1/17/2014
VR & SRS

1

1/24
VR  

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)

2

1/31
SRS

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

3

2/7
SRS

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)

  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.

4

2/14

VR

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)

5

2/21

VR

6

2/28

VR

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

   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

7

3/7

SRS

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

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 6.3.2.5 on oceans); *6.3.3. Methane*,
6.4.1. Intro to Projections of Future C cycles, Box 6.4 on how models are used.
6.4.3.4 Permafrost Carbon and FAQ 6.1 on rapid release of CH4
6.4.7. Future changes in methane emissions

8

3/14

MBS

Viruses in the ocean

Guest Matt Sullivan UofA EEB

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

3/21

9

3/28

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

OPTIONAL:

10
4/4
SRS

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:
      6.4.2.1. Global anakysis (of modeled C-cycle feedback, esp. Fig 6.20)
     Box 6.4 on how Carbon-Climate cycle models work

11

4/11

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.

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

OPTIONAL/BACKGROUND:
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.

12

4/18

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

13

4/25

14

5/2