The Rare Knowledgesphere

I sometimes get a self-depreciating response when I tell people what I do: “oh I could never do that,” “I wouldn’t even know where to begin,” or my least favorite; “I’m not smart enough to do that myself.”  Sure, I’m intelligent, but more importantly I am interested in my work and I put a lot of time and effort into practicing it.  I didn’t become a microbiologist overnight.  And more than that, in my career path I discovered a lot of people and opportunities that helped me get here.  I firmly believe that most people could do my job, given the right amount of education, determination, and support (and a heavy dose of enthusiasm for spread sheets).  As I move up the ladder, I’m increasingly in a position to educate, help others network, and bring students closer to their career goals.  One day I’ll be able to take on graduate and undergraduate researchers of my own, and I find myself asking, how will I find and recruit those students that just need an opportunity to become amazing scientists?  The ones that weren’t told by their teachers that they should be microbiologists but still have an aptitude for it, the ones that think they aren’t “smart enough” when really they just aren’t confident enough?

Lessons from the rare biosphere

One of the emergent theories in microbial ecology over the last few decades is that of the “rare biosphere.”  It’s the idea that microbial ecosystems are much more intricate than we realized, and there are a great many microorganisms present in any given environment that have very low populations.  We just couldn’t see them under a microscope or grow them in culture because their presence was washed out by more abundant microorganisms.  It wasn’t until the emergence of DNA-based technologies that we could really understand the depth of that diversity because this technology was able to sequence all or nearly all the DNA in the entire sample.

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An anaerobic chamber allows microbes to be grown in an oxygen-free environment, and the different color plates represent different media recipes.  Credit: Kristina Bond.

When culturing bacteria in the lab, one must try to mimic the original environment as closely as possible in order to get that microbe to grow.  It is incredibly difficult to please “everyone” on just one or even dozens of different culture media types, so you end up getting a biased idea of “who” lives in a natural environment based on what species are able to survive in the mock environment you’ve created.  DNA-based technologies don’t require live microorganisms; you can extract DNA or RNA strands directly from your environment and sequence them, although you will need a reference database of previously cultured and sequenced microorganisms to make the identification.  Sequencing has its own problems, of course, namely being able to discern between a rare microorganism whose DNA represents a very small percentage of your data, and a random sequencing error inherent to your technology that turns a known sequence into a fake novel one.  One way bioinformaticians tackle this is by removing rare sequences altogether, but as Sogin et al. argue, you might be getting rid of significant contributors to your ecosystem.

This is just one example of a major theme in science: how do we detect something if we don’t know it’s there?  How to do we differentiate what is real (but rare) from the technological errors and background noise?  We constantly improve our technology and revise our understanding of the physical world as we get better at investigating it.  But as we rely more and more on technology that we have created (which may operate on the biases we have designed into it), and we want to collect more information with less human effort, we need to remember that it’s our intuition and reasoning skills that make humans so good at data analysis and investigation in the first place. This led me to wonder if we weren’t making the same mistakes in education.

One of the most common errors we commit is to mistake education for intelligence.  Intelligence is partially a natural ability for learning and understanding, and partially cultivated by an atmosphere of curiosity and interest in learning.  Education, on the other hand, has to be earned.  While public schools and other learning resources in the United States exist to give all children an equal chance at education, in practice there are significant biases in quality and quantity in education.

The disparity between education and ability

Student to teacher ratio is correlated with student performance, and can vary widely by type of school (public, private, elementary or secondary), geographic location, urban or rural demographics, etc.  Because of that, the national trend for student to teacher ratios in public schools appears to have only slightly increased (more students per teacher) from where it was in 2002, with that increase only since 2008.  However, much of the increase in student to teacher ratios is localized, specifically in low-income districts, so there is a disproportionate affect by economic status.  Many teachers in low-income school districts cite budget cuts that result in overwhelmingly large class sizes to be the main reason they quit education (discussed here).  And a poor school budget does more than just crowd students, it depletes the school of educational resources which reduces the quality of the education and student performance.

