene in plants, RuBisCo, that can be used to identify the species of land plants.

Loading Gels at the Hill School

Loading Gels at the Hill School

 Using gel electrophoresis, we were able to load gels and run them quickly to see the results.  Most students successfully had amplicons – this was a great since they had not ever done DNA extraction or electrophoresis. The samples have been brought back to Rockville for sequencing and will be available for the students to analyze in about two-weeks.
Loading Gels like a Professional at the Hill School

Loading Gels like a Professional at the Hill School

We had a great visit with the students and are curious to see what plants they brought from around campus.

We look forward to working with them again in the future!

To support our Education program visit http://www.jcvi.org/cms/giving/overview

The Hill School: Day 1

DiscoverGenomics! Mobile Laboratory at the Hill School

DiscoverGenomics! Mobile Laboratory at the Hill School

The day started early with reagent and lab preparation before we even left for school OR had coffee.  We expected to do over 100 DNA Extractions as the first step in the DNA Barcoding. We arrived on campus as the first period was starting –we didn’t have class until after 9:00.

Grinding samples at the Hill School

Grinding samples at the Hill School

 It was a full house (bus) most of the day and busy getting through the DNA extraction.  Various specimens were brought in from around campus to determine their species.  It will be interesting to see the diversity of plants on campus.

Moving through the protocol at The Hill School

Moving through the protocol at The Hill SchoolThe Hill School

 

The Hill School

The Hill School

The Mobile Laboratory Hits the Road

After a hiatus this summer, the Mobile Laboratory hit the road again today for a trip to Pottstown, Pennsylvania.  Driving through the rolling hills of northern Maryland into southeastern Pennsylvania, it passed small towns and beautiful foliage.  Tomorrow and Tuesday, we will be working with students from the Hill School. 

The students will be exploring their campus by determining the species of plants they collect.  This process is often called “DNA Barcoding.”  DNA Barcoding is a standardized procedure using PCR, sequencing and bioinformatic analysis to determine the various species of plants, bacteria, etc. based on conserved genes.

Stay posted for more updates tomorrow!

What Happened to Sorcerer II?!?!

The last time I wrote a Sorcerer II blog was in November when we set sail from Spain to cross the Atlantic Ocean.  For all of you that have been worried that we have been at sea for 8 months, relax we made it!!  Over the next few days I will update everyone on what has happened and the upcoming plans for Sorcerer II.

First off, the Atlantic Crossing……….On November 13th we left Gibraltar and on November 17th arrived in the Canary Islands.

Canary Islands

Lanzarote Island

After a day on Lanzarote Island we sailed overnight to Las Palmas on Gran Canary, collecting two samples on the way.  We stayed in Las Palmas waiting for a good weather window for the big crossing.  During that time we traded out crew members, fully stocked the boat with food, supplies and fuel.  We also had time to meet our collaborators from the University of Las Palmas.  I gave a group from the University a tour of the boat and showed them the sampling equipment.

Giving a demo of the sample gear

Folks from University of Las Palmas

On November 22nd we took off for the USA USA USA!  There was one problem, a huge storm in the Northern Atlantic.  To avoid the storm we had to go much more south then originally planned, also this storm sucked all the wind up north, so we had very little wind to sail with.  With no wind and a much longer sail than planned, we couldn’t make it directly to Florida…………well we could have but we would have run out of fuel and food!  So on December 8th we arrived in St. Thomas USVI.  For two and a half weeks we motored our way from the Canary Islands to the USVI sampling and fishing.  Total fish count was 8 Mahi Mahi, 3 Wahoo and 2 Yellow Fin Tuna.

Route, Canary Islands to USVI

Les and Me with the catch of the day

Atlantic Ocean Sunset

John BBQ'ing dinner at sea

Crew Sampling

One more thing, during this crossing the following things all happened, the strange part is they all happened within 24 hours of each other!

1.  Little generator broke (not a big deal we have 2 generators), both were up and running in a few hours

2.  Auto-pilot went out……….could have been  a real pain  because we would have  had to hand steer 24 hours a day for the rest of the trip, this was on day 8, but it got fixed in a few hours as well.

3.  Water maker went down………no water for showers, dishes and oh yeah no drinking water……once again got fixed in a few hours

4.  Mainsail ripped, this was fixed a few days later, but for  those days we were pretty rolly out there with no mainsail to keep us steady.

5.  Busted pipe in my head (bathroom)………funny thing is I woke up around 4 am dreaming about waves then I woke up and still heard the waves; it was the water going back and forth in my bathroom floor!

6.  And the big daddy of them all…….. a full out engine room fire!!  Not just smoke or steam…….we are talking flames and extinguishers!  It was taken care of and the engine was up and running about 4 hours later.

On December 20th 2010 Sorcerer II arrived in Florida.  This wrapped up the 2009/2010 Europe Expedition.  During this time we collected 213 samples, filtered over 51,000 liters of water from 13 countries.  DNA from all 3 size fractions from the 213 samples have been extracted, although not all will be sequenced right away, a majority have been sequenced or are schedule to be sequenced this year.  I will write a future blog on the sequencing status of these 213 samples and how we are working with many collaborators from Europe to work up this data set.  I will also write about what has been going on with Sorcerer II since December 2010 and future plans for her.