Why Study Gut Microbes?

Why study gut microbes?  This is a question I am constantly addressed with while trying to explain my research interests.  My response?  Why not study gut microbes?!  The microbiome of living organisms has been termed the “forgotten organ”, with a collective metabolic activity equal to that of a virtual organ.  Gut microbes in particular are of crucial importance to their host, assisting in digestion of food matter, absorption of nutrients and development of a properly functioning immune system.  Studies estimate that the number of genes within the gastrointestinal microbiome is 100 times greater than that of the human genome. So, it comes as no surprise that scientists across multiple fields have been diving head first into the world of gut microbes, in hopes of better understanding everything from individual organisms to entire population structures.

My research focuses on immunomodulating gut bacteria, or groups of bacteria in the vertebrate gut that affect host immune homeostasis.  In particular, I am interested in a group of bacteria called segmented filamentous bacteria (SFB).  These tiny inhabitants of the intestines have amazing capabilities to directly influence the production of T helper cells that produce inflammatory cytokines in the body.  This is paramount in protecting the body from disease and infection.

But how does this relate back to conservation biology?  In order to effectively protect species, we must understand them at all levels, including the inner antics of their tiny commensal friends. These bacteria are heavily influenced by diet and environment, so it is assumed that in a changing world, the composition of the gut microbiota will change as well, ultimately affecting host health. Studying immunomodulating bacteria and what affects them, could give conservation biologists a more solid base for understanding the health status of species in a rapidly changing world. With the importance of gut microbes growing with every newly published study, it is clear that we must put increased focus on studying them through the lens of ecology and conservation.

Right now, I have two projects to investigate this unbelievably interesting stuff!  Dr. Pat Thomas (Vice President at the Bronx Zoo) and I have captured and transitioned wild house mice into captivity at the Bronx Zoo. Some of these mice are being fed a standard zoo diet, while others are being fed a diet more similar to what a house mouse would eat in the wild, varied by season.  The plan is for these mice to reproduce to produce multiple generations, mimicking the process that happens every day in captive facilities.  We will test for levels of SFB between the two diet treatments and over multiple generations.  The goal will be to investigate the effects of a captive diet on levels of SFB.  This information can hopefully provide zoos, (which are an increasingly important tool in the conservation toolkit) with information to better the health of their captive populations for future reintroductions. The second project focuses on mice in the wild.  I will be trapping wild white-footed mice from urban, suburban and rural field sites.  Levels of SFB will be compared between these populations to shed some light on how urbanization affects levels of SFB in wild populations of organisms.  These results could provide conservation biologists with information on how increased urbanization in the coming years may affect the health of species in the wild.

The bottom line is that there is much work to be done.  There are hundreds of distinct species present in the mammalian gastrointestinal tract with many specific functions crucial to their host.  Studying them could give us an astronomically enhanced understanding of how organisms function, and even how populations of organisms function.  So, in closing, that is why I study gut microbes! More to come from the field in the coming weeks!

-Erin Dimech

Prepping for Fiji Fieldwork

Prepping for the field!! Always an exciting, yet slightly stressful endeavor. I am a Master’s student in the Drew Lab, and will be spending 2 months in Fiji for fieldwork along with fellow MA student and friend Molly McCargar, and our amazing undergraduate student, Elora Lopez (who will be blogging in the field as well, at our undergrad research blog sister site, CUEBS). We’ve been preparing for this trip for what feels like ages, starting way back in January when we started putting together a symposium for a conference we’ll be attending in Fiji, began communicating with collaborators at University of the South Pacific, and started the whole process of getting permits and research visas. But when the semester finished in mid-May, the planning ramped up a million notches, and now we’re only 3 days away from heading off! Ah!! Are we prepared? Are we ready? Probably as much as we can be. As Kaggie showed us all earlier, you never know what is in store when you’re in the field – and cliché as it is, you always must expect the unexpected.