Therefore, just because someone appears uneducated does not mean they are not intelligent.   For example, Linus Pauling, who was competing with Britain’s Watson and Crick to discover the structure of DNA, didn’t obtain his high school diploma until after he won two Nobel Prizes simply because he didn’t finish some required high school history courses.  A recent study looked at grade point average (GPA), SATs (previously the Scholastic Aptitude Test), graduate record examinations (GREs- the standardized tests that most schools use as a graduate entrance qualifier), and whether test scores predicted how well someone performed as a graduate student.  Like undergraduate study, most graduate programs require a minimum GPA and GRE score even to be considered.  However, the study found that students with higher test scores didn’t actually perform better as graduate students.  In fact, here’s a whole website about geniuses that failed IQ or other aptitude tests that went on to change the world.  Here’s another about artists, politicians, and business tycoons who failed repeatedly before becoming household names.

Another problem is our biased view of the quality of an education based on the country of origin.  Indian mathematician and genius Srinivasa Ramanujan was born in a small village in the late 1880s.  He started performing advanced geometry and arithmetic at just 13 years old, and began focusing on mathematics in secondary school and at a local college.  At 26, he wrote to British mathematicians looking to discuss his ideas, and was dismissed out of hand by almost all of them.  G.H. Hardy, however, wrote back, and began a collaboration of ideas that led to an incredible body of work between the two of them.

The Rare Knowledgesphere- The one that almost got away

This idea of overlooking greatness is important to keep in mind when ranking people by their resume or test scores instead of by an interview.  After all, just because you attended Yale doesn’t mean you went to all your classes.  This concerns me, because we may be passing over potential undergraduate or graduate students who appear less educated on paper, but aren’t less intelligent or less apt.

So, how do we as educators and mentors get beyond this bias and find the students and researchers-to-be that slip through the cracks?  The ones that are out there that aren’t even on our radar.  I’ll let you know once I’ve figured it out.  But from my experience, it comes down to taking the time to interview and really get to know someone before accepting them as a graduate student, not just selecting the best looking resume. It especially means letting go of your ideas about the quality of someone’s education based on the type or location of their school, as well as stereotypes about their abilities.

And it means being creative about marketing your positions, to make sure you are reaching the individuals that aren’t actively looking for you.  This may sound counter-intuitive; why try to recruit someone to graduate study if they aren’t interested?  Again, I can speak from experience.  My undergraduate degree is in Animal Science, and my interests in graduate study at the time centered vaguely around wildlife conservation.  Instead, I entered a graduate program where my primary research and laboratory work were focused on microbiology, genetics, microbial ecology, and bioinformatics.  I had no formal academic or practical training in these areas.  But I joined, and I excelled, all because my mentor-to-be told me that I was capable.  And here I am today, in love with my science.

With all this in mind, stay tuned for my post in the next few weeks on what makes a person a good graduate student, if it isn’t test scores.

Featured Image Credit

2016 Year In Review

Looking back

2016 started with a bang when I launched this site and joined Twitter for the first time!  For the first quarter of the year, I was a post-doctoral researcher in the Yeoman Lab in the Department of Animal and Range Sciences at Montana State University.  I was working on a total of eight grants, ranging from small fellowships to million dollar projects, both as a principal investigator and as a co-PI.  I was also doing the bioinformatic analysis for multiple projects, totaling nearly 1,000 samples, as well as consulting with several graduate students about their own bioinformatic analyses.

In late spring, my position in the Yeoman lab concluded, and I began a post-doctoral position in the Menalled Lab in the Department of Land Resources and Environmental Sciences at MSU.  This position gave me the opportunity to dramatically increase my skill-set and learn about plant-microbe interactions in agricultural fields.  My main project over the summer was studying the effect of climate and other stresses on wheat production and soil microbial diversity, and this fall I have been investigating the legacy effects of these stressors on new plant growth and microbial communities.  I have extracted the DNA from all of my Fort Ellis summer trial soil samples, and look forward to having new microbial data to work with in the new year.  Based on the preliminary data, we are going to see some cool treatment effects!

Over the summer, I attended the American Society for Microbiology in Boston, MA in June, where I presented a poster on the microbial diversity in organic and conventional farm soil, and the Joint Annual Meeting for three different animal science professional societies in Salt Lake City, UT in July, where I gave my first two oral conference presentations. One was on the effect of a juniper-based diet on rumen bacteria in lambs, and the other was on the biogeography of the calf digestive system and how location-specific bacteria correlate to immune-factor expression.

