Saturday, October 25, 2014

Thinking about microbes & nitrogen...

Goose-down clouds with salmon bellies;
the evening comes down heavy and quiet and soon.
In the thin night air
soil microbes are starred with frost
and I, with my warm mug and new sweater,
dream of them buzzing in summer

Tuesday, May 29, 2012

Site scouting

A couple of weeks ago, on a nicer day than I could have asked for, I decided to go check out a few UNH-owned sites that I could use for my research.  First stop: Kingman Farm.  Crossing a large field, my mud boots sank into the soft, freshly-tilled soil as I carefully avoided stomping on the seedlings of whatever crop had been planted (oats or wheat, maybe).  Just past the field I found this patch of forest:
Forest next to Kingman Farm
Forest next to Kingman Farm
It seemed young, and perhaps recently logged, with lots of sunlight, ferns, tree seedlings, and wildflowers in the undergrowth.  I think you can see from the fresh green color of all the leaves that it was a lovely spring day in the woods of NH!  In the shady patch to the left of the biggest tree in that photo is where I scooped some moist leaf litter into a Ziploc bag to see what species of mites and collembola I can find at this site.

On the other side of the newly-planted field was a swampy area with mostly grass and cattails.  Each step there made me grateful for my mud boots, as the cool mud and welling water swallowed them up to above my ankles.  Behold: Kingman Farm Marsh!
A view of the marsh at Kingman Farm
A view of the marsh at Kingman Farm
Collecting a sample here was a little trickier, as all of the leaf litter is either very dry from the sun (the top layer of tan leaves you can see in the photo) or, just below the surface, sopping wet and intertwined with other long strands of decaying leaves.  Strangely feeling a bit like a zombie with a handful of oozing brains (a bit too much metaphor?) I filled another Ziploc bag just about where I was standing when I took the photo.

Heading over to the Burley-Demerritt Organic Dairy Research Farm, I ran into a friend who samples gaseous emissions from the soil there; she pointed me toward a particular part of the farm where she said I could find some good marshy action.  On the way, some young cows took an interest in me, following me from one side of their paddock to the other:
Yearling cows at the Organic Dairy
Yearling (or so?) cows at the Organic Dairy
They weren't interested in offerings of fresh grass, and moo-ed plaintively as I walked off.  Sorry ladies!  I don't have anything better for you...  Maybe we can hang out again some other time?  Sound good?

A little way from my Jersey cow friends, I found the marsh my (human) friend had promised.  It was anything a girl could ask for: a little pond, cattails, tussocks.... Just perfect!
The marsh at the Organic Dairy
The marsh at the Organic Dairy
Doesn't this part of the vegetation look rather different from the grasses that were in the marsh at Kingman Farm?  Being shorter, the decaying leaves from these plants seemed easier to collect, though there was also more muck in my Ziploc bag by the time I had filled it up.
Marsh vegetation at the Organic Dairy
Marsh vegetation at the Organic Dairy
From their Ziploc bags, I loaded my leaf/muck samples into some Berlese funnels, which shine a light that heats and dries out the material, much to the chagrin of the critters inside.  Trying to find cooler, moister climes, they head downward and fall to the bottom of the funnel where they collect in a little container.
Berlese funnels (not my photo)
Old-timey inventor of these funnels, Antonio Berlese.  Gotta love the moustache!
Interestingly, I found that at both marshes, there were lots of mites but they were only from one species, a very shiny, very round, very black species with kind of a pointy head.  Unlike the other mites I've collected so far who seem to wander aimlessly in the containers where I keep them, or merrily while away the hours  chewing on leaves, the majority of these bead-like mites gathered in a big cluster and formed a big, shiny, black patch.  Then they stood around and did nothing.  I wonder if they were actually standing together so they could turn into a mite raft when the water levels in the marsh rise to avoid being flooded by instead floating off to the safety of some taller plants?  Much like these fire ants:
Fire ant rafting behavior (not my photo)
A unique ability to form living rafts could explain why they're the only game in town in these marshes.  In the other places I look for mites, I tend to find quite a few different-looking species, none of which cut it in the marsh, I guess!

On other fronts, I've been calling and emailing folks left and right in an effort to find farmers who will let me sample soil and leaf litter from their land.  Every person in agricultural extension agencies, or at other farming organizations, probably grimaces slightly when they hear my name, at this point... But today I made the most headway, as I actually SPOKE to two real farmers, who were super gracious and said I could come by anytime!  I think I probably need 5 more sites than that, so the search continues...

Too bad I will probably not be using marshes after all (the single species mite thing kind of rules them out for me...), because I really like those sweet little cows at the Organic Dairy...

Thursday, December 22, 2011

UNH faculty honored as winter break begins

Check it out: UNH science faculty were recognized as being among the best researchers in the US!  It's especially nice to see the part at the bottom about how Dr. Serita Frey had the highest-cited paper.  Serita is also a fabulous professor (I took Soil Ecology with her this past semester) and I'm hoping to work with her during my future research here at UNH... It seems I'll be learning from the best!

