First run on the Barataria Transect

Yesterday I joined Jim Lee and Charlie Milan to help them execute sampling for the monthly Barataria Transect, one of Eugene Turner’s projects. His lab has been doing this transect, monthly, since 1994 to monitor water chemistry and some of the biology that occurs across this contiguous estuarine system. Over the years, various other sampling has been done, including work on the Macondo oil spill and toxic algal blooms. They brought me along so I could collect samples at the beginning of the transect in support of our microbial community survey of the Southern Louisiana coastline and our high-throughput culturing activities. I also brought my camera.

Grand Isle at sunset, facing southeast. Some oil platforms are visible in the distance.
Grand Isle at sunset, facing southeast. Some oil platforms are visible in the distance.
The quaint Grand Isle Suites where we stayed overnight. Our LSU van and 19' whaler are visible in front.
The quaint Grand Isle Suites where we stayed overnight. Our LSU van and 19′ whaler are visible in front.
Calibrating the YSI
Calibrating the YSI
The Sand Dollar Motel, where we launched
The Sand Dollar Motel, where we launched
An early sampling station
An early sampling station
Early segments of the transect are mostly water with faraway marsh
Early segments of the transect are mostly water with faraway marsh
Oil production in the northwest corner of Lake Salvador
Oil production in the northwest corner of Lake Salvador
Coolers and action-packers make the sampling go 'round
Coolers and action-packers make the sampling go ’round
A charming camp near one of our sampling sites.
A charming camp near one of our sampling sites.

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Jim doing turbidity measurements, old school
Jim doing turbidity measurements, old school

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HWY 90, also known as station 30.
HWY 90, also known as station 30.
Old HWY 90
Old HWY 90
Some of the local architecture
Some of the local architecture
Me and Jim
Me and Jim
A lonely cypress in Lac des Allemandes
A lonely cypress in Lac des Allemandes
The entrance to Bayou Chevreuil
The entrance to Bayou Chevreuil
Beautiful Bayou Chevreuil
Beautiful Bayou Chevreuil
Bayou Chevreuil
Bayou Chevreuil

-jct

Welcome Mike Henson!

Mike Henson has bravely chosen to do a Ph.D. here in the Thrash lab. He’s just finished a Master’s degree with Deric Learman at Central Michigan University (who recently gave a free online talk featuring Mike’s work over at MicroSeminar) and will be continuing to build his skills in both culture-dependent and -independent techniques. A big warm Southern welcome to Mike. Glad you’re here! For more about Mike click our People tab above or scamper on over to his twitter account: @HensonMW_08.

-jct

Platform dive 1 to service LUMCON hypoxia SONDEs

Yesterday I did my checkout dive with LUMCON’s dive safety officer Lora Pride. I’m working on getting certified for scientific diving, according to the AAUS standards, in support of some of our lab research goals. As part of the check out, we serviced a set of SONDEs that are mounted on the leg of an oil platform at the station we refer to as C6C. There are SONDEs at three depths (2.4 m, 10.7 m, 19 m) collecting real-time dissolved oxygen, temperature, conductivity, turbidity and fluorescence measurements (for a diagram click HERE). These SONDEs need to be changed out on a monthly basis (roughly), allowing for weather considerations. Yesterday we exchanged all three SONDEs on the platform for new ones, requiring us to dive in with calibrated units, remove the old ones, clear off the biofouling on the mounts, and install the new ones in the freshly cleaned mounts. I brought my camera along and documented some of this. The boat ride out is about an hour (at between 20-40!! kts- a much more exciting ride than the Pelican), on a 26′ Boston Whaler, one of LUMCONs small boats. I also collected water for inoculating a new HTC experiment.

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A beautiful day for diving. Our whaler ready to go.
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Closeup of our whaler with dive tanks visible.
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Busy day at C6C with supply boats and helicopters buzzing around.
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The section of the platform where our gear is mounted. The closest pylon has the moored SONDEs
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Station C6C, with supply boat visible.
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Getting a secondary calibration measurement of water temp/DO with a handheld YSI probe. The bottom water was certainly hypoxic, with DO < 0.5 mg/L.
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DSO Lora Pride
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A thoroughly encrusted SONDE
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Lora cleaning a SONDE mount
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Blurry photo of a new SONDE going in
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A little gobi poking out of a barnacle shell. I missed the focus on this guy, but it gives a good idea of the life on the platform leg.
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More of the sea life on the platform leg
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Coming home
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Part of our decaying coastline. What was perfectly green marsh a year ago is now dying. LA coastline is disappearing at a rate of one football field per hour. 

UPDATE (7/3/14): I’ve had some questions about the coastline decay mentioned in the final caption. There is a lot of information out there, but here’s a link to the Department of the Interior’s page on Louisiana’s coastline, and a link to a recent LA Times article detailing the various legal maneuvers between the State of Louisiana, the oil companies, and other interested parties.

-jct

Recent Collaborative Thrash Lab SAR11 research

There are some exciting developments in the world of SAR11 microbiology, and I’d like to take a moment to summarize recent research I’ve been involved in. All three papers have come out this year in The ISME Journal.

