MICROBIOLOGY: EXPEDITION SPECIFIC NOTES

[ 1 X402 ] [ 2 X393 ] [ 3 X395C ] [ 4 X385 ] [ 5 X378S ]

X402

Apr 5, 2024 COY Polymer Chamber - The rubber relief valves on the back of the chamber in the cold room lost their flexibility and would not seal, thus allowing oxygen contamination of the chamber. At first a valve was covered with tape but then more valves failed. The ETs built a heater box around the three valves that brought the area up to 20° C which softened the rubber up enough to seal. New valves were sent from COY and will be sent to the ship.

X393

Jul 27, 2022 Our lab officer had a suspicion that the label pictured below on "BIOLOGICAL ATMOSPHERE" gas bottles in TBULK would be incorrect. The bottles in question had been requested to be filled with 5% hydrogen, balance in nitrogen, no CO2. The label indicates that the gas mix contains 5% CO2. This is an old label that should have been changed out as the bottles were filled. A sample was drawn from a BIOLOGICAL ATMOSPHERE bottle into a gas tight syringe and injected into an NGA. No CO2 peak was observed at 10.4 minutes, which is the retention time for CO2. At 5% a significant peak should have been observed.

CO2-free bio gas mix is preferred by microbiologists, as CO2 acidifies the glove box atmosphere, which in turn lowers the pH of microbiological media.

Jul 24, 2022 Foldio360 Smart Turntable was used with iPhone 12 to generate 360-images of the MBIO hard rock samples before chiseling the rock into pieces.

Jun 24, 2022 A quick guide for purging the COY soft-shell was created. See COY Anaerobic Chambers.

Jun 20, 2022 The COY soft shell anaerobic chamber was set up on Upper Tween.

Jun 19, 2022 Hand guards were made from ethafoam rod for the rock box chisels. The microbiologists were very happy with these and never again complained about hitting their hands.

Jun 18, 2022 Labconco Vertical Clean Bench in the cold room was used for incubations. A paper strip was taped to the corner of the opening as a positive flow indicator (see the bottom right quarter of the image).

X395C

Jun 9, 2021 The old Fisherbrand Isotemp incubators were replaced in the MBIO area. Two new incubators were sent out to replace the two that had issues with excess ice formation.

Received Rock Boxes with hammer and set of chisels.

Microbiology Lab Notebook updated to include info on the new SS rock boxes, the walk-in enclosure, and DOE Van.

Anaerobic Chambers

Coy Polymer (Hard Shell) Chamber

The badly cracked COY hard shell chamber in the cold room was replaced with a new 3 ft. polymer chamber Tag# 91183. Old chamber Tag# 90589 to be sent home.

New 3 ft. chamber set up and tested with airlock controller and CAM-12 gas analyzer. The chamber holds the anaerobic environment very well.

Coy Vinyl (Soft Shell) Chamber

New Coy automatic airlock Tag#91182 arrived in shipment with new vinyl bag attached. We were going to remove the vinyl bag from the airlock but after setting up the chamber on the frame it was determined it would be potentially very difficult to get it all back together for 390/393. The decision was made to store the airlock with the bag attached in a plastic K-box. The bag is just gently folded up and the disk and aluminum frame pieces also stored inside. The rods are up in the batcave above UT landing.

Lab Notebook updated with new COY manuals, pictures and equipment lists.

X385

385 Guaymas Basin

The expedition was heavily focused on microbiology and geochemistry. Extensive pre-expedition planning and supply acquisition was done.

Portcall

Receiving and sorting of supplies

Anaerobic Chambers

Coy Polymer (Hard Shell) Chamber

The hard shell chamber has many cracks along the bottom edges. These are the source of a lot of gas exchange. The scientists taped over them from the inside and outside. The chamber still has a hard time maintaining anaerobic conditions.

Coy Vinyl (Soft Shell) Chamber

The soft shell chamber was assembled on the Upper Tween landing. A table was built to support the Coy table. The ship's welder made brackets to secure the table. Parts of the aluminum supports were missing but replacement pieces fabricated. A gas bottle rack on the lift holds high purity nitrogen and the biomix.

One half of Morono's Koach Clean Bench was installed in the chamber to clean the air. One side can be used in this situation because there is limited introduction of air into the chamber and so all of the air in the chamber can be cleaned.

The airlock was behaving erratically at times. It was plugged into ship power and that could have been the issue. It needs to be tested on regulated power.

The bag is still in good shape and can possibly be used again. The gloves need to be replaced as they have holes in them.

