[ES_JOBS_NET] PhD project: Elucidation of the microbial N-cycle in the subsurface – key microbial players and processes

Anna Görner anna.goerner at bgc-jena.mpg.de
Thu Aug 8 05:03:00 MDT 2013

The International Max Planck Research School for Global Biogeochemical
Cycles is offering an interesting PhD project on the

Elucidation of the microbial N-cycle in the subsurface – key microbial
players and processes

Supervisor: Prof. Dr. Kirsten Küsel (Friedrich Schiller University Jena)
Prof. Susan Trumbore (Max Planck Institute for Biogeochemistry), 
Ph.D., Dr. Martina Herrmann (Friedrich Schiller University Jena)

Project description

Elevated concentrations of nitrate in groundwater affecting the
suitability of groundwater for drinking water production represent a
global problem. Thus, understanding microbial nitrogen transformation
processes in subsurface compartments like aquifers is crucial.

Nitrite is a rapidly metabolized but central intermediate of the
nitrogen cycle, linking aerobic and anaerobic pathways. As a product of
aerobic ammonia oxidation, it can be further oxidized to nitrate by
nitrite-oxidizing bacteria. In turn, as a product of nitrate reduction,
it can be reduced to either ammonium (dissimilatory nitrate reduction to
ammonium, DNRA) or to gaseous nitrogen compounds by denitrification or
anaerobic oxidation of ammonia (anammox). Under suboxic conditions or at
oxic/anoxic interfaces, nitrite resulting from aerobic ammonia oxidation
can also directly be fueled into denitrification or anammox as reported
from the suboxic zone of the Black Sea. However, so far only little is
known about these metabolic interactions or the relevance of the anammox
process in aquifers. Similarly, a close metabolic coupling between
nitrite oxidizers and either ammonia-oxidizing bacteria or
ammonia-oxidizing archaea performing the first step of nitrification has
been reported from wastewater treatment plants or the open ocean.
However, nitrite oxidizers in aquifers have so far rarely been
investigated. Since anammox bacteria and a large number of known nitrite
oxidizers are chemolithoautotrophs, their activity would also provide
important links between the nitrogen cycle and the carbon cycle in

Previous research activities revealed the presence of both ammonia
oxidizing bacteria and ammonia oxidizing archaea in limestone aquifers
located in the Hainich region and confirmed nitrification activity in
the groundwater. Furthermore, these studies also showed the presence of
organisms with the genetic potential to perform denitrification as well
as anammox. Finally, analysis of the active total microbial communities
indicated the presence of members of the genera Nitrospira and
Nitrospina, which are likely to play a role in nitrite oxidation in the
limestone aquifer system.

The proposed project will address the following research questions:

(1) What is the relevance of anammox versus denitrification for the
removal of nitrite in limestone aquifers?

(2) What is the contribution of nitrite oxidation and anammox to
autotrophic carbon fixation?

In order to address these research questions, the candidate will perform
rate measurements of anammox, denitrification and nitrification using
15N-based techniques. Moreover, characterization of the microbial
communities involved in nitrite oxidation, denitrification and anammox
will be carried out using molecular approaches (qPCR-based analysis of
genes and transcripts, next generation sequencing), targeting both
ribosomal RNA genes and functional genes. These investigations will
focus on planktonic microbial communities in the groundwater as well as
on those communities that are associated with the aquifer matrix. Here,
both original rock material derived from drilling and rock material
deployed in passive samplers will be available for the investigation of
attached microbial communities. The candidate will participate in field
sampling campaigns of the CRC AquaDiva for sampling of groundwater and
passive sampler material. Investigations of environmental samples will
be complemented with mesocosm experiments and cultivation-based
approaches aiming at the isolation of nitrite-oxidizing bacteria from
the groundwater.

Working group & planned collaborations

The research group “Limnology/Aquatic Geomicrobiology” of Prof. Dr.
Kirsten Küsel works on the microbial ecology of the carbon, iron and
nitrogen cycle in aquatic and semiterrestrial environments, using both
molecular and cultivation-dependent approaches. The working group
provides excellent laboratory equipment for molecular work and for data
analysis from next generation sequencing. The research of the proposed
project will be performed in close association with the CRC AquaDiva

For carrying out mesocosm experiments and for the investigation of
autotrophic pathways, the candidate will work in close collaboration
with a postdoctoral scientist involved in the CRC AquaDiva. In addition,
the candidate will collaborate with Master and Bachelor students
involved in the CRC AquaDiva. For field work, the candidate will work
together with the hydrogeology working group at the FSU Jena. Analysis
of anammox communities using lipid biomarkers will be carried out in
collaboration with Dr. Valerie Schwab-Lavric.

The Research School

The successful candidate will become a member of the International Max
Planck Research School for Global Biogeochemical Cycles (IMPRS-gBGC).
The school provides excellent research possibilities for students to
obtain a PhD degree in a 3-years graduate program.

The elements key to life such as carbon, oxygen, hydrogen, and nitrogen
are continuously exchanged among the land, ocean and atmosphere in what
are known as global biogeochemical cycles. Research in the IMPRS-gBGC
discovers how these cycles function, how they are interconnected, and
how they can change with climate or human activity. In their thesis
projects, students deal with various crucial aspects of global
biogeochemical cycles and participate in ongoing research comprising
field observations, method development, experiments, and modeling.
Students will also benefit from a three-month external research visit,
specialised courses in e.g. statistics, Earth observation, modelling and
analytical techniques, as well as in soft skills and will have ample
opportunity to develop their personal career networks. The school is
thus an excellent starting platform for a successful career in a field
related to global biogeochemical cycles and Earth System Science.


Applications to the IMPRS-gBGC are open to well-motivated and
highly-qualified students from all countries. For this particular PhD
project we seek a candidate with

	• A Master’s degree in Biology, Microbiology, Molecular Ecology,
	Biogeochemistry or a related discipline, including a corresponding
	• Experience in standard molecular techniques (nucleic acid
	extraction, PCR, cloning) 
	• Experience in phylogenetic analyses and in the analysis of 
	next generation sequence data would be advantageous. 
	• Interest in interdisciplinary work in the field of
	the microbial ecology of aquifers 
	• Interest in working with model ecosystems at a laboratory scale (mesocosm experiments) 
	• Excellent oral and written communication skills in English

How to apply

Application deadline for these fully funded PhD positions is September
30, 2013. Top candidates will be invited to take part in our selection
symposium (December 03-04, 2013).

>> Apply online: www.imprs-gbgc.de

After you have been selected

The IMPRS-gBGC office will happily assist you with your transition to

Successful applicants are expected to join us in winter 2013/14 and will
receive a comfortable PhD stipend to cover all living expenses. There are no
tuition fees. Additional financial support is available for conference visits, 
participation in summer schools and a 3-month research visit to another top lab. 

Handicapped persons with comparable qualifications receive preferential

Anna Goerner - coordinator
International Max Planck Research School
	for Global Biogeochemical Cycles
MPI for Biogeochemistry
Hans-Knöll-Str. 10, 07745 Jena, Germany
phone:   +49 3641 576260
e-mail:  anna.goerner at bgc-jena.mpg.de


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