Sunday, June 25, 2017

Field Guide to Biocrust of Bandelier National Monument, NM

Here is the newly completed field guide to biocrust lichens and mosses of Bandelier National Monument in northern New Mexico.  We were able to find 23 different lichen and moss species within the Monument. While this is not an exhaustive list of all biocrust lichen and moss species within Bandelier, it is an example of the diversity of biocrust species present and provides the first taxa list for the Monument that can built upon in future work.

The guide is free to all and can be downloaded as a pdf here

Huge thanks to all the people who made this guide possible. Including our survey team Pete Chuckran, Armin Howell, Robin Reibold, Sarah Fischer, Channing Laturno, and Dustin Kebble. In additional to all the support and resources provided by Sasha Reed, Mike Duniway, Jayne Belnap, Kay Beeley, Jeremy Sweat, Craig Allen, Hilda Smith, Erika Geiger, our funding source the Natural Resource Preservation Program (NRPP) of the US Geological Survey, and Bandelier National Monument.

From left to right: Dustin Kebble, Kristina Young, Channing Laturno, Armin Howell, Robin Reibold, and Pete Chuckran

Tuesday, May 23, 2017

Fire Moss Research Expands to Valles Caldera National Preserve

Last week, with another semester in the books we embarked on our first trip of what looks to be a busy field season. Thanks to additional funding and logistical support provided by Dr. Robert Parmenter at Valles Caldera National Preserve we plan to put Fire Mosses to the test in the Jemez Mountains of northern New Mexico. This fall we will be attempting the first ever inoculation of greenhouse grown Fire Moss onto recently burned soils. To increase our chances of success and meet the preservation objectives of Valles Caldera, we will be growing locally collected moss in our greenhouse here at Northern Arizona University.

Mosses for growing in the Greenhouse
This new project is also a collaboration with Kara Gibson, a fellow graduate student here at NAU who is studying the impacts of thinning and burning forest restoration treatments on soil microbes within the Caldera. To explore the effects of and differences between greenhouse grown moss and field collected moss we will test the effectiveness of both treatments at, stabilizing soils, increasing infiltration, restoring soil microbial communities, restoring nutrient cycling, and facilitating vascular plant recovery in these degraded ecosystems.

We have also expanded a survey of Fire Moss natural colonization and soil stabilization on recent wildfires in northern Arizona to northern New Mexico. This survey will allow us to inform land managers about a missing piece in post fire recovery as well as direct current and future Fire Moss research and Burned Area Emergency Response implementation.
Carpets of Ceratodon purpureus (left) along with a new yet to be identified species. 

Although for this first trip the weather was not interested in cooperating, between the three different snow storms, we had a wonderful time exploring future field sites and sampling within the Las Conchas and Thompson Ridge wildfires. The Jemez Mountains, with their high elevation and vast Valle grasslands, feel like something you would find in Wyoming or Montana instead of the Southwestern US. The opportunity to explore Fire Mosses' potential in such a different climatic and edaphic landscape makes this a perfect addition to our research. Looking forward to many more trips up to such a special part of the world over the next two years!

A big thanks to Dustin Kebble and Kara Gibson for all of their help measuring and collecting moss!

Wednesday, October 19, 2016

Seeking a Master's student: biocrust biodiversity, does it offer resistance to climate change

Syntrichia caninervis, one of the stars of the new project (image: Jepson Herbarium, UC Berkely)

The School of Forestry, Northern Arizona University, seeks a motivated Master of Science (M.S.F.) student to conduct field and greenhouse experiments in Flagstaff, Arizona and field sites in southeast Utah starting in Fall 2017. The student will be co-advised by Matthew Bowker and Anita Antoninka on a new NSF-funded Dimensions of Biodiversity project in collaboration with 5 institutions (PI- Llo Stark, UNLV). The student will explore the relationship between biodiversity in moss and biocrust communities and their resistance to climate change stressors. The project will: 1. Conduct a greenhouse experiment to first develop “custom” biocrusts with varying levels of community diversity, and genetic diversity within a focal moss taxon (Syntrichia), then monitor the response of the communities to stress. 2. Track trade-offs in stress tolerance and reproduction in Syntrichia biocrusts experimentally transplanted on an elevation gradient. 3. Document the outcomes of long-term simulated climate change as expressed by stress tolerance and reproduction in Syntrichia. At least 2 years of funding are available to the student (Annual stipend of $17,950, tuition remission, and student health coverage) in addition to project costs. 
Research Environment: The School of Forestry is one of the top Forestry Schools in the nation, and a productive research environment, with faculty members specializing in a variety of ecological topics such as landscape ecology, ecological restoration, plant ecophysiology, entomology, hydrology, and soil ecology among other topics.