Thanks to a lot of hard work from myself and many collaborators, a number of research projects were accepted for publication in scientific journals, including the microbial diversity of agricultural soils, in reindeer on a lichen diet, and in relation to high-fat diets in mice, it also included work on virulent strains of Streptococcus pyogenes, and a review chapter on the role of methanogens in human gastrointestinal disease.

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Looking forward

A whopping thirteen manuscripts are still in review at scientific journals or are in preparation waiting to be submitted! Some of those are primarily my projects, and for others I added my skills to the work of other researchers.  Editing all those is going to keep me plenty busy for the next few months. I’ll also be writing several more grants in early 2017, and writing a blog post about the Herculean task that can be.

I’ll be concluding my greenhouse study by March of 2017, just in time to prepare for another field season at Fort Ellis, on the aforementioned climate change study that is my main focus. In January, I’ll be spending time in the lab helping to process and sequence DNA from my 270 soil samples, and begin the long task of data quality assurance, processing, and analysis.  I’m not worried, though, 270 samples isn’t the most I’ve worked with and bioinformatic analysis is my favorite part of the project!

This year, I am hoping to attend two conferences that I have never previously attended, and present data at both of them.  The first will be the 2017 Congress on Gut Function in Chicago, IL in April, and the second will be the Ecological Society of America’s Annual Meeting in Portland, OR in August.  Both conferences will give me the opportunity to showcase my work, network with researchers, and catch up with old friends.

If 2017 is anything like the past few years, it’s going to be full of new projects, new collaborators, new skills, and new opportunities for me, and I can’t wait!  So much of what I’ve accomplished over the last year has been possible because of the hard work, enthusiasm, and creativity of my colleagues, students, friends, and family, and I continue to be grateful for their support.  I’d also like to thank anyone who has been kind enough to read my posts throughout the last year; it’s been a pleasure putting my experiences into words for you and I appreciate the time and interest you put in.  I look forward to sharing more science with you next year!

Show Me the (Grant) Money!

Every political season brings about uncertainty regarding the future of policy, funding, and cultural beliefs, and the field of science is no exception. The surprising results this November have led many scientists and other academics to fear for their jobs and research in the coming years.

Part of this stems from a growing trend of members of the public distrusting scientists (discussed here), or the rise of false information regarding serious issues such as climate change, genetically modified organisms (GMOs), vaccinations, etc., that is leading to a disparity between what scientists accept as true and what the public accepts as true.  Regardless of which side of an issue you fall on, the consensus seems to be that the public is lacking scientific literacy and scientists are lacking in public outreach (hence the basis for my website).


Some of this disparity develops from public opinion and governmental policy, which can affect what research is deemed important enough to be funded.  For example, if an administration denies the existence and causes of climate change, it sends a message to the public that this research and this theory are invalid or unimportant.  Not only can this influence state and federal policy (1, 2), but usually means that the field is unlikely to receive state or federal research grant funding.  Not only does this prevent a better understanding of scientific issues, like climate change, but it prevents technological advances which improve quality of life and the economy, especially since a good deal of commercial technology companies utilize basic research from academic institutions as publications and raw date are typically publicly available.

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“The Changing Nature of U.S. Basic research: Trends in Performance”, SSTI.  U&C = universities and colleges.

It also means that people relying on research grants for salary (like myself, and most other post-doctoral researchers, research associates, graduate and undergraduate researchers, technicians, and some extension outreach personnel) find themselves without jobs.  Research-based salary also means that you are limited to a short contract based on the project, anywhere from a month to several years.  From experience, a short-term funded position (a year or less) means that you spend a significant amount of time applying to other jobs (a lengthy process) or writing more research grants (an incredibly lengthy process that I’ll discuss in a few months- which take at least 6 – 8 weeks just to write).  This can impede on your other job or social responsibilities.

