25th International Meeting on Organic Geochemistry IMOG 2011

P-426
Bacterial versus archaeal activity in episodically flooded soils –
A combined lipidomics/genomics approach
Cornelia Mueller-Niggemann 1 , Andrea Bannert 2 , Michael Schloter 2 , Kai Mangelsdorf 3 ,
Lorenz Schwark 1
1 Institute of Geosciences, Christian-Albrechts-University of Kiel, 24118 Kiel, Germany, 2 Department for
Terrestrial Ecogenetics, Helmholtz Centre München, 85764 Neuherberg, Germany, 3 GFZ Potsdam German
Research Centre for Geosciences, 14473 Potsdam, Germany (corresponding author:cmn@gpi.uni-kiel.de)
Microbial processes in episodically dry and flooded
soils, e.g. in rice paddy fields, are highly variable due
to alternating changes in environmental conditions.
The characterization of such complex biogeochemical
systems affords combined approaches, for example
microbial lipid analysis coupled to molecular genetics.
Nitrogen cycling in alternately dry and flooded rice
paddy soils is exceptionally rapid due to intensive
fertilization and substantial nitrogen loss via leaching.
It is now well established that ammonium oxidation,
the first step in the nitrification is carried out by
archaea and, bacteria. The key enzyme for this
process, the ammonium mono-oxgenase is found in
bacteria (amoA AOB) and in archaea (amoA AOA). At
present it is still disputed whether archaeal or
bacterial ammonium oxidation dominates in soil. A
predominance of archaea from the mesophilic phylum
thaumarchaeota (previously crenarchaeota) [1] has
been documented in several dry upland soils using
genomic and lipidomic techniques [2]. The key lipids
for detection of archaeal contribution to soil organic
matter are the isoprenoidal glyceroldialkylglycerol
tetraethers (GDGT). These specific GDGT may
originate from Euryarchaeota preferentially
participating in methanogenic and methanotrophic
processes, whereas crenarchaeol is exclusively
biosynthesed by Thaumarchaea. In contrast, the
isoalkanoidal GDGT found in sediments are attributed
to bacterial sources, whereby the likely sources are
denitrifying bacteria (see Mueller-Niggemann et al.,
this meeting).
We have analyzed a series of soils utilized under
alternating flooded and dry regimes in a coastal
region of China. These soils developed on a marine
tidal wetland substrate and differ in the duration of
cultivation time from 50 to 2000 years. This allows to
study the adaption of soil microbial communities to
changes in the nitrogen cycling regime. Microbial
ecology based on genomics demonstrates equal
abundances of amoA AOA and amoA AOB gene
copies in the marine realm. In paddy soils a
dominance of amoA AOA over amoA AOB is
established very rapidly, followed by a continuous
increase of amoA AOA over 2000 years of paddy
management. GDGT analysis of marine sediment
gave a high value of crenarchaeol derived from
ubiquitous mesophilic crenarchaea. In the paddy soils
a decline in crenarchaeol compared to caldarchaeol
and its isomers was attributed to the presence of
methanogenic/-trophic Euryarchaeota.
Comparison of amoA AOA gene copies and
isoprenoidal GDGT abundances shows a covariance
(Fig.1) better than for crenarchaeol with amoA AOA.
This may indicate an origin of crenarchaeol from
different archaeal lineages in marine sediment versus
paddy soils.
Abundance of both, archaeal GDGT and amoA AOA
gene copies show higher ammonium oxidation in the
paddy field cultivated for 300 versus 2000 years.
Archaea seem to outcompete bacteria in ammonium
oxidation only under N depletion. This is verified by
the dominance of archaea in the N-poor 300 year
paddy, versus the N-rich 2000 year paddy.
Combined genomic and lipidomic analysis of paddy
soils and substrates indicates a dependence of
microbial N-cycling by archaea or bacteria on the
highly variable N-availability in these man-made
agricultural ecosystems.
Fig.1. Comparison of archaeal abundance based on
amoA AOA gene copies and GDGT lipids.
[1] Spang et al. 2010, Trends in Microbiol., 331-340
[2] Leininger et al. 2006, Nature, 806-809
552