The Coy Hydrogen/Oxygen Analyzers

All of the analyzers will read hydrogen differently and it is important to determine what value is the “zero” value for the analyzer you are using. For instance, one of the analyzers the zero value is a 0.8% reading of H2 and on another the value is -0.2 of H2. The key here is to know when there is no hydrogen in the chamber because the oxygen values will also not read correctly if there is no hydrogen. When the chamber is first set up and before purging, note the value of the hydrogen reading on the monitor, this will be your zero value and put a note on the chamber for everyone to see. Purge with N2 then the biomix and the hydrogen value will respond. To ensure an anaerobic condition, always have hydrogen in the chamber and cycle renewed catalyst into the chamber.

Flammable Gas Station

Set up a flammable gas injection station on the Focsle Deck next to the Radvan. The station needed to be set up outside of the labstack since the gases contained 80% Hydrogen or Methane.

DOE van

The DOE van was sent out as a stable isotope lab. Counter tops were fabricated in College Station and installed during portcall. The Labconco ductless fume hood was sent out with new organic vapor filters. Two scientists sent their own incubators and a microscope. A Cahn balance was set up. Nitrogen and argon bottles were also set up.

Radvan

The Radvan was used by two scientists using S35 and C14. EHSD was in San Diego to help check in the radioisotopes. Protocols were established by the LO and scientists. The floors and benchtops were covered in the Versidry benchcoat which could be removed in the event of a spill or if contamination was suspected.

The large incubator by the door was removed to make room for two higher temperature incubators brought by one of the scientists. The 208V power was rerouted to the forward bulkhead so the incubators could be plugged in locally.

The Liquid Scintillation Counter (LSC) can only be run using the Easy GLP protocol. The user should be able to use the Easy Count protocol for unknown samples but the instrument gets an error and stops. The counter is in use for wipe tests and sample counts.

Tracer Pump

Both PFMD and PFMCH were used on the expedition. The supplier was not able to get all of the PFMCH to IODP in time for the shipment so a total of 12 Kg PFMD and 3 Kg of PFMCH was available for the expedition and almost all of it was used. The Tracer Watch camera that was installed was used to monitor the level of tracer. A log sheet was kept by the ALOs to estimate usage.

Mobile Microbiology Lab

The microbiologists set up a whole round sample cutting station on the work bench in the Upper Tween. They would take one side of IODP's Koach bench down to the UT and use it with Morono's other half of his bench. IODP's Koach bench was set up in the microbiology lab but one half would go back and forth. Flushed whole round samples were stored in the core reefer temporarily in coolers and boxes separated by sample codes. The coolers and boxes were then used to store and organize the refrigerated samples to be shipped.

Freezers

An additional -86C freezer was sent to the ship for a total of 4 -86C freezers. A fan was set up behind the freezers in the pallet stores to create more air flow and remove heat. The two -20C freezers in the core reefer were also utilized. Almost all freezer space was used.

N2 Generator

An o-ring in one of the process valves on the N2 generator failed causing excessive oxygen contamination to the nitrogen lines, ~18% O2. The repair was made quickly but it is unknown when the valve failed.

Water was found in the first pre-filter and some moisture in the second. The third filter had some condensation. The filters did their job to protect the generator.

Measurements of air in the nitrogen lines show ~2% oxygen on the NGA even after the generator was repaired. A service call is scheduled for the SDII port call. Dec 10, 2019 Update: The "2% oxygen" seen on the NGA was unlikely to be oxygen but argon. It was discovered that oxygen and argon elute within seconds from each other, thus, with our current NGA column setup we cannot separate oxygen and argon. There is almost 1% of argon in air. When the nitrogen generator removes oxygen as it makes nitrogen, it ends up concentrating argon, along with "concentrating" nitrogen, and this is likely to be the reason for us detecting 2% (20 000 ppm) argon in the generator nitrogen lines.

Recommendations

Coy Polymer (hard shell) chamber is extensively cracked and leaks. It needs to be repaired or replaced.
Possibly buy new Coy Type A vinyl bag for next Mbio cruise. The one we are using now was stored for years and is performing well. This item can be stored for long periods of time.
Stock lots of biomix gas if vinyl chamber will be used.
Stock lots of the basic mbio supplies.
Make custom order of tri-foil bags from current vendor that match the original foil bags.
Provide O2 scrubbers for bags and make sure they are used with any flushing procedure.
Purchase Winstat air ionizer BF-X2MB as an addition to the Koach Bench.
Create list of all JRSO mbio related equipment and make sure it is inspected and tested well before a big mbio cruise.
Replace scintillation counter

X378S

Transit Papeete to Panama

COY Hard Shell Chamber

Removed the back panel and sleeves in order to get full access to the inside of the chamber. Removed the tape that was used to cover the cracks on 385 and cleaned the chamber. Carefully taped over the cracks in the inside and outside of chamber.
Reassembled the chamber and installed a new set of sleeves and gloves replacing a set that had holes.
Tested the chamber for leaks with the hydrogen leak detector.
Trained TAS personnel on use of the chamber.

Tech Reports