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.

Thursday, May 26, 2016

Canyonlands Research Center Newsletter

Check out the cool work happening at Canyonlands Research Center, including our biocrust research! The pictures in the newsletter were post weeding, pre-weed cloth. Below you can see the weed cover, resulting in the addition of weed cloth at all gardens.

Tuesday, May 24, 2016

Moss experiments with Northland Preparatory Academy

Seventh grade blogger, Michal Swanson, has been documenting the year in science in Susan Brown's Northland Preparatory Academy classroom in her blog titled "I'm lichen it". The Bowker Lab has been featured a few times as a result of Dr. Antoninka's involvement with the class. She visited several times to help students learn about biocrusts, climate change, and to set up a semester-long experiment testing climate change effects on Syntrichia ruralis

Check out some of these posts (and feel free to browse others):
1. The semester long experiment we conducted to look at how mosses respond to altered climate
2. Moss revival (videos from Kyle Doherty).
3. An interview with Dr. Antoninka
4. Her visit to our NAU facilities

Great job Michal!

Wednesday, May 11, 2016

Tuesday, March 29, 2016

Rapid Cultivation of Fire Mosses

My first greenhouse experiment is complete! For this study I was interested in manipulating substrates and soil amendments to optimize the growth of my "fire mosses". Fire mosses colonize burned landscapes after severe forest fires and my research is focused on exploring their potential as a restoration tool. This being my first experiment with these species and in the greenhouse, I decided to try a little bit of everything with a nod toward burned material. Starting with the two most early serial species, Funaria hygrometrica and Bryum argentum, I added dry moss chunks as "inoculum" to an organic, garden topsoil substrate as well as a mixture of sand and coconut coir (which is an alternative to peat moss). These species can be dominant after high severity fire, so I tested soil amendments of ash from a friends stove and charcoal picked up from the local nursery, both of which are plentiful on burned landscapes. I was interested in how well burlap influenced the growth of mosses. If the mosses grew well on the burlap it could assist in harvesting and dispersal of greenhouse grown inoculum onto the landscape

The Experiment: complete with 216 units 
Channing adding "Inoculum" to a unit
In a side experiment I tested how well these mosses grew on the soils I had just collected them from. I thought this would allow me to see how good the greenhouse environment was for growing mosses, as well as, be a good comparison between natural soils and my engineered substrates. One unintended but awesome outcome of my natural soil experiment guessed it, lots of moss! No matter if I had added inoculum or not, Funaria was growing like mad from these soils, likely due to soil propigules left over after sieving out my inoculum.

Funaria (bright green) growing in a unit inoculate with Bryum only (silver green)
These ruderal (or, early successional) species grow very quickly under the right conditions and treatment effects were evident quite early on. Because of this, I decided to monitor my experiment every three weeks to track growth effectively. After 9 weeks some treatments were approaching full coverage which was very exciting to see in such a short time!

Funaria and Bryum Inoculated Unit at Week 1 (Left) and Week 9 (Right)

Saturday, February 27, 2016

SEGA: Progress and updates from a warm winter

With the warm February temperatures we have been experiencing in Northern Arizona, it is starting to feel more and more like May. May? Wow, the thought of Late Spring is alluring: SEGA will be up and running with Blue grama in the field for a second growing season and we will have planted Ponderosa pine for the tree's first growing season out of the glasshouse.

It seems like an appropriate time then, to give a brief update on SEGA. In case your new to our site and some of the work we do, SEGA stands for Southwestern Experimental Garden Array. The Array consists of two parallel elevation gradients: one on basalt derived soils and one on lime and sandstone derived soils. The elevation gradient allows us to manipulate Temperature and Precipitation.  The contrasting soil types allow us to test fascinating questions in regards to plant migration, soil microbes, and local adaptation to edaphic factors. How important is soil type to plants  migrating to new locations? Are soil microbes generalists or specialists to soil conditions and types? Can soil microbes facilitate plant adaptation to new climatic and soil environments?
The weather and irrigation infrastructure at SEGA sure makes for a great platform for cool experimental designs!

