Thesis (MSc (Microbiology))--University of Stellenbosch, 2010. / ENGLISH ABSTRACT: The relationship between various land management practices, soil properties and the soil
microbial communities are complex and little is known about the effect of these interactions
on plant productivity in agricultural systems. Although it would be advantageous to have a
single organism or property that can be used as a measure of soil health, it may not be
possible. Soil organisms which include both the microorganisms as well as soil fauna are
subjected to the effect of their immediate environment. This microenvironment in turn is
determined by the soil properties as well as above ground flora and their interactions. Most
soil indicators interact with each other, and these interactions can modify or influence the soil
properties. The complexities of the interactions between critical soil indicator values often
preclude its practical use by land managers and policy makers. However, soil microbial
communities (e.g. diversity and structural stability) may serve as a relative indicator of soil
quality. These communities are sensitive to land management practices and changes in the
microenvironment.
The objective of this study was to gain an understanding of the complex relationships by
investigating the effect of conventional, integrated and organic apple production systems on
the physical, chemical and biological (particularly soil microbial diversity) properties of the
soil. Automated Ribosomal Intergenic spacer analysis (ARISA) was used to characterise
fungal (F-ARISA) and bacterial (B-ARISA) communities from soil samples obtained from an
experimental apple orchard in Elgin, Grabouw. The intergenic spacer (ITS) region from the
fungal rRNA operon was amplified using ITS4 and fluorescently FAM (6-
carboxylfluorescein) labelled ITS5 primers. Similarly, the 16S-23S intergenic spacer region
from the bacterial rRNA operon was amplified using ITSR and FAM-labelled ITSF primers.
The sensitivity of the technique allowed us to discriminate between the soil microbial
communities of the different treatments. From our results we observed significant increase (p
< 0.05) in the fungal community diversity between the February and April samples, while the
bacterial community diversity was consistent (p > 0.05). Also, treatments with mulch showed
a significantly higher microbial diversity than the other treatments at a 5 % significance level.
Fungal communities showed significant correlation with the potassium concentration in the
soil, while bacterial communities depicted a significant correlation with the soil phosphorous
concentration. Based on the results we concluded that different management practices have a significant
effect on the soil microbial communities and that these communities are particularly sensitive
to small changes in the environment. However, there is still a need to determine what the
composition of the soil microbial communities are to be able to correlate our observations
with soil health. / AFRIKAANSE OPSOMMING: Die verhouding tussen verskillende landboubestuurspraktyke, grondeienskappe en die
mikrobiese gemeenskappe in grond is kompleks en weinig is bekend oor die uitwerking van
hierdie interaksies op die produktiwiteit van landboustelsels. Alhoewel dit voordelig sou
wees om ‘n enkele organisme of eienskap te kan hê wat die gesondheid van grond kan meet,
sal dit dalk nie moontlik wees nie. Grondorganismes wat die mikroörganismes sowel as die
grondfauna insluit, is onderworpe aan die invloed van hulle onmiddelike omgewings.
Hierdie mikro-omgewings op hulle beurt word weer beïnvloed deur die grondeienskappe
sowel as die die oppervlak flora en hulle wisselwerkinge. Meeste van die grondaanwysers
toon ook wisselwerkinge met mekaar, en hierdie wisselwerkinge kan die grondeienskappe
beïnvloed or selfs verander. Die kompleksiteit van die wisselwerkinge tussen kritiese grond
aanwysers is meestal die rede waarom dit nie deur grondbestuurders en beleidsmakers
gebruik word nie. Dit is ongeag die feit dat grond mikrobiese gemeenskappe (bv. diversiteit
en stukturele stabiliteit) mag dien as ‘n relatiewe aanwyser van grondkwaliteit. Hierdie
gemeenskappe is sensitief vir bestuurspraktyke en veranderinge in die mikro-omgewing.
Die doel van die studie was om die ingewikkelde verhoudings in die grondgemeenskappe te
bestudeer en die uitwerking van konventionele, geïntegreerde en organiese appel produksie
sisteme op die fisiese, chemiese en biologiese eienskappe (veral die grond mikrobiologiese
diversiteit) te bepaal. Geoutomatiseerde Ribosomale Intergeniese Spasie Analise (ARISA) is
gebruik om die fungus (F-ARISA) en bakteriese (B-ARISA) gemeenskappe van
grondmonsters wat vanaf ‘n proef appelboord in Elgin (Grabouw) verkry is, te bepaal. Die
intergeenspasie (ITS) area van die fungus rDNA operon is vermeerder deur die ITS4 en
fluoresserende FAM (6-karboxylfluorescein) gemerkte ITS5 inleiers te gebruik. Soortgelyk is
die 16S-23S intergeenspasie area van die bakteriese rDNA operon vermeerder deur ITSR en
FAM-gemerkte ITSF inleiers te gebruik.
Die sensitiwiteit van die tegniek laat ons toe om te onderskei tussen die grond mikrobiese
gemeenskappe vanaf verskillende grondbehandelings. Vanuit die resultate kon ons aflei dat
daar ‘n toename (p < 0.05) in die fungus gemeenskap diversiteit vanaf Februarie to April was
terwyl die bakteriese gemeenskap ‘n konstante diversteit getoon het (p > 0.05). Behandelings
met grondbedekking het ook ‘n beduidend hoër mikrobiese diversiteit getoon as ander
behandelings. Fungus gemeenskappe het beduidende korrelasies getoon met kalium konsentrasies in die grond, terwyl bakteriese gemeenskappe ‘n beduidende korrelasie getoon
het met grond fosfor konsentrasies.
Gebaseer op die resultate kon ons aflei dat verskillende bestuurspraktyke ‘n uitwerking kan
hê op die grond mikrobiese gemeenskappe en dat hierdie gemeenskappe sensitief is vir klein
veranderinge in die omgewing. Dit sal egter nog nodig wees om die spesifieke samestelling
van die grond mikrobiese gemeenskappe te bepaal voor ons hierdie waarnemings kan
korreleer met grondgesondheid.
| Identifer | oai:union.ndltd.org:netd.ac.za/oai:union.ndltd.org:sun/oai:scholar.sun.ac.za:10019.1/4133 |
| Date | 03 1900 |
| Creators | Caleb, Oluwafemi James |
| Contributors | Jacobs, K., Du Plessis, K., University of Stellenbosch. Faculty of Science. Dept. of Microbiology. |
| Publisher | Stellenbosch : University of Stellenbosch |
| Source Sets | South African National ETD Portal |
| Language | English |
| Detected Language | Unknown |
| Type | Thesis |
| Format | 131 p. : ill. |
| Rights | University of Stellenbosch |
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