2012 Summer Soil Institute

The 2012 Summer Soil Institute hosted at the Natural Resource Ecology Laboratory at Colorado State University is a 2 week intensive soil course designed for students to gain exposure to perspectives from world-renowned faculty to address critical questions related to soil chemistry and microbial ecology using current analytical techniques, experimental approaches, and instructional models.

SSI students spent the week 2 Tuesday and Wednesday afternoon sessions learning about qPCR and the Microplate Enzyme Assay Using Fluorescence-Based MUB & MUC-Linked Substrates.

For more information regarding Techniques, Topics, and Instructors for the 2012 Summer Soil Institute, please visit: http://soilinstitute.nrel.colostate.edu/index.html

The Art of Harvesting Knowledge:

During the 2nd International Enzymes in the Environment Workshop: Integrating Enzymes and Microbial Physiology into Biogeochemical Models, a ‘graphic facilitator’ was utilized to help us visually document  content presented during the talks as well as dialogue generated from the topic discussions during the World Café small round- table groups. This graphic facilitation was a great experience for all the participants and added value to the sharing and  integration of knowledge among workshop participants. 


Some of the graphic representations from the workshop are presented below:

Tuesday 05/15/2012 (Day 1):

Keynote Speaker: Josh Schimel

Wednesday 05/16/2012 Day 2:

Speaker Session 1A: New Paradigms

Speaker Session 1B: Current Applications

Working Group Session 1A: Priming

Working Group Session 1B: The Role of Nitrogen

End of Day 2: Reflections

Thursday 05/17/2012 Day 3:

Speaker Session 2: Challenges and Knowledge Gaps

Working Group Session 2A: Trade Offs

Working Group Session 2B: Scale

Working Group Session 2B: Defining Useful Data

Invitation to submit to a special issue in Biogeochemistry: Incorporating Enzymes and Microbial Physiology into Biogeochemical Models

The Enzymes in the Environment RCN has selected Biogeochemistry as the outlet for the special issue related to the workshop, and the chief editor has enthusiastically approved our proposal.  We anticipate 2-4 perspective/review papers to anchor the issue, and hope for several data and modeling submissions as well. We want you to submit your best work to what will be a high-profile, highly cited issue.  

Why submit to this special issue?

-Higher visibility (papers appearing in special issues get many more views and citations)

-We will help to coordinate the papers so that they complement each other, and cite each other.  When your paper is published, it may already have several citations.

-Rapid review:  We will enlist other contributors to help review your paper rapidly.  Your paper will be published online as soon as it is accepted, so it will not be held up by other papers in the issue.

We have established a tentative deadline of October 15^th, 2012.  The issue will be open to contributions from non-workshop participants. 

RCN workshop after Day 3 - unwinding at the end of a productive day with a tour of Fort Collins own New Belgium Brewery and a nice dinner at Choice City!

Working group breakout session titled Defining Useful Data led by Steve Del Grosso and Gwenaelle Lashermes. Start-off statement by Steve: Modelers want data that will improve the model fit! Useful data for models is dependent on the purpose of the model. Ecosystem scale models will likely not need the same parameters that micro-site lignin decomposition models will need. Enzyme activity Vmax and Km (enzyme kinetics) data is likely to be much more important for small scale models. Furthermore, one challenge with this is that there are plenty of Vmax values, but Km values are not as common due to method / lab logistics complications.

Visual summary of morning session.

The "World Cafe" is a success!

 For our breakout group discussions, we adopted the World Cafe format.  In brief, all participants split into tables of 4-5 people and discuss the same topic for 20 minutes, then we scramble the groups and continue the discussion for another 20 minutes.  We then have a full group discussion to synthesize the various discussions. The advantages of this technique are that everyone gets to participate, and as a result, we are able to address the topic with the collective genius in the room. 

Yesterday, we had discussed two topics:  1.  How to incorporate 'priming' into models and 2.  The role of N in decomposition models.  Everyone seemed to really enjoy the format, and the biggest challenge was keeping things on schedule because the conversations were going so well.  So, for today's meeting, we've adjusted the schedule a bit to give more time for the World Cafe discussions.

Day 1: Thoughts so far

As summarized by our graphic facilitator, Karina Mullen.

Ellen Kandeler presents talk titled: 

Modeling Carbon dynamics in a small scale microbial ecology of soils

Christina Kaiser presents talk titled:
From individuals to the community: Interactions between microbial functional group dynamics and C and N flows in a spatially explicit soil decomposition model

Daryl Moorhead presents his talk titled:

A theoretical model balance C-and N-acquiring exoenzyme activities driving decomposition

Klaus Butterbach-Bahl presenting talk titled:

Representation of N cycling processes in the biogeochemical model Landscape DNDC

Carol Arnosti from the University of North Carolina presenting talk: Microbial enzymes as selective gateways into the marine carbon cycle

Overview of Keynote talk (by Josh Schimel) at tonight’s RCN workshop banquet dinner 

Q: Why do we want to add microbial mechanisms to biogeochemical models?

A: Because we really think they matter!

To incorporate enzymes into models, 2 conditions are required:

1) Soil organic matter is rate limiting

2) C product pools have alternate fates!

Currently, models are not able to accurately represent both rates and magnitudes of changes in soil C dynamics!

Soil organic matter decomposition is dependent first on microbial access constraints, and secondly on then allocations. Soil C decomposition facilitated by biological factors is important to model at specific plant rhizospheres, in the soil organic horizon, and (possibly) in dead roots. Soil C decomposition modeling is not necessarily as useful with regard to fresh litter C or the mineral fraction of the soil consistent with physically protected OM.

Three common mechanistic models include 1) Functional, 2) Guild, and 3) Trait Based models.  Today, there are many tools to assess high resolution C pools (via IR and Mass spectrometry techniques) and microbial community species assemblages (via 454 pyrosequencing). From one gram of soil from a single soil core, we can identify thousands of different C structures and microbial species. However, these relationships are impossibly difficult for us to discern because nature is too complex for man to fully understand. There is much that we can learn by embracing multidisciplinary fields such as Landscape Ecology, mathematics, and biogeochemistry. The future in understanding these soil C relationships with biology is to simplify using biogeochemical models.

RCN Workshop: Josh Schimel Keynote talk

Participants from around the World joined us tonight for the 2nd International Enzymes in the Environment workshop. The festivities included a social hour at Fort Collins own El Monte Grill.

The workshop welcome speech and workshop introduction by Matt Wallenstein (RCN workshop co-chair as well as assistant professor at the Natural Resource Ecology Laboratory at CSU), followed by the workshop-keynote talk presented by Josh Schimel (professor at UC Santa Barbara).

To learn more about Matt and Josh, visit their lab websites at:

Matt Wallenstein Lab (http://warnercnr.colostate.edu/~mawallen/)

Josh Schimel Lab (http://www.lifesci.ucsb.edu/eemb/labs/schimel/)

Workshop on Incorporating Enzymes and Microbes into Biogeochemical Models

After months of planning, the workshop begins today with a keynote from Josh Schimel and welcome reception.  Check back here for updates throughout the week.