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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.

Made available in DSpace on 2016-04-26T19:39:29Z (GMT). No. of bitstreams: 1 2006-Luciano Lopes Reis.pdf: 1765828 bytes, checksum: e031c34734485e7d84bd20e5fcc0d59b (MD5) Previous issue date: 2006-02-24 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior / This study had as objective to monitor the process of environmental reclamation of tanks filled with residues from bauxite washings, vegetated by hydro-sowing legume trees species inoculated with rhizobia, and asbuscular mycorrhizal fungi. Nutrient fertilizers, without nitrogen, were added at the mixture at sowing. Later it was planted a mixture of native tree species seedlings, with a high proportion of N2-fixing legumes, in an experiment with additional increasing levels of fertilizers and liming, except for nitrogen. The deposits of sterile bauxite subsoil, vegetated with the mix of native species, with high proportion of legumes capable of N2 fixation and mineral fertilization, were evaluated at different periods of time, for the chemical and biological attributes of soil and plants. Samples of soil, leaves, litter, and soil invertebrates fauna were taken in 2002, 2003 and 2004, to measure nutrient availability in soil; foliar nutrient level of indicator plants; soil microbial biomass and activity; soil fauna activity, diversity and ecological indexes; and evaluation of vegetal coverage of the SP1 residue tank. The results of foliar analyses indicated that even at the highest level of fertilizer and lime additions in the SP1 residue tank were not sufficient to meet the adequate plant nutrition requirements, indicating the need of higher input of nutrients. By using multivariate statistical analyses of the data, it was possible to distribute the studied systems along Cartesian axis, where the native forest area, used as testimony, and old vegetated mining sites (planted in 1984, 1992 and 1994) were clustered together; while the most recent vegetated mining sites and the tanks filled with residues formed a distant cluster. Among the index attributes studied Al+3, total C, total N, K, soil pH, microbial carbon and respiration; and Ca and Mg from litter were the principal factors determining the ordering and distinction between reclamation sites. The reclamation methodology used in the residue tank SP1, which combined the hydro-sowing with application of low solubility fertilizers, using a mix of seeds from medium cycle legume trees inoculated and with mycorrhizae, with later planting of native seedlings and manual dispersion of seeds, showed to be an important technique to stimulate natural vegetation growth. Also, the technique resulted in a high capacity of addition of decidual material, and the legume tree Acacia holosericea showed the best capacity for soil coverage and input of nutrients. / Com o objetivo de monitorar o processo de recupera??o ambiental de tanques de dep?sito de rejeito da lavagem da bauxita, revegetados atrav?s da hidrossemeadura de leguminosas fixadoras de N2 e com adi??o de fungos micorrizicos, mais aporte de nutrientes. Posteriormente, foi feito o plantio de mudas nativas em experimento de n?veis de aduba??o e calagem, sem aplica??o de nitrog?nio. Os dep?sitos de subsolo est?ril em bauxita revegetados com mistura de esp?cies nativas, com grande propor??o de leguminosas fixadoras de N2 e aduba??o mineral na cova, avaliados em diferentes idades, foram utilizados atributos qu?micos e biol?gicos do solo e planta. Foram realizadas coletas de solo, de folhas, de serapilheira e da fauna de invertebrados do solo, nos anos de 2002, 2003 e 2004, para determina??o da disponibilidade de nutrientes no solo; dos teores foliares de nutrientes das plantas indicadoras; da biomassa e atividade microbiana; da atividade, diversidade de grupos e ?ndices ecol?gicos da comunidade da fauna do solo; e avalia??o da cobertura vegetal do tanque de rejeito SP1. Os resultados da an?lise foliar das esp?cies indicadoras e de disponibilidade de nutrientes no solo indicaram que nem os maiores n?veis de aduba??o e calagem utilizados no experimento do tanque de rejeito SP1 foram suficientes para permitir uma adequada nutri??o ?s plantas, indicando a necessidade de novos aportes de nutrientes. Atrav?s da aplica??o de ferramentas de estat?stica multivariada aos dados, foi poss?vel ordenar os sistemas estudados ao longo de eixos cartesianos, onde a ?rea de mata nativa, usada como testemunha, e reflorestamentos sobre res?duos de minera??o com maior idade (realizados nos anos de 1984, 1992 e 1994) se ordenam pr?ximos uns dos outros, enquanto que os reflorestamentos sobre est?ril mais recentes e ?reas dos tanques de rejeito se ordenam distantes destes, formando grupamentos entre si. Dentre os atributos indicadores utilizados, o Al+3, C total, N total, K e pH do solo; a respira??o e carbono microbiano; e o Ca e Mg da serapilheira foram os mais determinantes para o ordenamento e distin??o entre os sistemas em recupera??o. A metodologia de recupera??o utilizada no tanque de rejeito SP1 que combinou a pr?tica da hidrossemeadura com aplica??o de formas de adubos pouco sol?veis, utiliza??o de coquetel de sementes de leguminosas arb?reas de ciclo m?dio inoculadas e micorrizadas, posterior plantio de mudas nativas e lan?amento manual de sementes, mostrou-se como importante t?cnica propulsora da regenera??o natural. A t?cnica tamb?m resultou em elevada capacidade de aporte de material decidual, sendo a leguminosa arb?rea Acacia holosericea, a esp?cie que apresentou melhor capacidade de cobertura do solo e aporte de nutrientes.