Preferred Qualifications: Bachelor of Science in Forestry, Biology, Environmental Science or related field, supplemented with research experience (undergraduate thesis, capstone or internship, or employment-related experience). Candidates with greenhouse or field research experience will be strongly favored. Candidates with previous experience in soil ecology and/or bryophyte/biocrust ecology will also be favored. The candidate must satisfy all requirements set by the School of Forestry, and Northern Arizona University.

Admissions requirements (Deadline March 15, 2017):

    GPA of 3.0 or greater on a 4.0 scale in all college and university work
    GRE scores in the top 40th percentile
    If English is not your native language:
    a score of at least 80 on the internet-based TOEFL or
    550 on the paper-based TOEFL or
    213 on the computer-based TOEFL
    Three letters of recommendation

How to apply:  First contact us directly ( to state your research interests, and motivations for attending graduate school, with “moss diversity graduate student inquiry” in the header. Please provide a resume or C.V., and provide your GRE scores (if taken) and GPA. If we agree that you are a good match for the position, we will encourage you to apply to the program.

Useful Links

Dr. Bowker’s web page -

School of Forestry -

SOF M.S. program -

Monday, July 25, 2016

Webinar on biocrust restoration

The Bowker lab recently contributed a feature article to the Society of Ecological Restoration's newsletter on biocrust restoration.  The article can be found here:

As a complement to the article, members of the Bowker lab will be giving a webinar, sharing progress and plans for restoring biocrusts using the following approach: 1) Develop optimal culturing techniques; 2) Maximize field survivorship; 3) Develop, build and test field delivery mechanisms; and 4) Integrate techniques with current restoration practices.

The webinar will be from Thursday, August 4th, at 4-5pm EDT.  Please join us!

Monday, July 18, 2016

crustCover R Package

The Bowker Lab has developed an R package to characterize and quantify biocrust cover with photo data. This package is called crustCover, and is an adaptation of the methods in Fischer et al. (2012), which describes techniques to use visible light cameras in conjunction with a lens filter to calculate NDVI. This package is a work in progress, and input from the biocrust community on bugs encountered or ideas for improvements would be greatly appreciated. Please send reports or request for improvements to 

Friday, June 24, 2016

Plant-Soil Feedbacks, Ponderosa Pine, and SEGA -- A new study from the Bowker Lab

SEGA? Am I really talking about a video game platform on our research blog? Really? NO! Though, I am not sure which I invested more time in - crusading through the old school Sonic the Headchog video game series or prepping and launching this experiment. 

OK, OK, in all seriousness, this experiment is really stinking cool, and we finally got it launched! 

First of all, lets backup and define SEGA, acronyms are tossed around so lavishly we just assume everyone knows what they mean, but I genuinely hope everyone in the research world learns about SEGA. The Southwest Experimental Garden Array, or SEGA, is a new research tool managed by Northern Arizona University in partnership with the Bureau of Land Management, The United States Forest Service, Babbitt Ranches, The Grand Canyon Trust, University of Arizona, and Arizona State University. SEGA is effectively a series of common gardens spanning seven life zones, from high elevation Mixed Conifer to low elevation cool and warm deserts . SEGA utilizes this strong elevation gradient with a twist, soils. Soil types on the Colorado Plateau are highly variable so SEGA has two of these elevation gradients, one on predominately limestone and sedimentary derived soils, and one on basaltic soils. One of the coolest aspects of SEGA is the depth of onsite weather instrumentation - we have a live feed on virtually any weather variable you can think of across all the sites. Better yet, live irrigation that can be controlled remotely or programmed to match spikes in soil moisture at different sites - yes, that's right, we can simulate precipitation events based on real-time weather data.  

The warm desert SEGA site and its weather instrumentation. 

What is this laberous project that has been taking me away from video games and into the field? We are especially interested in plant responses to changing and dynamic climates, however, we are interested in the added complexity of soil and plant-soil organism interactions. Given any shift in a plant's environment, plants have three options for a response: 1) die 2) move 3) adapt. Most plants, like our study organism in this study - Pinus ponderosa (ponderosa pine), are highly dependent on soil organisms. Soil organisms include bacteria, nematodes, collembela, and mycorrhizal fungi (myco = fungus, rhizo = root, so mycorrhizal fungi are root fungi). These unique fungi live on or inside plant's roots and explore the soil environment for key nutrients like nitrogen and phosphorous or soil water. So we add the questions 1) If a plant migrates to a new environment, does soil type matter? 2) If a plant migrates to a new environment, is it limited by the absence of its natal, or home team, soil organisms? 3) Do different soil types change plant responses to changes in climate?

Preparring to plant in the field required deep holes to bury the pots in - better just bring in heavy equipment! 