Prior to the jump in federal funding during the Cold War, research was funded by universities themselves and smaller organizations. Most large-scale research grants in the last 50 years, however, have been federally funded.  Organizations such as the United States Department of Agriculture (USDA), the National Science Foundation (NSF), the National Institutes of Health (NIH), the National Aeronautics and Space Administration (NASA), the US Department of Defense (DoD), the US Department of Energy (DoE), and others release funding calls on a regular basis.  Some funding calls are general and will accept any project type, but many are specific to a particular field or research question (e.g. climate change, cancer, etc.).  There are many other organizations or companies which will fund research in a very specific field (such as Sustainable Agriculture Research and Education (SARE), which funds organic and sustainable agriculture), or provide small fellowships.  Philanthropic organizations also fund research, usually targeted towards a specific disease or special interest, and tend to be small but which can help bring funding to obscure fields.

While the total dollar amount of money put into research and development (R & D) in the US has dramatically increased over the last 50 years, the amount the federal government has been putting in has remained relatively stable over the last 10 years.  Some cite the availability of other funding sources, such as universities themselves, as making up more of the costs.  However, this also comes with a price, as the reduction in state funding has been cited as the cause for rising tuition, and universities are unwilling to reduce tuition even after funding has been reinstated.

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The increase in funding has largely been in biomedical and engineering fields, with other areas of research remaining relatively stable.

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It’s also important to remember that there are more people going into research jobs now,  although this number has been largely stagnant over the last 10 years, and even with the increases in working researchers, only 5.9% of the US workforce was in a STEM field in 2015.  Long-term, without a concurrent increase in funding this increase in working researchers can increase job competition and stress.

Laboratory equipment and technology is much more complex and expensive than it was even a decade ago.  The percentage of funding going into basic research, from multiple funding sources, has also declined over the last 10 years, which means research projects have to focus on short-term goals instead of long-term, complex projects that gather more data.  Basic research aims to understand a system, rather than manipulate it or develop a product, and is the necessary first step which opens up decades of further, more applied, research.

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The increase in number of researchers and projects/researcher, coupled with funding stagnation, can massively increase grant competition.  Over the past few years, it has been holding steady at 22% for NSF, and 18-25% for NIH, although their data is more complicated because they saw an increase in budget and an increase in total number of PIs funded, yet a reduction in percent of projects funded (indicating that more many more grants were submitted overall).  The USDA is also more complicated to track because of the number of grant programs within the USDA, each of which put forward different targeted grant funding calls each year.  In 2013, USDA AFRI had a 10% funding success rate.  Manually checking grant funding calls reveals grant-specific success rates, upwards of 30% funding success; however, many of these grants with a higher rate of success also require you to match their funding with funding from another source.  So if you have a 1/3 chance of getting that USDA grant, and a 1/5 chance of getting a matching NIH grant, your actual chances of getting all that funding are 1/3 x 1/5 = 1/15.


Taken altogether, the clearest trend regarding research in the US is that it’s an integral part to our  way of life and it’s not going anywhere.  Whatever your political views, it’s important that scientists, citizens, and politicians come together across the aisle to do what’s best for the future of the US, and that’s going to necessitate a strong support of scientific work.

 

 

 

 

End of the fall semester is in sight!

Finals are upon us and that can only mean that I’ve committed myself to reading a stack of manuscripts that students wrote as the final project for the bioinformatics lab I am teaching!  This semester we took raw 16S rRNA sequencing data, analyzed it, interpreted it, and here are the results. Many of my students had never used command line based programs at the beginning of the semester, and now they can discuss the merits of different clustering techniques- I am so proud of them!

Just My Enterotype

A review chapter that I put together last year is now available online or by purchasing the textbook!  The chapter explores the current breadth of knowledge about methanogenic archaea that live in the human digestive tract and their involvement in human gut diseases. These archaea produce methane using hydrogen and carbon products that bacteria create during fermentation, and it’s unclear how the interaction of host immune system, bacterial diversity, and archaeal diversity can trigger disease or convalescence.

It’s based on a preliminary study I did with my Ph.D. advisor https://acbs.cals.arizona.edu/people/andre-denis-wright and gastroenterologist https://www.uvm.edu/medicine/medicine/gastro/?Page=profile.php&bioID=22563 on the connection between methanogen diversity in the intestines and exhaled breath methane.

