Fieldwork at Black Rock Forest

This past month I have been working at Black Rock Forest, a research and educational forest located in Cornwall, NY. I am interested in the changes in mesofauna, soil-dwelling animals that are about a few millimeters in size, to forest disturbances. If you want to learn more about soil biodiversity and why my project is important, you can watch my video featured in Breaking Bio Blitz in the previous post. This post will focus on my fieldwork and the methods I have been using to collect all the animals living on the soil.

The forest disturbance part of my project was inspired by an on-going long-term experiment at Black Rock Forest. Named the “Future of Oak Forests Study,” this project was initiated in 2008, and includes different tree girdling experiments, with an emphasis on the girdling of red oak trees to simulate an increasingly common scenario where sudden oak death takes over a forest. A smaller portion of this experiment includes herbivore exclosures, where parts of the forest are fenced off in order to prevent feeding by large and medium herbivores which, at Black Rock, are deer. You can read about the experiment here.


Photo: A girdled red oak tree, Black Rock Forest, October 2013

Working in these experimental plots is a unique experience. In certain areas, you are surrounded by girdled trees, which are trees that have been sawed around the trunk at breast height so the trees are still standing but are functionally dead. In herbivore exclosures, the vegetation, light intensity and overall appearance of the forest is very different.

Many studies in this experiment area have obviously focused on the aboveground response of vegetation to the removal and death of oaks and the removal of major herbivores. I am interested in what was going on in the soil and leaf litter. In order to collect mesofauna, which are so small that you can only really see their general form with the naked eye, I had to collect leaf litter at the surface of the forest floor and soils at different depths. I used a soil corer, which is made up to two, very heavy parts: a slam hammer, to drive down into the soil and a metal cylinder, to collect the soil. By placing the metal cylinder upright on top of the soil, after the leaf litter has been removed, I lift the hammer and drive it down into the ground about 10 centimeters, which is sometimes a lot more difficult than one would expect. Once the cylinder was full of soil (and not rocks, which I found to be very problematic in certain areas of the forest), I had to gently extract it from the ground and place the soil into (properly labeled) bags. I took many, many cores in different part of the experimental area for both mesofauna collection as well as soil physical and chemical properties analysis.

IMG_3811 IMG_3814

Photos: My Berlese funnel set-up, Black Rock Forest, July 2014

Once I collected all my soils and leaf litter, the mesofauna had to be collected from the different mediums. The outstanding and universally applied method of doing this type of arthropod extraction is a Berlese funnel. The principle of a Berlese funnel is to use both heat and light to drive the animals out of the medium and into vials of ethanol to be collected and sorted later. The leaf litter and soils were placed into large funnels resting below a light bulb, the source of heat and light, with the end of the funnel falling into a vial of ethanol. By letting the soils and leaf litter dry out for three days, I expected to get most of the arthropods and other animals to migrate away from the light bulb and fall into the ethanol. As of right now, all my soils and leaf litter have been “extracted” and I have a bunch of ethanol vials filled with mesofauna and other animals and arthropods to be counted and sorted. I’m hoping to be able to identify the major mesofauna groups (as well as a few subgroups) and determine whether or not the forest disturbances are having a significant effect on these communities.

Though I’m sad that my fieldwork and funnel days are over, I am looking forward to seeing all the litter critters that have been living in the leaf litter and soil under the microscope as I start the next part of my summer research.


-Natalie Bray


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!

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.



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 [] 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.