Sunday, December 22, 2013

The Initiation

It has certainly been an interesting few months. Upon arrival at NCSU to study soil science I figured I would have some time to absorb information about my project, sit down to plan out a timeline of events, and THEN actually start working.

Getting to this point was the easy part. See more below.
Nope. Turns out that's not how graduate studies work - especially not mine. I had a couple of weeks to plan, but between classes, reading, research, and familiarizing myself with the locality I felt like I didn't spend nearly enough time learning what I was doing. Combine that with the impending shutdown of all of the facilities I was using and you get a rush to complete the initial stages of a project. I was basically learning as I was doing. That's a sometimes fun, sometimes dangerous approach. Thankfully I had the help great lab technicians and researchers who had already been in the trenches and could walk me through the important research procedures.

My project studies the symbiosis between soil bacteria and plants - specifically rhizobia and legumes (Fabaceae family). Rhizobia enter the roots of legumes and grow inside plant tissue that forms what are referred to as "nodules". Plants provide food (sugar) to the rhizobia while the rhizobia provide nutrition (nitrogen) to the plants. Most of the time rhizobia are already present in the soil, but sometimes the soil is inoculated with rhizobia to improve the chances of nodule formation.

It seems simple at first, but as I read more about nodulation, I learned that it is anything but that. I used to read about nodulation in my undergraduate studies and think about it at a macrobiology scale. My current research, however, is focused on nodulation from a microbiology scale. It is an interesting switch in perspective that has made me gain more of an interest in microbiology. When I really think about it, people don't truly understand things until they are able to break them down into their simplest components, and my current focus on microbiology has certainly been enlightening.

On one hand I am reading things about applications of nodulation as it applies to agriculture and on the other hand I am reading about microbial metabolism and genetics. Over the past 50 years agriculture has gained more of a focus on genetics and microbiology and I feel that current rhizobia research is going in that direction. Just as some researchers were able to apply microbiology to make breakthroughs in plant resistance and growth, I think a breakthrough in rhizobia research could help improve soil fertility - at least in a way that is more natural than dumping chemicals all over it.

This is generally the point where people get distracted by other things so before you go you should know that I am done with the first stage of my research. I am specifically looking at competition between individual rhizobia strains for nodulation of Hairy Vetch. That is, if such competition exists. For all I know the nodulation could be a first-come-first-served occurrence. I won't know much until I actually begin the analysis. Now I see first-hand why news stories about scientific research can say one thing one month and something different the next month. Research results can be fickle even if you are doing things properly.

2013/11/04 - Entering the growth chamber

One week in the growth chamber
Thanks to Mary I was able to use these adorable mini-trellises to support the plants.

A few weeks in the chamber. Thankfully all the units contained a growing plant

Last day in the growth chamber was 2013/12/18. Some visible variation, but not enough to make reliable predictions.

Non-inoculated control - Inoculated treatment - Nitrogen enhanced

Some plants have 50 nodules. Some have Over 150. It depends on what kind of mood they were in.

That's it for now. The next step is heavily focused on molecular biology. I will likely be bothering the other lab researchers as much as possible to make sure I get things right.

Friday, December 13, 2013

A typical fun day

Mary started her day with lab inventory and found this old piece of equipment that came with the lab way before we moved in. It is now looks perfect to be used as a home of cute little flowers.

I saw it again in my office.
I guess Natalie came up with some cool ideas for it.

We're so excited to receive some TaqPolymerase samples but didn't think that they would be this generous!!

Dry ice came with the package is always fun.


I think December is the best month of the year to celebrate birthdays.
This time we gathered to wish for Payton.
Happy birthday!!!

Sunday, December 8, 2013

End in Sight

Friday was JiJY’s birthday!  We managed to surprise her by celebrating a day early, and Sarah even made awesome pink cupcakes.  

I always associate the end of fall semester with festivities, and between Thanksgiving, a few lab birthdays, and winter break coming up, it definitely seems like it’s time.  This week is finals, so we’re almost there!  And while winter break may be a chance for some students to give their brains a vacation for a while, most of us in the Grossman Lab will probably be scurrying around with time to finally dedicate solely to research.  Lots of new projects are coming along, and this will be a great time to give them more attention.  Good luck on finals!

Wednesday, December 4, 2013

Raleigh's Trash is Treasure

Spotlight on a Raleigh small business

This week, as we are all thinking of returning home for the holidays, we are reminded of the exciting things happening around us in Raleigh.  At a house just down the street from the University, lives a whole gaggle of our lab's compadres.  JiJY (pictured) lives there with one housemate named Justin Senkbeil.

Justin is a co-founder and CEO of a local company called Compost Now.  This company goes door-to-door picking up kitchen scraps from Raleigh residents and turning it into compost, that you can later have delivered back to your home.  Pretty cool huh?

Check out their website:  It is almost as cool as their Raleigh-centric T-shirts.  Way to go Raleigh!