 

 

Imposter Syndrome

There’s been a lot of attention paid online lately to “Imposter Syndrome”. It’s that sneaking doubt that makes you feel like you don’t belong somewhere because you aren’t qualified, and eventually someone will realize the mistake and fire you.  In short: that you are an Imposter.  It’s extremely common among graduate students and young faculty.  In fact, I haven’t met a graduate student that didn’t doubt themselves and whether they deserved their place in a research program at some point in their studies.  Most studies on this phenomenon have been relatively small and in specific populations of people, thus estimates of affected individuals range from 40 to 70%, at some point in one’s life.

cat-imposterFrom my experience, in academia, Imposter Syndrome stems from feeling overwhelmed by the amount of information that you need to learn, or the amount that you need to accomplish.  The interdisciplinary approach to graduate studies has increased the number of scientific fields you now need to be familiar with, and compounds the amount of material that you have to memorize.  This seems to leave many students feeling inadequate and dumb, because they are unable to perfectly recall every fact they learned in two or three years worth of graduate courses.  For post-doctoral researchers and assistant professors, your To-Do list only grows longer by the day, as the reduction in federal funding increases the competition for fewer and fewer job postings and more pressure to distinguish yourself.  These tasks seem insurmountable, and that you simply aren’t up to them.  You start to doubt your abilities, and think that there has been some mistake.  You think, someone will realize how dumb I am, and that I don’t deserve to be here.

At best, Imposter Syndrome makes you nervous, at worst, it can lead to a lot of work-place stress and low self esteem.  It can also prevent you from taking risks in your research, or being ambitious in the positions you apply for, or make you feel guilty about taking time off when you feel that you should be using the time for career development.

 

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Imposter Syndrome, or more clinically, Imposter Phenomenon, has been studied for several decades, and is reviewed thoroughly here.  Originally it was thought to be a symptom found only in professional women who weren’t emotionally strong enough to deal with the stress of the workplace.  Later, after it was described by Dr. Pauline Clance in 1985, and observed in many different careers and both genders, we came to understand that this sexist stereotype was in fact common to high-achievers, “perfectionists”, and those with anxiety and the motivation to succeed.

Correlations have also been found between feeling like an imposter and low or conflicting family member support, low self-esteem or general self-doubt, neurotic behaviors, or when there are negative consequences to achieving success.  For example, if a person is ostracized by friends or family for working hard, studying, getting an education, or generally wanting a “better life” than the cohort has.   This can also occur when there is jealousy or competition between coworkers, where a promotion or other success would alienate you.

Own your success

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When graduate students express feelings of self-doubt to me, I remind them that they already got into grad school.  Their graduate program was satisfied by their application, their PI or advisor chose them for their accomplishments.  I remind them that in academia, you can’t compare yourself to anyone else.  Everyone has come from different backgrounds, has different work experience, took different classes, read different papers, and has different research and career goals.  Maybe you got PhD but you don’t want to do research, only teach.  Maybe you only want to do research.  Maybe you want to publish ten papers a year, or maybe you only want to publish once a year because that is more consistent with the pace of your research and the type of work that you do.  Maybe you have more post-docs who work on complicated questions, or maybe you have undergraduates and your projects are smaller.  Some research fields (especially literal fields) can’t be rushed, and it’s unrealistic to expect prolific publications from everyone.  Cognitive behavior therapy guidelines for dealing with Imposter Syndrome recommend distancing yourself from the need for validation from others, to improve your self-awareness about your own abilities and needs, and to lessen the feeling that you need to hide the real you.

There is no litmus test for whether you are a “good graduate student”, or a “successful researcher”, except for your own demanding self-assessment.  All you can do is try to set realistic goals for yourself.  And not vague, large ones, such as “I want to publish 5 papers this year”.  Be more specific, and more short-term: “This week, I want to finish the Methods section of this paper, and hopefully have a working draft of this manuscript by the end of the month”.  I also find it helpful to keep a written record of what I’ve done.  Maybe keep a running To-Do list, and at the end of the week, month, or year, look back and see all of the things you have crossed off.  This is most helpful to me when I find that projects are getting delayed, or analyses need to be redone, or I generally feel like I am spinning my wheels.  Or, when I write a number of grants but some of them don’t even get submitted.  I still did all that work, but if I don’t have that item crossed off my list, I don’t have a visual reminder that I accomplished something.