Arbuscular mycorrhizal fungi (AMF) play a crucial role in improving the growth of a vast majority of plants. Past researchers have discovered that agricultural practices have a significant negative effect on the diversity of AMF. Arbuscular mycorrhizal fungi are reported to enhance plant nutrient uptake, stress tolerance, and soil aggregate formation which are key aspects of productive low-input farming. The objective of this study was to investigate the effects of four pesticides on the ability of AMF to colonize the roots of okra plants (Abelmoschus esculentus). The pesticides being tested include two synthetic chemicals (glyphosate and carbaryl) and two organic chemicals (neem oil and citrus oil). The tested parameters included crop yield, plant biomass, leaf matter CNP, and the percentage of mycorrhizal colonization in roots. The results of this study show that the organic chemicals had no significant effect on AMF colonization while the synthetic chemicals did have somewhat of a negative effect on colonization.

This diploma thesis focuses on the use of thermogravimetry as quick and low-cost method in the analysis of soil quality. Most of the currently used methods for analyzing some soil properties are, unlike thermogravimetry, demanding especially for pretreatment and analysis time. Previous research has shown an interesting correlation between thermogravimetry data and some soil properties, but to obtain these correlations, it is necessary to keep the analyzed soils at 76% relative humidity. The aim of this work was to determine whether similar correlations can also by achieved at lower relative humidities. Therefore, soil samples in this work were thermogravimetrically analyzed at 43% relative humidity. That humidity is closer to laboratory conditions and it is also easier to be reached by most of commercially available thermogravimeters. Next aim of this thesis was to find whether thermogravimetric data correlate with other soil properties, especially microbiological indicators of soil quality. Results showed that thermogravimetry of soil samples correlates with standard methods even at 43% humidity. Furthermore, it was found that they also correlate with selected microbiological parameters, such as anaerobic ammonification or urease activity. These results suggest the possibility of using thermogravimetry analysis at broader spectrum of soil properties, without the need for pretreatment of samples and at different (relevant) soil moisture.

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Integrating crop and livestock is being considered to improve soil health by carbon sequestration. A two-year study (2019-2021) at CPBES in Newton, MS was aimed to evaluate soil microbial diversity in the warm, humid regions, specifically southeastern USA. Amplicons targeting bacterial 16S rRNA genes and fungal ITS2 regions were sequenced. Taxonomic assignment and microbial diversity characterization were performed using QIIME2®. Soil fungal diversity showed significant differences (alpha diversity, p = 0.031 in yr. 2020 and beta diversity, p = 0.037 in yr. 2021). Canonical Correspondence Analysis (CCA) and Mantel test showed significant influence on fungal diversity due to carbon (rm = 0.2581, p = 0.022), nitrogen (rm = 0.2921, p = 0.0165) in yr. 2021, and on bacterial diversity due to EE-GRSP (rm = 0.22, p = 0.02) in yr. 2020. Long term study of ICLS can help us better understand the shift in microbiome to improve crop production sustainably.

Several studies have reported agronomic benefits by improving soil health/quality, but uncertain knowledge remains when determining specific impacts on water quality off-field. This study investigated the links between runoff water quality and soil health/quality in agricultural fields of the Mississippi delta under three land management scenarios: Conservation Reserve Program (CRP), vegetative buffer (VB), and row crops (RC). Using the Soil Management Assessment Framework (SMAF), a Soil Quality Index (SQI) was obtained based on ten soil health/quality indicators from 2008 and 2012 datasets. The SMAF identified significant differences in soil health/quality improvements among scenarios over a four-year period. Varied relationships between water quality parameters, SQI, and soil health/quality indicators were determined. Individually, physical and chemical soil indicators were also correlated with runoff water quality. Overall, the evidenced relationship between soil health/quality and water quality parameters was stronger in areas under CRP.