Tag: soil diversity

In preparation for the ESA conference next week

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I’m counting down the days for my first Ecological Society of America (ESA) conference next week in Portland, OR.  Over the last few weeks, I’ve been diligently working to finish as much analysis as possible on the data from my recent post-doc, as I am presenting a poster on Wednesday, August 9th from 4:30 to 6:30 pm; PS 31-13 – Soil bacterial diversity in response to stress from farming system, climate change, weed diversity, and wheat streak virus.

Several of my new colleagues will also be presenting on their recent work, including a talk from Roo Vandegrift on the built environment and the microbiome of human skin, and one from Ashkaan Fahimipour on the dynamics of food webs.

The theme for this year’s ESA meeting is “Linking biodiversity, material cycling and ecosystem services in a changing world”, and judging from the extravagant list of presenting authors, it’s going to be an extremely large meeting.  It’s worth remembering that large conferences like these bring together researchers from each rung of the career ladder, and many of the invited speakers will be presenting on work that might have been done by dozens of scientists over decades.  Seeing only the polished summary can be intimidating, lots of scientists I’ve spoken to can feel intimidated by these comprehensive meeting talks because the speakers seem so much smarter and more successful than you.  It’s something I jokingly refer to as “pipette envy”: when you are at a conference thinking that everyone does cooler science than you.  Just remember, someone also deemed your work good enough to present at the same conference!

Harvesting a feast of data

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My greenhouse trial on the legacy effects of farming systems and climate change has concluded!  Over this past fall and winter, I maintained a total of 648 pots across three replicate trials (216 trials per).  In the past few weeks, we harvested the plants and took various measurements: all-day affairs that required the help of several dedicated undergraduate researchers.

In case you were wondering why research can be so time and labor intensive, over the course of the trials we hand-washed 648 pot tags twice, 648 plant pots twice, planted 7,776 wheat seeds across two conditioning phases, 1,944 wheat seeds and 1,944 pea seeds for the response phase.  We counted seedling emergence for those seeds every day for a week after each of the three planting dates in each of the three trials (9 plantings all together).  Of those 11,664 plants, we hand-plucked 7,776 seedlings and grew the other 3,888 until harvesting which required watering nearly every day for over four months.  At harvest, we counted wheat tillers or pea flowers, as well as weighed the biomass on those 3,888, and measured the height on 1,296 of them.  And this is only a side study to the larger field trial I am helping conduct!  All told, we have a massive amount of data to process, but we hope to have a manuscript ready by mid-summer – stay tuned!

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Preparing for my first greenhouse trial

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As the 2016 growing season comes to a close in Montana, here in the lab we aren’t preparing to overwinter just yet.  In the last few weeks, I have been setting up my first greenhouse trial to expand upon the work we were doing in the field.  My ongoing project is to look at changes in microbial diversity in response to climate change.  The greenhouse trial will expand on that by looking at the potential legacy effects of soil diversity following climate change, as well as other agricultural factors.

First, though, we had to prep all of our materials, and since we are looking at microbial diversity, we wanted to minimize the potential for microbial influences.  This meant that the entire greenhouse bay needed to be cleaned and decontaminated.  To mitigate the environmental impact of our research, we washed and reused nearly 700 plant pots and tags in order to reduce the amount of plastic that will end up in the Bozeman landfill.

Each pot needed to be scrubbed with disinfectant soap and then soaked in bleach.
Lines of pots drying on the rack.
I scrubbed 700 labels clean in order to reuse them.

We also needed to autoclave all our soil before we could use it, to make sure we are starting with only the microorganisms we are intentionally putting in.  These came directly from my plots in the field study, and are being used as an inoculum, or probiotic, into soil as we grow a new crop of wheat.

This is trial one of three, each of which has three phases, so by the end of 2016 I’ll have cleaned and put soil into 648 pots with 648 tags; planted, harvested, dried and weighed 11,664 plants; and sampled, extracted DNA from, sequenced, and analyzed 330 soil and environmental samples!

Each pot gets six tiny winter wheat seeds planted.
Trial 1: 216 pots ready to grow!
After only a few days, seedlings are beginning to emerge.

 Stay tuned for more updates and results (eventually) from this and my field study!

What I do for a living Part 3: Soil Ecology and Weed Management

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In May, 2016, I started a post doctoral position in a laboratory that focuses on weed management in agricultural systems, especially organic farms which don’t use chemical fertilizer or herbicide. My role is to integrate microbial ecology. For example, is the soil microorganism diversity different in fields that compete better against weeds than in fields that can’t? Are there certain microorganisms that make it easier for weeds to grow, and how do they do that? Can we suppress weeds by manipulating bacteria or fungi in the soil?

So far, I’ve been doing field work for my project, as well as assisting other lab members in their own projects, as many large scale greenhouse or field experiments require large groups of helpers to accomplish certain tasks. I’m also new to weed ecology, and I wanted to learn as much as possible. Thus, I put on some sunscreen and one of those vendor t-shirts you get when you order a certain dollar amount, and got to work.

Some of our projects investigate the link between crop health and climate change.  To simulate climate change, we create rain-out shelters to mimic dry conditions, and plastic shielding to mimic hotter conditions.

Making climate change simulators.
The gypsum block will absorb soil moisture, and we can measure conductivity off of that.
This one is very dry.

One of the treatments is to infect crops with wheat streak mosaic virus, to determine whether climate change will affect the plant’s ability to fight infection, and whether it will change soil microbiota. To do this, we needed to infect our crops, which meant growing infected plants in the laboratory and selectively spreading them in the field as a slurry.

Blended wheat.
We need to filter out the particles or they will clog the sprayer. Also pictured: Dr. Fabian Menalled.

 

A similar project is using mites as a virus transmission vector, so we attached mite-infected wheat to healthy wheat.

Kyla and I are attaching wheat to other wheat with paperclips.
We hope the wheat mite get infected.

Another project is collecting data about ground beetle diversity in organic versus conventionally farmed soil. For this, we planted pitfalls traps in fields to collect and identify beetles.

Throughout many of the ongoing lab projects, I’ll be investigating the effect of treatments on soil health and diversity.

The core sampler is used to collect soil from certain depths.
The soil is then put in sterile containers until analysis.

My project is part of a larger experiment, which also involves assessing crop and weed communities.  For this, we need to randomly sample plants in the field and collect all above-ground plant material (to measure biomass as weight), as well as the biomass of each individual weed species to measure diversity (number of different weed species) and density (how large the plants are actually growing).

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And, of course, there is plenty of weed species identification!