SWES 410 / 510
EEB 427 / 527

Microbial Biogeochemistry and Global Change

Spring Semester 2014


Meeting time: Friday, 12:30 - 3:00 pm. Location: Saguaro Hall, room 223 (then room 219 for discussion)


Date  Lecture Topic Discussion Leader Discussion Readings (* = primary reading)


introduction to Course & Organizational meeting    



a. Why study Microbial biogeochemistry?

b. Molecular Microbial Ecology: key concepts & methods overview

(presentation + extras)

Moira Hough

 Falkowski, P.G., Fenchel, T. & Delong, E.F. 2008. The microbial
engines that drive Earth’s biogeochemical cycles. Science

 Offre, Spang, and Schleper. 2013. Archaea in Biogeochemical
Cycles. Annu. Rev. Microbiol.
Optional: MICRO-CARD-FISH summary (mentioned in Offre et al. 2013)



Biogeochemistry: key concepts & methods overview

   a. Biogeochemical cycles (Saleska)
   b. Thermodynamics of microbially mediated reactions
      (by guest lecturer Prof. Jon Chorover, UA SWES)

Note: We will have the paper discussion first this week, followed by the lectures, to accomodate Prof. Chorover's schedule.

Andri Rachmadi

  Burgin, Yang, Hamilton, Silver. 2011. How the microbial energy
economy couples elemental cycles in diverse ecosystems, Front.
Ecol Environ.
[this readable and informative review builds on the
part of last week's lecture on metabolic diversity, and fills in details
on the thermodynamics discussed in Prof. Chorover's lecture this week.]

 Li. 2007. Quantifying greenhouse gas emissions from soils:
Scientific basis and modeling approach.
   [this work presents the DNDC model, an example of how thermodynamic
rules allow us to make model-based predictions for microbially produced
gases (greenhouse gases CO2, CH4, N2O) without actually representing the
communities involved.

   This raises a question that is a theme of the course: how much do we
need to know about the details of microbial communties in order to understand/
predict ecosystem-to-global scale biogeochemistry relevant to global change?
Li 2007 in effect stakes out the hypothesis that says: "not much!"



Isotopes as tracers of biogeochemical processes

Background/Reference: isotopes in:
  Carbon & Water in plants (Werner et al. 2012)
  Methane (Chanton et al., 2004)
  Nitrous Oxide ( Bags et al., 2008)


guest Joshua Weitz, Georgia Tech

  Follows et al. 2007. Emergent Biogeography of Microbial Communities in
an Ocean model. Science.

This includes Supplemental material (with model description and additional
model results), which we will discuss in detail, so please read as
closely as the main text (don't be scared off by the math, we will go
through the important parts in class).

   Follows et al takes us to another level beyond last week's Li 2007:
explict representation of microbial communities. This is of course necessary
if the modeling goal includes microbial biogeography, as it does here.
But Follows et al framework also provides a way to investigate the question of
how important is the biogeography for biogeochemistry.




Methods to link microbial processes to biogeochemistry
Juliana Gil Loaiza 

McCalley et al (submitted). Microbial community responses to permafrost
thaw regulate atmospheric methane dynamics

Ingalls et al. 2006. Quantifying archaeal community autotrophy in the
mesopelagic ocean using natural radiocarbon
(see also the related commentary by Ed DeLong, which nicely sets the work in context)




The C cycle from the microbes’ side, take 1: autotrophy Noelle Espinosa Orphan et al., 2001. Methane-consuming archaea revealed by
directly coupled isotopic and phylogenetic analysis
(see related News Focus)




The C cycle from the microbes’ side, take 2: heterotrophy

Martha Gebhardt

   Swan et al., 2011. Potential for Chemolithoautotrophy Among
Ubiquitous Bacteria Lineages in the Dark Ocean
(uses single cell genomics to further explore chemoautotrphy in
the ocean, building upon Ingalls et al.)
   Prosser & Nicol. 2012. Archaeal and bacterial ammonia-oxidisers
in soil: the quest for niche specialisation and differentiation
(reviews key chemoautotrophs in waters and soils, linking our
exploration of C and N cycles





C cycle: from the biogeochemistry perspectiveincluding guest lecture on Fungal decomposition by Naupaka Zimmerman, postdoc in the Arnold Lab;

Gary Trubl

IPCC, Assessment Report 5 (2013). Ch. 6. Carbon and Other Biogeochemical Cycles
Focus only on following sections:
   Read Exec Sum, then focus on: 6.1. Introduction;
6.3.1. CO2 emissions; 6.3.2 (skipping on oceans); *6.3.3. Methane*,
6.4.1. Intro to Projections of Future C cycles, Box 6.4 on how models are used. Permafrost Carbon and FAQ 6.1 on rapid release of CH4
6.4.7. Future changes in methane emissions




Viruses in the ocean

Guest Matt Sullivan UofA EEB

Koiya Tuttle

Hurwitz et al 2013. Metabolic reprogramming by viruses in the sunlit
and dark ocean
Suttle 2005. Viruses in the Sea

OPTIONAL: Breitbart 2012. Marine viruses: truth or dare


Spring Break    



The N cycle: the microbiological perspective

Sarah Doore

Fierer, et al. 2012. Comparative Metagenomic, phylogenetic,
physiological analyses of soil microbes & nitrogen
Fowler et al. Global N cycle in 21st century



The N cycle: the biogeochemistry perspective Ben Wieser

IPCC Chapter 6, (now with N-related annotations) findings related to N-cycle effects on biogeochemical feedbacks to climate:

Re-read Executive Summary (esp. parts about N), then focus on:
6.1.3. Connections between C & N cycles (esp. Box 6.2, Fig 6.4)
- note nutrient limitation effects on land C sink, e.g. Box 6.3 and "summary
   of processes missing from C-cycle models" (p. 504)
6.3.4. Global N and N2O budgets in the 1990s
6.4.6. N-cycle impaces on C-cycle
  (for this, review background on CMIP5, including: Global anakysis (of modeled C-cycle feedback, esp. Fig 6.20)
     Box 6.4 on how Carbon-Climate cycle models work



The Water cycle : microphysics of precipitation patterns (lecture outline)
Guest Lecture: Francina Dominguez, UA ATMO

This lecture will review the microphysics of precipitation.  This is far from the background of many in this class, but it is this kind of information that microbiologists (in collaboration with atmospheric scientists) will need to understand in order to develop good hypotheses for the role that microbes might play in atmospheric processes.

John McMullen

Ekstrom et al. 2010. Possible role of microbes in cloud formation
Womack et al. 2010. Biodiversity and Biogeograhpy of the atmosphere

DeLeon-Rodriguez et al. 2013. Microbiome of the upper troposphere
Konstantinidis. 2014. Do airborne microbes matter for the atmosphere?
Christner, 2012. Cloudy with a chance of microbes. Microbe magazine 7:70-75
Amato. 2012. Clouds Provide Atmospheric Oases for Microbes. Microbe.



No lecture


Reading 1:
Wieder et al. 2013, Global soil carbon projections are improved by modelling microbial processes
Wieder et al online Supplement
Schimel, News & Views piece re Wieder et al, Microbes and global carbon

Reading 2
Groenigen et al., 2013. Using metabolic tracer techniques to assess the impact of tillage and
straw management on microbial carbon use efficiency in soil



Student Project presentations    



Student project presentations  



(started 23 January 2014)
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