Testing out the 99 cent GoPro rig I made in California - it works! Doesn't float though...

Testing out the 99 cent GoPro rig I made – it works! Doesn’t float though…

I’m actually currently writing this in Columbia’s IT office, as I wait for all of eternity for a tech to troubleshoot our little field laptop – one of the many small but time-consuming tasks we’ve had to cross off our list to get ready for the field. Other to-do items have involved visiting police stations, printing and laminating colorful pictures of fish, and buying items like a mini liquid nitrogen dewar and pH/salinity meters. We’ve had to get medical clearance for our research permits and prep dive gear and field equipment, buy odds and ends for cameras and technical gear, and we’re all prepping our personal gear as well. And then there’s all the email correspondence with people in Fiji to make sure we have permission to collect samples in certain villages and get everything in order for some of the more remote sites we’ll be visiting, like the Lau and Yasawa island groups. Needless to say, it’s been a busy few weeks.

Field notebooks in bulk!! The best.

Field notebooks in bulk!! The best.

We have a couple more exciting things on our agenda in addition to fieldwork and sample collection – first, I will be teaching a week-long marine conservation course at USP with our principle investigator, Josh Drew, (which we named Fiji WISE) and second, our group will be leading a symposium and doing talks at the Society for Conservation Biology Oceania Section conference in early July (called SCBO 14 for short). We’ll be spending three weeks in Suva, Fiji’s capital, prepping for and running Fiji WISE, and meeting with various people before enjoying the conference. I’m really excited to meet up with our WCS Fiji contacts and the US Embassy peeps who are helping us run Fiji WISE, as well as doing a few talks at local high schools to maximize our outreach. We’ll also be working on a few manuscripts for publication, and I’ll be blogging and posting videos for people to follow along! (Shameless plug: if you’re on twitter, make sure to check out #CUintheField14!)

A visual of how much gear we schlep around while in the field

A visual of how much gear we schlep around while in the field

THEN after all the Suva business is over, the fieldwork begins! We’ll be visiting four locations around Fiji – Nagigi in Vanua Levu, Neselesele in Taveuni, Vanuabalavu in Lau, and Yasawa Island in the Yasawas. Four weeks of sample collection (which involves diving, spearfishing, sediment coring, gut dissections, and interacting with fisherpeople – so stoked!) and then we’ll be back in Suva to obtain permits and pack everything up before heading back to the States! Phew. It’s going to be amazing.

Map of our sampling sites! (ignore the lowest dot in Kadavu, we had to remove that one in March)

Map of our sampling sites! (ignore the lowest dot in Kadavu, we had to remove that one in March)

The Lau island group, aka literal paradise.

The Lau island group, aka literal paradise.

Stay tuned for more updates from Molly and I in Fiji, and from the rest of our cohort as well!

What is soil and why does it matter?

I love soils, and all the animals that live in and on top of it. I spent most of my undergraduate work focusing on soil ecology and working both in the lab and in the field on projects related to arthropods, earthworms, and soils in forests and urban areas. This summer I am working at Black Rock Forest located in Cornwall, New York, an amazing research and teaching forest, where I will be collecting soils and the arthropods and assessing the effects of forest disturbances on these soil-dwelling animal communities. Before I describe my research project, I want to share why soil is so important, though it is often undervalued and under-appreciated.

IMG_3381Photo: Black Rock Forest, October 2013

Soil sustains life on Earth. People often take for granted that soil exists beneath their feet. Soil is not only important for healthy forests and crops but they provides habitat for a huge variety of organisms. Let’s say you walk into a forest or a garden or a field and scoop up a handful of dirt. What would you find? At first, you would probably just think you had simple handful of uninteresting material that just help prop up plants and trees. In reality, you have a complex mixture of chemical compounds and animals that make up one of the most important mediums in an ecosystem.