Friday, November 29, 2013

A Perfect Day for Gas Sampling

Black Friday
November 29, 2013

It is the day after Thanksgiving, Black Friday, and I'm standing in the middle of a field contemplating the quiet beauty of late autumn. While others scramble to score the best deals in the malls of America, I think about the last time I stood in these fields. Corn, corn and more corn was all I could see around and above me. Corn surrounded me, forming tunnels through a vast corn fort. Huddled between the rows, I crawled under layers of leaves to reach the chambers where we test for nitrous oxide coming out of the soil.

Today the corn is gone, and the whole farm is a wide open space interrupted only by groups of trees in riparian buffers and experimental forests. Between my feet and the trees are acres of dried stubble and freshly sprouted cover crops shimmering in the sun. Bases of corn stalks with their tentacle roots float like octopi in a sea of green.

My job today, as part of the greenhouse gas group, is to measure nitrous oxide emissions from the soil. I place an air-tight chamber over the soil and use a syringe to extract gas at specific time points. The air makes a high-pitched whine as it rushes into the syringe, reassuring me that something is happening even though I can't see the gases moving around. I'm working on my first of three sets of chambers that I'll test today. 

At each set I pour myself a cup of hot tea from my thermos. There's an odd window of downtime between sampling points that's too short to get engrossed in something, but too long to just do nothing. So I sip tea and gaze across the fields, imagining that this is my farm. I feel proud of this vast swatch of land blanketed by winter rye. Then I realize a real farmer would probably be standing there thinking of all the work that is yet to be done, or be in the shed fixing machines. 

Watching each blade of rye vibrate in the wind I'm drawn into a meditative state. Today I'm grateful for the clear blue skies and the warm sun as I do this work. I'm grateful for the crickets still chirping in late November. I'm grateful for a reason to spend the day outside and enjoy the weather before winter sets in. Had I not been here sampling, I would have been busy with inside work, oblivious to the sheer beauty of the day outside despite the cold. 

The roar of the Kubota drowns out my thoughts as I drive down grassy lanes to my final sampling set. At my last stop, I set up the chambers and wait. I have just enough tea for one more cup, and I snack on sweet potato biscuits from last night's Thanksgiving feast. I could imagine a group of landscape painters setting up a plein air session out here. 

Back home I go on what is usually my morning walk. My route looks different and new in the evening light, and I realize how much I enjoy being outside year round. 

If you haven't taken the time to spend an afternoon outside lately, go for a walk and enjoy the golden light and the crisp autumn air. 

Thursday, November 21, 2013

Birthday surprise!!

Another lab tradition is birthday party. We usually try to keep it as a secret to the birthday person.

Amanda's birthday is on Thursday 21 but since she was not going to be in the lab so we threw in an early surprise party for her after her work at the phytotron on Monday.

Sarah got the bagels and coffee for us before she left to the field

Peyton, Natalie and I (JiJY), the decor crew.

Introducing our new lab icon, Mr. Unicorn!

Here comes the birthday girl!!!


Wednesday, November 20, 2013

Grossman Lab at the Raleigh City of Oaks Marathon

Mary here, and I just wanted to share what great support our lab group gives to potentially foolish ideas.  Fall in Raleigh is beautiful,  and the perfect time of the year to spend time outside!  This fall, in between finishing up my lab work for my PhD, and writing papers, I decided to train for a marathon!  Foolish!

So, on November 3rd, I ran in the Raleigh City of Oaks Marathon.  It was the absolutely most perfect day for a run, wonderful weather, great route.

My parents were in town, and my mom ran with me for a bit starting at the last half mile.

As I approached the finish line, I saw these guys!
 Amanda, Bon, Sarah (Angela and Jijy - not in photo) were all there to cheer me on!

My final time was 4 hours and 35 minutes.

Such great friends and colleagues!  Thanks for all your support, I guess if I can finish a marathon, I can finish a PhD!

Tuesday, October 29, 2013

Fall Post Harvest Wrap-Up

This year's corn has all been harvested.  Corn is no longer is green like the picture below.  We can once again see across all the fields.  To celebrate the end of Field Season 2013........ we took some soil samples.

(Above) Peyton pushes wet soil through the sieve to get them ready for Microbial Biomass Fumigation extractions.

(Right) Amanda samples fields for Nitrous Oxide Emissions.

How did a caterpillar get in the lab?

Monday, October 28, 2013

All abuzz about Tampa

The week before a conference is always a bit of mayhem around academic departments. Everyone is running around printing posters, presenting dry-runs of oral talks, discussing flight arrangements and making plans to meet up with friends and colleagues from across the globe. This year's annual Soil Science Society of America meetings will be in Tampa, FL November 3-6. Sarah and Julie have complementary presentations this year. Sarah will present the results of her M.S. work looking at the effects of inoculation on common legume cover crops in our region - with some surprising results! Come check out her poster on Wednesday afternoon at the Microbial Community Dynamics In Farming Systems: II poster session. Julie will present earlier in the day at the oral session of the same name Microbial Community Dynamics In Farming Systems: I, reporting on some work to evaluate strains a potential inoculants for the important cover crop legume hairy vetch in the Southeast. Also joining us from our lab will be Peyton and Natalie to see what all the excitement is about. We look forward to seeing you all in Tampa next week!

The joys of poster editing!