Briefly, I just want to share a taste of the labor that went into this project. Soils are tough - most research in this field has been done in small containers in the glasshouse, because if you really want to understand the effects of soil biota and soil independently from one another, you have to start with sterile soil - and soil is far from sterile. Secondly, to grow trees for an extended time in the field requires large containers, and large containers require a lot of soil. So, firstly, we collected field soil from our three sites. All the soil was steam sterilized for 48 hours, twice. That means, field collected, shoveled into a sterilizer, shoveled back into a sterilizer, and finally shoveled into those massive pots. Then we "inoculated" with our soil organisms - how do you inoculate, you ask? In this case it's easy, we just sprinkled a single centimeter of live soil from the field on the surface of the soil. Lastly, we seeded our locally collected Ponderosa pine seed into the live soil inoculum. We then grew our seedlings into saplings for two seasons in the glasshouse. So now we have trees growing in soil from their site of origin, or in soil from a site that is two degrees centigrade warmer or a site two centigrade cooler, and soil organisms from each of the sites as well. We prepared the sites for planting by digging trenches the depth of the pots ( ~ three feet deep) and eventually plopped the pots in the ground and back filled the holes so the soil surface is flush across the site and pot. So I am one man, a fairly strong one - but none of this would have been possible without help.

I unload pots from the UHUAL trailer, excited to be getting a good work out!
Photo Courtesy of Emily Thompson

So let me ramble for a second about the importance of volunteering and all the other avenues of support we have had. The Grand Canyon Trust and their volunteer program has been quintessential to implementing this project. From the installation of fences, to the arduous effort of back-filling trenches to get the Ponderosa planted, I honestly do not know where I would be without volunteer support, well - still digging, probably. Not only do volunteers provide valuable physical assistance, but they become patrons and liaison for the science we are doing and the community. I cannot thank the dozens of volunteers that have helped with this enough. I sincerely appreciate your effort and more importantly your story. Every volunteer I have interacted with came interested in science, ready to work hard, and with a fascinating story. Most of you have been non-scientists and your engagement in our science is so important. My gratitude towards volunteers is an appreciation for our mutual relationship and the stories we share.

Grand Canyon Trust Volunteers help finish the planting of Ponderosa pine at the cool, mixed conifer site. 

The end result is 190 trees growing in the field under these different climatic conditions, and being force to grow with different soil organisms and in unique soil types.  This is really a classical plant-soil feedback experiment with a climatic twist, or a classical climate themed common garden study with a soil feedback twist. With the trees in the ground, we are excited to continually monitor our plants in terms of growth and physiology over the years to come. We expect to be able to grow the trees for several years before they out grow their containers.

100 trees happily planted on the Brow of the Kaibab Plateau at the warm PiƱion Juniper site

I should note that we have a nearly identical experiment that has been in the ground for over a year, also on SEGA, using the infamous perennial grass, Boutelous gracilis (blue grama). So far, after the first year, we have observed that plants growing with their "home team" soil organisms grow the largest regardless of climate. Plants forced to grow in new climates (whether warmer or cooler) are much smaller than those growing at their home site. This reduction in size is reduced when growing with their "home team" soil organisms. Lastly, certain soil types, specifically a young basalt "cinder" soil, are seemingly nightmarish for a population of blue grama that came from much older soils. The "home team" advantage is also strongly diminished in this soil type suggesting its not just the plants that are struggling.

We hypothesize that in more stressful soil conditions, as a product of nutrient or soil limitation, the plant-soil organism mutualism will be of enhanced importance.  As soil environments become more benign, it is likely that competitive interactions or lack of dependency on soil organisms will result in a diminished importance of the "home-team". Our study system on SEGA allows us to test the many facets of plant-soil organism interactions over climate gradients through multiple growing seasons and I am extremely excited to continue to share progress with you all!

This graphic represents data from a related experiment to show how plants grown in more a mild drought (a and b) and extreme drought like conditions (c and d) are much larger when grown with their home team (a and c) soil organisms as opposed to novel soil organisms (b and d). Notice how under extreme drought, and with their home team (c) plants invested more in their mycorrhizal partners and grew just as large as plants grown under moderate drought! The soil organisms are buffering the plants from extreme stress! 

This work is important in this is important in that fe studies have examined and manipulated the role of soil organisms in facilitating plant growth and survival across a climatic gradient. Additionally, in the context of vegetation management programs, very rarely are soils and soil organisms considered in planting scenarios, whether following invasion of exotic species or in the context of restoration or post-fire rehabilitation. This work is helping us better understand the benefit of using soil organisms in vegetation management and exploring new tools that could be used as a climate solution to the often dismal outlook of widespread vegetation mortality. 

Thanks for reading! 

A scenic vista with Saddle Mountain and the Kaibab Plateau along the horizon

Friday, June 10, 2016

Lab grad Chris Ive's research featured on Earth Notes (KNAU)

Chris Ive's successfully defended back in late April, and completed some foundational work on one of our more exciting research lines: using post-fire colonizing soil mosses as a restoration material. The radio short Earth Notes also thought it was exciting and produced this nice program after interviewing Chris. Listen here.