The soil you are holding has been in the making for a long time. Soil does not just appear. Over time, based on the parent material, which is the rock type you start out with on your landscape, the climate acts on the soil: rain and wind changes the chemistry of the rock. The scientific processes that describe the changes from rock to soil are called leaching and weathering. These processes alter the chemistry of the rock so that the compounds from the rock, mixed with the organic compounds from the surface, turn into what we recognize as soil.

When you reached down and grabbed your handful of soil, it was most likely exposed and easy to pick up. Because soils are directly in contact with the air, there are many exchanges between soil and atmosphere. Plants take in carbon dioxide (CO2) during photosynthesis and use the carbon to live. When a plant dies, the carbon in that plant is recycled into the soil and through complex chemical reactions, soil releases that carbon into the atmosphere. Most people are familiar with carbon because of carbon dioxide and its emissions in the atmosphere contributing to human-caused global climate change. In fact, CO2 emissions from soil are the greatest contributor to atmospheric COHowever, it’s important to remember that soils are a natural source of CO2, as opposed to the many anthropogenic sources.

IMG_3377Photo: Black Rock Forest, October 2013

What else is in the soil in your hand? You’ve likely picked up a living organism or two that you can easily identify, like an ant or an earthworm. You might assume that’s all that’s living in your hand. Most of these organisms are small, like little mites or springtails about a millimeter in size or even smaller on the microscopic scale, like a fungus or bacteria. Soil is one of the most important habitats for a wide variety of organisms from burrowing mammals to crawling arthropods to basically invisible microorganisms. All organisms in the soil not only transform their soil habitat by creating holes or burrows through which water can flow but they also provide services for each other. For example, certain organisms eat dead plant material and by eating this dead material, they change the form of the material – what we would call nutrients – so that new growing plants can take that transformed material and use them to grow. This is called nutrient recycling. By maintaining this natural nutrient recycling process, soils can continue to supply nutrients to plants and animals.

hypvia01Photo: Collembola or springtail, only a few millimeters in size from www.collembola.org

When you think less about biology and ecology and more about sustainability and agriculture, soils become arguably even more important. The biological health of soils is tightly linked to social and economic issues today. Something that people often forget is that soils are the medium in which we grow many of our crops. Food production depends heavily on soils and the nutrients in them, referred to as soil fertility, which is why we care so much about fertilizers and the general chemical composition of soils. Current threats to soils include degradation, erosion, and contamination. As discussed previously, soils taken many hundreds of years to develop and current practices are not favorable for maintaining healthy soils.

The scoop of soil you originally picked up should now appear to be a complex assortment of different elements and organisms. This medium is the keystone of most forests, agricultural land and habitats. All of the complex processes in soil provide numerous services and contribute to global biodiversity. Recognizing what soil is and what how incredible it is will help to prevent further damage to this indispensable resource.

 

-Natalie Bray

The Truth About Fieldwork

Fieldwork is about how well you can adapt. If you can’t adapt, can’t make plans on the fly, have no creativity and a quick temper you’ll never make it in fieldwork. And that is because fieldwork is never what you expect it to be. Even if you already know your field site well anything can happen out in the field and you always have to be on your toes. An example, you ask? Well the perfect one happened on base a mere few days ago.

            With some of the newly arrived volunteers gone for a day in town, Brie, a GVI staff member, and I were changing a gas bottle for the fridges. We requested some of the older volunteers to take the empty gas tank over to the garage and bring a new one over. A few minutes later we hear one of them shout “Yo…. Fire!” (to give him a little credit, he did have a slight panic in his voice). Looking over towards the generator we saw high flames pouring out of the window. Now, I also understand that people exaggerate. Especially people who want a good story. I definitely have been known to do this before. However, in this instance, no exaggeration is needed. Flames were pouring out the window. Now, unless you are a trained fire fighter, nothing really prepares you for that moment, aka, what the HELL are you going to do with high flames pouring out of the generator room, which is full of diesel and oil covering the floors? In an act of pure stupidity or bravery (I like to think the latter, but I know it was the former), I quickly grabbed the nearest fire extinguisher and ran straight into the generator room. Having spent hours of my childhood staring at fire extinguishers dreaming of yanking out the pin and spraying the extinguisher fumes everywhere just for the hell of it, I knew the general idea of what I needed to do, even if I never had needed to actually use one (I strongly urge for all of you to look at your own fire extinguisher and do the same, it does make a difference if you’re in an emergency). Keeping the volunteers at a safe distance away from the flames and building, we used 7 entire fire extinguishers to kill the fire. That’s right, 7. If you still thought I was exaggerating about how big the flames were, now you know. 