And keeping a tally of everything you’ve done- not just the things that get published, can help you prove your worth and your effort when it comes time for job assessment.  Whether it’s a weekly meeting with your PI where you need to account for how you’ve spent your time, an annual performance review, or the tenure process.  If you have a written record of all the things you have done, all the little things that you spent your time on, you have proof that you have been productive.  Remember that success and failure are often out of your hands- especially in research.  Sometimes all you can do is try your best and hope that your fairy grant-mother rates your proposal wish as “outstanding”.

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Cinderella, 1950

A collaborative study on virulent Streptococcus got published!

Dr. Benfang Lei is an associate professor here at Montana State University in the Department of Microbiology and Immunology, who has previously collaborated with my previous post-doc advisor, Dr. Carl Yeoman.  As a lab member at the time, I consulted with Dr. Lei about the whole-genome shotgun sequencing that his lab group had performed on several Streptococcus pyogenes isolates.  S. pyogenes is pathogenic in humans and, among other symptoms, causes fever for which it is named.  Some of Dr. Lei’s isolates were much more virulent than others, and his study was to identify differences in the genome that would account for this.  I helped perform some of the genome processing and analysis, and am happy to be a small part of such an interesting study.

Wenchao, Feng, Dylan Minor, Mengyao Liu, Jinquan Li, Suzanne Ishaq, Carl Yeoman, and Benfang Lei. 2016. Null Mutations of Group A Streptococcus Orphan Kinase RocA: Selection in Mouse Infection and Comparison with CovS Mutations in Alteration of in vitro and in vivo Protease SpeB Expression and Virulence. Infection and Immunity.

My first soil microbial ecology paper was just published!

After a long year of data analysis and interpretation, my first paper on soil microbial ecology was just published in Microbial Ecology, found here.  Previously, I presented the data at a poster at this summer’s ASM conference in Boston.  The project led to further collaborations and, of course, led to my current post-doc position!


 “Impact of Cropping Systems, Soil Inoculum, and Plant Species Identity on Soil Bacterial Community Structure”

Suzanne L. Ishaq, Stephen P. Johnson,Zach J. Miller, Erik A. Lehnhoff, Sarah Olivo, Carl J. Yeoman, Fabian D. Menalled. 2016. Microbial Ecology: 1-18.

Abstract

Farming practices affect the soil microbial community, which in turn impacts crop growth and crop-weed interactions. This study assessed the modification of soil bacterial community structure by organic or conventional cropping systems, weed species identity [Amaranthusretroflexus L. (redroot pigweed) or Avena fatua L. (wild oat)], and living or sterilized inoculum. Soil from eight paired USDA-certified organic and conventional farms in north-central Montana was used as living or autoclave-sterilized inoculant into steam-pasteurized potting soil, planted with Am. retroflexus or Av. fatua and grown for two consecutive 8-week periods to condition soil nutrients and biota. Subsequently, the V3-V4 regions of the microbial 16S rRNA gene were sequenced by Illumina MiSeq. Treatments clustered significantly, with living or sterilized inoculum being the strongest delineating factor, followed by organic or conventional cropping system, then individual farm. Living inoculum-treated soil had greater species richness and was more diverse than sterile inoculum-treated soil (observed OTUs, Chao, inverse Simpson, Shannon, P  < 0.001) and had more discriminant taxa delineating groups (linear discriminant analysis). Living inoculum soil contained more Chloroflexi and Acidobacteria, while the sterile inoculum soil had more Bacteroidetes, Firmicutes, Gemmatimonadetes, and Verrucomicrobia. Organically farmed inoculum-treated soil had greater species richness, more diversity (observed OTUs, Chao, Shannon, P  < 0.05), and more discriminant taxa than conventionally farmed inoculum-treated soil. Cyanobacteria were higher in pots growing Am. retroflexus, regardless of inoculum type, for three of the four organic farms. Results highlight the potential of cropping systems and species identity to modify soil bacterial communities, subsequently modifying plant growth and crop-weed competition.

Keywords

16S rRNA, Avena fatua, Amaranthus retroflexus, Conventional farming, Illumina MiSeq, Organic farming, Soil microbial diversity

Preparing for my first greenhouse trial

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.

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!

After only a few days, seedlings are beginning to emerge.

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