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The single-cell genomes from Thrash et al., 2014, aligned linearly according to scaffold size, showing (outside-in) GC content, scaffold boundaries, coding regions according to pan-genome status, and shared elements unique to the subclade Ic with orange lines

The final main project of my postdoc with Steve Giovannoni was a characterization of a deep-water subclade of the larger SAR11 group using single-cell genomics and metagenomics. This was a collaboration between our lab and that of Ramunas Stepanauskas and Ed DeLong, and although it began at Oregon State, the work carried over (like many projects do) into my appointment at LSU. The main findings of the paper were that this “subclade Ic” dominated deep-water metagenomic reads compared to extant surface-originated genomes, and that a few gene-content specific variations could be identified that may distinguish these organisms from the surface strains, but that, on the whole, the main observable differences were in global genomic footprints such as expected average genome size, average coding region size, intergenic spacer size, and preferential amino acid substitutions. The deep water ecotype, subclade Ic, has obviously been evolving separately from the surface subclades for some time based on these accumulated variations and phylogenomic branch lengths, however, it also appears these organisms share a similar metabolic niche with the surface strains: they are predicted to be obligate aerobic organisms with a particular appetite for common metabolic intermediates found in the cellular milieu of most organisms: simple carboxylic and amino acids and C1 and methylated compounds.

Read more here: Thrash, J. Cameron, Ben Temperton, Brandon K. Swan, Zachary C. Landry, Tanja Woyke, Edward F. DeLong, Ramunas Stepanauskas and Stephen J. Giovannoni. (2014) Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype. The ISME Journal. doi:10.1038/ismej.2013.243.

 

Steve was also invited to write a Winogradski Review article in coordination with him recently being given the prestigious Jim Tiedge Award from ISME. Ben Temperton, who is also a former postdoc of Steve’s, and who worked closely with me on the subclade Ic study, above, was a co-author. Steve took the opportunity to review many of the observed variations between streamlining selection on free-living, small genomes like SAR11 and Prochlorococcus, and the small genomes of obligate intracellular symbionts like Rickettsia. Importantly, the review also pointed out that examples of streamlining selection are becoming more prevalent as data from single-cell genomics and assembled metagenomes continues to pour in. Indeed, the odd nutrient requirements that are sometimes a result of streamlining selection may be at the heart of the difficulty in cultivating many of these organisms in the lab.

Read more here: Giovannoni, Stephen J., J. Cameron Thrash, and Ben Temperton. (2014) Implications of streamlining theory for microbial ecology. The ISME Journal. doi:10.1038/ismej.2014.60

 

Dovetailing nicely with the theoretical concepts brought up in Steve’s review was a third piece from our lab, a detailed study on an unusual vitamin requirement in SAR11 that was discovered by Paul Carini, currently postdoc-ing with Alyson Santoro. This work identified that members of many SAR11 subclades are unable to make the vitamin thiamine by typical synthetic means, because they lack a single gene in an otherwise complete pathway, thiC. As a result, they are unable to synthesize 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP), a direct precursor to thiamine. However, Paul also discovered that SAR11 has the capacity to use free HMP in media to relieve thiamine limitation, and identified a putative transporter for HMP in several SAR11 genomes. Additionally, HMP measurements from the Sargasso Sea and cultivation experiments pointed to a possible natural source of HMP from cyanobacteria, thus providing an explanation for how SAR11 can remain successful without the key thiC gene.

Read more here: Carini, Paul, Emily O. Campbell, Jeff Morré, Sergio Sañudo-Wilhelmy, J. Cameron Thrash, Samuel Bennett, Ben Temperton, Tadhg Begley and Stephen J. Giovannoni. (2014) Discovery of a SAR11 growth requirement for thiamin’s pyrimidine precursor and its distribution in the Sargasso Sea. The ISME Journal. doi:10.1038/ismej.2014.61

-jct

LSUCC in full effect

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Jessica preparing medium components
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David and Brette making glycerol stocks
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Poised like an eagle ready to take flight: the Guava, at rest.

This semester, Jessica, Brette, and David have been working hard getting the high-throughput culturing lab (HTCL) up and running. Today Brette and David put samples of their first putative isolates in the freezer, thus christening the official LSU culture collection (LSUCC). We are naming this in the tradition of Stephen J. Giovannoni’s HTCC at Oregon State University, and that of the culture collections his former lab members Mike Rappé, Bob Morris, Uli Stingl and Jang-Cheon Cho. The HTCL relies on a couple principle features: dilution-to-extinction isolation techniques, and high-throughput/high accuracy counting of small cells at low cell densities. The former is assisted by use of a laminar flow hood, the latter with a Millipore Guava benchtop flow cytometer. The basic steps in the HTCL methodology are detailed in Connon & Giovannoni, 2002, and Stingl et al., 2007. Stay tuned as new microorganisms isolated by the HTCL at LSU are identified.

-jct

BioGrads Graduate Student Symposium Nov. 15th

The 15th annual LSU Biological Sciences Graduate Student Symposium is happening on Friday, November 15th. This is a one-day conference put on by the grad students, and open to all. Come out and see what cool science is being done by biology grads at LSU. There will be posters in the morning, an afternoon filled with 15 min talks, and a beer and jambalaya social afterwards. Below are links to the schedule and abstracts for more information.

Schedule of Events 2013

Student Abstracts

-jct

The lab is coming together…

The lab is slowly coming together, and at this point most of the initial major equipment is present, if not unwrapped yet!

A panorama standing in front of the fume hood, the door to the culturing room is in the center.

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The culturing room without it’s crown jewel (Guava).

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But it’s here and ready for install…

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We’ve got a few other working items recently arrived:

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Mmm… water….

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My office

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-jct