 

           Image Image

 

So after that whole saga you would think that everyone would be done for the day. Or at least the vehicles and machinery would give us a break. Unfortunately, not to be out done by the generator, on of the bakkies on drive started smoking and burnt the battery wire. With minimal staff on base, and minimal functioning vehicles, Melanie and I delivered a new bakkie for Brie to continue on her drive while we waited with the broken/burnt bakkie for another vehicle to tow us back. By the time we have gotten the bakkie out of the dip and towing back to base the sun was setting. It’s frustrating when you get pushed back an entire day just because of things no one can control, however that sunset, like every sunset in Africa, just makes it completely worth it. And I think that is what I love most about fieldwork and being out in the bush. Every day is completely unexpected. You don’t know where the animals are going to move, you don’t know how they are going to react, you don’t know if your vehicle will get stuck or not… and you don’t know if your generator will explode randomly. But that’s good. It keeps you on your toes and forces you to constantly make plan A’s, B’s, C’s etc. A skillset that everyone should have.

And lets be honest, no one would love fieldwork if it was boring…

Image

(photos are of the presumed source of where the fire started, the seven fire extinguishers we used, and the aftermath of the generator room after being sprayed by fire retardant chemicals!)

—Kaggie Orrick, Masters candidiate, posted from South Africa

Did You Know?

Fun Facts about South African Animals by Kaggie Orrick

Did you know that porcupines can stay afloat in water because their quills keep them buoyant?

Did you know a rhinos horn is actually made of keratin, which also makes up your fingernails and hooves of cattle?

Did you know that a leopards tail is rounded while a cheetahs tail is flattened so it can act as a rudder and keep it balanced while is sprints?

Did you know elephants can communicate from kilometers away by feeling the vibrations through the ground? They can also hear each other from up to 8 kilometers away via trumpeting. 

Did you know that a type of amphibian called an African plantanna can tell you if your pregnant or not? (a dose of a pregnant womans pee will cause the female plantanna to lay eggs within 8 to 12 hours…)

Did you know you can tell the difference between a cat track and a dog track by counting the number of lobes on the back of the pad (dogs have two, cats have three: I would show you all a picture however my internet is too slow for photos at the moment!)

 

 

More fun facts and interesting information about my research to come!

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Nitrogen Fixation Rate of Genus Robinia in Northeast U.S.

Hi everyone, I am Eleen – (soon-to-be) second-year master student at Columbia University Ecology, Evolution, and Environmental Biology department. I study ecosystem ecology, broadly interested in nutrient cycling. My current work is focusing on Nitrogen (N) cycling in temperate forest ecosystems.