As winter break begins, I want to take a moment to wish everyone a happy holiday.  I'll be celebrating Chanukah, Solstice, and Christmas (in that order) this year, so I have most of my seasonally-festive bases covered.  Otherwise, if you need to find me over break, look no further than my computer where I'll be reading as much as I can and working on my experiment (see my last post).  I'll also sink my teeth into Joshua Schimel's book, Writing Science: How to Write Papers that Get Cited and Proposals That Get Funded, which my advisor just gave me; it looks quite well-written (one should hope so!) and I'm looking forward to perusing its words of wisdom.

Oh, and did I mention I'm heading to Puerto Rico for a quick vacation?  This winter break is going to be epic!!

Thursday, December 8, 2011

Nearing the end of my first semester...

The first semester in my Ph.D. program has been going great!  I'm just one final exam away from finishing my classes.  Most of my peers only take 1 or 2 classes per semester, but I wanted to start knocking credits off early--I have to complete 36 during my program--so I took 3 classes this time around.
  1. Ethics in Research and Scholarship, which fulfilled a requirement of my program, as well as a college-wide requirement for Ph.D. students.  It's a complex topic, and this class covered some foundations in a broad range of ethical issues related to conducting research, many of which I had never considered before,
  2.  Research Methodology & Statistics I, taught by an excellent prof from the Psychology department who really made the subject come alive.  Although I took a Stats class as an undergrad, it's through this class that I feel I'm really starting to understand it.
  3. Soil Ecology, another great class taught by my (I hope) future committee member Serita Frey, all about the microbes and other organisms that live in the soil, their interactions, life strategies, and involvement in terrestrial--and global--ecological processes, including carbon and nitrogen cycling (my favorite!).
I'll be keeping busy over winter break setting up a greenhouse experiment I'd like to start as soon as possible.  If I heard him right, my advisor has given me the go-ahead to look into doing a metagenomic study as part of my experiment, which is an exciting and cutting-edge method of understanding which microbes are in the soil and what roles they're playing, which we can get at by determining what genes they carry and which ones they actively use.  I'm also scouring the scientific literature on the interactions between plant roots and soil microbes, and how these interactions affect soil nutrients, especially nitrogen.  If I can synthesize our existing knowledge about this topic in an interesting conceptual framework, I'll be able to write a nice review paper and try to get it published!

Next semester I'll be hitting the ground running with three more classes... Research Methodology & Statistics II (after which I'll be ready for some more complicated stuff... I'm thinking a Multivariate Stats class...), Microbial Ecology & Evolution (definitely looking forward to that), and my advisor Stuart's "hot topics" graduate seminar on soil carbon (should be really interesting, and I'm looking forward to taking a class with him).

Oh, and check it out: I put together a webpage for my lab!  It's pretty basic, but it gets the job done.  Visit the Soil Biogeochemistry & Fertility Lab and let me know what you think.

Monday, August 22, 2011

Digging in the Midwest, NH seacoast, and chickens!

Well, it has been a fun-filled July and August!

I got to sally forth from the lab to accompany two postdocs on a trip to the Kellogg Biological Station's Long-Term Ecological Research site on cropping biodiversity. Our mission, which we chose to accept, was:
  1. To boldly install soil mesocosms attached to lysimeters (check out the photo below). An intact soil core in the mesocosm is re-buried in its original hole; in another month or so, our postdoc will add wheat litter with isotopically-labelled carbon to the soil surface in the mesocosm, which will allow him to trace where the carbon goes--into microbes, attached to clay particles, in aggregates, in molecules of interesting/complex chemistry, etc. Any carbon lost by leaching out during rainfall events will be caught in the lysimeter.

  2. The mesocosm (on the right) is attached by tubing to the lysimeter housing (center) in a plot currently under soybean rotation. A control mesocosm not attached to a lysimeter is on the left. Those are my arms!

  3. To boldly gather roots and shoots from biofuel crops including corn, switchgrass, big bluestem, and miscanthus, as well as a big cooler full of soil, for our other postdoc's lab incubation experiment to look at decomposition dynamics of above- and below-ground residues.
    I'm dwarfed by this stand of miscanthus, which is native to Europe and is even taller than this at full height!

It was great to get out into the field for the first time. It was hard work digging so many holes (and even harder to pound the mesocosms in...), but rewarding to be a part of.

Digging in the dirt!

Aside from that, I helped out for a couple of days with fellow PhD-student's enzyme assay (which mostly involved making litter slurries and pipetting into hundreds of 96-well plates), and have mostly spent my time reading textbooks and papers. Recent and future search topics include: priming; P limitation in agriculture; Things Written By People In My Lab; soil fungal and bacterial niches; plant-soil interactions; scale-up; spatial statistics; and soil fauna and food webs.

In other news, New Hampshire has been treating me well! I took myself to the NH seashore on Sunday for the afternoon, lounging about in a true summery American fashion.


I also had my first pet-sitting gig this weekend, caring for some local chickens!

When I let them out of the coop in the morning, the chickens gleefully guzzled water and roamed throughout the yard

Wednesday, August 10, 2011

What controls soil processes?

Reflections upon reading "The Biology of Soil" by Richard Bardgett...

What controls soil processes?  Of course the answer has to be:

It depends!

There is never an easy explanation, is there?  I suppose that is what makes something worth studying, though.

Also, it seems to make soil (along with deep ocean) one of our Earth's final frontiers.  Have I stumbled into an Ecologist's goldmine?  I hope so!