Overview
Inside the
tree nursery two different irrigation systems are used. The first one is a
classical sprinkler which uses water from the pond inside the facility and the
second one is a drip irrigation system that uses fresh water. The different usage
of water has mainly to do with the water quality. For the drip irrigation
system clear water is necessary or otherwise the nozzles would be overgrown
with algae and in need for replacement in a short amount of time.
Next to the
site, a little stream called “Talbach” is flowing into the river Aare. Possible
interactions with the plant nursery and their pond inside the site with the stream
should also be investigated.
Goal
This blog
entry tries to answer the following main research question:
“Which prerequisites need to be available in
order to do a comparison of the different irrigation systems in pot-substrate and
their impact for the microbiological community in soil and water?”
In order to
do so, a molecular method with its pros and cons are compared against each
other. The goal is to find the best analysis technique for the given task and
time. To validate if the chosen method is feasible in the project week, an
estimated time table is shown.
Additionally,
the influence of the used irrigation water, which is stored in the pond on the
Talbach, should be assessed.
Possible methods
The irrigation
systems and their used water (fresh water or waste water), have a direct impact
on the microbiological community in soil. A shift in the microbiological composition,
especially in disturbance scenarios e.g. heat, can be observed depending on the
used irrigation water. (Frenk et al.)
It is not
clear how strong the impact of the pond for the stream Talbach is. Therefor it is
necessary to analyse the stream at two different points. Sample point 1 should
have no water from the pond in it and is therefore uncontaminated. Sample point
3 is further downstream and came in contact with water from the pond. Sample
point 2 is there to have an estimation of the water composition and its quality
in the retention basin.
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Figure 1: Overview of the different sample points at
the site.
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The two separate
research questions can be analysed with the following method.
A fast and
uncomplicated way to analyse a microbiological community is PCR-DGGE. (Madigan) Firstly, the DNA has to be
extracted from the soil or water samples. For that, special kits and procedures
are available. (Angel et al.) The isolated DNA can then be
further analysed.
For that, a
PCR is done with a primer-set for general bacterial community. This could be
the primer 341F-GC containing a 40-bp GC clamp for better separation in DGGE or
907R. After amplification the samples are added to a DGGE gel containing 20% to
70% urea with TAE as running buffer (2 M Tris base, 1 M glacial acetic acid, 50
mM EDTA). (Frenk et al.)
Because the
goal is to see a shift in the microbiological community and not a detailed
phylogenetic tree, a sequencing of the different amplificants is not necessary.
The method
is simple and fast to perform but can only give a rough overview of the
different bacterial species in the sample. Species which are low in density are
most likely not visible on the denaturing gel.
Time table
To see if
the method is feasible in the given time a time table was created.
References
Angel, Roey, et al. ‘Methanogenic Archaea Are
Globally Ubiquitous in Aerated Soils and Become Active under Wet Anoxic
Conditions’. The ISME Journal, vol. 6, no. 4, Apr. 2012, pp. 847–62. PubMed
Central, doi:10.1038/ismej.2011.141.
Frenk, Sammy, et al. ‘Quality of Irrigation Water Affects Soil
Functionality and Bacterial Community Stability in Response to Heat
Disturbance’. Appl. Environ. Microbiol., vol. 84, no. 4, Feb. 2018, pp.
e02087-17. aem.asm.org, doi:10.1128/AEM.02087-17.
Madigan, Michael T. Brock Biology of Microorganisms. Fourteenth edition, Pearson, 2015.