One of the major supply of N in terrestrial forest ecosystem is N fixation by free-living or symbiotic microbes that live in the root nodules of N-fixing plants. My research is primarily focusing on symbiotic N fixation (SNF): SNF is a process of converting atmospheric N2 into plant-available N by microbes. It is crucial in global n cycle, especially important in temperate forests, where N commonly limits primary production. SNF is also essential in conservation because of its capability of jump-starting recovery in abandoned and nutrient-poor systems to facilitate nutrient restoration and succession. In coterminous U.S., the estimated N input combining both N deposition and other types of N fixation besides symbiotic N fixation is <20kg N/ha year (Holland and Braswell 2004, Reed et al 2011). Based on a rough estimate, N fixers have the potential to be the greatest N input source on a continental scale (Sprent and Parsons 2000). Based on the recent Forest Inventory Analysis (FIA) data analysis (Liao and Menge Unpublished), there are in total 12831 N fixing trees recorded since 1980s. Genus Robinia (Figure 1) is the most common of six native N-fixing genera across U.S.: on a regional scale, this genus is particularly important in northeast region (Figure 2) where it comprises 95.6% of N fixer biomass. Despite the recognized importance, we currently do not have an accurate understanding of SNF rates of genus Robinia in this region or how they vary with tree age. My summer plan is to conduct a systematic analysis of Robinia SNF rates across tree ages in a northeast temperate forest.

(Figure1: Robinia at Central Park)

 

Robinia distributionRobinia distribution

(Figure 2: Distribution of Robinia across U.S. Color shows percent basal area. (Menge et al 2010))

There are different ways of measuring SNF rates- each has advantages and limitations. The most commonly used methods include 15N enrichment experiment, acetylene reduction assay, and d15N natural abundance method. 15N enrichment experiment allows ecosystem-level analysis but is high-costly. Acetylene reduction assay because of its invasive nature by excising nodules off might not capture the actual SNF rates under natural settings. In my summer research, a combined analysis of 15N isotope natural abundance and dendrological dating record will be used to approach SNF rate of Robinia across age groups. I will sample 15 pairs of adult Robinia trees and neighboring non-N-fixing trees at Black Rock Forest (BRF), assuming they access the same soil nutrient pool. By coring the trees, dividing tree cores into different age groups, and comparing the isotope signals of Robinia and reference non-N-fixing tree I will be able to understand the amount of N fixed and the rate of SNF of genus Robinia in this forest and thus provide an estimate of SNF rates in northeast region.

Before going down to the field and start coring trees, I will spend/have been spending my time compiling literature that have reported SNF rates of Robinia and other N-fixing genera across coterminous U.S. In addition to literature review, I also will continue figuring out the best way to extract isotope signals from tree cores. Ultimately the data with literature estimates of SNF rates and experimental measurements of SNF rates will be combined with FIA database to estimate SNF at a continental scale, providing the first ever map of nationwide SNF estimates.

 

Reference:

Holland, E. A., B. H. Braswell, J. Sulzman, and J.-F. Lamarque. 2004. Nitrogen Depositio to the United States and Western Europe. Data set. Available on-line [http://www.daac.ornl.gov] from Oak Ridge National Laboratory Distributed Active Archive Center, Oak Ridge, Tennessee, U.S.A.n on

Menge, D.N.L., DeNoyer J.L., and Lichstein J.W. 2010. Phylogenetic constraints do not explain the rarity of nitrogen-fixing trees in late-successional temperate forests. PLoS ONE 5(8): e12056.

Reed, S. C., C. C. Cleveland, and A. R. Townsend. 2011. Functional Ecology of Free-Living Nitrogen Fixation: A Contemporary Perspective. Annual Review of Ecology, Evolution, and Systematics 42:489–512.

Sprent, J., and R. Parsons. 2000. Nitrogen fixation in legume and non-legume trees. Field Crops Research 65:183–196.

Preparations of a Lab Rat

Welcome to the first text post of the summer! I’m Natalie Hofmeister, one of two Natalies in this group, and this summer I’ll be writing about my work in the Rubenstein lab here at Columbia. Given that most of us are in transit or getting settled at field sites, I’m starting us off with a run-down of what I’ve been doing to prepare for the summer. In a two-year Master’s program like Columbia’s, we complete the bulk of our thesis research during the summer in between academic years. However, there is a lot of preparation to be done before the summer begins: writing grants, planning methods, ordering equipment and supplies, and – of course – lots of reading. For me, preparation meant a semester of primer design and testing before I could get to data collection.