Additional work on SEGA is hoping to better understand population genetics and epigenetics of Southwestern White Pine and the genetic mechanisms that promote resistance to drought and White Pine Blister Rust, an introduced fungal pathogen. The hope is that by better understanding some of these traits, land managers would be able to preserve the range of white pine in the face of pathogen encroachment and densification combined with increased drought frequency and severity. This project is led by Dr. Kristen Waring and her current graduate student Jessica DaBell if you want more information. 
I decided to help sow seeds with the White Pine research crew- another 40 down... 10,000+ to go! 

But for now, back to microbes. So far we find consistent evidence that there is high specificity in plants and soil microbes; not any old microbe will do, plants need the microbes from their site origin. This finding supports Nancy Johnson's "no place like home" hypothesis. As we continue our studies, our Ponderosa Pine seedlings are beginning to break bud with the warm weather and lengthening of days. Stay tuned for updates as we launch field season and continue to monitor our plants in the Field! 
Bud burst on a Ponderosa Pine Seedling has
resulted in some stunning fresh growth. This tree is
growing in soil from its home site, but with
a soil organism community from an unique site.  

Root for the home team! That leader is taking off!
This pine is grown with its home team soil organisms
and in its original soil. 

Thursday, February 18, 2016

Picturing biocrusts during the wintertime

The conditions in Moab, UT have been pretty ideal for crusts this winter.  6+ inches of snow stuck around for a while, then slowly melted, leaving north facing slopes with wet soil surfaces while the sun is shining. These conditions have resulted in some of the most robust looking crusts I have ever see.  Robust crusts like these, and the 2015 Biogeochemistry paper by Anthony Darrouzet-Nardi et al. which observed substantial net photosynthesis rates underneath snow, seem to suggest there is exciting work to be done about seasonality of biocrust growth and the importance of winter snow cover to these systems. Enjoy the pretty pictures of crusts!
Note the sporophytes emerging! 

Wednesday, February 10, 2016

New Blog Feature: Web Apps

To explore new dimensions of science communication and data visualization, the Bowker Lab group is now developing informative web apps for a few of our research efforts. These are now located under the 'Web Apps' tab at the top of the page. Currently, we are featuring biocrust survey data from our MPG partnership:

Each of our survey points, to date, is represented on the map, and you can click on the points to reveal the species composition, with links to photos of each species. You can also explore the effects of environmental gradients, visualized as differing colors, on measures of biodiversity, depicted as dot size.

We hope that these data exploration tools will get more folks excited about biocrusts, and, in this case, assist land managers in conservation efforts!

Saturday, February 6, 2016

Some recent papers from the lab (late 2015, early 2016)

Antoninka, A.J., Bowker, M.A., Reed, S.C., Doherty, K.D. 2015. Production of greenhouse-grown biocrust mosses and associated cyanobacteria to rehabilitate dryland soil function. Restoration Ecology doi:10.1111/rec/12311.

Results of one of our first experiments in the bryotron, the work that has convinced us there's a bright future in culturing biocrusts for rehabilitation. This photo has become the face of our lab.

Antoninka, A.J., Ritchie, M.E., Johnson, N.C. 2015. The hidden Serengeti - Mycorrhizal fungi respond to environmental gradients. Pedobiologia 58:165-176.

Rainfall and soil gradients differentially affect various members of the arbuscular mycorrhizal community. 

Delgado-Baquerizo, M., Maestre, F.T., Gallardo, A., Bowker M.A., et al. (over 50 authors) 2016. Human impacts and aridity differentially alter soil N availability in drylands worldwide. Global Ecology and Biogeography 25:36-45.

Another product from the global drylands database featuring, I think, the first SEM Manu constructed and a clever way that he summarized human impacts spatially. The guy is on fire.

Sunday, January 24, 2016