My thesis focuses on signatures of evolution in the glucocorticoid receptor, a gene that is critically important in the production of the stress response. To look at variation in this gene (NR3C1, which stands for nuclear receptor subfamily 3, group C, member 1*), the first step was designing primers for each of the eight exons. Beginning in January 2014, I spent many hours on the computer and in the laboratory, designing and optimizing primers. Luckily, I had a great teacher (Joe Solomon, thanks for your help!), and after a few months I now have primers for all eight exons and I’m ready to start collecting data.

*Finding that all of these strange combinations of letters and numbers in molecular biology actually mean something definitely made life a lot easier to understand.

Superb starlings, one of the species I study (Pedro Fernandes, Cornell Lab of Ornithology).

Superb starlings, one of the species I study (Pedro Fernandes, Cornell Lab of Ornithology).

So, what goes on behind-the-scenes? Many molecular projects go through the same steps I did this spring, so I’ll try to demystify what we do in the lab.

1. Half of my time this spring was spent designing primers and aligning NR3C1 sequences on Geneious. Obviously, I needed to begin my project by learning to use the software that could analyze all of my sequences. So, I started at the computer, trouble-shooting in Geneious. First, I aligned the superb starling transcriptome (constructed by Joe Solomon) to putative sequences of NR3C1 in the zebra finch and the chicken. Once I developed a hypothesis of the starling NR3C1, I designed primers for each exon using the built-in commands in Geneious. The image below shows an example of a primer with the selection criteria we use to judge which primer is best; generally speaking, you want a primer with about 45% GC content and low scores for dimer and hairpin formation.

An example of primer design in Geneious from the manual (v5.3.6).

An example of primer design in Geneious (Geneious Manual v5.3.6).

 

2. I spent the other half of my spring testing those primers. Usually, in testing primers you start with a temperature optimization to test the primers at many different annealing temperatures, and then proceed to magnesium optimizations to clean up the bands on a gel. Unfortunately, these optimizations don’t always get you pretty bands. Below, I show two unpretty gels and one lovely gel (with the bands boxed in red).

These are a few of the gels I ran to test primers this spring. The left-most gel was one of the worst (see the streaking), while the gel on the right shows clear and bright bands.

These are a few of the gels I ran to test primers this spring. The left-most gel was one of the worst (see the streaking), while the gel on the right shows clear and bright bands.

I used touchdown PCR to get the beautiful bands in the gel on the far right. I’d been working on a particularly troublesome exon for a few weeks when my PI suggested I try touchdown PCR (TD-PCR). This protocol gradually decreases the annealing temperature of a reaction, literally “touching down” by one degree in each subsequent cycle, which selectively amplifies the product that amplified at the highest annealing temperature. For more information on TD-PCR, see Korbie and Mattick 2008.

 

Next step: moving on to this guy! I'll be sequencing on a machine like this one (the ABI 3730) at AMNH this month.

Next step: moving on to this guy! I’ll be sequencing on a machine like this one (the ABI 3730) at AMNH this month.

 

Now that I’ve finished up this preliminary work, I’ll be shuttling back and forth between the Rubenstein lab and the Sackler lab at AMNH, where I’ll complete the actual sequencing of NR3C1 (using a machine like the one shown above). Stay tuned for some (hopefully forthcoming) results!

Breaking Bio Blitz – Cynthia Malone

Hello everyone and welcome to CU in the Field! As you will see in the About Me section, this is a blog run by some of Columbia University’s Conservation Biology Masters students, where we will be posting as often as we can about our summer research endeavors. Stay tuned for photos, videos, blog posts, and video interviews we conducted with Breaking Bio, a great group of biologists who put out podcasts about biology, science, and academic life. Here is the first Breaking Bio Blitz interview with the lovely Cynthia Malone, who is studying oil palm plantations in Cameroon!

Featured Photo credit: 100r.org